WO2021231648A2 - Cancer therapeutics comprising chemokine or its analog - Google Patents
Cancer therapeutics comprising chemokine or its analog Download PDFInfo
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- WO2021231648A2 WO2021231648A2 PCT/US2021/032088 US2021032088W WO2021231648A2 WO 2021231648 A2 WO2021231648 A2 WO 2021231648A2 US 2021032088 W US2021032088 W US 2021032088W WO 2021231648 A2 WO2021231648 A2 WO 2021231648A2
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
- A61K2039/507—Comprising a combination of two or more separate antibodies
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
- C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
Definitions
- the isolated chemokine mimetic is a CCL5 mimetic or pharmaceutically acceptable salt thereof. In some embodiments, the isolated chemokine mimetic or pharmaceutically acceptable salt thereof is administered in a pharmaceutical composition further comprising a pharmaceutically acceptable carrier or excipient. [0018] In some embodiments, said administering is via intratumoral injection, intravenous injection, subcutaneous injection, or a combination thereof. In some embodiments, said administering is via intratumoral injection. In some embodiments, the method further comprises the step of administering to the subject an anti-PD-L1 antibody or an anti-PD-1 antibody. In some embodiments, the method further comprises the step of administering to the subject a TGF ⁇ inhibitor.
- FIG.4A Mice bearing MC38 tumors were administered PBS or CCL5 (1ug/dose) IT three times per a week for 6 doses and on day 12 tumors were harvested and analyzed by flow cytometry Left: percent of CCR5+ cells within the CD8+ T cell population (live cells, CD3+, CD4-, CD8+, CCR5+) in PBS or CCL5 treated tumors. Right: percent of CCR5+ cells within the NK cell (live cells, NK1.1+, CD3-, CCR5+) population. Black cross bars represent median values.
- FIG.4D Average tumor volume + SEM for each treatment group is shown. P-value was determined using Wilcoxon rank sum test.
- FIG.4E Spider plots showing tumor volume for individual mice over time.
- FIG.4F Survival plot for the same study. P-value was determined using log-rank test.
- FIG.4G Average tumor volume + SEM for CCL5 administered alone compared to PBS (Control).
- FIGs 5A-5D Intratumorally administered CCL5 enhances intratumoral levels of CCD5+ CD8 T cells and mature CD11b+ NK cells. Mice bearing s.c.
- FIG.5D tSNE plots of flow data showing the expression of CCR5 within PBS control (left) or CCL5 treated tumors (right), or where populations are differentiated according to expression of marker genes as indicated in the key (bottom). Heat maps showing expression of each flow marker are in FIG.7G.
- FIG.6A Average tumor volume + SEM is shown. P-value was determined using Wilcoxon rank sum test.
- FIG. 6B Spider plots showing tumor volume for individual mice over time.
- FIGs.7A-7I Anti-PD-L1 plus anti-TGF ⁇ led to tumor growth inhibition of EMT6 tumors.
- FIGs.7A-7B Mice bearing EMT6 tumors were treated with PBS, anti-PD-L1 (10 mg/kg for the first dose with each subsequent dose at 5 mg/kg), anti-TGF ⁇ (10 mg/kg) or anti-PD-L1 plus anti-TGF ⁇ . For all treatments the first dose was administered i.v. on day 0 and the eight subsequent doses were administered i.p. three times per week.
- n 12 mice per group including 3 mice per a group taken down early on day 8 for pre-planned scRNA-seq analysis.
- FIG.7A Average tumor volume + SEM is shown. P-values were determined using Wilcoxon rank sum test. Mice used for scRNA-seq were not included in this average as these mice were euthanized for terminal experiments on day 8.
- FIG.7C Single cell transcriptomes for all CD45- cells visualized on a Uniform Manifold Approximation and Projection (UMAP) plot. Cell clusters are numbered.
- FIG.7G Dot plot showing chemokine gene expression in different cell types under different treatments. The size of the dots indicates percent cells expressing the chemokine gene, while the color contrast of the dots indicates average gene expression level.
- FIG.7H Survival plot for the EMT6 study. P-values were determined using log-rank test.
- FIG.7I CD3 IHC score in EMT6 tumors. Each point is the IHC score representing the density of CD3+ cells from an individual mouse.
- FIG.8A-8B CCL5 expression correlates with TIL score.
- the scatter plot shows the correlation between CCL5 expression and pathology image-based tumor infiltrating lymphocyte (TIL) score in breast cancer (BRCA) in TCGA. Each point represents a TCGA tumor sample. Both axes are shown in Z-score space. TIL score is inferred computationally from H&E-stained pathology images of the tumor samples.
- FIG.10E Spider plots showing CT26 tumor volume for individual mice over time.
- FIG.10F Survival plot for the study. P-values were determined using log-rank test. Non-significant p-values are not shown for all panels.
- FIG.11A-11G scRNA-seq of EMT6 tumors from mice treated with anti-PD-L1 ⁇ anti-TGF- ⁇ .
- FIG.11A Number of up- (top panel) and down- (bottom panel) regulated genes in various cell types, when comparing each treatment sample to the PBS sample.
- FIG. 11B UMAP plot showing the two subclusters of fibroblasts.
- FIG.11F Gene concept network showing representative enriched terms for the genes downregulated in Fib_0 in the aPD-L1 plus aTGF- ⁇ group. The downregulated genes associated with the pathway are shown, with the color contrast of the nodes representing log2 fold change in gene expression relative to the PBS group.
- FIG.11G Heatmap showing relative (z-scored per row) gene expression levels for representative differentially expressed genes in Fib_0.
- FIG.12A-12B Quality control of single cell RNA-seq of anti-PD-L1 ⁇ anti-TGF- ⁇ treated EMT6 tumor-bearing mice.
- FIG.14D Functional enrichment analysis of genes upregulated in the Mac_0 subcluster, for each of the treatment group when compared to the PBS group.
- the size and color contrast of the circles indicate the number of upregulated genes and the -log10 adjusted p-value, respectively, for the enriched terms indicated on the y-axis.
- FIG.14E Gene concept network showing representative enriched terms for the genes upregulated in Mac_0 in the aPD-L1 plus aTGF- ⁇ group. The upregulated genes associated with the pathway are shown, with the color contrast of the nodes representing log2 fold change in gene expression relative to the PBS group.
- FIG.15A-15C Tumor volumes (mm 3 ) from mice with chemokines CXCL9, CCL5, CXCL9 and CCL5, WARS, WARS + WARS at DOI, or control (PBS) alone or in combination with aPD-1.
- FIG.15A shows a comparison of tumor volumes (mm 3 ) from mice only treated with chemokines CXCL9, CCL5, CXCL9 and CCL5, WARS, WARS + WARS at DOI, or control (PBS). Mean tumor volume ⁇ SEM is shown.
- FIG.15B shows comparison of tumor volumes (mm 3 ) from mice treated with chemokines CXCL9, CCL5, CXCL9 and CCL5, WARS, or WARS + WARS at DOI in combination with aPD-1. Mean tumor volume ⁇ SEM is shown.
- the last observation was carried forward. Data is shown through day 18, as some animals were euthanized and had their tumors collected at our request on day 19 for potential future analysis.
- the columns “pct.1” and “pct.2” represent percent cells expressing the gene in the first treatment group and the second treatment group, respectively.
- the column “avg_logFC” represents log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the antibody treated group. P-values, as shown in the “p_val” column, were determined using Wilcoxon rank sum test.
- the column “p_val_adj” shows adjusted p- value, based on bonferroni correction using all genes in the dataset. [0046] Table 2. Enriched terms as determined by functional enrichment analysis using DE genes from the EMT6 single cell RNA-seq experiment.
- the functional enrichment analysis was performed using all up- or down-regulated genes (indicated in the “genes_used” column) from the CD45+ or CD45- cells (indicated in the “cells” column), for a given treatment group comparison (indicated in the “comparison” column).
- the categories tested were biological process (BP), molecular function (MF), and cellular component (CC), as shown in the “ONTOLOGY” column.
- Table 3 Differentially expressed (DE) genes in fibroblasts. Differential expression analysis was performed within each fibroblast subcluster, indicated in the “cluster” column. The “comparison” column indicates the treatment group comparison in which a given DE gene was observed.
- the columns “pct.1” and “pct.2” represent percent cells expressing the gene in the first treatment group and the second treatment group, respectively.
- the column “avg_logFC” represents log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first treatment group.
- the column “p_val_adj” shows adjusted p-value, based on Bonferroni correction using all genes in the dataset. [0048] Table 4. Differentially expressed (DE) genes in macrophages. Differential expression analysis was performed within each macrophage subcluster, indicated in the “cluster” column.
- the “comparison” column indicates the treatment group comparison in which a given DE gene was observed.
- the columns “pct.1” and “pct.2” represent percent cells expressing the gene in the first treatment group and the second treatment group, respectively.
- the column “avg_logFC” represents log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first treatment group. Pvalues, as shown in the “p_val” column, were determined using Wilcoxon rank sum test.
- the column “p_val_adj” shows adjusted p-value, based on Bonferroni correction using all genes in the dataset.
- CCL5 can be a protein encoded by the CCL5 gene of other mammals, such as a non-human primate (e.g., a monkey), a rodent (e.g., a mouse or a rat), a dog, a camel, a cat, a cow, a goat, a horse, or a sheep.
- CCL5 can be a protein naturally expressed by cells, a recombinant or synthetic protein.
- chemokine analog refers to a protein including an active fragment of a chemokine or a modification thereof.
- a chemokine analog is a polypeptide having one or more amino acid additions, deletions or substitutions compared to the chemokine.
- the term “chemokine mimetic” as used herein refers to a chemokine; a chemokine analog; a fusion of the chemokine or its analog to a second peptide or polypeptide; or the chemokine or its analog conjugated to a conjugate moiety.
- the chemokine mimetic is a fusion of the chemokine or its analog to a second peptide or polypeptide, optionally with a linker peptide therebetween.
- the chemokine mimetic comprises a chemokine or its analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is not an in- frame fusion. In various embodiments, the chemokine mimetic comprises a chemokine or its analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is an in-frame fusion.
- active fragment refers to a fragment of the chemokine (e.g., N-terminal fragments, C-terminal fragments) that is sufficient for activation of or binding to its receptor.
- an “active-fragment” of a chemokine can include fragments of the chemokine amino acid sequence that are important for receptor binding and activation.
- CCL5 analog refers to a protein including an active fragment of CCL5 or a modification thereof.
- a CCL5 analog is a polypeptide having the sequence of SEQ ID NO: 2.
- a CCL5 analog is a polypeptide having one or more amino acid additions, deletions or substitutions compared to SEQ ID NO: 2.
- CCL5 mimetic refers to CCL5; a CCL5 analog; a fusion of CCL5 or CCL5 analog to a second peptide or polypeptide; or CCL5 or CCL5 analog conjugated to a conjugate moiety.
- the CCL5 mimetic is a fusion of CCL5 or a CCL5 analog to a second peptide or polypeptide, optionally with a linker peptide therebetween.
- the CCL5 mimetic comprises CCL5 or a CCL5 analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is not an in-frame fusion.
- the CCL5 mimetic comprises CCL5 or a CCL5 analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is an in-frame fusion.
- active fragment refers to a fragment of CCL5 (e.g., N-terminal fragments, C-terminal fragments) that is sufficient for activation of or binding to its receptor (e.g., CCR1, CCR3, CCR5).
- an “active-fragment” of CCL5 can include fragments of the CCL5 amino acid sequence that are important for receptor binding and activation.
- bi-specific antibody and “multi-specific antibody” are used herein in the broadest sense understood in the art and include, but are not limited to, the molecular formats described in Spies et al., Molecular Immunology 67:95-106 (2015), incorporated herein by reference in its entirety, and certain types of immunoglobulin molecules comprising one or more antigen-binding domains that specifically bind to two or more different antigens or epitopes.
- An antigen-binding domain is a portion of antigen binding protein that is capable of binding to an antigen or epitope.
- bi-specific antibody targeting PD-L1 and TGF ⁇ can be M7824, an anti-PD-L1/TGF ⁇ Trap fusion protein.
- bi- specific antibodies disclosed in US9,676,863, incorporated by reference in its entirety herein are used.
- the term “PD-L1,” “PD-L1 protein,” and “PD-L1 antigen” are used interchangeably herein to refer to human PD-L1, or any variants (e.g., splice variants and allelic variants), isoforms, and species homologs of human PD-L1 that are naturally expressed by cells, or that are expressed by cells transfected with a polynucleotide encoding PD-L1.
- the PD-L1 protein is a PD-L1 protein naturally expressed by a primate (e.g., a monkey or a human), a rodent (e.g., a mouse or a rat), a dog, a camel, a cat, a cow, a goat, a horse, or a sheep.
- the PD-L1 protein is human PD-L1 (hPD-L1; SEQ ID NO: 3).
- PD-L1 antibody used interchangeably herein with “anti-PD-L1 antibody”, as used herein refers to an antibody comprising one or more antigen-binding domains that specifically bind to an antigen or epitope of PD-L1.
- PD-L1 antibodies which have been developed for therapeutic use can be used in various embodiments of the present disclosure.
- the PD-L1 antibodies include, but not are limited to, atezolizumab, avelumab, and durvalumab. [0063] Any of the PD-L1 antibodies or antigen binding domains disclosed in PCT/US19/68826, which is incorporated herein by reference in its entirety herein, can be used.
- VH variable heavy chain
- an antibody or antigen-binding protein is selected from A201-A228.
- an antibody or antigen-binding protein having one or more CDR sequences of any one of A201-A228 is used.
- the V L and the V H are a cognate pair.
- TGF ⁇ TGF ⁇ protein
- TGF ⁇ antigen any variants (e.g., splice variants and allelic variants), isoforms (e.g., TGF ⁇ 1-3), and species homologs of human TGF ⁇ that are naturally expressed by cells, or that are expressed by cells transfected with a TGF ⁇ gene.
- TGF ⁇ inhibitor is a small molecule.
- TGF ⁇ inhibitors which have been developed for therapeutic use can be used in various embodiments of the present disclosure.
- the TGF ⁇ inhibitors include, but not are limited to, fresolimumab.
- the TGF ⁇ inhibitors include, but not are limited to, galunisertib, fresolimumab, lucanix, vigil, TGFbRII, TGFBRII-Fc (e.g., TGFBRII trap) and trabedersen. 6.2.
- Other interpretational conventions [0069] Ranges recited herein are understood to be shorthand for all of the values within the range, inclusive of the recited endpoints.
- a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50.
- reference to a compound that has one or more stereocenters intends each stereoisomer, and all combinations of stereoisomers, thereof. 6.3. Overview of experimental results [0071] The present disclosure provides therapeutic methods for enhancing T cell and/or NK cell infiltration and response to PD-1/PD-L1 blockade for treatment of cancer.
- Applicant measured transcriptional changes induced by therapeutic regimen using anti-PD-L1 and anti-TGF ⁇ antibodies and identified that anti-TGF ⁇ antibody blocks TGF ⁇ - producing tumor cells from inducing cancer-associated fibroblasts to express collagen and other matrix remodeling genes. Additionally, Applicant found anti-PD-L1 with or without anti-TGF ⁇ induced expression of several chemokines associated with the recruitment of cytotoxic T cells. Additionally, Applicant found a TGF ⁇ inhibitor with or without anti-PD-L1 induced expression of several chemokines associated with the recruitment of cytotoxic T cells.
- chemokines are associated with lymphocyte, T cell, NK cell and dendritic cell infiltration in human tumors, with CCL5 being most highly correlated with immune infiltration across tumor types. This suggested that chemokines, in particular CCL5, will enhance T cell and/or NK cell infiltration and efficacy of PD-1/PD-L1 blockade.
- Intratumoral administration of CCL5 in fact, increased the frequency of CCR5+ CD8 T cells within the tumor and administration of CCL5 alone, or CCL5 plus atezolizumab (anti- PD-L1 antibody) inhibited tumor growth in the otherwise excluded murine tumor model MC38.
- CCL5 alone can help immune cell infiltration into tumors
- CCL5 can help immune cell infiltration into tumors and enhance response to PD- L1 blockade, by either limiting the physical barrier or providing exogenous immune cell recruitment signals, or both
- CCL5 mimetic alone activates NK cell or T cell activity and recruits activating T cells and/or NK cells to a tumor microenvironment.
- intratumoral administration of an anti-TGF ⁇ in combination with systemic administration of anti-PD-L1 antibody significantly reduces tumor volume.
- the combination intratumoral administration of an anti-TGF ⁇ in combination with systemic administration of anti-PD-L1 antibody can be used to treat cancer. 6.4.
- the isolated chemokine mimetic is two or more isolated chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof.
- the chemokine mimetic is a CCL5 mimetic.
- the CCL5 analog comprises an active fragment of a human CCL5 peptide.
- the chemokine mimetic is a CXCL9 mimetic.
- the CXCL9 analog comprises an active fragment of a human CXCL9 peptide.
- the chemokine mimetic is a combination of CCL5 and CXCL9 mimetic. [0080] In some embodiments, the chemokine mimetic is a CXCL13 mimetic. In some embodiments, the CXCL13 analog comprises an active fragment of a human CXCL13 peptide. [0081] In some embodiments, the chemokine mimetic is a CXCL10 mimetic. In some embodiments, the CXCL10 analog comprises an active fragment of a human CXCL10 peptide. [0082] In some embodiments, the chemokine mimetic is a CXCL11 mimetic.
- the CXCL11 analog comprises an active fragment of a human CXCL11 peptide.
- the chemokine mimetic is a WARS mimetic.
- the WARS analog comprises an active fragment of a human WARS peptide.
- the chemokine mimetic is a CL-1 mimetic.
- the XCL-1 analog comprises an active fragment of a human XCL-1 peptide.
- the CCL5 mimetic is a human CCL5 peptide, wherein the CCL5 peptide has a sequence of SEQ ID NO: 1.
- the CCL5 mimetic is a CCL5 analog.
- the CCL5 analog is a polypeptide having the sequence of SEQ ID NO: 1.
- the CCL5 analog comprises an active fragment of a human CCL5 peptide.
- the active fragment of human CCL5 comprises amino acids 12-22 of SEQ ID NO: 1.
- the active fragment of human CCL5 comprises one or more of the following amino acid residues selected from the group consisting of: P2, Y3, D6, T7, F12, I15, and R17.
- the CXCL10 mimetic is a CXCL10 analog having a longer half-life in vivo as compared to CXCL10.
- the CXCL11 mimetic is a CXCL11 analog having a longer half-life in vivo as compared to CXCL11.
- the WARS mimetic is a WARS analog having a longer half-life in vivo as compared to WARS.
- the XCL-1 mimetic is an XCL-1 analog having a longer half-life in vivo as compared to XCL-1.
- the CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic is a conjugate of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, XCL-1, or WARS, or a CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS analog to a conjugate moiety.
- the CCL5 mimetic is a conjugate of CCL5 or a CCL5 analog to a conjugate moiety.
- the conjugate of CCL5 or CCL5 analog comprises a binding site.
- the conjugate moiety is an antibody or antigen-binding fragment specific to a target tissue for treatment. In some embodiments, the conjugate moiety is an antibody or antigen-binding fragment specific to a tumor antigen. [0093] In some embodiments, the conjugate moiety is selected from the group consisting of: XTEN, a proline-alanine-serine polymer (PAS), a homopolymer of glycine residues (HAP), a gelatin-like protein (GLP), a signal peptide and an elastin-like peptide (ELP).
- PAS proline-alanine-serine polymer
- HAP homopolymer of glycine residues
- GLP gelatin-like protein
- ELP elastin-like peptide
- the CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic comprises one or more modified or non-naturally occurring amino acids, selected from the group consisting of: a steric enantiomer (D isomer), a rare amino acid of plant origin, a non-naturally occurring amino acid or amino acid mimetic, or have been modified by any one or more modifications selected from acetylation, acylation, phosphorylation, dephosphorylation, glycosylation, myristollation, amidation, aspartic acid/asparagine hydroxylation, phosphopantethane attachment, methylation, methylthiolation, prensyl group attachment, intein N-/C-terminal splicing, ADP-ribosylation, bromination, citrullination, deamination, dihydroxylation, formylation, geranyl-geranilation, glycation, palmitoylation, ⁇
- D isomer a
- the CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic is chemically-synthesized and comprises one or more non-peptide bonds.
- Polynucleotides encoding a chemokine mimetic and cells comprising the polynucleotides [0096] In another aspect, the present disclosure provides a polynucleotide encoding the chemokine mimetic.
- Codon-optimization refers to the exchange in a sequence of interest of codons that are generally rare in highly expressed genes of a given species by codons that are generally frequent in highly expressed genes of such species, such codons encoding the same amino acids as the codons that are being exchanged.
- codons that are generally frequent in highly expressed genes of such species, such codons encoding the same amino acids as the codons that are being exchanged.
- the skilled artisan will be able to design and utilize suitable codon optimizations of the polynucleotide disclosed herein.
- Within the scope of the present disclosure are also the polynucleotide having a sequence obtained due to the degeneration of the genetic code of the nucleotide sequences of the chemokine mimetics described herein.
- the polynucleotide is in a viral or a non-viral vector.
- the vector can be used to deliver the polynucleotide to a target cell in vitro or in vivo.
- the polynucleotide is in a viral construct.
- the polynucleotide is in a plasmid.
- the viral or non-viral vector comprises a nucleotide sequence encoding CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic, e.g., a coding sequence of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS.
- the present disclosure provides a cell comprising a chemokine mimetic disclosed herein.
- the cell comprises a polynucleotide encoding a chemokine mimetic.
- the cell is generated by transformation of the cell with a viral or non-viral vector containing the polynucleotide encoding a chemokine mimetic.
- a pharmaceutical composition comprising a chemokine mimetic described herein.
- a pharmaceutical composition comprises a polynucleotide encoding a chemokine mimetic, or a cell comprising a chemokine mimetic, instead of a chemokine mimetic protein.
- the chemokine mimetic, polynucleotide or cellin the pharmaceutical composition can be formulated in any appropriate pharmaceutical composition for administration by any suitable route of administration.
- Suitable routes of administration include, but are not limited to, oral, intravenous, and intratumoral routes of administration. The most suitable route may depend upon the condition and disorder of the recipient.
- the formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods known in the art of pharmacy.
- a composition can be administered alone or in combination with other treatments, for administration either simultaneously or sequentially dependent upon the condition to be treated.
- the pharmaceutical composition can be administered in combination with one or more drugs targeting a different check point receptor, such as CTLA-4 inhibitor (e.g., anti-CTLA-4 antibody) or TIGIT inhibitor (e.g., anti-TIGIT antibody).
- CTLA-4 inhibitor e.g., anti-CTLA-4 antibody
- TIGIT inhibitor e.g., anti-TIGIT antibody
- a composition can be administered alone or in combination with an antibody, such as an anti-TGFb antibody, an anti-PD-L1 antibody, or an anti-PD-1 antibody.
- a pharmaceutical composition comprising a chemokine mimetic further comprises one or more additional therapeutic agents.
- the present disclosure provides a pharmaceutical composition comprising a TGF ⁇ inhibitor.
- the pharmaceutical composition is formulated for intratumoral administration.
- the present disclosure provides a pharmaceutical composition comprising a PD-L1 antibody.
- the pharmaceutical composition is formulated for systemic administration.
- Formulations of the present methods suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets each containing a predetermined amount of the active ingredient; as a powder or granules; as a solution or a suspension in an aqueous liquid or a non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion.
- the active ingredient may also be presented as a bolus, electuary, pump, or paste.
- Formulations for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain antioxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient.
- Formulations for parenteral administration also include aqueous and non-aqueous sterile suspensions, which may include suspending agents and thickening agents.
- the formulations may be presented in unit-dose of multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of a sterile liquid carrier, for example saline, phosphate-buffered saline (PBS) or the like, immediately prior to use.
- a sterile liquid carrier for example saline, phosphate-buffered saline (PBS) or the like.
- Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described.
- the pharmaceutical composition may comprise one or more pharmaceutical excipients.
- any suitable pharmaceutical excipient may be used, and one of ordinary skill in the art is capable of selecting suitable pharmaceutical excipients. Accordingly, the pharmaceutical excipients provided below are intended to be illustrative, and not limiting. Additional pharmaceutical excipients include, for example, those described in the Handbook of Pharmaceutical Excipients, 8th Revised Ed. (2017), incorporated by reference in its entirety.
- the pharmaceutical composition described herein can be used for treatment of cancer or infection.
- the pharmaceutical composition can be in any form appropriate for human or veterinary medicine, including a liquid, an oil, an emulsion, a gel, a colloid, an aerosol, nanoparticle (e.g., lipid nanoparticle), lipid bilayer, or a solid.
- the pharmaceutical composition can be formulated for administration by any route of administration appropriate for human or veterinary medicine, including enteral and parenteral routes of administration.
- the pharmaceutical composition is formulated for oral administration, for buccal administration, or for sublingual administration.
- the pharmaceutical composition is formulated for intravenous, intramuscular, intratumoral, subcutaneous administration, or a combination thereof.
- the pharmaceutical composition is formulated for intravenous infusion.
- the pharmaceutical composition is formulated for intrathecal or intracerebroventricular administration.
- the active ingredient will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability.
- a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability.
- isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection.
- Preservatives, stabilisers, buffers, antioxidants and/or other additives can be included, as required.
- the pharmaceutical composition is in a unit dosage form.
- the unit dosage form is in a vial, ampule, bottle, or pre-filled syringe.
- the unit dosage form contains 0.01 mg, 0.1 mg, 0.5 mg, 1 mg, 2.5 mg, 5 mg, 10 mg, 12.5 mg, 25 mg, 50 mg, 75 mg, or 100 mg of a chemokine mimetic.
- the unit dosage form contains 125 mg, 150 mg, 175 mg, or 200 mg of the chemokine mimetic.
- the unit dosage form contains 250 mg of the chemokine mimetic.
- the pharmaceutical unit dosage form contains 0.1 to 10 ⁇ g of thechemokine mimetic per 50 mm 3 to 1000 mm 3 tumor area.
- the pharmaceutical composition in the unit dosage form is in liquid form.
- the unit dosage form contains between 0.1 mL and 50 ml of the pharmaceutical composition.
- the unit dosage form contains 1 ml, 2.5 ml, 5 ml, 7.5 ml, 10 ml, 25 ml, or 50 ml of pharmaceutical composition.
- the unit dosage form is a vial containing 1 ml of the pharmaceutical composition at a concentration of 0.01 mg/ml, 0.1 mg/ml, 0.5 mg/ml, or 1mg/ml of a chemokine mimetic.
- the unit dosage form is a vial containing 2 ml of the pharmaceutical composition at a concentration of 0.01 mg/ml, 0.1 mg/ml, 0.5 mg/ml, or 1mg/ml.
- the pharmaceutical composition in the unit dosage form is in solid form, such as a lyophilate, suitable for solubilization.
- Unit dosage form embodiments suitable for subcutaneous, intradermal, intratumoral, or intramuscular administration include preloaded syringes, auto-injectors, and autoinject pens, each containing a predetermined amount of the pharmaceutical composition described hereinabove.
- the unit dosage form is a preloaded syringe, comprising a syringe and a predetermined amount of the pharmaceutical composition.
- the syringe is adapted for subcutaneous administration.
- the syringe is suitable for self-administration.
- the preloaded syringe is a single use syringe.
- the preloaded syringe contains about 0.1 mL to about 0.5 mL of the pharmaceutical composition. In certain embodiments, the syringe contains about 0.5 mL of the pharmaceutical composition.
- the syringe contains about 1.0 mL of the pharmaceutical composition. In particular embodiments, the syringe contains about 2.0 mL of the pharmaceutical composition. In some embodiments, the syringe contains from 2.0 mL to 5.0 mL of the pharmaceutical composition.
- the pharmaceutical composition is administered in an amount sufficient to increase filtration of immune cells and enhance the anti-tumor activity of an anti-PD-L1 antibody, TGF- ⁇ inhibitor, or both. 6.7. Dosage Regimens [00128] In various embodiments, the pharmaceutical compositions described in the present disclosure is administered at a dose sufficient to treat a disease or condition, such as cancer, by itself or in combination with an additional therapeutic agent.
- the chemokine mimetic is administered at a dose sufficient to treat a disease or condition, such as cancer, by itself or in combination with an additional therapeutic agent.
- the chemokine mimetic is present in the pharmaceutical composition at a concentration of at least 0.01 mg/ml, at least 0.05 mg/ml, at least 0.1mg/ml, at least 0.5mg/ml, or at least 1mg/ml.
- the chemokine mimetic is present in the pharmaceutical composition at a concentration of at least 0.5 mg/ml, 1 mg/ml, 2 mg/ml, 3 mg/ml, 4 mg/ml, 5 mg/ml, 10 mg/ml, 15 mg/ml, 20 mg/ml, or 25 mg/ml. In certain embodiments, the chemokine mimetic is present in the pharmaceutical composition at a concentration of at least 30 mg/ml, 35 mg/ml, 40 mg/ml, 45 mg/ml or 50 mg/ml. [00131] In some embodiments, the chemokine mimetic is administered in an amount of at least 0.001 mg/kg.
- the chemokine mimetic is administered in an amount of at least 0.01 mg/kg. In certain embodiments, the chemokine mimetic is administered in an amount of at least 0.05 mg/kg. In certain embodiments, the chemokine mimetic is administered in an amount of at least 0.5 mg/kg. In certain embodiments, the chemokine mimetic is administered orally in an amount of at least 1 mg/kg. In certain embodiments, the dose is at least 2 mg/kg, at least 3 mg/kg, at least 4 mg/kg, at least 5 mg/kg, at least 6 mg/kg, at least 7 mg/kg, at least 8 mg/kg, at least 9 mg/kg, or at least 10 mg/kg.
- the dose of the chemokine mimetic is at least 0.01 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 0.1 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 0.05 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 0.5 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 1 mg/kg.
- the dose of chemokine mimetic is at least 1.5 mg/kg, at least 2 mg/kg, at least 2.5 mg/kg, at least 3 mg/kg, at least 3.5 mg/kg, at least 4 mg/kg, at least 4.5 mg/kg, at least 5 mg/kg, at least 5.5 mg/kg, at least 6 mg/kg, at least 6.5 mg/kg, at least 7 mg/kg, at least 7.5 mg/kg, at least 8 mg/kg, at least 8.5 mg/kg, at least 9 mg/kg, at least 9.5 mg/kg, or at least 10 mg/kg.
- the dose is at least 5 mg/kg, at least 10 mg/kg at least 15 mg/kg, at least 20 mg/kg, at least 25 mg/kg, 30 mg/kg, at least 35 mg/kg, at least 40 mg/kg, at least 45 mg/kg, at least 50 mg/kg, at least 55 mg/kg, at least 60 mg/kg, at least 65 mg/kg, at least 70 mg/kg, at least 75 mg/kg, at least 80 mg/kg, at least 85 mg/kg, at least 90 mg/kg, at least 95 mg/kg, at least 100 mg/kg, at least 125 mg/kg, at least 150 mg/kg, at least 160 mg/kg, at least 175 mg/kg, or at least 200 mg/kg.
- the dose is 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg.
- the dose is 0.001 mg/kg to 100 mg/kg per day.
- the dose is 2 mg/kg to 100 mg/kg per day.
- the dose is 25 mg/kg to 1000 mg/kg per day.
- the dose of the chemokine mimetic is at least 0.5 mg/kg.
- the dose is at least 1 mg/kg. In certain embodiments, the dose is at least 40 mg/kg, at least 40 mg/kg, at least 50 mg/kg, at least 100 mg/kg, at least 150 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 500 mg/kg, 750 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 25 mg/kg to 1,000 mg/kg per day.
- the flat dose is 0.001 mg, 0.01 mg, 0.1 mg, 0.2 mg, 0.3 mg, 0.4 mg, 0.5 mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, or 1 mg. In some embodiments, the flat dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, or 10 mg. In some embodiments, the flat dose is 11 mg, 12 mg, 13 mg, 14 mg, 15 mg, 16 mg, 17 mg, 18 mg, 19 mg, or 20 mg. In some embodiments, the flat dose is 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 46 mg, 47 mg, 48 mg, 49 mg, or 50 mg.
- the flat dose is 40 mg, 42 mg, 44 mg, 46 mg, 48 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, or 100 mg. In some embodiments, the flat dose is 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, or 1000 mg. In some embodiments, the flat dose ranges from 0.1 to 40 mg. In some embodiments, the flat dose ranges from 12 to 30 mg. In some embodiments, the flat dose is 0.1 – 1 mg, 1 – 10 mg, 10 – 15 mg, 15 – 20 mg, 20 – 30 mg, 30 – 40 mg, or 40 – 50 mg.
- the flat dose is 1 – 50 mg, 50 – 100 mg, 100 mg – 200 mg, 200 mg – 300 mg, 300 mg – 400 mg, 400 mg – 500 mg, 500 mg – 600 mg, 600 mg – 700 mg, 700 mg – 800 mg, 800 mg – 900 mg, or 900 mg – 1000 mg.
- the dose is 1-5000 mg.
- the flat dose is 12-30 mg.
- the flat dose is 1-11 mg.
- the flat dose is 12-40 mg.
- the dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 325 mg, 350 mg, 375 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 950 mg, or 1000 mg.
- the dose is determined based on the tumor volume. In some embodiments, the dose is 0.01 to 100 ⁇ g for 50 – 1000mm 3 tumor volume. In some embodiments, the dose is 0.1 to 10 ⁇ g for 50 – 1000mm 3 tumor volume. In some embodiments, the dose is 0.1 to 10 ⁇ g for 50 mm 3 tumor volume. In some embodiments, the dose is 0.1 to 10 ⁇ g for 100 mm 3 tumor volume. In some embodiments, the dose is 0.1 to 10 ⁇ g for 500 mm 3 tumor volume. In some embodiments, the dose is 0.1 to 10 ⁇ g for 1000 mm 3 tumor volume. [00140] The chemokine mimetic can be administered in a single dose or in multiple doses.
- the chemokine mimetic can be administered in multiple doses, e.g., to different tumor sites or throughout a tumor.
- the chemokine mimetic is administered once a day, once every 2 days, once every 3 days, once every 4 days, once every 5 days, once every 6 days, once every 7 days, once every 14 days, once every 21 days, once every 28 days, or once a month.
- chemokine mimetic is administered twice a day, twice every 2 days, twice every 3 days, twice every 4 days, twice every 5 days, twice every 6 days, twice every 7 days, twice every 14 days, twice every 21 days, twice every 28 days, or twice a month.
- the chemokine mimetic is administered 1 time a week, 2 times a week, 3 times a week, four times a week, or five times a week.
- the present disclosure provides a pharmaceutical composition comprising the combination of an anti-PD-L1 antibody and TGF ⁇ inhibitor (e.g.,anti-TGF ⁇ antibody).
- the anti-PD-L1 antibody and TGF ⁇ inhibitor is administered at individual doses sufficient to treat a disease or condition, such as cancer, in when administered together in combination.
- the pharmaceutical composition can be admininistered for a combination therapy.
- aspects of the present disclosure also include a method of treating cancer by: administering systemically to a subject with cancer, an effective amount of an anti-PD-L1 antibody; and administering intratumorally to the subject, an TGF ⁇ inhibitor (e.g., anti-TGF ⁇ antibody).
- an TGF ⁇ inhibitor e.g., anti-TGF ⁇ antibody
- the pharmaceutical composition includes the combination of an anti-PD-L1 antibody (e.g., for administering systemically) and an TGF ⁇ inhibitor (e.g., anti-TGF ⁇ antibody) (e.g., for administering intratumorally).
- the anti-PD-L1 antibody is present in the pharmaceutical composition at a concentration of at least 0.01 mg/ml, at least 0.05 mg/ml, at least 0.1mg/ml, at least 0.5mg/ml, or at least 1mg/ml. In certain embodiments, the anti-PD- L1 antibody is present in the pharmaceutical composition at a concentration of at least 0.5 mg/ml, 1 mg/ml, 2 mg/ml, 3 mg/ml, 4 mg/ml, 5 mg/ml, 10 mg/ml, 15 mg/ml, 20 mg/ml, or 25 mg/ml.
- the anti-PD-L1 antibody is present in the pharmaceutical composition at a concentration of at least 30 mg/ml, 35 mg/ml, 40 mg/ml, 45 mg/ml or 50 mg/ml. [00143] In some embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.001 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.01 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.05 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.5 mg/kg.
- the anti-PD-L1 antibody is administered orally in an amount of at least 1 mg/kg.
- the dose is at least 2 mg/kg, at least 3 mg/kg, at least 4 mg/kg, at least 5 mg/kg, at least 6 mg/kg, at least 7 mg/kg, at least 8 mg/kg, at least 9 mg/kg, or at least 10 mg/kg.
- the dose of the anti-PD-L1 antibody is at least 0.01 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.1 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.05 mg/kg.
- the dose of the anti-PD-L1 antibody is at least 0.5 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 1 mg/kg. In various embodiments, the dose of anti-PD-L1 antibody is at least 1.5 mg/kg, at least 2 mg/kg, at least 2.5 mg/kg, at least 3 mg/kg, at least 3.5 mg/kg, at least 4 mg/kg, at least 4.5 mg/kg, at least 5 mg/kg, at least 5.5 mg/kg, at least 6 mg/kg, at least 6.5 mg/kg, at least 7 mg/kg, at least 7.5 mg/kg, at least 8 mg/kg, at least 8.5 mg/kg, at least 9 mg/kg, at least 9.5 mg/kg, or at least 10 mg/kg.
- the dose is at least 5 mg/kg, at least 10 mg/kg at least 15 mg/kg, at least 20 mg/kg, at least 25 mg/kg, 30 mg/kg, at least 35 mg/kg, at least 40 mg/kg, at least 45 mg/kg, at least 50 mg/kg, at least 55 mg/kg, at least 60 mg/kg, at least 65 mg/kg, at least 70 mg/kg, at least 75 mg/kg, at least 80 mg/kg, at least 85 mg/kg, at least 90 mg/kg, at least 95 mg/kg, at least 100 mg/kg, at least 125 mg/kg, at least 150 mg/kg, at least 160 mg/kg, at least 175 mg/kg, or at least 200 mg/kg.
- the dose is 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg.
- the dose is 0.001 mg/kg to 100 mg/kg per day.
- the dose is 2 mg/kg to 100 mg/kg per day.
- the dose is 25 mg/kg to 1000 mg/kg per day.
- the dose of the anti-PD-L1 antibody is at least 0.5 mg/kg.
- the dose is at least 1 mg/kg. In certain embodiments, the dose is at least 40 mg/kg, at least 40 mg/kg, at least 50 mg/kg, at least 100 mg/kg, at least 150 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 500 mg/kg, 750 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 25 mg/kg to 1,000 mg/kg per day.
- the dose is 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg.
- the dose is 0.001 mg/kg to 100 mg/kg per day.
- the dose is 2 mg/kg to 100 mg/kg per day.
- the dose is 25 mg/kg to 1000 mg/kg per day.
- the dose of the TGF ⁇ inhibitor is at least 0.5 mg/kg.
- the TGF ⁇ inhibitor is administered 1 time a week, 2 times a week, 3 times a week, four times a week, or five times a week. 6.8.
- Methods of Treating Cancer [00164] Aspects of the present disclosure include a method of treating cancer by administering a chemokine mimetic, e.g., an isolated CCL5 mimetic.
- the method can be used for treatment of cancer by recruiting mature NK cells and activated CD8 T cells to the tumor microenvironment.
- the method can be used for treatment of inflammation, or other disorders, such as treating infections.
- the method can also be used for recruiting, activating, and/or maturing NK cells.
- Example 1 PD-L1 plus TGF ⁇ blockade reduces tumor growth and enhances immune cell infiltration
- Human PD-L1 knock-in mice bearing MC38 tumors expressing Hu-PD-L1 (Hu-PD-L1 MC38) were treated with vehicle, anti-PD-L1 or a combination of anti-PD-L1 plus anti-TGF ⁇ .
- the EMT6 orthotopic tumor model provided with an opportunity to characterize the single cell molecular responses to anti-PD-L1 ⁇ anti-TGF- ⁇ treatment in a setting where anti-TGF- ⁇ addition overcomes resistance to anti-PD-L1 therapy.
- Eight days after the first dose three mice per a group with representative tumors were euthanized and their tumors were harvested, dissociated, and flow sorted for CD45+ immune cells and CD45- non-immune cells, which were subjected to single cell RNA sequencing (scRNA-seq) using the 10x Genomics platform. After quality control (FIG.12), single cell transcriptomic profiles were generated for 27,797 high-quality cells, including including 17,665 CD45+ and 9,795 CD45- cells.
- collagen and metalloproteinase genes such as Col1a1, Col1a2, Cthrc1, P3h4 and Mmp23 were down-regulated in fibroblasts following dual antibody blockade (FIG.2E, 2F).
- TGF ⁇ blockade synergizes with anti-PD-L1 to reprogram the peritumoral stromal fibroblasts ⁇ Mariathasan:2018dx ⁇ .
- a cell-cell communication network was generated involving all TGF ⁇ ligands and receptors using CellPhoneDB ⁇ Efremova:2020cb ⁇ .
- TGF ⁇ ligands include B cells, dendritic cells, macrophages, NK cells and interestingly, tumor cells.
- Tumor cell-expressed TGF ⁇ molecules were predicted to interact with TGF ⁇ receptors on fibroblast cells, macrophages and tumor cells themselves. Interestingly, these interactions were largely abolished following anti-TGF ⁇ treatment, alone or in combination with anti-PD-L1 (FIG.7F). This suggests that tumor cell produced TGF ⁇ can induce fibroblasts to express collagen and other extracellular matrix genes resulting in a physical barrier to T cell exclusion and that TGF ⁇ blockade counteracts this immune suppression.
- chemokines were upregulated in the macrophages of the anti-PD-L1 sample (Cxcl9, Ccl5, Ccl4, Cxcl14), the anti-TGF ⁇ sample (Ccl12, Ccl4) and the anti-PD-L1 plus anti-TGF ⁇ sample (Cxcl10, Cxcl9, Ccl4, Ccl5, Ccl3, Ccl2, Ccl7) (FIG.2I).
- chemokines were upregulated in fibroblasts, neutrophils and T cells in tumors from anti-PD-L1 and anti-PD-L1 plus anti-TGF ⁇ treated mice (FIG.7G). Additionally, anti- PDL-L1 plus anti-TGF ⁇ combination treatment led to upregulation of additional chemokines such as Cxcl1 and Cxcl2 above and beyond those induced by either single treatment alone (Table 1). Chemokines lay a critical role in recruiting various immune cells to create an inflamed TME ⁇ Vilgelm:2019jw, Nagarsheth:2017dp ⁇ .
- Mac_0 Cells in Mac_0 were characterized by expression of complement-related genes (C1qa, C1qb, C1qc) and cytokines (Spp1, Ccl12), while cells in Mac_1 expressed higher levels of several tumor-associated macrophages- related genes such as Arg1, Cebpb, and Ier3 (FIG.14C).
- C1qa complement-related genes
- Spp1, Ccl12 cytokines
- FIG.14C tumor-associated macrophages- related genes
- Differential expression and functional enrichment analysis showed that anti-PD-L1, administered alone or in combination with anti-TGF- ⁇ , resulted in enhanced immune responses in Mac_0.
- TIL tumor-infiltrating lymphocyte
- Saltz et al. used a deep learning image recognition algorithm to quantify tumor infiltrating lymphocytes from H&E-stained pathology images for 13 TCGA cancer types ⁇ Saltz:2018ig, Thorsson:2018ji ⁇ .
- Aran et al. developed a gene signature-based method termed xCell to infer immune cell abundance based on tumor gene expression profiles ⁇ Aran:2017do ⁇ .
- the immune cell abundance scores was of focus for three cytotoxicity relevant cell types: CD8+ T cells, dendritic cells and NK cells.
- CCL5 CXCL9, CXCL13, CXCL10 CXCL11, and CCL19 were, also, among the top chemokine genes associated with the gene expression-based immune scores across multiple cancer types (FIG.3C).
- FIG.8A correlation of CCL5 expression in breast cancer (BRCA) with the image-based infiltration scores is shown in FIG.8A.
- these chemokines were weakly associated with the gene expression-based immune scores for immunosuppressive Tregs and M2 macrophages (FIG.8B).
- CCL5 and CXCL9 were consistently the top chemokines associated with immune infiltration scores, as determined by the image-based and the gene signature-based methods (FIG.3B, 3C).
- CCL5 in combination with anti-PD-L1 significantly reduced tumor growth relative to all individual arms (p ⁇ 0.05;FIG.4D, 4E).
- Mice that received intratumoral CCL5 plus anti-PD-L1 combination therapy also had significantly prolonged survival compared to compared to all individual arms (p ⁇ 0.02;(FIG.4F).
- intratumorally administered CCL5 is able to overcome resistance to anti-PD-L1 therapy.
- An MC38 syngeneic tumor model was used in order to evaluate anti-tumor activity of intratumorally (i.t.) administered recombinant CCL5, CXCL9, or WARS.
- CCL5 and CXCL9 are properly primed (i.e. recruiting T cells to the tumor will not induce productive anti- tumor response if no anti-tumor T cells are activated).
- Tumor ulceration Tumor ulceration was defined as a break in the skin through the basement membrane exposing the dermis and associated vasculature and nerves. Mice with ulceration greater than 50% of the tumor total surface area or impacting the overall health and well-being were euthanized. As antibiotic use is known to affect immuno-oncology drug efficacy, no antibiotic ointment was added to tumors.
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Abstract
The present disclosure provides a method of treating cancer using a chemokine, e.g., a CCL5 mimetic. The chemokine can be used individually or in combination with other therapeutics, such as anti-PD-1 antibodies, anti-PD-Ll antibodies, and/or a ΤGFβ inhibitor (e.g., anti- ΤGFβ antibody). The present disclosure also provides a method of treating cancer using a a combination therapy with systemic administration of an anti-PD-Ll antibody and intratumoral administration of a ΤGFβ inhibitor (e.g., anti-ΤGFβ antibody).
Description
Cancer Therapeutics Comprising Chemkine or its Analog 1. CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No.63/023,790, filed May 12, 2020, the entire disclosure of which is hereby incorporated by reference in its entirety. 2. BACKGROUND [0002] Antibodies blocking the PD-1/PD-L1 immune checkpoint pathway have been approved as first-line treatments for a range of cancer types including non-small-cell lung carcinoma (NSCLC), urothelial cancer, head and neck squamous cell carcinoma (HNSCC), microsatellite instability-high cancer and melanoma. However, while effective in some patients, with some patients experiencing dramatic remissions, these immune checkpoints inhibitors are not effective in others. There is a need to improve the response rate to these agents in order to benefit more patients. 3. SEQUENCE LISTINGS [0003] The instant application contains a Sequence Listing which has been submitted via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 12, 2021, is named “48492 WO SEQ LISTING_ST25” and is 2153 kilobytes in size. 4. SUMMARY [0004] The present disclosure provides a method of treating cancer using a chemokine, e.g., an isolated CCL5 mimetic. The present disclosure also provides a method of treating an infection using a chemokine, e.g., an isolated CCL5 mimetic. The chemokine can be used individually or in combination with other therapeutics, such as anti-PD-1 orPD-L1 antibodies, or TGFβ inhibitors. The combination therapy can be combined with administration of more than one additional therapeutics (e.g., TGFβ inhibitor (e.g., anti-TGFβ antibody) and anti-PD-1 or PD-L1 antibody) to further induce T cell infiltration. [0005] The combination therapy is based on the discovery by the Applicant that chemokines, such as CCL5 and CXCL9, are highly correlated with immune cell infiltration in various human cancers. Without wishing to be bound by a theory, chemokines are believed to enhance infiltration of immune cells to improve efficacy of anti-PD-1/PD-L1 therapy. This is consistent with earlier studies which demonstrated that anti-tumor activity of anti-PD-1/PD-
L1 therapies correlates with T cell infiltration in tumors and T cell excluded tumors are less likely to respond to immune checkpoint blockade targeting the PD-1/PD-L1 pathway. The present disclosure shows that intratumorally administered CCL5 could enhance the anti- tumor activity of anti-PD-L1 antibody. [0006] Accordingly, the present disclosure provides a method of increasing immune cell infiltration and migration into a target of interest by administering a chemokine such as CCL5, e.g., an isolated CCL5 mimetic. Specifically, the method can be used for treatment of cancer by recruiting mature NK cells and activated CD8 T cells to the tumor microenvironment. The method can be used for treatment of inflammation or other disorders. The chemokines and their variants can be also used in combination with an ADCC-inducing antibody or in cancer or non-cancer application of adoptive cell therapy. [0007] In an aspect, the present disclosure provides a pharmaceutical composition, comprising: a CCL5 mimetic, or pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier. [0008] In some embodiments, the CCL5 mimetic is a human CCL5 peptide, wherein the CCL5 peptide has a sequence of SEQ ID NO: 1. In some embodiments, the CCL5 mimetic is a CCL5 analog. In some embodiments, the CCL5 analog is a polypeptide having the sequence of SEQ ID NO:1. In some embodiments, the CCL5 analog comprises an active fragment of a human CCL5 peptide. In some embodiments, the active fragment of human CCL5 comprises amino acids 12-22 of SEQ ID NO: 1. In some embodiments, the active fragment of human CCL5 comprises one or more of the following amino acid residues selected from the group consisting of: P2, Y3, D6, T7, F12, I15, and R17. In some embodiments, the CCL5 mimetic comprises a polypeptide having at least 70%, 75%, 80%, 85%, 90%, or 95% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2. In some embodiments, the CCL5 mimetic is a CCL5 analog having a longer half-life in vivo as compared to CCL5. [0009] In some embodiments, the CCL5 mimetic is a conjugate of CCL5 or a CCL5 analog to a conjugate moiety. In some embodiments, the conjugate moiety is selected from polyethylene glycol (PEG) and hyaluronic acid. In some embodiments, the conjugate moiety is selected from the group consisting of HAS, human IgG, scFv, transferrin, albumin, and an Fc domain of an immunoglobulin. In some embodiments, the conjugate moiety is selected from the group consisting of: XTEN, a proline-alanine-serine polymer (PAS), a
homopolymer of glycine residues (HAP), a gelatin-like protein (GLP), a signal peptide and an elastin-like peptide (ELP). In some embodiments, the CCL5 mimetic comprises one or more modified or non-naturally occurring amino acids, selected from the group consisting of: a steric enantiomer (D isomer), a rare amino acid of plant origin, a non-naturally occurring amino acid or amino acid mimetic, or have been modified by any one or more modifications selected from acetylation, acylation, phosphorylation, dephosphorylation, glycosylation, myristollation, amidation, aspartic acid/asparagine hydroxylation, phosphopantethane attachment, methylation, methylthiolation, prensyl group attachment, intein N-/C-terminal splicing, ADP-ribosylation, bromination, citrullination, deamination, dihydroxylation, formylation, geranyl-geranilation, glycation, palmitoylation, Į-methyl-amino acids, CĮ- methyl amino acids, and NĮ-methyl amino acids. [0010] In some embodiments, the CCL5 mimetic is chemically-synthesized and comprises one or more non-peptide bonds. In some embodiments, the pharmaceutically acceptable salt of a CCL5 mimetic, wherein the salt is hydrochloride, trihydrochloride, sulfate, mesylate, or tosylate. [0011] In some embodiments, the CCL5 mimetic activates NK cell or T cell activity. In some embodiments, the CCL5 mimetic recruits activating T cells and/or NK cells to a tumor microenvironment. [0012] In some embodiments, the pharmaceutical composition is formulated for parenteral administration. In some embodiments, the pharmaceutical composition is formulated for intratumoral injection, intravenous injection or subcutaneous injection. [0013] In another aspect, the present disclosure provides a kit for treatment of cancer, comprising: the pharmaceutical composition of the present disclosure and an additional therapeutic agent. In some embodiments, the additional therapeutic agent is an anti-PD-L1 antibody, an anti-PD-1 antibody, or a TGFβ inhibitor. In some embodiments, the additional therapeutic agent is a bispecific antibody against PD-L1 and TGFβ or against PD-1 and TGFβ. In some embodiments, the additional therapeutic agent comprises an anti-PD-L1 antibody and an anti-TGFβ antibody. In some embodiments, the additional therapeutic agent comprises an anti-PD-1 antibody and an anti-TGFβ antibody. In some embodiments, the additional therapeutic agent comprises an anti-PD-L1 antibody, wherein the anti-PD-L1 antibody is atezolizumab.
[0014] In some embodiments, the additional therapeutic agent is an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is ipilimumab. In some embodiments, the additional therapeutic agent is an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is GIGA-564. In some embodiments, the additional therapeutic agent is an anti- CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is GIGA-2328. Anti-CTLA4 antibodies that can be used in combination with the chemokine mimetics or analogs thereof of the present disclosure can be found in PCT Application Publication No.: WO2020140084A1, which is thereby incorporated by reference in its entirety. In certain embodiments, the anti-CTLA4 antibody has a heavy chain amino acid sequence set forth in SEQ ID NO:5909. In certain embodiments, the anti-CTLA4 antibody has a light chain amino acid sequence set forth in SEQ ID NO:5910. In certain embodiments, the anti-CTLA4 antibody is afucosylated. [0015] In some embodiments, the additional therapeutic agent comprises a T cell or an NK cell. In some embodiments, the additional therapeutic agent comprises a CAR-NK or CAR- macrophage cell. In some embodiments, the T cell is a CAR-T or TCR-T cell. In some embodiments, the additional therapeutic agent is an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof. In some embodiments, the additional therapeutic agent is an agent activating NK cell or T cell activity. In some embodiments, the additional therapeutic agent is an agent that recruits activating T cells and/or NK cells to a tumor microenvironment. In some embodiments, the additional therapeutic agent is a vaccine, a chemotherapeutic agent, a small molecule inhibitor, or a nucleic acid. In some embodiments, the additional therapeutic agent is a vaccine, chemotherapeutic agent, nucleic acid therapeutic, or small molecule inhibitor. [0016] In yet another aspect, the present disclosure provides a method of treating cancer, comprising the step of: administering to a subject with the cancer a therapeutically effective amount of an isolated chemokine mimetic, or pharmaceutically acceptable salt thereof. In some embodiments, the isolated chemokine mimetic is selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, and an analog thereof. In some embodiments, the isolated chemokine mimetic is two or more isolated chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. [0017] In some embodiments, the isolated chemokine mimetic is a CCL5 mimetic or pharmaceutically acceptable salt thereof. In some embodiments, the isolated chemokine
mimetic or pharmaceutically acceptable salt thereof is administered in a pharmaceutical composition further comprising a pharmaceutically acceptable carrier or excipient. [0018] In some embodiments, said administering is via intratumoral injection, intravenous injection, subcutaneous injection, or a combination thereof. In some embodiments, said administering is via intratumoral injection. In some embodiments, the method further comprises the step of administering to the subject an anti-PD-L1 antibody or an anti-PD-1 antibody. In some embodiments, the method further comprises the step of administering to the subject a TGFβ inhibitor. In some embodiments, the method further comprises the steps of administering anti-PD-L1 antibody and an anti-TGFβ antibody. In some embodiments, the method further comprises the step of administering a bi-specific antibody targeting both PD- L1 and TGFβ. In some embodiments, the method further comprises the step of administering a bi-specific antibody targeting both PD-1 and TGFβ. [0019] In some embodiments, the method further comprises the step of administering to the subject an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is ipilimumab. In some embodiments, the method further comprises the step of administering to the subject a T cell or an NK cell, optionally wherein the T cell is a CAR-T, CAR-NK,TCR-T cell. In some embodiments, the method further comprises the step of administering to the subject an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof. In some embodiments, the method further comprises the step of administering to the subject an agent activating NK cell or T cell activity. In some embodiments, the method further comprises the step of administering to the subject an agent selected from: a vaccine, a chemotherapeutic agent, a small molecule inhibitor, and a nucleic acid. [0020] In some embodiments, the cancer is selected from the group consisting of: multiple myeloma, adrenocortical carcinoma, acute myeloid leukemia, Bladder Urothelial Carcinoma, glioma, breast invasive carcinoma, glioma, Cervical squamous cell carcinoma, endocervical adenocarcinoma, cholangiocarcinoma, chronic myelogenous leukemia, colon adenocarcinoma, esophageal carcinoma, glioblastoma multiforme, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, lymphoid neoplasm diffuse large B-cell lymphoma, mesothelioma, ovarian serous cystadenocarcinoma, pancreatic adenocarcinoma, pheochromocyoma, paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma,sarcoma, skin cutaneous melanoma, mucosal melanoma, stomach adenocarcinoma, testicular germ cell tumors, thyomas, thyroid
carcinoma, uterine carcinosarcoma, uterine corps endometrial carcinoma, microsatellite instability-high cancer, basal cell carcinoma, Merkel cell carcinoma, and uveal melanoma. [0021] In some embodiments, the method further comprises the steps of: intratumorally administering a therapeutically effective amount of an isolated chemokine mimetic, or pharmaceutically acceptable salt thereof, to a subject who has been determined to have expression levels in a biological sample of one or more genes selected from the group consisting of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, CD8, CD3, TCRȕ, TCR1, WARS, CD11c, NKp46, NCR1, CD11B, FcRs, collagen genes, CTLA4, CD56, CD16, CD7 CD127, Tbet, Eomes, granzymes, and perforin that are lower than or higher than a predetermined threshold level. [0022] In some embodiments, the biological sample is a tumor biopsy. In some embodiments, the biological sample is a liquid biopsy. In some embodiments, the biological sample is a blood sample. In some embodiments, the biological sample is a sample containing cells isolated from a subject comprising a disease or condition (e.g., cancer or an infection). In some embodiments, the biological sample is a sample containing cells isolated from a donor. In certain embodiments, the biological sample is a sample containing T cells and/or NK cells isolated from subject comprising a disease or condition (e.g., cancer) or a donor. In some embodiments, the method further comprises the prior step of determining the expression levels of one or more genes selected from the group consisting of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, CD8, CD3, TCRȕ, TCR1, CD11c, WARS, NKp46 and NCR1, granzymes, and perforin in the biological sample. [0023] In some embodiments, the method further comprises the prior step of detecting CD8+ T cells, NK cells, mature NK cells, lymphocytes, fibroblasts, Tregs, or dendritic cells in the biological sample. In some embodiments, the CD8+ T cells, NK cells, mature NK cells, lymphocytes, fibroblasts, Tregs, or dendritic cells are detected by immune histochemistry. [0024] In some embodiments, the chemokine mimetic is selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. In some embodiments, the chemokine mimetic is a CCL5 mimetic or pharmaceutically acceptable salt thereof. In some embodiments, the chemokine mimetic is CCL5 or a CCL5 analog. [0025] In some embodiments, the chemokine mimetic or pharmaceutically acceptable salt thereof is administered in a pharmaceutical composition further comprising a
pharmaceutically acceptable carrier or excipient. In some embodiments, said administering is via intratumoral injection, intravenous injection or subcutaneous injection. In some embodiments, the method further comprises the step of administering to the subject an anti- PD-L1 antibody or an anti-PD-1 antibody. In some embodiments, the method further comprises the step of administering to the subject a TGFβ inhibitor. In some embodiments, the method further comprises the step of administering an anti-PD-L1 antibody and a TGFβ antibody. In some embodiments, the method further comprises the step of administering a bi- specific antibody targeting both PD-L1 and TGFβ. In some embodiments, the method further comprises the step of administering a bi-specific antibody targeting both PD-1 and TGFβ. [0026] In some embodiments, the method further comprises the step of administering to the subject an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is ipilimumab. In some embodiments, the method further comprises the step of administering to the subject a T cell or an NK cell, optionally wherein the T cell is a CAR-T, CAR-NK,TCR-T cell. In some embodiments, the method further comprises the step of administering to the subject an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof. In some embodiments, the method further comprises the step of administering to the subject an agent activating NK cell or T cell activity. In some embodiments, the method further comprises the step of administering to the subject a vaccine, nucleic acid, small molecule inhibitor, or chemotherapeutic agent. [0027] In some embodiments, the cancer is selected from the group consisting of: multiple myeloma, adrenocortical carcinoma, acute myeloid leukemia, Bladder Urothelial Carcinoma, glioma, breast invasive carcinoma, glioma, Cervical squamous cell carcinoma, endocervical adenocarcinoma, cholangiocarcinoma, chronic myelogenous leukemia, colon adenocarcinoma, esophageal carcinoma, glioblasoma multiforme, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, lymphoid neoplasm diffuse large B-cell lymphoma, mesothelioma, ovarian serous cystadenocarcinoma, pancreatic adenocarcinoma, pheochromocyoma, paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma,sarcoma, skin cutaneous melanoma, stomach adenocarcinoma, testicular germ cell tumors, thyomas, thyroid carcinoma, uterine carcinosarcoma, uterine corps endometrial carcinoma, microsatellite instability-high cancer, basal cell carcinoma, Merkel cell carcinoma, uveal melanoma, mucosal melanoma.
[0028] The present disclosure also provides a method of treating cancer by administering a combination therapy using an anti-PD-L1 antibody in combination with TGFβ inhibitor (e.g., anti-TGFβ antibody). Specifically, the anti-PD-L1 antibody is administered to a subject systemically, and the anti-TGFβ antibody is administered to a subject intratumorally. [0029] The combination therapy is based on the discovery by the Applicant that TGFβ inhibitors, when administered intratumorally, can reduce or limit the toxicity levels associated with them. Without wishing to be bound by a theory, the combination therapy including administration of systemic anti-PD-L1 and intratumoral a TGFβ inhibitor are believed to enhance infiltration of immune cells to improve efficacy of anti-PD-1/PD-L1 therapy. The present disclosure shows that intratumorally administered anti-TGFβ in combination with systemic administration of anti-PD-L1 could enhance the anti-tumor activity of anti-PD-L1 antibody. 5. BRIEF DESCRIPTION OF THE DRAWINGS [0030] FIGs.1A-1F. Anti-PD-L1 plus anti-TGFβ leads to regression of HuPD-L1-MC38 tumors in Hu-PD-L1 KI mice. HuPD-L1 KI mice bearing HuPD-L1-MC38 tumors (n=6 per a group) were dosed (IP) biweekly for three weeks with PBS, anti-PD-L1 (2mg/kg) or anti-PD- L1 (2mg/kg) plus anti-TGFβ (10mg/kg) combination. (FIG.1A) Average tumor volume + SEM is shown. P-values were determined using Wilcoxon rank sum test. (FIG.1B) Spider plots showing tumor volume for individual mice over time. (FIG.1C) Survival plot for the same study. P-values were determined using log-rank test. (FIG.1D) Mice from (FIGs.1A- 1C) for which treatment resulted in a complete response (anti-PD-L1, n = 1; anti-PD-L1 plus anti-TGFβ, n = 3) were re-challenged with s.c. HuPD-L1-MC38 tumor cells at the opposite flank. Treatment naïve, wildtype mice (n = 6) were used as a control. Average tumor volume + SEM is shown. P-values shown is for anti-PD-L1 plus anti-TGFβ vs. naïve control (Wilcoxon rank sum test), comparing tumor sizes on day 77 between naïve and aPD-L1 + aTGF-ȕ groups. (FIG.1E) CD3+ cell count in tumors by immunohistochemistry (IHC). Each point represents the number of CD3+ cells counted in the tumor from an individual mouse. Counts were obtained by counting three 200^m2 fields at 10X magnification. The horizontal black bars of the box plots indicate median cell count, while the lower and upper hinges correspond to the first and third quartiles, respectively. P-values were determined using Wilcoxon rank sum test. (FIG.1E Continued) CD3 IHC score in MC38 tumors. Each point is the IHC score representing the density of CD3+ cells from an individual mouse.
(FIG.1F) Representative CD3 IHCs images (10X magnification) from each treatment group. The brown cells are CD3 positive cells. The scale bars indicate 250^m. [0031] FIGs.2A-2I. scRNA-seq of EMT6 tumors from mice treated with anti-PD-L1 and/or anti-TGFβ. (FIG.2A) Single cell transcriptomes for all cells visualized on a Uniform Manifold Approximation and Projection (UMAP) plot. Cells are labeled based on cell type annotations, as indicated in the legend. (FIG.2B) UMAP plots for cells from individual treatment groups. Cell types are annotated with the same color contrast scheme as FIG.2A. (FIG.2C) Percent composition of cells types within the CD45- cells (top) and the CD45+ (bottom) cells. The different treatment groups are shown in different contrasting colors, as indicated in the legend. (FIG.2D) Functional enrichment analysis of genes down-regulated in CD45- cells, for each of the treatment group when compared to the PBS group. The size and color contrast of the circles indicate the number of down-regulated genes and the -log10 adjusted p-value, respectively, for the enriched terms indicated on the y-axis. (FIG.2E) Gene concept network showing representative enriched terms for the genes down-regulated in CD45- cells in the anti-PD-L1 plus anti-TGFβ group. The down-regulated genes associated with the pathway are shown, with the color contrast of the nodes representing log2 fold change in gene expression relative to the PBS group. (FIG.2F) Heatmap showing relative (z- scored per row) gene expression levels for representative differentially expressed genes in fibroblasts. (FIG.2G) Functional enrichment analysis of genes up-regulated in CD45+ cells, for each of the treatment group when compared to the PBS group. The size and color contrast of the circles indicate the number of up-regulated genes and the -log10 adjusted p-value, respectively, for the enriched terms indicated on the y-axis. (FIG.2H) Gene concept network showing representative enriched terms for the genes up-regulated in CD45+ cells in the anti- PD-L1 plus anti-TGFβ group. The up-regulated genes associated with the pathway are shown, with the color contrast of the nodes representing log2 fold change in gene expression relative to the PBS group. (FIG.2I) Heatmap showing relative (z-scored per row) gene expression levels for differentially expressed chemokine genes in macrophages. [0032] FIGs.3A-3C. Association of chemokine gene expression with inferred immune cell infiltration in TCGA cancer types. (FIG.3A) Computational workflow to identify chemokine genes associated with immune cell abundance in TCGA tumor samples. Two parallel methods are used to infer immune cell abundance: image-based estimation from pathology slides and gene signature-based estimation from RNA-seq. Linear regression models are used to find chemokine genes whose expression levels are associated with inferred immune
infiltration. (FIG.3B) Heatmap showing chemokines (rows) significantly associated with the pathology image-based TIL scores across different TCGA cancer types (columns). The color contrast indicates regression coefficients from the linear models (positive regression coefficients indicate positive association between chemokine expression and immune infiltration). (FIG.3C) Heatmap showing chemokines (rows) significantly associated with the gene signature-based immune scores across different TCGA cancer types (columns). The 3 panels represent associations with CD8 T cells, dendritic cells, and NK cells scores, respectively. The chemokines (rows) are ordered descendingly by the sum of the regression coefficients across all cancer types and all 3 immune cell types (i.e. all columns). [0033] FIGs.4A-4G. Intratumoral (IT) CCL5 in combination with systemic anti-PD-L1 treatment of mice bearing MC38 tumors led to tumor growth inhibition and increased survival. (FIG.4A) Mice bearing MC38 tumors were administered PBS or CCL5 (1ug/dose) IT three times per a week for 6 doses and on day 12 tumors were harvested and analyzed by flow cytometry Left: percent of CCR5+ cells within the CD8+ T cell population (live cells, CD3+, CD4-, CD8+, CCR5+) in PBS or CCL5 treated tumors. Right: percent of CCR5+ cells within the NK cell (live cells, NK1.1+, CD3-, CCR5+) population. Black cross bars represent median values. P-values were determined using Wilcoxon rank sum test. FIGs.4B-4C show flow cytometry-based expression of key genes in tSNE identified populations. Plots show heat maps of the indicated marker for each parameter used in tSNE analysis in PBS control (FIG.4B) or recombinant CCL5 (FIG.4C) treated samples. (FIGs.4D-4F) Mice bearing MC38 tumors were administered PBS (intratumoral, IT, 3 times a week for 3 weeks), CCL5 (IT, 1 ug/animal, 3 times a week for 3 weeks), anti-PD-L1 (1mg/kg, IP, twice a week for 3 weeks) or a combination of CCL5 and anti-PD-L1. n = 12 mice per group. (FIG.4D) Average tumor volume + SEM for each treatment group is shown. P-value was determined using Wilcoxon rank sum test. (FIG.4E) Spider plots showing tumor volume for individual mice over time. (FIG.4F) Survival plot for the same study. P-value was determined using log-rank test. (FIG.4G) Average tumor volume + SEM for CCL5 administered alone compared to PBS (Control). [0034] FIGs 5A-5D. Intratumorally administered CCL5 enhances intratumoral levels of CCD5+ CD8 T cells and mature CD11b+ NK cells. Mice bearing s.c. MC38 tumors were administered PBS or CCL5 (1 μg/dose) intratumorally three times per a week for 5 doses, and on day 12 tumors were harvested and analyzed by flow cytometry. (FIG.5A) Left: percent of CCR5+ cells within the CD8+ T cell population (live cells, CD4-, CD8+) Right:
percent of CCR5+ cells within the NK cell population (live cells, NK1.1+, CD3-). Black cross bars represent median values. P-values were determined using Wilcoxon rank sum test. (FIG.5B) Density plots (with outlier cells indicated as dots) of populations from a tSNE analysis of flow cytometry of single cell suspensions of tumors treated with intratumoral PBS (control, left) or recombinant CCL5 treated samples. Data is from live, single cells and tSNE was calculated from using data from live, single cells and data from staining with fluorescent antibodies specific for CD4, CD8, CD11b, Ly6C, Ly6G, CD3, NK1.1, CD11c, PD1, CCR5, CD44 and FOXP3 and also data from SSC. Filled black arrows indicate cell populations increased in the CCL5 treated samples. Filled black arrow 1 points to a population of CD11b+ NK cells that are substantially elevated in the CCL5 treated samples. Filled black arrow 2 points to a population of that is Ly6C-hi, SSC-int/hi, Ly6G-lo, CD11c-lo, CCR5-lo, CD11b-lo. Filled black arrow 3 points to a population that is CD11b+, Ly6G-lo, Ly6C-lo. This population is CCR5 - or lo. This indicates that CCL5 can increase the frequency of cell populations in the tumor that are not CCR5+. The open arrows denote populations that decrease upon treatment with CCL5. Open arrow 4 points to a population that has relatively high SSC. This population may not be of hematopoietic origin. Open arrow 5 points to a population that is Ly6C+ CD11b-lo. Of additional note the tSNE analysis suggests that the CCR5+ CD8 T cells are more activated with some of these cells also expressing CD44 and PD1. Density plots (with outlier cells indicated as dots) of populations from the tSNE analysis in control or CCL5 treated samples. Arrows 1 and 6 indicate CD11b+ NK cells (population 23 from FIG.5D). (FIG.5C) Frequency of NK cells (live, single cells, NK1.1+ CD3-) which express CD11b, a marker of mature, more functional NK cells, as determined by flow cytometry. Black cross bars represent median values. P-value was determined using Wilcoxon rank sum test. (FIG.5D) tSNE plots of flow data showing the expression of CCR5 within PBS control (left) or CCL5 treated tumors (right), or where populations are differentiated according to expression of marker genes as indicated in the key (bottom). Heat maps showing expression of each flow marker are in FIG.7G. [0035] FIGs.6A-6B. Anti-PD-L1 plus anti-TGFβ induced tumor growth inhibition of CT26 tumors. Mice bearing CT26 tumors (n = 10 per a group) were dosed IP two times a week for 3 weeks with PBS or anti-PD-L1 (2mg/kg) + anti-TGFβ (10mg/kg). (FIG.6A) Average tumor volume + SEM is shown. P-value was determined using Wilcoxon rank sum test. (FIG. 6B) Spider plots showing tumor volume for individual mice over time.
[0036] FIGs.7A-7I. Anti-PD-L1 plus anti-TGFβ led to tumor growth inhibition of EMT6 tumors. (FIGs.7A-7B) Mice bearing EMT6 tumors were treated with PBS, anti-PD-L1 (10 mg/kg for the first dose with each subsequent dose at 5 mg/kg), anti-TGFβ (10 mg/kg) or anti-PD-L1 plus anti-TGFβ. For all treatments the first dose was administered i.v. on day 0 and the eight subsequent doses were administered i.p. three times per week. n = 12 mice per group including 3 mice per a group taken down early on day 8 for pre-planned scRNA-seq analysis. (FIG.7A) Average tumor volume + SEM is shown. P-values were determined using Wilcoxon rank sum test. Mice used for scRNA-seq were not included in this average as these mice were euthanized for terminal experiments on day 8. (FIG.7B) Spider plots showing tumor volume for individual mice over time. Mice sacrificed for scRNA-seq (n = 3 per group) are shown in grey. (FIG.7C) Single cell transcriptomes for all CD45- cells visualized on a Uniform Manifold Approximation and Projection (UMAP) plot. Cell clusters are numbered. (FIG.7D) Violin plot showing Fap expression level in the different CD45- cell clusters. (FIG.7E) Inferred copy number for the different CD45- cell types, shown on the y-axis, along the mouse genome, shown on the x-axis. (FIG.7F) Cell-cell communication network involving all TGFβ ligands and receptors, as analyzed using CellPhoneDB. The x-axis displays the cell pairs expressing the ligand and the receptor, respectively, while the y-axis displays the corresponding ligand and receptor pairs expressed by the cell types indicated on the x-axis. The size and color contrast of the points show the significance of the interactions and log2 mean expression values of the ligand-receptor pairs, respectively, as indicated in the key. (FIG.7G) Dot plot showing chemokine gene expression in different cell types under different treatments. The size of the dots indicates percent cells expressing the chemokine gene, while the color contrast of the dots indicates average gene expression level. (FIG.7H) Survival plot for the EMT6 study. P-values were determined using log-rank test. (FIG.7I) CD3 IHC score in EMT6 tumors. Each point is the IHC score representing the density of CD3+ cells from an individual mouse. The horizontal black bars of the box plots indicate median score, while the lower and upper hinges correspond to the first and third quartiles, respectively. P-values were determined using Wilcoxon rank sum test. Non-significant p-values are not shown for all panels. [0037] FIG.8A-8B. CCL5 expression correlates with TIL score. The scatter plot shows the correlation between CCL5 expression and pathology image-based tumor infiltrating lymphocyte (TIL) score in breast cancer (BRCA) in TCGA. Each point represents a TCGA tumor sample. Both axes are shown in Z-score space. TIL score is inferred computationally
from H&E-stained pathology images of the tumor samples. Representative images for a high TIL sample and a low TIL sample are shown. (FIG.8B). Heatmap showing association of chemokines with gene signature-based immune scores for regulatory T cells (Tregs) and M2 macrophages. The order of the chemokines on the y-axis are as shown in FIG.3C, while the x-axis indicates TCGA cancer types. The color contrast indicates regression coefficients from the linear models (positive regression coefficients indicate positive association between chemokine expression and immune infiltration). [0038] FIG.9A-9B Anti-PD-L1 plus anti-TGF-ȕ in the murine tumor model HuPD-L1- MC38. (FIGs.9A-9B) Mice bearing s.c. HuPD-L1-MC38 tumors (n = 6 per group) were dosed I.P. biweekly for three weeks with PBS, aPD-L1 (2 mg/kg; atezolizumab), aTGF-ȕ (10 mg/kg; 1D11), or aPD-L1 plus aTGF-ȕ. (FIG.9A) Average MC38 tumor volume ± SEM is shown. P-values were determined using Wilcoxon rank sum test, comparing tumor sizes on day 17. Non-significant p-values are not shown. (FIG.9B) Spider plots showing tumor volume for individual mice over time. [0039] FIG.10A-10F. Anti-PD-L1 plus anti-TGF-ȕ in the murine tumor model CT26. (FIGs.10A-10C) Mice bearing CT26 tumors were dosed intraperitoneally (I.P.) two times a week for 3 weeks with PBS (n = 10), aPD-L1 (2 mg/kg; atezolizumab; n = 12), aTGF-ȕ (10 mg/kg; 1D11; n = 10), or aPD-L1 + aTGF-ȕ (n = 12). (FIG.10A) Average tumor volume ± SEM is shown. P-value was determined using Wilcoxon rank sum test, using tumor sizes on day 28. (FIG.10B) Spider plots showing CT26 tumor volume for individual mice over time. (FIG.10C) Survival plot for the study. P-values were determined using log-rank test. (FIG. 10D-10F) Mice bearing CT26 tumors were dosed two times a week for 3 weeks with PBS (I.P.; n = 10; same PBS arm as in A-C), aPD-L1 (2 mg/kg; atezolizumab; I.P.) + PBS (intratumorally, I.T.) (n = 12), aTGF-ȕ (10 mg/kg; 1D11; I.T.; n = 6), or aPD-L1 (I.P.) + aTGF-ȕ (I.T.) (n = 12). (FIG.10D) Average tumor volume ± SEM is shown. P-values were determined using Wilcoxon rank sum test, using tumor sizes on day 28. (FIG.10E) Spider plots showing CT26 tumor volume for individual mice over time. (FIG.10F) Survival plot for the study. P-values were determined using log-rank test. Non-significant p-values are not shown for all panels. [0040] FIG.11A-11G scRNA-seq of EMT6 tumors from mice treated with anti-PD-L1 ± anti-TGF-ȕ. (FIG.11A) Number of up- (top panel) and down- (bottom panel) regulated genes in various cell types, when comparing each treatment sample to the PBS sample. (FIG. 11B) UMAP plot showing the two subclusters of fibroblasts. (FIG.11C) Fraction of
fibroblasts in Fib_0 (solid) and Fib_1 (striped) in each treatment group. (FIG.11D) Representative marker genes in the fibroblast subclusters. The size of the dots indicates percent cells expressing the gene, while the color contrast of the dots indicates average gene expression level. (FIG.11E) Functional enrichment analysis of genes downregulated in the Fib_0 subcluster, for each of the treatment group when compared to the PBS group. The size and color contrast of the circles indicate the number of downregulated genes and the -log10 adjusted p-value, respectively, for the enriched terms indicated on the y-axis. (FIG.11F) Gene concept network showing representative enriched terms for the genes downregulated in Fib_0 in the aPD-L1 plus aTGF-ȕ group. The downregulated genes associated with the pathway are shown, with the color contrast of the nodes representing log2 fold change in gene expression relative to the PBS group. (FIG.11G) Heatmap showing relative (z-scored per row) gene expression levels for representative differentially expressed genes in Fib_0. [0041] FIG.12A-12B. Quality control of single cell RNA-seq of anti-PD-L1 ± anti-TGF-ȕ treated EMT6 tumor-bearing mice. (FIG.12A) Violin plots showing the distribution of the number of genes (left) and percent read count that mapped to mitochondrial genes (right) per cell, before removing low quality cells. (FIG.12B) The same plots after removing cells with more than 10% mitochondrial reads and fewer than 200 or more than 5,000 expressed genes, as low and high number of gene counts may indicate low quality cells and cell multiplets, respectively. [0042] FIG.13A-13B. scRNA-seq marker gene expression. (FIG.13A) Heatmap showing relative gene expression of top marker genes most differentially expressed in each cell type relative to other cell types. (FIG.13B) Left: Single cell transcriptomes for all cells visualized on a UMAP plot. Right: Relative expression of selected marker genes displayed on the UMAP plot. [0043] FIG.14A-14F scRNA-seq analysis of macrophage subclusters. (FIG.14A) UMAP plot showing the four subclusters of macrophages. (FIG.14B) Fraction of macrophages in each subcluster in each treatment group. The subclusters are annotated with the same color scheme as FIG.14A. (FIG.14C) Representative marker genes in the macrophage subclusters. The size of the dots indicates percent cells expressing the gene, while the color contrast of the dots indicates average gene expression level. (FIG.14D) Functional enrichment analysis of genes upregulated in the Mac_0 subcluster, for each of the treatment group when compared to the PBS group. The size and color contrast of the circles indicate the number of upregulated genes and the -log10 adjusted p-value, respectively, for the
enriched terms indicated on the y-axis. (FIG.14E) Gene concept network showing representative enriched terms for the genes upregulated in Mac_0 in the aPD-L1 plus aTGF-ȕ group. The upregulated genes associated with the pathway are shown, with the color contrast of the nodes representing log2 fold change in gene expression relative to the PBS group. (FIG.14F) Heatmap showing relative (z-scored per row) gene expression levels for differentially expressed chemokine genes in Mac_0. [0044] FIG.15A-15C. Tumor volumes (mm3) from mice with chemokines CXCL9, CCL5, CXCL9 and CCL5, WARS, WARS + WARS at DOI, or control (PBS) alone or in combination with aPD-1. FIG.15A shows a comparison of tumor volumes (mm3) from mice only treated with chemokines CXCL9, CCL5, CXCL9 and CCL5, WARS, WARS + WARS at DOI, or control (PBS). Mean tumor volume ± SEM is shown. For animals euthanized due to a tumor volume of >2000 mm3, the last observation was carried forward. Data is shown through day 18, as some animals were euthanized and had their tumors collected at our request on day 19 for potential future analysis. FIG.15B shows comparison of tumor volumes (mm3) from mice treated with chemokines CXCL9, CCL5, CXCL9 and CCL5, WARS, or WARS + WARS at DOI in combination with aPD-1. Mean tumor volume ± SEM is shown. For animals euthanized due to a tumor volume of >2000 mm3, the last observation was carried forward. Data is shown through day 18, as some animals were euthanized and had their tumors collected at our request on day 19 for potential future analysis. FIG.15C shows the percent change in body weight after treatment with chemokines only or chemokines in combination with aPDLaPD-L1. Mean body weight change± SEM is shown. For animals euthanized due to a tumor volume of >2000 mm3, the last observation was carried forward. Data is shown through day 18, as some animals were euthanized and had their tumors collected at our request on day 19 for potential future analysis. [0045] Table 1. Differentially expressed (DE) genes determined from the EMT6 single cell RNA-seq experiment. Differential expression analysis was performed within each cell type, indicated in the “cell” column. The “comparison” column indicates the treatment group comparison in which a given DE gene was observed. The columns “pct.1” and “pct.2” represent percent cells expressing the gene in the first treatment group and the second treatment group, respectively. The column “avg_logFC” represents log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the antibody treated group. P-values, as shown in the “p_val” column,
were determined using Wilcoxon rank sum test. The column “p_val_adj” shows adjusted p- value, based on bonferroni correction using all genes in the dataset. [0046] Table 2. Enriched terms as determined by functional enrichment analysis using DE genes from the EMT6 single cell RNA-seq experiment. The functional enrichment analysis was performed using all up- or down-regulated genes (indicated in the “genes_used” column) from the CD45+ or CD45- cells (indicated in the “cells” column), for a given treatment group comparison (indicated in the “comparison” column). The categories tested were biological process (BP), molecular function (MF), and cellular component (CC), as shown in the “ONTOLOGY” column. [0047] Table 3. Differentially expressed (DE) genes in fibroblasts. Differential expression analysis was performed within each fibroblast subcluster, indicated in the “cluster” column. The “comparison” column indicates the treatment group comparison in which a given DE gene was observed. The columns “pct.1” and “pct.2” represent percent cells expressing the gene in the first treatment group and the second treatment group, respectively. The column “avg_logFC” represents log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first treatment group. P- values, as shown in the “p_val” column, were determined using Wilcoxon rank sum test. The column “p_val_adj” shows adjusted p-value, based on Bonferroni correction using all genes in the dataset. [0048] Table 4. Differentially expressed (DE) genes in macrophages. Differential expression analysis was performed within each macrophage subcluster, indicated in the “cluster” column. The “comparison” column indicates the treatment group comparison in which a given DE gene was observed. The columns “pct.1” and “pct.2” represent percent cells expressing the gene in the first treatment group and the second treatment group, respectively. The column “avg_logFC” represents log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first treatment group. Pvalues, as shown in the “p_val” column, were determined using Wilcoxon rank sum test. The column “p_val_adj” shows adjusted p-value, based on Bonferroni correction using all genes in the dataset. [0049] The figures depict various embodiments of the present invention for purposes of illustration only. One skilled in the art will readily recognize from the following discussion
that alternative embodiments of the structures and methods illustrated herein may be employed without departing from the principles of the invention described herein. 6. DETAILED DESCRIPTION 6.1. Definitions [0050] Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. As used herein, the following terms have the meanings ascribed to them below. [0051] The term “chemokine” as used herein refers to a family of small cytokines, or signaling proteins secreted by cells. Specifically, the term includes the chemokines listed in Table 1 and Table 2. Chemokines include, not are not limited to, CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and analogs thereof. [0052] The term “CCL5” as used herein refers to Chemokine (C-C motif) ligand 5, also referred to as RANTES. In preferred embodiments, CCL5 is a protein encoded by the human CCL5 gene. CCL5 can be a protein having the sequence of SEQ ID NO: 1 (available from NCBI with accession number P13501 (SEQ ID NO: 1)). However, CCL5 can be a protein encoded by the CCL5 gene of other mammals, such as a non-human primate (e.g., a monkey), a rodent (e.g., a mouse or a rat), a dog, a camel, a cat, a cow, a goat, a horse, or a sheep. CCL5 can be a protein naturally expressed by cells, a recombinant or synthetic protein. [0053] The term “chemokine analog” as used herein refers to a protein including an active fragment of a chemokine or a modification thereof. In some embodiments, a chemokine analog is a polypeptide having one or more amino acid additions, deletions or substitutions compared to the chemokine. [0054] The term “chemokine mimetic” as used herein refers to a chemokine; a chemokine analog; a fusion of the chemokine or its analog to a second peptide or polypeptide; or the chemokine or its analog conjugated to a conjugate moiety. For example, in various embodiments, the chemokine mimetic is a fusion of the chemokine or its analog to a second peptide or polypeptide, optionally with a linker peptide therebetween. In various embodiments, the chemokine mimetic comprises a chemokine or its analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is not an in- frame fusion. In various embodiments, the chemokine mimetic comprises a chemokine or its
analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is an in-frame fusion. [0055] The term “active fragment” of a chemokine refers to a fragment of the chemokine (e.g., N-terminal fragments, C-terminal fragments) that is sufficient for activation of or binding to its receptor. Thus, an “active-fragment” of a chemokine can include fragments of the chemokine amino acid sequence that are important for receptor binding and activation. [0056] The term “CCL5 analog” as used herein refers to a protein including an active fragment of CCL5 or a modification thereof. In some embodiments, a CCL5 analog is a polypeptide having the sequence of SEQ ID NO: 2. In some embodiments, a CCL5 analog is a polypeptide having one or more amino acid additions, deletions or substitutions compared to SEQ ID NO: 2. [0057] The term “CCL5 mimetic” as used herein refers to CCL5; a CCL5 analog; a fusion of CCL5 or CCL5 analog to a second peptide or polypeptide; or CCL5 or CCL5 analog conjugated to a conjugate moiety. For example, in various embodiments, the CCL5 mimetic is a fusion of CCL5 or a CCL5 analog to a second peptide or polypeptide, optionally with a linker peptide therebetween. In various embodiments, the CCL5 mimetic comprises CCL5 or a CCL5 analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is not an in-frame fusion. In various embodiments, the CCL5 mimetic comprises CCL5 or a CCL5 analog covalently attached to a non-protein conjugate moiety or to a peptide or polypeptide that is an in-frame fusion. [0058] The term “active fragment” of CCL5 refers to a fragment of CCL5 (e.g., N-terminal fragments, C-terminal fragments) that is sufficient for activation of or binding to its receptor (e.g., CCR1, CCR3, CCR5). Thus, an “active-fragment” of CCL5 can include fragments of the CCL5 amino acid sequence that are important for receptor binding and activation. [0059] The term “antibody” is used herein in its broadest sense understood in the art and includes, but is not limited to, all polypeptides described as antibodies in Sumit et al., Antibodies 2:452-500 (2013), incorporated herein by reference in its entirety, and other types of immunoglobulin molecules comprising one or more antigen-binding domains that specifically bind to an antigen or epitope. “Antibody” specifically includes intact antibodies (e.g., intact immunoglobulins), antibody fragments, and multi-specific antibodies. One example of an antigen-binding domain is an antigen-binding domain formed by a VH -VL dimer.
[0060] The term “bi-specific antibody” and “multi-specific antibody” are used herein in the broadest sense understood in the art and include, but are not limited to, the molecular formats described in Spies et al., Molecular Immunology 67:95-106 (2015), incorporated herein by reference in its entirety, and certain types of immunoglobulin molecules comprising one or more antigen-binding domains that specifically bind to two or more different antigens or epitopes. An antigen-binding domain is a portion of antigen binding protein that is capable of binding to an antigen or epitope. For example, bi-specific antibody targeting PD-L1 and TGFβ can be M7824, an anti-PD-L1/TGFβ Trap fusion protein. In some embodiments, bi- specific antibodies disclosed in US9,676,863, incorporated by reference in its entirety herein, are used. [0061] The term “PD-L1,” “PD-L1 protein,” and “PD-L1 antigen” are used interchangeably herein to refer to human PD-L1, or any variants (e.g., splice variants and allelic variants), isoforms, and species homologs of human PD-L1 that are naturally expressed by cells, or that are expressed by cells transfected with a polynucleotide encoding PD-L1. In some embodiments, the PD-L1 protein is a PD-L1 protein naturally expressed by a primate (e.g., a monkey or a human), a rodent (e.g., a mouse or a rat), a dog, a camel, a cat, a cow, a goat, a horse, or a sheep. In some embodiments, the PD-L1 protein is human PD-L1 (hPD-L1; SEQ ID NO: 3). [0062] The term “PD-L1 antibody”, used interchangeably herein with “anti-PD-L1 antibody”, as used herein refers to an antibody comprising one or more antigen-binding domains that specifically bind to an antigen or epitope of PD-L1. PD-L1 antibodies which have been developed for therapeutic use can be used in various embodiments of the present disclosure. The PD-L1 antibodies include, but not are limited to, atezolizumab, avelumab, and durvalumab. [0063] Any of the PD-L1 antibodies or antigen binding domains disclosed in PCT/US19/68826, which is incorporated herein by reference in its entirety herein, can be used. For example, the PD-L1 antibody or antigen binding protein can comprise: a variable light chain (VL) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 5-29 and a variable heavy chain (VH) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 30-54; or a variable light chain (VL) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 207-359 and a variable heavy chain (VH) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence
selected from SEQ ID NOS: 360-512; or a variable light chain (VL) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a VL sequence of any one of the clones in the library deposited under ATCC Accession No. PTA-125513 and a variable heavy chain (VH) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a VH sequence of any one of the clones in the library deposited under ATCC Accession No. PTA-125513. In some embodiments, an antibody or antigen-binding protein is selected from A101-A125. In some embodiments, an antibody or antigen-binding protein having one or more CDR sequences of any one of A101-A125 is used. In some embodiments, the VL and the VH are a cognate pair. [0064] The terms “PD-1,” “PD-1 protein,” and “PD-1 antigen” are used interchangeably herein to refer to human PD-1, or any variants (e.g., splice variants and allelic variants), isoforms, and species homologs of human PD-1 that are naturally expressed by cells, or that are expressed by cells transfected with a pdcd1 gene. In some embodiments, the PD-1 protein is a PD-1 protein naturally expressed by a primate (e.g., a monkey or a human), a rodent (e.g., a mouse or a rat), a dog, a camel, a cat, a cow, a goat, a horse, or a sheep. In some embodiments, the PD-1 protein is human PD-1 (hPD-1; SEQ ID NO: 4). [0065] The term “PD-1 antibody”, used interchangeably herein with “anti-PD-1 antibody,” as used herein refers to an antibody comprising one or more antigen-binding domains that specifically bind to an antigen or epitope of PD-1. PD-1 antibodies which have been developed for therapeutic use can be used in various embodiments of the present disclosure. The PD-1 antibodies include, but not are limited to, nivolumab, pembrolizumab, and cemiplimab. [0066] Any of the PD-1 antibodies or antigen binding domains disclosed in PCT/US19/068824, which is incorporated by reference in its entirety herein, can be used. For example, the PD-1 antibody or antigen binding protein can comprise: a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 1462-1489 and a variable heavy chain (VH) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 1490-1517; or a variable light chain (VL) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 1687-2209 and a variable heavy chain (VH) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a sequence selected from SEQ ID NOS: 2210- 2732; or a variable light chain (VL) comprising a sequence at least 97%, 98%, 99%, or 100% identical to a VL sequence of any one of the clones in the library deposited under ATCC Accession No. PTA-125509 and a variable heavy chain (VH) comprising a sequence at least
97% identical to a VH sequence of any one of the clones in the library deposited under ATCC Accession No. PTA-125509. In some embodiments, an antibody or antigen-binding protein is selected from A201-A228. In some embodiments, an antibody or antigen-binding protein having one or more CDR sequences of any one of A201-A228 is used. In some embodiments, the VL and the VH are a cognate pair. [0067] The terms “TGFȕ,” “TGFȕ protein,” and “TGFβ antigen” are used interchangeably herein to refer to human TGFβ, or any variants (e.g., splice variants and allelic variants), isoforms (e.g., TGFβ 1-3), and species homologs of human TGFβ that are naturally expressed by cells, or that are expressed by cells transfected with a TGFβ gene. In some embodiments, the TGFβ protein is a TGFβ protein naturally expressed by a primate (e.g., a monkey or a human), a rodent (e.g., a mouse or a rat), a dog, a camel, a cat, a cow, a goat, a horse, or a sheep. In some embodiments, the TGFβ protein is human TGFβ. [0068] The term “TGFȕ inhibitor” as used herein refers to an agent that can inhibit TGFβ pathway. TGFβ inhibitor can be an antibody comprising one or more antigen-binding domains that specifically bind to an antigen or epitope of TGFβ or TGFβ receptor. In some cases, TGFβ inhibitor is not an antibody. In some cases, TGFβ inhibitor is a small molecule. Various TGFβ inhibitors which have been developed for therapeutic use can be used in various embodiments of the present disclosure. The TGFβ inhibitors include, but not are limited to, fresolimumab. The TGFβ inhibitors include, but not are limited to, galunisertib, fresolimumab, lucanix, vigil, TGFbRII, TGFBRII-Fc (e.g., TGFBRII trap) and trabedersen. 6.2. Other interpretational conventions [0069] Ranges recited herein are understood to be shorthand for all of the values within the range, inclusive of the recited endpoints. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50. [0070] Unless otherwise indicated, reference to a compound that has one or more stereocenters intends each stereoisomer, and all combinations of stereoisomers, thereof. 6.3. Overview of experimental results [0071] The present disclosure provides therapeutic methods for enhancing T cell and/or NK cell infiltration and response to PD-1/PD-L1 blockade for treatment of cancer.
[0072] Applicant measured transcriptional changes induced by therapeutic regimen using anti-PD-L1 and anti-TGFβ antibodies and identified that anti-TGFβ antibody blocks TGFβ- producing tumor cells from inducing cancer-associated fibroblasts to express collagen and other matrix remodeling genes. Additionally, Applicant found anti-PD-L1 with or without anti-TGFβ induced expression of several chemokines associated with the recruitment of cytotoxic T cells. Additionally, Applicant found a TGFβ inhibitor with or without anti-PD-L1 induced expression of several chemokines associated with the recruitment of cytotoxic T cells. Analysis of TCGA transcriptomes confirmed that a series of chemokines are associated with lymphocyte, T cell, NK cell and dendritic cell infiltration in human tumors, with CCL5 being most highly correlated with immune infiltration across tumor types. This suggested that chemokines, in particular CCL5, will enhance T cell and/or NK cell infiltration and efficacy of PD-1/PD-L1 blockade. [0073] Intratumoral administration of CCL5, in fact, increased the frequency of CCR5+ CD8 T cells within the tumor and administration of CCL5 alone, or CCL5 plus atezolizumab (anti- PD-L1 antibody) inhibited tumor growth in the otherwise excluded murine tumor model MC38. [0074] These data demonstrated that (1) CCL5 alone can help immune cell infiltration into tumors, (2) CCL5 can help immune cell infiltration into tumors and enhance response to PD- L1 blockade, by either limiting the physical barrier or providing exogenous immune cell recruitment signals, or both and (3) CCL5 mimetic alone activates NK cell or T cell activity and recruits activating T cells and/or NK cells to a tumor microenvironment. [0075] Furthermore, Applicant provides surprising evidence that intratumoral administration of an anti-TGFβ in combination with systemic administration of anti-PD-L1 antibody significantly reduces tumor volume. Thus, the combination intratumoral administration of an anti-TGFβ in combination with systemic administration of anti-PD-L1 antibody can be used to treat cancer. 6.4. Chemokine Mimetics [0076] Aspects of the present disclosure include pharmaceutical compositions, methods of use, and kits comprising one or more chemokine mimetics alone or in combination with an antibody, vaccine, nucleic acid, or small molecule inhibitor; and pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
[0077] In some embodiments, the chemokine mimetic is a mimetic of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, or XCL-1. In some embodiments, the chemokine mimetic is selected from one or more of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. In some embodiments, the isolated chemokine mimetic is two or more isolated chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. [0078] In some embodiments, the chemokine mimetic is a CCL5 mimetic. In some embodiments, the CCL5 analog comprises an active fragment of a human CCL5 peptide. [0079] In some embodiments, the chemokine mimetic is a CXCL9 mimetic. In some embodiments, the CXCL9 analog comprises an active fragment of a human CXCL9 peptide. In some embodiments, the chemokine mimetic is a combination of CCL5 and CXCL9 mimetic. [0080] In some embodiments, the chemokine mimetic is a CXCL13 mimetic. In some embodiments, the CXCL13 analog comprises an active fragment of a human CXCL13 peptide. [0081] In some embodiments, the chemokine mimetic is a CXCL10 mimetic. In some embodiments, the CXCL10 analog comprises an active fragment of a human CXCL10 peptide. [0082] In some embodiments, the chemokine mimetic is a CXCL11 mimetic. In some embodiments, the CXCL11 analog comprises an active fragment of a human CXCL11 peptide. [0083] In some embodiments, the chemokine mimetic is a WARS mimetic. In some embodiments, the WARS analog comprises an active fragment of a human WARS peptide. In some embodiments, the chemokine mimetic is a CL-1 mimetic. In some embodiments, the XCL-1 analog comprises an active fragment of a human XCL-1 peptide. [0084] In certain embodiments, the CCL5 mimetic is a human CCL5 peptide, wherein the CCL5 peptide has a sequence of SEQ ID NO: 1. In certain embodiments, the CCL5 mimetic is a CCL5 analog. In yet other embodiments, the CCL5 analog is a polypeptide having the sequence of SEQ ID NO: 1. In certain embodiments, the CCL5 analog comprises an active fragment of a human CCL5 peptide. In certain embodiments, the active fragment of human CCL5 comprises amino acids 12-22 of SEQ ID NO: 1.
[0085] In some embodiments, the active fragment of human CCL5 comprises one or more of the following amino acid residues selected from the group consisting of: P2, Y3, D6, T7, F12, I15, and R17. [0086] In certain embodiments, the CCL5 mimetic comprises a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2. [0087] In some embodiments, the CCL5 mimetic is a CCL5 analog having a longer half-life in vivo as compared to CCL5. In some embodiments, the CXCL9 mimetic is a CXCL9 analog having a longer half-life in vivo as compared to CXCL9. In some embodiments, the CXCL13 mimetic is a CXCL13 analog having a longer half-life in vivo as compared to CXCL13. In some embodiments, the CXCL10 mimetic is a CXCL10 analog having a longer half-life in vivo as compared to CXCL10. In some embodiments, the CXCL11 mimetic is a CXCL11 analog having a longer half-life in vivo as compared to CXCL11. In some embodiments, the WARS mimetic is a WARS analog having a longer half-life in vivo as compared to WARS. In some embodiments, the XCL-1 mimetic is an XCL-1 analog having a longer half-life in vivo as compared to XCL-1. [0088] In some embodiments, the CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic is a conjugate of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, XCL-1, or WARS, or a CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS analog to a conjugate moiety. [0089] In some embodiments, the CCL5 mimetic is a conjugate of CCL5 or a CCL5 analog to a conjugate moiety. [0090] In some embodiments, the conjugate of CCL5 or CCL5 analog comprises a binding site. In certain embodiments the binding site is an antibody or antigen-binding fragment. In particular embodiments, the binding site is a tumor-targeting antibody or antigen-binding fragment thereof. [0091] In certain embodiments, the conjugate moiety is selected from polyethylene glycol (PEG) and hyaluronic acid. [0092] In certain embodiments, the conjugate moiety is an antibody or antigen-binding fragment thereof. In certain embodiments, the conjugate moiety is selected from the group consisting of HAS, human IgG, scFv, F(ab), (Fab’)2, transferrin, albumin, and an Fc domain of an immunoglobulin. In some embodiments, the conjugate moiety is an antibody or
antigen-binding fragment specific to a target tissue for treatment. In some embodiments, the conjugate moiety is an antibody or antigen-binding fragment specific to a tumor antigen. [0093] In some embodiments, the conjugate moiety is selected from the group consisting of: XTEN, a proline-alanine-serine polymer (PAS), a homopolymer of glycine residues (HAP), a gelatin-like protein (GLP), a signal peptide and an elastin-like peptide (ELP). [0094] In some embodiments, the CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic comprises one or more modified or non-naturally occurring amino acids, selected from the group consisting of: a steric enantiomer (D isomer), a rare amino acid of plant origin, a non-naturally occurring amino acid or amino acid mimetic, or have been modified by any one or more modifications selected from acetylation, acylation, phosphorylation, dephosphorylation, glycosylation, myristollation, amidation, aspartic acid/asparagine hydroxylation, phosphopantethane attachment, methylation, methylthiolation, prensyl group attachment, intein N-/C-terminal splicing, ADP-ribosylation, bromination, citrullination, deamination, dihydroxylation, formylation, geranyl-geranilation, glycation, palmitoylation, Į- methyl-amino acids, CĮ-methyl amino acids, and NĮ-methyl amino acids. [0095] In some embodiments, the CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic is chemically-synthesized and comprises one or more non-peptide bonds. 6.5. Polynucleotides encoding a chemokine mimetic and cells comprising the polynucleotides [0096] In another aspect, the present disclosure provides a polynucleotide encoding the chemokine mimetic. In some embodiments, the polynucleotide is DNA (e.g., such as dsDNA, ssDNA, cDNA), RNA (e.g., such as dsRNA, ssRNA, mRNA), combinations thereof, or derivatives (e.g., as PNA) thereof. In some embodiments, mRNA or DNA encodes the chemokine mimetic (e.g., a CCL5 chemokine mimetic). In some embodiments, the polynucleotide further comprises a sequence homologous to a target genomic region for site- specific integration. [0097] In some embodiments, the pharmaceutical composition comprises a polynucleotide comprising a nucleotide sequence encoding the chemokine mimetic selected from CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS. [0098] In certain embodiments, the polynucleotide comprises a nucleotide sequence encoding a CCL5 mimetic. In certain embodiments, the polynucleotide comprises a nucleotide sequence encoding a CXCL9 mimetic. In certain embodiments, the polynucleotide comprises
a nucleotide sequence encoding a CXCL13 mimetic. In certain embodiments, the polynucleotide comprises a nucleotide sequence encoding a CXCL10 mimetic. In certain embodiments, the polynucleotide comprises a nucleotide sequence encoding a CXCL11 mimetic. In certain embodiments, the polynucleotide comprises a nucleotide sequence encoding a WARS mimetic. [0099] In some embodiments, the polynucleotide encoding a chemokine mimetic is codon optimized for expression in mammalian cells, preferably for expression in human cells. [00100] Codon-optimization refers to the exchange in a sequence of interest of codons that are generally rare in highly expressed genes of a given species by codons that are generally frequent in highly expressed genes of such species, such codons encoding the same amino acids as the codons that are being exchanged. The skilled artisan will be able to design and utilize suitable codon optimizations of the polynucleotide disclosed herein. [00101] Within the scope of the present disclosure are also the polynucleotide having a sequence obtained due to the degeneration of the genetic code of the nucleotide sequences of the chemokine mimetics described herein. [00102] In some embodiments, the polynucleotide is in a viral or a non-viral vector. The vector can be used to deliver the polynucleotide to a target cell in vitro or in vivo. In some embodiments, the polynucleotide is in a viral construct. In some embodiments, the polynucleotide is in a plasmid. [00103] In certain embodiments, the viral or non-viral vector comprises a nucleotide sequence encoding CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS mimetic, e.g., a coding sequence of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, or WARS. [00104] In another aspect, the present disclosure provides a cell comprising a chemokine mimetic disclosed herein. In some embodiments, the cell comprises a polynucleotide encoding a chemokine mimetic. In some embodiments, the cell is generated by transformation of the cell with a viral or non-viral vector containing the polynucleotide encoding a chemokine mimetic. 6.6. Pharmaceutical Compositions [00105] In one aspect, the present disclosure provides a pharmaceutical composition comprising a chemokine mimetic described herein. In some cases, a pharmaceutical composition comprises a polynucleotide encoding a chemokine mimetic, or a cell comprising a chemokine mimetic, instead of a chemokine mimetic protein.The chemokine mimetic,
polynucleotide or cellin the pharmaceutical composition can be formulated in any appropriate pharmaceutical composition for administration by any suitable route of administration. Suitable routes of administration include, but are not limited to, oral, intravenous, and intratumoral routes of administration. The most suitable route may depend upon the condition and disorder of the recipient. The formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods known in the art of pharmacy. [00106] A composition can be administered alone or in combination with other treatments, for administration either simultaneously or sequentially dependent upon the condition to be treated. For example, the pharmaceutical composition can be administered in combination with one or more drugs targeting a different check point receptor, such as CTLA-4 inhibitor (e.g., anti-CTLA-4 antibody) or TIGIT inhibitor (e.g., anti-TIGIT antibody). In some embodiments, a composition can be administered alone or in combination with an antibody, such as an anti-TGFb antibody, an anti-PD-L1 antibody, or an anti-PD-1 antibody. In some embodiments, a pharmaceutical composition comprising a chemokine mimetic further comprises one or more additional therapeutic agents. [00107] In another aspect, the present disclosure provides a pharmaceutical composition comprising a TGFβ inhibitor. In some embodiments, the pharmaceutical composition is formulated for intratumoral administration. [00108] In another aspect, the present disclosure provides a pharmaceutical composition comprising a PD-L1 antibody. In some embodiments, the pharmaceutical composition is formulated for systemic administration. [00109] Formulations of the present methods suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets each containing a predetermined amount of the active ingredient; as a powder or granules; as a solution or a suspension in an aqueous liquid or a non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion. The active ingredient may also be presented as a bolus, electuary, pump, or paste. [00110] Formulations for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain antioxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient. Formulations for parenteral administration also include aqueous and non-aqueous sterile suspensions,
which may include suspending agents and thickening agents. The formulations may be presented in unit-dose of multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of a sterile liquid carrier, for example saline, phosphate-buffered saline (PBS) or the like, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described. [00111] The pharmaceutical composition may comprise one or more pharmaceutical excipients. Any suitable pharmaceutical excipient may be used, and one of ordinary skill in the art is capable of selecting suitable pharmaceutical excipients. Accordingly, the pharmaceutical excipients provided below are intended to be illustrative, and not limiting. Additional pharmaceutical excipients include, for example, those described in the Handbook of Pharmaceutical Excipients, 8th Revised Ed. (2017), incorporated by reference in its entirety. [00112] The pharmaceutical composition described herein can be used for treatment of cancer or infection. [00113] The pharmaceutical composition can be in any form appropriate for human or veterinary medicine, including a liquid, an oil, an emulsion, a gel, a colloid, an aerosol, nanoparticle (e.g., lipid nanoparticle), lipid bilayer, or a solid. [00114] The pharmaceutical composition can be formulated for administration by any route of administration appropriate for human or veterinary medicine, including enteral and parenteral routes of administration. [00115] In various embodiments, the pharmaceutical composition is formulated for oral administration, for buccal administration, or for sublingual administration. [00116] In some embodiments, the pharmaceutical composition is formulated for intravenous, intramuscular, intratumoral, subcutaneous administration, or a combination thereof. In certain embodiments, the pharmaceutical composition is formulated for intravenous infusion. [00117] In some embodiments, the pharmaceutical composition is formulated for intrathecal or intracerebroventricular administration. [00118] For intravenous, cutaneous or subcutaneous injection, or injection at the site of affliction, the active ingredient will be in the form of a parenterally acceptable aqueous
solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilisers, buffers, antioxidants and/or other additives can be included, as required. [00119] In some embodiments, the pharmaceutical composition is in a unit dosage form. In some embodiments, the unit dosage form is in a vial, ampule, bottle, or pre-filled syringe. In some embodiments, the unit dosage form contains 0.01 mg, 0.1 mg, 0.5 mg, 1 mg, 2.5 mg, 5 mg, 10 mg, 12.5 mg, 25 mg, 50 mg, 75 mg, or 100 mg of a chemokine mimetic. In some embodiments, the unit dosage form contains 125 mg, 150 mg, 175 mg, or 200 mg of the chemokine mimetic. In some embodiments, the unit dosage form contains 250 mg of the chemokine mimetic. [00120] In typical embodiments, the pharmaceutical unit dosage form contains 0.1 to 10 μg of thechemokine mimetic per 50 mm3 to 1000 mm3 tumor area. [00121] In typical embodiments, the pharmaceutical composition in the unit dosage form is in liquid form. In various embodiments, the unit dosage form contains between 0.1 mL and 50 ml of the pharmaceutical composition. In some embodiments, the unit dosage form contains 1 ml, 2.5 ml, 5 ml, 7.5 ml, 10 ml, 25 ml, or 50 ml of pharmaceutical composition. [00122] In particular embodiments, the unit dosage form is a vial containing 1 ml of the pharmaceutical composition at a concentration of 0.01 mg/ml, 0.1 mg/ml, 0.5 mg/ml, or 1mg/ml of a chemokine mimetic. In some embodiments, the unit dosage form is a vial containing 2 ml of the pharmaceutical composition at a concentration of 0.01 mg/ml, 0.1 mg/ml, 0.5 mg/ml, or 1mg/ml. [00123] In some embodiments, the pharmaceutical composition in the unit dosage form is in solid form, such as a lyophilate, suitable for solubilization. [00124] Unit dosage form embodiments suitable for subcutaneous, intradermal, intratumoral, or intramuscular administration include preloaded syringes, auto-injectors, and autoinject pens, each containing a predetermined amount of the pharmaceutical composition described hereinabove. [00125] In various embodiments, the unit dosage form is a preloaded syringe, comprising a syringe and a predetermined amount of the pharmaceutical composition. In
certain preloaded syringe embodiments, the syringe is adapted for subcutaneous administration. In certain embodiments, the syringe is suitable for self-administration. In particular embodiments, the preloaded syringe is a single use syringe. [00126] In various embodiments, the preloaded syringe contains about 0.1 mL to about 0.5 mL of the pharmaceutical composition. In certain embodiments, the syringe contains about 0.5 mL of the pharmaceutical composition. In specific embodiments, the syringe contains about 1.0 mL of the pharmaceutical composition. In particular embodiments, the syringe contains about 2.0 mL of the pharmaceutical composition. In some embodiments, the syringe contains from 2.0 mL to 5.0 mL of the pharmaceutical composition. [00127] In some embodiments, the pharmaceutical composition is administered in an amount sufficient to increase filtration of immune cells and enhance the anti-tumor activity of an anti-PD-L1 antibody, TGF-ȕ inhibitor, or both. 6.7. Dosage Regimens [00128] In various embodiments, the pharmaceutical compositions described in the present disclosure is administered at a dose sufficient to treat a disease or condition, such as cancer, by itself or in combination with an additional therapeutic agent. [00129] In various embodiments, the chemokine mimetic is administered at a dose sufficient to treat a disease or condition, such as cancer, by itself or in combination with an additional therapeutic agent. [00130] In some embodiments, the chemokine mimetic is present in the pharmaceutical composition at a concentration of at least 0.01 mg/ml, at least 0.05 mg/ml, at least 0.1mg/ml, at least 0.5mg/ml, or at least 1mg/ml. In certain embodiments, the chemokine mimetic is present in the pharmaceutical composition at a concentration of at least 0.5 mg/ml, 1 mg/ml, 2 mg/ml, 3 mg/ml, 4 mg/ml, 5 mg/ml, 10 mg/ml, 15 mg/ml, 20 mg/ml, or 25 mg/ml. In certain embodiments, the chemokine mimetic is present in the pharmaceutical composition at a concentration of at least 30 mg/ml, 35 mg/ml, 40 mg/ml, 45 mg/ml or 50 mg/ml. [00131] In some embodiments, the chemokine mimetic is administered in an amount of at least 0.001 mg/kg. In certain embodiments, the chemokine mimetic is administered in an amount of at least 0.01 mg/kg. In certain embodiments, the chemokine mimetic is administered in an amount of at least 0.05 mg/kg. In certain embodiments, the chemokine mimetic is administered in an amount of at least 0.5 mg/kg. In certain embodiments, the
chemokine mimetic is administered orally in an amount of at least 1 mg/kg. In certain embodiments, the dose is at least 2 mg/kg, at least 3 mg/kg, at least 4 mg/kg, at least 5 mg/kg, at least 6 mg/kg, at least 7 mg/kg, at least 8 mg/kg, at least 9 mg/kg, or at least 10 mg/kg. [00132] In various embodiments, the dose of the chemokine mimetic is at least 0.01 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 0.1 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 0.05 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 0.5 mg/kg. In various embodiments, the dose of the chemokine mimetic is at least 1 mg/kg. In various embodiments, the dose of chemokine mimetic is at least 1.5 mg/kg, at least 2 mg/kg, at least 2.5 mg/kg, at least 3 mg/kg, at least 3.5 mg/kg, at least 4 mg/kg, at least 4.5 mg/kg, at least 5 mg/kg, at least 5.5 mg/kg, at least 6 mg/kg, at least 6.5 mg/kg, at least 7 mg/kg, at least 7.5 mg/kg, at least 8 mg/kg, at least 8.5 mg/kg, at least 9 mg/kg, at least 9.5 mg/kg, or at least 10 mg/kg. In certain embodiments, the dose is at least 5 mg/kg, at least 10 mg/kg at least 15 mg/kg, at least 20 mg/kg, at least 25 mg/kg, 30 mg/kg, at least 35 mg/kg, at least 40 mg/kg, at least 45 mg/kg, at least 50 mg/kg, at least 55 mg/kg, at least 60 mg/kg, at least 65 mg/kg, at least 70 mg/kg, at least 75 mg/kg, at least 80 mg/kg, at least 85 mg/kg, at least 90 mg/kg, at least 95 mg/kg, at least 100 mg/kg, at least 125 mg/kg, at least 150 mg/kg, at least 160 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 0.001 mg/kg to 100 mg/kg per day. In certain embodiments, the dose is 2 mg/kg to 100 mg/kg per day. In certain embodiments, the dose is 25 mg/kg to 1000 mg/kg per day. [00133] In various embodiments, the dose of the chemokine mimetic is at least 0.5 mg/kg. In certain embodiments, the dose is at least 1 mg/kg. In certain embodiments, the dose is at least 40 mg/kg, at least 40 mg/kg, at least 50 mg/kg, at least 100 mg/kg, at least 150 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 500 mg/kg, 750 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 25 mg/kg to 1,000 mg/kg per day. [00134] In some embodiments, the chemokine mimetic is administered at a dose of 0.001 mg/kg, 0.01 mg/kg, 0.02 mg/kg, 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg or 0.1 mg/kg. In some embodiments, the chemokine mimetic or analog thereof is administered at a dose of 0.1 mg/kg, 0.1 mg/kg, 0.2 mg/kg, 0.3
mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, or 1.0 mg/kg. In some embodiments, the chemokine mimetic or analog thereof is administered at a dose of 1.5 mg/kg, 2 mg/kg, 2.5 mg/kg, 3 mg/kg, 3.5 mg/kg, 4 mg/kg, 4.5 mg/kg, or 5 mg/kg. In some embodiments, the chemokine mimetic or analog thereof is administered at a dose of 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, 12 mg/kg, 15 mg/kg, 20 mg/kg, 30 mg/kg, 40 mg/kg, or 50 mg/kg. In some embodiments, the chemokine mimetic or analog thereof is administered at a dose of 10 mg/kg, 50 mg/kg, 8 mg/kg, 100 mg/kg, 150 mg/kg, 200 mg/kg, 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, or 450 mg/kg, 500 mg/kg, 550 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg. [00135] In some embodiments, the chemokine mimetic or analog thereof is administered in a dose that is independent of patient weight or surface area (flat dose). [00136] In some embodiments, the flat dose is 0.001 mg, 0.01 mg, 0.1 mg, 0.2 mg, 0.3 mg, 0.4 mg, 0.5 mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, or 1 mg. In some embodiments, the flat dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, or 10 mg. In some embodiments, the flat dose is 11 mg, 12 mg, 13 mg, 14 mg, 15 mg, 16 mg, 17 mg, 18 mg, 19 mg, or 20 mg. In some embodiments, the flat dose is 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 46 mg, 47 mg, 48 mg, 49 mg, or 50 mg. In some embodiments, the flat dose is 40 mg, 42 mg, 44 mg, 46 mg, 48 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, or 100 mg. In some embodiments, the flat dose is 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, or 1000 mg. In some embodiments, the flat dose ranges from 0.1 to 40 mg. In some embodiments, the flat dose ranges from 12 to 30 mg. In some embodiments, the flat dose is 0.1 – 1 mg, 1 – 10 mg, 10 – 15 mg, 15 – 20 mg, 20 – 30 mg, 30 – 40 mg, or 40 – 50 mg. In some embodiments, the flat dose is 1 – 50 mg, 50 – 100 mg, 100 mg – 200 mg, 200 mg – 300 mg, 300 mg – 400 mg, 400 mg – 500 mg, 500 mg – 600 mg, 600 mg – 700 mg, 700 mg – 800 mg, 800 mg – 900 mg, or 900 mg – 1000 mg. [00137] In various embodiments, the dose is 1-5000 mg. In various embodiments, the flat dose is 12-30 mg. In various embodiments, the flat dose is 1-11 mg. In various embodiments, the flat dose is 12-40 mg. In certain embodiments, the dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 325 mg, 350 mg, 375 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg,
700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 950 mg, or 1000 mg. In certain embodiments, the dose is 1500 mg, 2000 mg, 2500 mg, 3000 mg, 3500 mg, 4000 mg, 4500 mg, or 5000 mg. [00138] In various embodiments, the dose is 25-2000 mg. In certain embodiments, the dose is 25 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 350 mg, 375 mg, 400 mg, 425 mg, 450 mg, 475 mg, 500 mg, 525 mg, 550 mg, 575 mg, 600 mg, 625 mg, 650 mg, 675 mg, 700 mg, 725 mg, 750 mg, 775 mg, 800 mg, 825 mg, 900 mg, 925 mg, 950 mg, 975 mg, or 1000 mg. [00139] In some embodiments, the dose is determined based on the tumor volume. In some embodiments, the dose is 0.01 to 100 μg for 50 – 1000mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 50 – 1000mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 50 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 100 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 500 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 1000 mm3 tumor volume. [00140] The chemokine mimetic can be administered in a single dose or in multiple doses. In certain embodiments, the chemokine mimetic can be administered in multiple doses, e.g., to different tumor sites or throughout a tumor. In various embodiments, the chemokine mimetic is administered once a day, once every 2 days, once every 3 days, once every 4 days, once every 5 days, once every 6 days, once every 7 days, once every 14 days, once every 21 days, once every 28 days, or once a month. In various embodiments, chemokine mimetic is administered twice a day, twice every 2 days, twice every 3 days, twice every 4 days, twice every 5 days, twice every 6 days, twice every 7 days, twice every 14 days, twice every 21 days, twice every 28 days, or twice a month. In various embodiments, the chemokine mimetic is administered 1 time a week, 2 times a week, 3 times a week, four times a week, or five times a week. [00141] In another aspect, the present disclosure provides a pharmaceutical composition comprising the combination of an anti-PD-L1 antibody and TGFβ inhibitor (e.g.,anti-TGFβ antibody). The anti-PD-L1 antibody and TGFβ inhibitor is administered at individual doses sufficient to treat a disease or condition, such as cancer, in when administered together in combination. The pharmaceutical composition can be admininistered for a combination therapy. For example, aspects of the present disclosure also include a method of treating cancer by: administering systemically to a subject with cancer, an
effective amount of an anti-PD-L1 antibody; and administering intratumorally to the subject, an TGFβ inhibitor (e.g., anti-TGFβ antibody). The pharmaceutical composition includes the combination of an anti-PD-L1 antibody (e.g., for administering systemically) and an TGFβ inhibitor (e.g., anti-TGFβ antibody) (e.g., for administering intratumorally). [00142] In some embodiments, the anti-PD-L1 antibody is present in the pharmaceutical composition at a concentration of at least 0.01 mg/ml, at least 0.05 mg/ml, at least 0.1mg/ml, at least 0.5mg/ml, or at least 1mg/ml. In certain embodiments, the anti-PD- L1 antibody is present in the pharmaceutical composition at a concentration of at least 0.5 mg/ml, 1 mg/ml, 2 mg/ml, 3 mg/ml, 4 mg/ml, 5 mg/ml, 10 mg/ml, 15 mg/ml, 20 mg/ml, or 25 mg/ml. In certain embodiments, the anti-PD-L1 antibody is present in the pharmaceutical composition at a concentration of at least 30 mg/ml, 35 mg/ml, 40 mg/ml, 45 mg/ml or 50 mg/ml. [00143] In some embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.001 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.01 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.05 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered in an amount of at least 0.5 mg/kg. In certain embodiments, the anti-PD-L1 antibody is administered orally in an amount of at least 1 mg/kg. In certain embodiments, the dose is at least 2 mg/kg, at least 3 mg/kg, at least 4 mg/kg, at least 5 mg/kg, at least 6 mg/kg, at least 7 mg/kg, at least 8 mg/kg, at least 9 mg/kg, or at least 10 mg/kg. [00144] In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.01 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.1 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.05 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.5 mg/kg. In various embodiments, the dose of the anti-PD-L1 antibody is at least 1 mg/kg. In various embodiments, the dose of anti-PD-L1 antibody is at least 1.5 mg/kg, at least 2 mg/kg, at least 2.5 mg/kg, at least 3 mg/kg, at least 3.5 mg/kg, at least 4 mg/kg, at least 4.5 mg/kg, at least 5 mg/kg, at least 5.5 mg/kg, at least 6 mg/kg, at least 6.5 mg/kg, at least 7 mg/kg, at least 7.5 mg/kg, at least 8 mg/kg, at least 8.5 mg/kg, at least 9 mg/kg, at least 9.5 mg/kg, or at least 10 mg/kg. In certain embodiments, the dose is at least 5 mg/kg, at least 10 mg/kg at least 15 mg/kg, at least 20 mg/kg, at least 25 mg/kg, 30 mg/kg, at least 35 mg/kg, at least 40 mg/kg, at least 45 mg/kg, at least 50 mg/kg, at least 55 mg/kg, at least 60 mg/kg, at least 65 mg/kg, at least 70 mg/kg, at least 75 mg/kg, at least 80 mg/kg, at least 85 mg/kg, at least 90 mg/kg, at
least 95 mg/kg, at least 100 mg/kg, at least 125 mg/kg, at least 150 mg/kg, at least 160 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 0.001 mg/kg to 100 mg/kg per day. In certain embodiments, the dose is 2 mg/kg to 100 mg/kg per day. In certain embodiments, the dose is 25 mg/kg to 1000 mg/kg per day. [00145] In various embodiments, the dose of the anti-PD-L1 antibody is at least 0.5 mg/kg. In certain embodiments, the dose is at least 1 mg/kg. In certain embodiments, the dose is at least 40 mg/kg, at least 40 mg/kg, at least 50 mg/kg, at least 100 mg/kg, at least 150 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 500 mg/kg, 750 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 25 mg/kg to 1,000 mg/kg per day. [00146] In some embodiments, the anti-PD-L1 antibody is administered at a dose of 0.001 mg/kg, 0.01 mg/kg, 0.02 mg/kg, 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg or 0.1 mg/kg. In some embodiments, the anti-PD-L1 antibody or analog thereof is administered at a dose of 0.1 mg/kg, 0.1 mg/kg, 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, or 1.0 mg/kg. In some embodiments, the anti-PD-L1 antibody or analog thereof is administered at a dose of 1.5 mg/kg, 2 mg/kg, 2.5 mg/kg, 3 mg/kg, 3.5 mg/kg, 4 mg/kg, 4.5 mg/kg, or 5 mg/kg. In some embodiments, the anti-PD-L1 antibody or analog thereof is administered at a dose of 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, 12 mg/kg, 15 mg/kg, 20 mg/kg, 30 mg/kg, 40 mg/kg, or 50 mg/kg. In some embodiments, the anti-PD-L1 antibody or analog thereof is administered at a dose of 10 mg/kg, 50 mg/kg, 8 mg/kg, 100 mg/kg, 150 mg/kg, 200 mg/kg, 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, or 450 mg/kg, 500 mg/kg, 550 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg. [00147] In some embodiments, the anti-PD-L1 antibody is administered in a dose that is independent of patient weight or surface area (flat dose). [00148] In some embodiments, the flat dose is 0.001 mg, 0.01 mg, 0.1 mg, 0.2 mg, 0.3 mg, 0.4 mg, 0.5 mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, or 1 mg. In some embodiments, the flat dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, or 10 mg. In some
embodiments, the flat dose is 11 mg, 12 mg, 13 mg, 14 mg, 15 mg, 16 mg, 17 mg, 18 mg, 19 mg, or 20 mg. In some embodiments, the flat dose is 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 46 mg, 47 mg, 48 mg, 49 mg, or 50 mg. In some embodiments, the flat dose is 40 mg, 42 mg, 44 mg, 46 mg, 48 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, or 100 mg. In some embodiments, the flat dose is 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, or 1000 mg. In some embodiments, the flat dose ranges from 0.1 to 40 mg. In some embodiments, the flat dose ranges from 12 to 30 mg. In some embodiments, the flat dose is 0.1 – 1 mg, 1 – 10 mg, 10 – 15 mg, 15 – 20 mg, 20 – 30 mg, 30 – 40 mg, or 40 – 50 mg. In some embodiments, the flat dose is 1 – 50 mg, 50 – 100 mg, 100 mg – 200 mg, 200 mg – 300 mg, 300 mg – 400 mg, 400 mg – 500 mg, 500 mg – 600 mg, 600 mg – 700 mg, 700 mg – 800 mg, 800 mg – 900 mg, or 900 mg – 1000 mg. [00149] In various embodiments, the dose is 1-5000 mg. In various embodiments, the flat dose is 12-30 mg. In various embodiments, the flat dose is 1-11 mg. In various embodiments, the flat dose is 12-40 mg. In certain embodiments, the dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 325 mg, 350 mg, 375 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 950 mg, or 1000 mg. In certain embodiments, the dose is 1500 mg, 2000 mg, 2500 mg, 3000 mg, 3500 mg, 4000 mg, 4500 mg, or 5000 mg. [00150] In various embodiments, the dose is 25-2000 mg. In certain embodiments, the dose is 25 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 350 mg, 375 mg, 400 mg, 425 mg, 450 mg, 475 mg, 500 mg, 525 mg, 550 mg, 575 mg, 600 mg, 625 mg, 650 mg, 675 mg, 700 mg, 725 mg, 750 mg, 775 mg, 800 mg, 825 mg, 900 mg, 925 mg, 950 mg, 975 mg, or 1000 mg. [00151] In some embodiments, the dose is determined based on the tumor volume. In some embodiments, the dose is 0.01 to 100 μg for 50 – 1000mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 50 – 1000mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 50 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 100 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 500 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 1000 mm3 tumor volume.
[00152] The anti-PD-L1 antibody can be administered in a single dose or in multiple doses. In certain embodiments, the anti-PD-L1 antibody can be administered in multiple doses, e.g., to different tumor sites or throughout a tumor. In various embodiments, the anti- PD-L1 antibody is administered once a day, once every 2 days, once every 3 days, once every 4 days, once every 5 days, once every 6 days, once every 7 days, once every 14 days, once every 21 days, once every 28 days, or once a month. In various embodiments, anti-PD-L1 antibody is administered twice a day, twice every 2 days, twice every 3 days, twice every 4 days, twice every 5 days, twice every 6 days, twice every 7 days, twice every 14 days, twice every 21 days, twice every 28 days, or twice a month. In various embodiments, the anti-PD- L1 antibody is administered 1 time a week, 2 times a week, 3 times a week, four times a week, or five times a week. [00153] In some embodiments, the TGFβ inhibitor is present in the pharmaceutical composition at a concentration of at least 0.01 mg/ml, at least 0.05 mg/ml, at least 0.1mg/ml, at least 0.5mg/ml, or at least 1mg/ml. In certain embodiments, the TGFβ inhibitor is present in the pharmaceutical composition at a concentration of at least 0.5 mg/ml, 1 mg/ml, 2 mg/ml, 3 mg/ml, 4 mg/ml, 5 mg/ml, 10 mg/ml, 15 mg/ml, 20 mg/ml, or 25 mg/ml. In certain embodiments, the TGFβ inhibitor is present in the pharmaceutical composition at a concentration of at least 30 mg/ml, 35 mg/ml, 40 mg/ml, 45 mg/ml or 50 mg/ml. [00154] In some embodiments, the TGFβ inhibitor is administered in an amount of at least 0.001 mg/kg. In certain embodiments, the TGFβ inhibitor is administered in an amount of at least 0.01 mg/kg. In certain embodiments, the TGFβ inhibitor is administered in an amount of at least 0.05 mg/kg. In certain embodiments, the TGFβ inhibitor is administered in an amount of at least 0.5 mg/kg. In certain embodiments, the TGFβ inhibitor is administered orally in an amount of at least 1 mg/kg. In certain embodiments, the dose is at least 2 mg/kg, at least 3 mg/kg, at least 4 mg/kg, at least 5 mg/kg, at least 6 mg/kg, at least 7 mg/kg, at least 8 mg/kg, at least 9 mg/kg, or at least 10 mg/kg. [00155] In various embodiments, the dose of the TGFβ inhibitor is at least 0.01 mg/kg. In various embodiments, the dose of the TGFβ inhibitor is at least 0.1 mg/kg. In various embodiments, the dose of the TGFβ inhibitor is at least 0.05 mg/kg. In various embodiments, the dose of the TGFβ inhibitor is at least 0.5 mg/kg. In various embodiments, the dose of the TGFβ inhibitor is at least 1 mg/kg. In various embodiments, the dose of TGFβ inhibitor is at least 1.5 mg/kg, at least 2 mg/kg, at least 2.5 mg/kg, at least 3 mg/kg, at least 3.5 mg/kg, at least 4 mg/kg, at least 4.5 mg/kg, at least 5 mg/kg, at least 5.5 mg/kg, at least 6 mg/kg, at
least 6.5 mg/kg, at least 7 mg/kg, at least 7.5 mg/kg, at least 8 mg/kg, at least 8.5 mg/kg, at least 9 mg/kg, at least 9.5 mg/kg, or at least 10 mg/kg. In certain embodiments, the dose is at least 5 mg/kg, at least 10 mg/kg at least 15 mg/kg, at least 20 mg/kg, at least 25 mg/kg, 30 mg/kg, at least 35 mg/kg, at least 40 mg/kg, at least 45 mg/kg, at least 50 mg/kg, at least 55 mg/kg, at least 60 mg/kg, at least 65 mg/kg, at least 70 mg/kg, at least 75 mg/kg, at least 80 mg/kg, at least 85 mg/kg, at least 90 mg/kg, at least 95 mg/kg, at least 100 mg/kg, at least 125 mg/kg, at least 150 mg/kg, at least 160 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 0.001 mg/kg to 100 mg/kg per day. In certain embodiments, the dose is 2 mg/kg to 100 mg/kg per day. In certain embodiments, the dose is 25 mg/kg to 1000 mg/kg per day. [00156] In various embodiments, the dose of the TGFβ inhibitor is at least 0.5 mg/kg. In certain embodiments, the dose is at least 1 mg/kg. In certain embodiments, the dose is at least 40 mg/kg, at least 40 mg/kg, at least 50 mg/kg, at least 100 mg/kg, at least 150 mg/kg, at least 175 mg/kg, or at least 200 mg/kg. In certain embodiments, the dose is 250 mg/kg, 500 mg/kg, 750 mg/kg, or 1000 mg/kg. In certain embodiments, the dose is 25 mg/kg to 1,000 mg/kg per day. [00157] In some embodiments, the TGFβ inhibitor is administered at a dose of 0.001 mg/kg, 0.01 mg/kg, 0.02 mg/kg, 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg or 0.1 mg/kg. In some embodiments, the TGFβ inhibitor or analog thereof is administered at a dose of 0.1 mg/kg, 0.1 mg/kg, 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, or 1.0 mg/kg. In some embodiments, the TGFβ inhibitor or analog thereof is administered at a dose of 1.5 mg/kg, 2 mg/kg, 2.5 mg/kg, 3 mg/kg, 3.5 mg/kg, 4 mg/kg, 4.5 mg/kg, or 5 mg/kg. In some embodiments, the TGFβ inhibitor or analog thereof is administered at a dose of 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, 12 mg/kg, 15 mg/kg, 20 mg/kg, 30 mg/kg, 40 mg/kg, or 50 mg/kg. In some embodiments, the TGFβ inhibitor or analog thereof is administered at a dose of 10 mg/kg, 50 mg/kg, 8 mg/kg, 100 mg/kg, 150 mg/kg, 200 mg/kg, 250 mg/kg, 300 mg/kg, 350 mg/kg, 400 mg/kg, or 450 mg/kg, 500 mg/kg, 550 mg/kg, 600 mg/kg, 650 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 850 mg/kg, 900 mg/kg, 950 mg/kg, or 1000 mg/kg. [00158] In some embodiments, the TGFβ inhibitor is administered in a dose that is independent of patient weight or surface area (flat dose).
[00159] In some embodiments, the flat dose is 0.001 mg, 0.01 mg, 0.1 mg, 0.2 mg, 0.3 mg, 0.4 mg, 0.5 mg, 0.6 mg, 0.7 mg, 0.8 mg, 0.9 mg, or 1 mg. In some embodiments, the flat dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, or 10 mg. In some embodiments, the flat dose is 11 mg, 12 mg, 13 mg, 14 mg, 15 mg, 16 mg, 17 mg, 18 mg, 19 mg, or 20 mg. In some embodiments, the flat dose is 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 46 mg, 47 mg, 48 mg, 49 mg, or 50 mg. In some embodiments, the flat dose is 40 mg, 42 mg, 44 mg, 46 mg, 48 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, or 100 mg. In some embodiments, the flat dose is 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, or 1000 mg. In some embodiments, the flat dose ranges from 0.1 to 40 mg. In some embodiments, the flat dose ranges from 12 to 30 mg. In some embodiments, the flat dose is 0.1 – 1 mg, 1 – 10 mg, 10 – 15 mg, 15 – 20 mg, 20 – 30 mg, 30 – 40 mg, or 40 – 50 mg. In some embodiments, the flat dose is 1 – 50 mg, 50 – 100 mg, 100 mg – 200 mg, 200 mg – 300 mg, 300 mg – 400 mg, 400 mg – 500 mg, 500 mg – 600 mg, 600 mg – 700 mg, 700 mg – 800 mg, 800 mg – 900 mg, or 900 mg – 1000 mg. [00160] In various embodiments, the dose is 1-5000 mg. In various embodiments, the flat dose is 12-30 mg. In various embodiments, the flat dose is 1-11 mg. In various embodiments, the flat dose is 12-40 mg. In certain embodiments, the dose is 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 325 mg, 350 mg, 375 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 950 mg, or 1000 mg. In certain embodiments, the dose is 1500 mg, 2000 mg, 2500 mg, 3000 mg, 3500 mg, 4000 mg, 4500 mg, or 5000 mg. [00161] In various embodiments, the dose is 25-2000 mg. In certain embodiments, the dose is 25 mg, 50 mg, 75 mg, 100 mg, 125 mg, 150 mg, 175 mg, 200 mg, 225 mg, 250 mg, 275 mg, 300 mg, 350 mg, 375 mg, 400 mg, 425 mg, 450 mg, 475 mg, 500 mg, 525 mg, 550 mg, 575 mg, 600 mg, 625 mg, 650 mg, 675 mg, 700 mg, 725 mg, 750 mg, 775 mg, 800 mg, 825 mg, 900 mg, 925 mg, 950 mg, 975 mg, or 1000 mg. [00162] In some embodiments, the dose is determined based on the tumor volume. In some embodiments, the dose is 0.01 to 100 μg for 50 – 1000mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 50 – 1000mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 50 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 100 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10
μg for 500 mm3 tumor volume. In some embodiments, the dose is 0.1 to 10 μg for 1000 mm3 tumor volume. [00163] The TGFβ inhibitor can be administered in a single dose or in multiple doses. In certain embodiments, the TGFβ inhibitor can be administered in multiple doses, e.g., to different tumor sites or throughout a tumor. In various embodiments, the TGFβ inhibitor is administered once a day, once every 2 days, once every 3 days, once every 4 days, once every 5 days, once every 6 days, once every 7 days, once every 14 days, once every 21 days, once every 28 days, or once a month. In various embodiments, TGFβ inhibitor is administered twice a day, twice every 2 days, twice every 3 days, twice every 4 days, twice every 5 days, twice every 6 days, twice every 7 days, twice every 14 days, twice every 21 days, twice every 28 days, or twice a month. In various embodiments, the TGFβ inhibitor is administered 1 time a week, 2 times a week, 3 times a week, four times a week, or five times a week. 6.8. Methods of Treating Cancer [00164] Aspects of the present disclosure include a method of treating cancer by administering a chemokine mimetic, e.g., an isolated CCL5 mimetic. [00165] The method can be used for treatment of cancer by recruiting mature NK cells and activated CD8 T cells to the tumor microenvironment. The method can be used for treatment of inflammation, or other disorders, such as treating infections. The method can also be used for recruiting, activating, and/or maturing NK cells. [00166] In some cases, the method of treating cancer comprises the step of administering a subject with the cancer a therapeutically effective amount of a polynucleotide encoding a chemokine mimetic or a cell expressing a chemokine mimetic, instead of administering a chemokine mimetic as a protein. [00167] In some embodiments, the method further comprises the step of administering an additional therapeutic agent before or after administration of a chemokine mimetic or a chemokine polynucleotide or cell. In some embodiments, a chemokine mimetic (protein, polynucleotide or cell) and an additional therapeutic agent are administered concurrently. [00168] In some embodiments, the combination therapy of a chemokine mimetic (protein, polynucleotide, or cell) and an additional therapeutic agent enables reduction of the therapeutic dose of the additional therapeutic agent. For example, when a CCL5 mimetic and
an anti-PD-L1 antibody are used together, a therapeutic dose of the anti-PD-L1 antibody can be reduced compared to anti-PD-L1 mono-therapy. [00169] The chemokines and their variants can be also used in combination with an ADCC-inducing antibody, ADCP-inducing antibody, or in cancer or non-cancer application of adoptive cell therapy. [00170] In one aspect, the present disclosure includes a method of treating cancer, comprising the step of: administering to a subject with the cancer a therapeutically effective amount of an isolated chemokine mimetic, or pharmaceutically acceptable salt thereof. [00171] In typical embodiments, the isolated chemokine mimetic is selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. In certain embodiments, the isolated chemokine mimetic is two or more isolated chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. [00172] In some embodiments, isolated chemokine mimetic is a CCL5 mimetic. In certain embodiments, the isolated chemokine mimetic is administered in a pharmaceutical composition further comprising a pharmaceutically acceptable carrier or excipient. [00173] In some embodiments, the isolated chemokine is administered via intratumoral injection, intravenous injection or subcutaneous injection. [00174] In some embodiments, the isolated is administered is via intratumoral injection. [00175] In some embodiments, the method further comprises the step of administering to the subject an anti-PD-L1 antibody or an anti-PD-1 antibody. In certain embodiments, the anti-PD-L1 antibody or anti-PD-1 antibody is administered systemically. In certain embodiments, the anti-PD-L1 antibody or anti-PD-1 antibody is administered intratumorally. [00176] In some embodiments, the method further comprises the step of administering to the subject a TGFβ inhibitor. In certain embodiments, the TGFβ inhibitor is administered systemically. In certain embodiments, the TGFβ inhibitor is administered intratumorally. [00177] In some embodiments, the method further comprises the steps of administering anti-PD-L1 antibody and an anti-TGFβ inhibitor. [00178] In some embodiments, the method further comprises the step of administering a bi-specific antibody targeting both PD-1 and TGFβ.
[00179] In some embodiments, the method further comprises step of administering to the subject an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is ipilimumab. In some embodiments, the antibody is an anti-CTLA4 antibody disclosed in PCT/US2019/068820, incorporated by reference in its entirety herein. In certain embodiments, the anti-CTLA4 antibody has a heavy chain amino acid sequence set forth in SEQ ID NO:5909. In certain embodiments, the anti-CTLA4 antibody has a light chain amino acid sequence set forth in SEQ ID NO:5910. In certain embodiments, the anti-CTLA4 antibody is afucosylated. [00180] In some embodiments, the method further comprises the step of administering to the subject a T cell, an NK cell, macrophage, B cell, or dendritic cell, optionally wherein the T cell is a CAR-T, CAR-NK, CAR-macrophage, or CAR-T cell. [00181] In some embodiments, the method further comprises the step of administering to the subject an IL-15, IL-15 complex, IL-7, IL-2, or a variant thereof. [00182] In some embodiments, the method further comprises the step of administering to the subject an agent activating NK cell, T cell activity, or dendritic cell activity. In some embodiments, the method further comprises the step of administering to the subject a vaccine, nucleic acid therapeutic, small molecule inhibitor, or chemotherapeutic agent. [00183] In some aspects, the present disclosure provides a method of treating cancer, comprising the steps of: intratumorally administering a therapeutically effective amount of an isolated chemokine mimetic, or pharmaceutically acceptable salt thereof, to a subject who has been determined to have expression levels in a biological sample of one or more genes selected from the group consisting of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, CD8, CD3, TCRȕ, TCR1, CD11c, XCL-1, WARS, NKp46 and NCR1, granzymes, and perforin that are lower than or higher than a predetermined threshold level. [00184] In some embodiments, the biological sample is a tumor biopsy. In certain embodiments, the biological sample is a blood sample. In yet other embodiments, the biological sample is a liquid biopsy. In some embodiments, the biological sample is a sample containing cells isolated from a subject comprising a disease or condition (e.g., cancer). In some embodiments, the biological sample is a sample containing cells isolated from a donor. In certain embodiments, the biological sample is a sample containing T cells and/or NK cells isolated from subject comprising a disease or condition (e.g., cancer) or a donor.
[00185] In some embodiments, the method comprises the prior step of determining the expression levels of one or more genes selected from the group consisting of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, CD8, CD3, TCRȕ, TCR1, CD11c, XCL-1, WARS, NKp46, NCR1, CD11B, FcRs, collagen genes, CTLA4, CD56, CD16, CD7 CD127, Tbet, Eomes, granzymes, and perforin in the biological sample. [00186] In some embodiments, the method comprises the prior step of detecting CD8+ T cells, NK cells, mature NK cells, lymphocytes, fibroblasts, Tregs, or dendritic cells in the biological sample. In certain embodiments, the CD8+ T cells, NK cells, lymphocytes, or dendritic cells are detected by immune histochemistry. [00187] In some embodiments, the chemokine mimetic is selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. In certain embodiments, the chemokine mimetic is two or more chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof. [00188] In certain embodiments, the method further comprises the step of administering to the subject a vaccine, nucleic acid therapeutic, chemotherapeutic agent, or a small molecule inhibitor. [00189] In some embodiments, the cancer is selected from the group consisting of: multiple myeloma, adrenocortical carcinoma, acute myeloid leukemia, Bladder Urothelial Carcinoma, glioma, breast invasive carcinoma, glioma, Cervical squamous cell carcinoma, endocervical adenocarcinoma, cholangiocarcinoma, chronic myelogenous leukemia, colon adenocarcinoma, esophageal carcinoma, glioblastoma multiforme, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, lymphoid neoplasm diffuse large B-cell lymphoma, mesothelioma, ovarian serous cystadenocarcinoma, pancreatic adenocarcinoma, pheochromocyoma, paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma,sarcoma, skin cutaneous melanoma, stomach adenocarcinoma, testicular germ cell tumors, thyomas, thyroid carcinoma, uterine carcinosarcoma, uterine corps endometrial carcinoma, microsatellite instability-high cancer, basal cell carcinoma, Merkel cell carcinoma, mucosal melanoma, and uveal melanoma. [00190] Aspects of the present disclosure also include a method of treating cancer by: administering systemically to a subject with cancer, an effective amount of an anti-PD-L1
antibody; and administering intratumorally to the subject, an TGFβ inhibitor (e.g., anti-TGFβ antibody). The method includes a combination therapy which comprises systemic administration of an anti-PD-L1 antibody and intratumoral administration of an TGFβ inhibitor (e.g., anti-TGFβ antibody). [00191] The method can be used for treatment of cancer by recruiting mature NK cells and activated CD8 T cells to the tumor microenvironment. The method can be used for treatment of inflammation, or other disorders, such as treating infections. The method can also be used for recruiting, activating, and/or maturing NK cells. 6.9. Antibodies [00192] In some embodiments, a pharmaceutical composition comprises an additional therapeutic agent. In some embodiments, the pharmaceutical composition comprises one or more additional active ingredients in addition to or separate from the chemokine mimetic of the present invention. The one or more additional active ingredients can be a drug targeting a different check point receptor, such as CTLA-4 inhibitor (e.g., anti-CTLA-4 antibody), PD- L1 inhibitor (e.g., anti-PD-L1 antibody), PD-1 inhibitor (e.g., anti-PD-1 antibody), a TGFβ inhibitor (e.g., anti-TGFβ antibody), or a bispecific antibody (e.g., against PD-L1 and TGFβ or against PD-1 and TGFβ). [00193] In some embodiments, the therapeutic agent comprises a T cell or an NK cell. In certain embodiments, the T cell is a CAR-T, CAR-NK, or TCR-T cell. [00194] In some embodiments, the therapeutic agent comprises a dendritic cell or macrophage. [00195] In certain embodiment, the therapeutic agent is an agent activating NK cell, T cell activity, dendritic cell activity, or a combination thereof. [00196] In certain embodiments, the additional therapeutic agent is an IL-15, IL-15 complex, IL-2, IL-7 or a variant thereof. [00197] In certain embodiments, the additional therapeutic agent is selected from a vaccine, chemotherapeutic agent, nucleic acid therapeutic, or a small molecule inhibitor. In certain embodiments, the small molecule inhibitor is an inhibitor of TGF-ȕ. [00198] In certain embodiments, the additional therapeutic agent is one or more ADCC-inducing antibodies and/or ADCP-inducing antibodies.
6.10. Kits [00199] In another aspect, the present disclosure provides a kit for treatment of cancer, comprising a pharmaceutical composition comprising a chemokine mimetic or analog thereof. [00200] In another aspect, the present disclosure provides a kit for treatment of an infection, comprising a pharmaceutical composition comprising a chemokine mimetic or analog thereof [00201] In certain embodiments, the kit further comprises a second pharmaceutical composition comprising an additional therapeutic agent. In typical embodiments, the additional therapeutic agent is an anti-PD-L1 antibody, an anti-PD-1 antibody, or a TGFβ inhibitor. In certain embodiments, the therapeutic agent is a bispecific antibody against PD- L1 and TGFβ or against PD-1 and TGFβ. In certain embodiments, the additional therapeutic agent comprises an anti-PD-L1 antibody and an anti-TGFβ antibody. In certain embodiments, the additional therapeutic agent comprises an anti-PD-1 antibody and an anti-TGFβ antibody. In certain embodiments, the additional therapeutic agent comprises an anti-PD-L1 antibody, wherein the anti-PD-L1 antibody is atezolizumab. [00202] In another aspect, the present disclosure provides a kit comprising a first pharmaceutical composition comprising a TGFβ inhibitor and a second pharmaceutical composition comprising an anti-PD-L1 antibody. In some embodiments, the first pharmaceutical composition comprising a TGFβ inhibitor is formulated for intratumoral administration and a second pharmaceutical composition comprising an anti-PD-L1 antibody is formulated for systemic administration. [00203] In some embodiments, the kit comprises a second and a third pharmaceutical composition. For example, the kit can comprise a second pharmaceutical composition comprising an anti-PD-L1 antibody or an anti-PD-1 antibody, and a third pharmaceutical composition comprising a TGFβ inhibitor. [00204] In certain embodiments, the additional therapeutic agent is an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is ipilimumab. In certain embodiment, the additional therapeutic agent is an ADCC/ADCP inducing antibody.
[00205] In certain embodiments, the additional therapeutic agent comprises a T cell or an NK cell. In certain embodiments, the T cell is a CAR-T, CAR-NK, CAR-macrophage, or TCR-T cell. [00206] In certain embodiments, the additional therapeutic agent is an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof. [00207] In certain embodiments, the additional therapeutic agent is an agent activating NK cell, T cell activity, dendritic cell activity, or a combination thereof. [00208] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are in a single container. In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are separate pharmaceutical compositions in two or more separate containers. [0100] The kit can comprise one or more unit doses of the first pharmaceutical composition. The kit can further comprise one or more unit doses of the second pharmaceutical composition. In some embodiments, the kit comprises one or more vials containing the first pharmaceutical composition, and one or more vials containing the second pharmaceutical composition. The kit can further comprise one or more unit doses of the third pharmaceutical composition. [0101] The kit can further comprise an instruction explaining the method of administering the first pharmaceutical composition, the second pharmaceutical composition, the second pharmaceutical composition, or all of the three. The method can be any of the administration methods provided herein. [0102] The kit described herein can be used for treatment of cancer or infection. 6.11. Examples [00209] The following examples are provided by way of illustration not limitation. Materials and Methods [00210] Murine models: Murine experiments were approved by the Institutional Animal Care and Use Committees of Explora BioLabs, Crown Bioscience or Champions Oncology. [00211] Experiments using Hu-PD-L1 KI mice were done at Crown Biosciences (Taicang Jiangsu Province, China) and mice were obtained from Shanghai Model Organisms Center, Inc., Shanghai Lingchang Biotechnology Co., Ltd.1 x 106 MC38 cell expressing
human PD-L1 (Hu-PD-L1 MC38) were implanted subcutaneously into the flank of HuPD-L1 knock-in C57/BL6 mice (female, 9-11 weeks old). The mice were randomized into 3 treatment groups (n = 6 per group) when average tumor volume reached 90.48mm3. Dosing was initiated on the same day (day 0). The mice were dosed (intraperitoneal, IP) biweekly for 3 weeks with PBS, anti-PD-L1 (Atezolizumab, Roche, 2mg/kg) or a combination of anti-PD- L1 (2mg/kg) and anti-TGFβ (mouse IgG1 clone 1D11 from BioXCell, 10mg/kg). Individual animals were removed from the study as their tumor volumes measured greater than 3000 mm3. All mice that did not have a complete response within the initial 28 day observation period were euthanized and tumors were collected to generate formalin-fixed paraffin- embedded (FFPE) blocks. Mice with full tumor regression (tumor volume of 0.00 mm3) after 4 weeks were re-challenged on study day 49. Six wildtype C57BL/6 mice (16-18 weeks of age) from Shanghai Lingchang Biotechnology Co., Ltd were used as a naïve control for the re-challenge experiment. Mice for the re-challenge experiment were inoculated subcutaneously at the opposite flank (left lower flank) with 1 x 106 HuPD-L1-MC38 cells. Following tumor implantation, tumor volume and body weight were measured twice a week for an additional 4 weeks. Two-sided Wilcoxon rank sum test was used to determine if the differences in average tumor volume are statistical significance. Survival analysis was performed using the R package survminer (version 0.4.5) and p-values were determined using log-rank test. [00212] The EMT6 tumor study was performed at Champions Oncology, Inc.250,000 EMT6 cells suspended in 0.1mL 1x PBS were implanted orthotopically in the 4th right mammary fat pad of female BALB/C mice (Taconic). When tumors reached an average tumor volume of 176.56 mm3 with a range of 15 – 400 mm3, animals were matched by tumor volume into blinded groups (n = 12 mice per group) used for dosing. The four treatment groups were PBS, anti-PD-L1 (10 mg/kg for the first dose with each subsequent dose at 5 mg/kg, Atezolizumab, Roche), anti-TGFβ (10 mg/kg, mouse IgG1 clone 1D11, BioXCell), or a combination of anti-PD-L1 plus anti-TGFβ. For all treatments the first dose was administered i.v. on day 0 and the eight subsequent doses were administered i.p. using a dose volume of 5 ml/kg three times per a week. Tumor volumes were measured three times weekly. Mice were observed for 28 days post initiation of dosing, with individual animals being removed from the study as their tumor volumes measured >2000 mm3. On day 8, three mice per group (chosen based on day-6 tumor volumes that were representative of the entire group) were sacrificed. Whole tumors from the selected mice were sterilely harvested,
removing adjacent skin but leaving the exterior surface of the tumor intact. If there was a large amount of mammary fat attached to the tumor or if the tumor had invaded the adjacent tissue, the tumor was cut away from the tissue and approximately 1-2mm of the tissues was kept attached to the tumor, so that the boundary between the tumor and non-tumor tissues was not disturbed. Tumors were placed into MACS tissue storage solution buffer (Miltenyi 130-100-008) on ice packs and shipped overnight for scRNA-seq processing. [00213] The CT26 tumor study was performed at Explora BioLabs by GigaGen staff. 500,000 CT26 cells suspended in 0.1mL 1x PBS were implanted s.c into the right hind flank of female BALB/c mice (Taconic). On day 11 post implantation, when tumors were an average tumor volume of 70.6 mm3, animals randomized into blinded groups (n = 10 per a group) based on tumor volume into blinded groups. Mice received PBS or a combination of Atezolizumab (anti-PD-L1, 2mg/kg) and anti-TGFβ (10mg/kg, clone 1D11, BioXcell). Starting on day 11, mice were treated i.p. two times a week for three weeks. Tumor were measured three times weekly. Mice were observed for 33 days post implantation, with individual animals being removed from the study as their tumor volumes measured greater than 2000mm3. [00214] The MC38 tumors study was performed at Champions Oncology, Inc.5 x 105 MC38 cells suspended in 100 ul of PBS were injected s.c. into the left flank of female C57BL/6 mice (Taconic). When tumors reached an average tumor volume of 71.1mm3 with a range of 32 – 113mm3, animals were randomized into blinded groups (n = 12 mice per group) on day 0. The four treatment groups were given PBS, recombinant human CCL5 (R&D systems, 278-RN-050/CF), PBS plus anti-PD-L1 (Atezolizumab, Roche), and CCL5 plus anti-PD-L1, respectively. PBS and CCL5 (1 ^g/animal) were administered intratumorally (IT), three times a week for three weeks. The recombinant human CCL5 has the sequence of SEQ ID NO: 2. Anti-PD-L1 (1mg/kg) was administered IP, twice a week for three weeks. Dosing started on day 1. Tumor volumes were measured three times weekly. Mice were observed for 28 days, with individual animals being removed from the study as their tumor volumes measured >2000 mm3. Two-sided Wilcoxon rank sum test was used to determine statistical significance in difference in average tumor volume. [00215] Immunohistochemistry: Formalin-fixed tumors from studies at Crown Biosciences or Champions Oncology were trimmed and paraffin embedded by those organizations, respectively. Tumors from the CT26 study were formalin fixed for 24h before being transferred to ethanol and transferred to Allele Biotechnology (San Diego) where they
were trimmed and paraffin embedded. All immunohistochemistry (IHC) was performed by Allele Biotechnology.4 ^m sections were cut and placed on glass slides for Haemotoxylin and Eosin (H&E) or antibody staining as indicated. A board-certified veterinary pathologist with experience in laboratory animals and toxicologic pathology and who was blinded from the study evaluated the slides from the huPD-L1 KI mouse study. Briefly, IHC findings were reviewed for intensity of staining (0 to 5, where 0 = no staining and 5 = most intense staining) and for number of positive cells per 200 ^m2 field at 10X magnification counting 3 fields for each slide. Statistical significance in the difference in CD3+ cell count was determined using Wilcoxon rank sum test. [00216] Single cell RNA sequencing: EMT6 mammary fat pad tumors and the neighboring tissue were collected from mice such that the entire tumor and the interface between tumor and normal tissue was preserved and tissue was stored overnight in MACS Tissue Storage Solution (Miltenyi Biotec Cat #: 130-100-008) at 4qC. The following day tumor tissue was minced and dissociated using the mouse Tumor Dissociation Kit (Miltenyi Biotec) and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). The “37C_m_TDK_2” and “m_imptumor_01” programs were used for the primary and secondary gentle MACS dissociation programs. Tumor suspensions were filtered through a 70μm MACS Smart Strainers (Miltenyi Biotec) and washed with PBS containing 0.5% BSA and 2mM EDTA. Cells were pelleted by centrifugation at 500 g for 7 min. A red blood cell lysis step was performed by incubating cells for 2 minutes with 1X Red Blood Cell Lysis Solution (Miltenyi Biotech). Cells were washed again and then cell viability was measured using the Nexcelom Cellometer K2 Fluorescent Viability Cell Counter and the ViaStain AOPI Staining Solution (Nexcelom). Single cell suspensions were then cryopreserved using CryoStor CS10 solution (STEMCELL technologies) and stored in liquid nitrogen. [00217] The day samples were to be run on the 10X Genomics Chromium instrument, cells were thawed and FACS sorted for DAPI- CD45+ (live, hematopoietic cells) and DAPI- CD45- (live, non-hematopoietic cells) populations. Briefly, cells were thawed in a 37qC water bath, resuspended in 10 ml of RPMI (Gibco cat # 22400-089) with 10% FBS (Gibco # 26140-095), centrifuged at 500g for 5 minutes, washed in PBS containing 0.5% BSA and 2mM EDTA, and counted using the Nexcelom Cellometer. Approximately 1 x 106 cells were transferred to a new tube, washed in PBS with 0.5% BSA and 2mM EDTA, and centrifuged at 500g for 5 minutes. The liquid was poured off from the cells (leaving approximately 100ul in each tube) and 5 μl of mouse Fc Blocking Reagent (rat anti-Mouse CD16/CD32 BD) was
added to samples and incubated for 5 minutes at 4C.162.5 μl of Brilliant Stain Buffer (BD) containing 12.5 μl of mouse CD45-PE clone 30-F11 (BioLegend) was added to cells and incubated on ice for 30 minutes protected from light. Cells were washed, resuspended in 1X DAPI solution (in PBS plus 0.5% BSA and 2mM EDTA) (BioLegend) at a concentration of 5 x 106 cells/ml, and filtered into 5mL FACS tubes with cell-strainer caps (Falcon). Cells were sorted using the BD FACSMelody using the 100μm nozzle. Mouse splenocytes were used as a positive control to determine the voltage needed to identify CD45+ immune cells in the initial side scatter area and forward scatter area gate that would be used for tumor cell suspensions. Singlet and DAPI- (live cell) gates were then applied. Stained single cell suspensions from EMT6 tumors were then sorted and approximately 1 x 105 Live CD45+ and 1 x 105 Live CD45- cells were collected at 4qC. Cells were washed in RPMI with 10% FBS, centrifuged at 500g for 5 minutes, and counted as described above. Cells were resuspended in RPMI with 10% FBS at 7 x 105 cells/ml and were placed on ice. CD45+ and CD45- sorted cells from each of the four groups were run on the 10X Genomics Chromium device using the Single Cell 3^ Reagent Kit v3 (work performed at SeqMatic). Libraries were sequenced at SeqMatic with an Illumina NovaSeq SP 100 cycle kit (read 128 bp, read 291 bp). [00218] Single cell RNA-seq data analysis: Raw sequencing FASTQ files were processed using the Cell Ranger (version 3.1.0) analysis pipeline. Briefly, alignment and filtering of sequencing reads, barcode counting, and UMI counting were performed using the cellranger count command. The reads were aligned to the Mus musculus reference genome assembly GRCm38 (mm10). The outputs of cellranger count for all samples were aggregated using the command cellranger aggr, normalizing the runs to the same sequencing depth. Secondary analyses were performed using the Seurat package (version 3.1.2) in R (version 3.6.0) {Stuart:2019id}. First, quality control was performed by removing cells with fewer than 200 or more than 5,000 expressed genes, as low and high number of gene counts may indicate low quality cells and cell multiplets, respectively. Cells with more than 10% mitochondrial gene expression were removed. This resulted in 27,797 cells, including 18,002 CD45+ and 9,795 CD45- cells. sctransform was used to normalize the expression data and to regress out mitochondrial mapping percentage as a confounding source of variation {Hafemeister:2019ba}. Principal component analysis was performed using the RunPCA function in Seurat. Principal components 1 to 30 were provided as an input for non-linear dimensionality reduction via Uniform Manifold Approximation and Projection (UMAP) using the RunUMAP function.
[00219] For cell type annotation, the R package SingleR was used, which leveraged reference transcriptomic datasets of pure cell types to infer the cell of origin of each of the single cells independently {Aran:2019ei}. The ImmGen (immgen.org) reference dataset was used. The cells were first annotated using the main cell type labels generated by SingleR. Since the ImmGen reference did not include tumor cell as a cell type, it was required to manually discern tumor cells from host non-immune cells within the CD45- cells. Therefore the CD45- cells was reanalyzed using RunUMAP, followed by clustering using the FindNeighbors and FindClusters functions in Seurat. These functions applied shared nearest neighbor (SNN) based clustering on the scRNA-seq data, identifying 15 clusters of cells. Cells in cluster 7 were annotated as fibroblasts based on expression of fibroblast marker gene, Fap. Cells previously annotated by SingleR as endothelial cells or epithelial cells were assigned their original SingleR labels. All other CD45- cells were annotated as tumor cells. To validate the annotations, copy number alterations were analyzed for the CD45- cells using InferCNV {Anonymous:wa}, using epithelial and endothelial cells as reference cells. This revealed copy number aberrations in the tumor cells but not in the fibroblast cells. [00220] Differential gene expression and functional enrichment analysis: Differential gene expression analysis was performed within each cell type using the FindMarkers function in Seurat. Each treatment group was compared to the PBS control, using Wilcoxon rank sum test to identify differentially expressed (DE) genes (log fold change > 0.25, adjusted p value < 0.05) between the two groups of cells. The aPD-L1 plus aTGFβ treatment group was also compared to the single treatment groups. [00221] ClusterProfiler (version 3.12.0) {Yu:2012ec} was used to perform functional enrichment analysis. For each treatment group, foreground gene lists containing genes up- or down-regulated in any CD45+ and CD45- cell types were generated, respectively. These gene lists were tested against background gene lists containing all expressed genes (expressed in at least 5 cells) in CD45+ and CD45- cells, respectively. The enrichment analysis was performed using the enrichGO function in ClusterProfiler using the org.Mm.eg.db database and the gene ontology (GO) categories biological process (BP), molecular function (MF), and cellular component (CC). Multiple testing correction was performed using the Benjamini and Hochberg method. The enriched pathways were visualized as gene concept networks using the cnetplot function of the enrichplot package (version 1.4.0) {enrichplotVisualiz:2019ty}. [00222] Cell-cell communication using CellphoneDB: Cell-cell communication analysis was performed using CellphoneDB {Efremova:2020cb}, a repository of curated
receptors, ligands and their interactions. First, all mouse genes from this study were mapped to their human orthologs using biomaRt {Durinck:2009ki}. scRNA-seq count tables and cell type annotations for each treatment group were used as inputs for running CellphoneDB, using the method “statistical analysis” and default parameters. Receptor-ligand interactions were visualized as dot plots using ggplot2 (version 3.2.1) {Wickham:2016bq}. [00223] Association of chemokine expression and immune cell abundance in TCGA: Intratumoral immune cell abundance was inferred using either an image-based approach or a gene signature-based approach. For the image-based approach, 4,612 published TIL scores estimated from TCGA H&E images were downloaded {Saltz:2018ig, Thorsson:2018ji}. Briefly, Saltz et al. developed deep learning-based image recognition to classify and quantify lymphocytes on H&E diagnostic images from 13 TCGA cancer types (LUAD, BRCA, PAAD, COAD, LUSC, PRAD, UCEC, READ, BLCA, STAD, CESC, SKCM and UVM). The deep learning model training process was repeated until pathologists judged that the lymphocyte classification was adequate. The TIL scores were reported as “TIL Regional Fraction” in Table 1 by Thorsson et al. {Thorsson:2018ji}. For the gene signature-based approach, pre-calculated xCell immune cell scores were downloaded for 9,358 TCGA samples (www(dot)xcell(dot)ucsf(dot)edu/) {Aran:2017do} and filtered for immune cell types of interest: CD8+ T cells, dendritic cells (aDC), NK cells, Tregs, and M2 macrophages. [00224] For TCGA tumor gene expression data, RNA-seq quantifications (in Fragments Per Kilobase of transcript per Million mapped reads, FPKM) were downloaded from the TCGA portal (www(dot)portal(dot)gdc(dot)cancer(dot)gov/) for 32 cancer types (ACC, BLCA, BRCA, CESC, CHOL, COAD, DLBC, ESCA, GBM, HNSC, KICH, KIRC, KIRP, LGG, LIHC, LUAD, LUSC, MESO, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM, STAD, TGCT, THCA, THYM, UCEC, UCS, UVM). Chemokine genes were filtered by retaining only expression data for genes whose names started with CXC, CCL, CX3C or XC. Within each cancer type, genes that were not or lowly expressed (median expression across all samples < 0.01 FPKM) were excluded from further analysis. [00225] For each TCGA cancer type, the chemokine gene expression data frame was combined with either the image-based or the gene signature-based immune score data frame. Only samples with data present in both data frames were analyzed. A pseudo count of 0.01 was added to the expression and immune scores, followed by log2 and z-score transformation, in preparation for linear regression analysis. Linear regression analysis was
performed for each chemokine gene using immune score as the dependent variable and chemokine gene expression as the independent variable. P-values were adjusted for multiple testing using the Benjamini and Hochberg method. Chemokines significantly associated with immune scores were further ranked by the sum of their regression coefficients across different cancer types. The results were visualized as heatmaps using ggplot2 (version 3.2.1) {Wickham:2016bq}. All data manipulations and analyses were performed in R 3.6.0. [00226] Flow cytometry: For flow cytometry MC38 tumors were harvested, cut into small pieces approximately of 2-4 mm and dissociated using the MACS Miltenyi Biotec Tumor Dissociation Kit according to manufacturer instructions. Dissociated cell suspensions were filtered through a 70um strainer with 10mL of RPMI 1640 media and centrifuged at 300xg for 7 minutes. Cells were resuspended in MACs buffer and Red Blood Cell Lysis Solution was added to remove erythrocytes and dead cells. Cells were pelleted, washed, and resuspended with MACS buffer. Cells were then plated into 96 well plates and stained with fluorescently labelled antibodies: CD11b (BUV395, clone M1/70, BD), CD4 (BUV496, clone RM4-5, BD), CD8 (9BUV661, clone 53-6.7, BD), CD3 (BUV805, clone 17A2, BD), CD11c (BV421, clone N418, BD), CD45 (BV480, 30F11, BD), Ly6G (BV605, clone 1A8, BD), CD44 (BV786, clone IM7, BD), Ly6C (AF488, clone HK1.4, BL), PD1 (BB700, clone j43, BD), FOXP3 (PE, clone FJK-16S, Fisher), NK1.1 (PECy7, clone PK136, BL), CCR5 (CD195) (APC, Clone 2D7, BD), and FVS780. Populations were named based on expression of the indicated marker(s). [00227] Data availability: Single cell RNA-seq fastq sequence files are deposited at the Sequence Read Archive (www(dot)ncbi(dot)nlm(dot)nih(dot)gov/sra/), under BioProject ID PRJNA615238. [00228] Supplemental materials: Table 1 lists the differentially expressed (DE) genes identified in the single cell RNA-seq of tumor samples from mice treated with anti-PD-L1 and/or anti-TGFβ. Table 2 contains the list of enriched terms as determined by functional enrichment analysis using the DE genes from Table 1. Example 1: PD-L1 plus TGFȕ blockade reduces tumor growth and enhances immune cell infiltration [00229] Human PD-L1 knock-in mice bearing MC38 tumors expressing Hu-PD-L1 (Hu-PD-L1 MC38) were treated with vehicle, anti-PD-L1 or a combination of anti-PD-L1 plus anti-TGFβ. Anti-PD-L1 significantly limited tumor growth (p = 0.0087; FIGs.1A-1B),
while anti-TGF-ȕ alone was not efficacious (FIGs.9A-9B). Additionally, combination treatment with anti-PD-L1 plus anti-TGFβ was significantly more efficacious than anti-PD- L1 alone (p = 0.038) and led to tumor regression in 66.67% of animals by day 28 (FIGs.1A, 1B). Both anti-PD-L1 and anti-PD-L1 plus anti-TGFβ also improved survival relative to control (FIG.1C).1 of 6 (16.67%) mice from the anti-PD-L1 group and 3 of 6 (50%) mice from the anti-PD-L1 plus anti-TGFβ group had a complete response and were re-challenged with Hu-PD-L1 MC38 cells, implanted subcutaneously on the opposite flank from the original tumor. Tumor-naïve, wild-type C57BL/6 mice were used as controls. All previously cured mice, but not the naïve mice, were protected from tumor re-challenge, indicating the presence of anti-tumor immune memory (FIG.1D). [00230] To investigate if PD-L1 plus TGFβ blockade had an effect on T cell infiltration, CD3 immunohistochemistry (IHC) was performed on tumors from the treated mice. Anti-PD-L1 plus anti-TGFβ significantly increased T cell infiltration while anti-PD-L1 alone did not (FIG.1E, 1F). Tumor growth inhibition was also observed upon anti-PD-L1 plus anti-TGFβ treatment in a different mouse colon carcinoma tumor model, CT26 (FIG. 6A, 6B). Overall, these results established that dual blockade of PD-L1 and TGFβ effectively controlled tumor growth and improved T cell infiltration into the tumor. It was thus reasoned that in vivo inhibition of PD-L1 plus TGFβ could be used as an experimental model to identify genes important for immune cell infiltration and anti-tumor response, and this information could be used to uncover strategies to enhance immunotherapy. [00231] In a different mouse colon carcinoma tumor model, CT26, significant tumor growth inhibition was also observed upon anti-PD-L1 (atezolizumab, which cross reacts with murine PD-L1) plus anti-TGF-ȕ treatment, whether anti-TGF-ȕ was given intraperitoneally (I.P.) or intratumorally (I.T.) (FIG.10). [00232] To study this therapeutic regimen in an orthotopic tumor type, mice harboring EMT6 breast tumors orthotopically grown in the mammary fat pad were treated with PBS, anti-PD-L1 (atezolizumab), anti-TGF-ȕ, or anti-PD-L1 (atezolizumab) plus anti-TGF-ȕ. While efficacy from either single agent was not observed, anti-PD-L1 plus anti-TGF-ȕ significantly reduced tumor size relative to PBS or anti-TGF-ȕ alone (p<0.03; FIGs.7A, 7B). Further, the combination treatment improved the survival relative to all individual arms (p<0.01; FIG.7H). Anti-PD-L1 plus anti-TGF-ȕ in combination, but neither monotherapy alone, enhanced CD3 immune cell infiltration relative to all individual arms (p<0.03; FIG. 7I).
Example 2: Single cell RNA-seq of tumors from anti-PD-L1 and anti-TGFȕ treated mice [00233] To identify potential novel therapeutic strategies, the present inventors aimed to characterize the molecular responses upon anti-PD-L1 and/or anti-TGFβ treatment at the single cell level, using the syngeneic breast tumor model, EMT6. Mice harboring EMT6 tumors were treated with either PBS, anti-PD-L1, anti-TGFβ or anti-PD-L1 plus anti-TGFβ. While efficacy was not observed from the single agents, anti-PD-L1 plus anti-TGFβ significantly reduced tumor size relative to PBS (p = 0.024) (FIG.7A, 7B). The EMT6 orthotopic tumor model provided with an opportunity to characterize the single cell molecular responses to anti-PD-L1 ± anti-TGF-ȕ treatment in a setting where anti-TGF-ȕ addition overcomes resistance to anti-PD-L1 therapy. Eight days after the first dose, three mice per a group with representative tumors were euthanized and their tumors were harvested, dissociated, and flow sorted for CD45+ immune cells and CD45- non-immune cells, which were subjected to single cell RNA sequencing (scRNA-seq) using the 10x Genomics platform. After quality control (FIG.12), single cell transcriptomic profiles were generated for 27,797 high-quality cells, including including 17,665 CD45+ and 9,795 CD45- cells. Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction of the transcriptomes revealed distinct clusters of cells present in all treatment groups (FIG.2A, 2B). Cell type labels were assigned using SingleR, which annotated cell type based on reference transcriptomes of pure cell types in the ImmGen database {Heng:2008jj}. To discern tumor cells from host stromal cells, fine UMAP clustering was performed on the CD45- cells, generating 15 distinct clusters (FIG.7C). Cells in cluster 7 had high expression of the fibroblast marker, Fap, and were annotated as fibroblasts (FIG.7D). The remaining cells were annotated as tumor cells or assigned their original SingleR labels as endothelial or epithelial cells. Copy number analysis confirmed that the annotated tumor cells exhibited aberrant copy number while the fibroblasts did not (FIG.7E). In total, 12 cells types that had both unique and overlapping marker gene expression patterns were identified (FIG.13). When comparing the different treatment groups, differences in cell type composition was observed. For example, the anti-PD-L1, anti-TGFβ and anti-PD-L1 plus anti-TGFβ samples had lower numbers of macrophages (9.2 – 20.3% of CD45+ cells) compared to the PBS control (33.3% of CD45+ cells). On the contrary, relative to the PBS sample where B cells represented 9.5%% of the CD45+ cells, the three treatment groups had higher number of B cells (23.8%-32.1%, respectively, of the CD45+ cells) (FIG.2C).
[00234] Next, differential gene expression analysis was performed between each drug treatment group and the control sample, within each annotated cell type. Anti-PD-L1, anti- TGFβ and anti-PD-L1 plus anti-TGFβ treatments resulted in 568, 123 and 358 differentially expressed genes, respectively, across different cell types, respectively (Table 1). To assess the overall impact of the drug treatments on the non-immune and immune compartments, functional enrichment analysis of the differentially expressed genes within the CD45- and CD45+ cells were performed, respectively. While single agent inhibition of PD-L1 did not result in down-regulation of specific functional categories for the CD45- cells, TGFβ blockade led to down-regulation of WNT-signaling related pathways including Wnt-protein binding and frizzled binding (FIG.2D, Table 2). Interestingly, WNT/beta-catenin pathway was previously shown to contribute to T cell exclusion {Spranger:2015ge}. More strikingly, dual blockade of PD-L1 plus TGFβ led to significant down-regulation of matrix remodeling associated functional categories including extracellular matrix, contractile fiber and collagen- containing extracellular matrix (FIG.2D). For example, collagen and metalloproteinase genes such as Col1a1, Col1a2, Cthrc1, P3h4 and Mmp23 were down-regulated in fibroblasts following dual antibody blockade (FIG.2E, 2F). This is consistent with previous observation that TGFβ blockade synergizes with anti-PD-L1 to reprogram the peritumoral stromal fibroblasts {Mariathasan:2018dx}. To elucidate the interactions between various cell types involved in TGFβ signaling, a cell-cell communication network was generated involving all TGFβ ligands and receptors using CellPhoneDB {Efremova:2020cb}. CellPhoneDB analysis implicated multiple cell types as the source of TGFβ ligands, including B cells, dendritic cells, macrophages, NK cells and intriguingly, tumor cells. Tumor cell-expressed TGFβ molecules were predicted to interact with TGFβ receptors on fibroblast cells, macrophages and tumor cells themselves. Interestingly, these interactions were largely abolished following anti-TGFβ treatment, alone or in combination with anti-PD-L1 (FIG.7F). This suggests that tumor cell produced TGFβ can induce fibroblasts to express collagen and other extracellular matrix genes resulting in a physical barrier to T cell exclusion and that TGFβ blockade counteracts this immune suppression. [00235] Functional enrichment analysis of the up-regulated genes within the CD45+ cells showed clear enhanced immune responses following anti-PD-L1 and anti-TGFβ treatments, whether administered alone or in combination. For example, anti-PD-L1 plus anti-TGFβ induced upregulation of genes involved in response to bacterium (eg. H2-K1, B2m, Cd274, Il1b), response to interferon-gamma (eg. H2-Aa, Stat1, Irf1) and positive
regulation of cytokine production (eg. Cd74, Cd83, Ccl4) (FIG.2G, 2H, Table 2). Notably, multiple chemokines were upregulated in the macrophages of the anti-PD-L1 sample (Cxcl9, Ccl5, Ccl4, Cxcl14), the anti-TGFβ sample (Ccl12, Ccl4) and the anti-PD-L1 plus anti-TGFβ sample (Cxcl10, Cxcl9, Ccl4, Ccl5, Ccl3, Ccl2, Ccl7) (FIG.2I). This is consistent with previous in vivo studies showing anti-PD-1/L1 treatment favors polarization of macrophages towards a more immunostimulatory state {Gubin:2018iw, Xiong:2019fx}. Further analysis revealed that chemokines were upregulated in fibroblasts, neutrophils and T cells in tumors from anti-PD-L1 and anti-PD-L1 plus anti-TGFβ treated mice (FIG.7G). Additionally, anti- PDL-L1 plus anti-TGFβ combination treatment led to upregulation of additional chemokines such as Cxcl1 and Cxcl2 above and beyond those induced by either single treatment alone (Table 1). Chemokines lay a critical role in recruiting various immune cells to create an inflamed TME {Vilgelm:2019jw, Nagarsheth:2017dp}. The increase in chemokine expression in anti-PD-L1 and anti-PD-L1 plus anti-TGFβ treated samples suggests that chemokines may facilitate the success of checkpoint blockade treatments. Indeed, both pre- treatment and post-treatment CXCL9 and CXCL10 expression levels have been shown to be correlated with response to anti-PD-1 and anti-PD-L1 treatment, in melanoma and urothelial cancer patients, respectively {Rosenberg:2016hh, Lim:2018jy, Chow:2019gj}. [00236] Because multiple tumors were pooled for each treatment group for the scRNA-seq analysis, it is possible that some of the gene expression differences observed could be skewed by a single tumor sample, leading to a higher number of false positives from this analysis. Among CD45- cells, the combo treatment resulted in the highest number of down-regulated genes in fibroblasts (FIG.11A). To further investigate the changes in fibroblasts, unsupervised re-clustering of fibroblasts was performed, revealing two subclusters. Cluster Fib_0 was associated with higher expression of genes including Clec3b, Tnxb, Col14a1, Pi16, and Lbp, while cluster Fib_1 was associated with higher expression of Tnc, Gapdh, Spp1, Cxcl14, and Timp1 (FIGs.11B-11D). Differential gene expression and functional enrichment analysis was performed within the fibroblast subclusters. Interestingly, within Fib_0, dual blockade of PD-L1 plus TGF-ȕ led to significant downregulation of matrix remodeling associated functional categories including collagen fibril organization, extracellular matrix organization, and fibrillar collagen trimer (FIG.11E). For example, collagen and metalloproteinase genes such as Col1a2, Col5a2, Col1a1, P3h4, Cthrc1, and Mmp2 were downregulated in Fib_0 following combination blockade (FIGs.11F-11G; Table 3).
[00237] Among CD45+ cell types, macrophages had the highest number of up- regulated genes following anti-PD-L1 plus anti-TGF-ȕ treatment (FIG.11A). Fine clustering of macrophages revealed four subclusters, with subclusters Mac_0 and Mac_1 representing more than 90% of the cells (FIGs.14A-14B). Cells in Mac_0 were characterized by expression of complement-related genes (C1qa, C1qb, C1qc) and cytokines (Spp1, Ccl12), while cells in Mac_1 expressed higher levels of several tumor-associated macrophages- related genes such as Arg1, Cebpb, and Ier3 (FIG.14C). Differential expression and functional enrichment analysis showed that anti-PD-L1, administered alone or in combination with anti-TGF-ȕ, resulted in enhanced immune responses in Mac_0. For example, both anti- PD-L1 and anti-PD-L1 plus anti-TGF-ȕ induced upregulation of genes involved in antigen processing and presentation, adaptive immune response, response to bacterium, and response to interferon-gamma (FIGs.14D-14E). Anti-TGF-ȕ, administered alone or in combination with anti-PD-L1, induced upregulation of genes involved in monocyte chemotaxis, response to chemokine, and eosinophil migration (FIG.14D). Notably, many chemokines were upregulated in the Mac_0 population of the anti-PD-L1 sample (Ccl5, Cxcl9, Ccl4) and the anti-TGF-ȕ sample (Ccl2, Ccl12, Ccl4), while multiple chemokines showed further upregulation after anti-PD-L1 plus anti-TGF-ȕ combination treatment (Ccl5, Ccl2, Ccl7, Ccl3, Cxcl10) (FIG.14F; Table 4). [00238] Further analysis revealed that chemokines were upregulated in fibroblasts, neutrophils, and T cells in anti-PD-L1 and anti-PD-L1 plus anti-TGF-ȕ treated tumors (FIG. 7G). Additionally, anti-PD-L1 plus anti-TGF-ȕ combination treatment led to upregulation of additional chemokines such as Cxcl1 and Cxcl2 in tumor cells above and beyond those induced by either single treatment alone (Table 1). Chemokines lay a critical role in recruiting various immune cells to create an inflamed tumor microenvironment. The enhanced chemokine expression in samples after anti-PD-L1 plus anti-TGF-ȕ combination treatment suggests that chemokines may facilitate the success of checkpoint blockade treatments. [00239] A major goal in immunotherapy is to find strategies to enhance immune cell infiltration. While anti-TGFβ monoclonal antibodies in combination with anti-PD-L1s have been shown to enhance immune infiltration and efficacy in preclinical models, these molecules have been plagued by toxicity leading to the halting of several clinical trials with these agents. However, these data suggest the possibility that a chemokine administered therapeutically may improve immune cell infiltration and efficacy of anti-PD-L1 antibodies.
Example 3: CCL5 expression and CXCL9 expression are associated with immune cell infiltration across human cancer types [00240] To prioritize chemokines most likely to enhance efficacy of anti-PD-L1 antibodies, an unbiased computational approach was taken to identify chemokines associated with immune cell infiltration in different human cancer types in The Cancer Genome Atlas (TCGA). For this tumor-infiltrating lymphocyte (TIL) scores for TCGA tumor samples were utilized, which have been previously quantified using two distinct methods. For one method Saltz et al. used a deep learning image recognition algorithm to quantify tumor infiltrating lymphocytes from H&E-stained pathology images for 13 TCGA cancer types {Saltz:2018ig, Thorsson:2018ji}. Independently, Aran et al. developed a gene signature-based method termed xCell to infer immune cell abundance based on tumor gene expression profiles {Aran:2017do}. Specifically, the immune cell abundance scores was of focus for three cytotoxicity relevant cell types: CD8+ T cells, dendritic cells and NK cells. Using linear regression models, association between gene expression levels for a panel of chemokine genes (i.e. genes starting with CXC, CCL, CX3C or XC) was tested for with the immune infiltration scores, based on both the image-based scoring method and the gene signature- based scoring method (FIG.3A). Chemokines significantly (multiple testing adjusted p- values < 0.05) associated with immune infiltration scores were further ranked based on their association strengths (i.e. regression coefficients) across cancer types (FIG.3A). [00241] The expression levels of six chemokine genes were significantly associated with the image-based immune scores, across all 13 tested cancer types (FIG.3B). Of these CCL5, CXCL9, CXCL13, CXCL10 CXCL11, and CCL19) were, also, among the top chemokine genes associated with the gene expression-based immune scores across multiple cancer types (FIG.3C). For example, correlation of CCL5 expression in breast cancer (BRCA) with the image-based infiltration scores is shown in FIG.8A. In contrast, these chemokines were weakly associated with the gene expression-based immune scores for immunosuppressive Tregs and M2 macrophages (FIG.8B). Notably, CCL5 and CXCL9 were consistently the top chemokines associated with immune infiltration scores, as determined by the image-based and the gene signature-based methods (FIG.3B, 3C). CCL5 and CXCL9 expression levels were significantly associated with inferred CD8+ T cells, dendritic cells and NK cells abundance across multiple cancer types (FIG.3C). Example 4: CCL5 enhances immune cell infiltration and synergizes with anti-PD-L1 in vivo
[00242] Given its chemotactic roles, it was hypothesized that intratumoral delivery of recombinant CCL5 or CXCL9 proteins may enhance immune cell recruitment and control tumor growth. While multiple intratumoral cell subsets express CCR5 (FIG.5D; Additional file 1, FIGs.4B-4C), intratumorally administering recombinant CCL5 to s.c. MC38 tumors resulted in an increased frequency of CD8+ T cells in the tumor that were CCR5 positive twelve days after starting dosing (p = 0.03; FIG.5D, 4A; FIGs.4B-4C), though no significant difference was seen for total CD8+ T cells (FIG.5D). There was also a trend towards an increase in the frequency of NK cells expressing CCR5 (p = 0.09; FIG.5D, 4A; FIGs.4B- 4C) but not for total NK cells (FIG.5D). Furthermore, it was found that intratumoral CCL5 resulted in an increased frequency of NK cells expressing CD11b+ (p = 0.04; FIG.5B, 5C; FIGs.4B-4C). Though after multiple hypothesis correction (Bonferroni), none of the p-values in Figure 4A or 5C remain significant (p>0.05). Together these data suggest that intratumorally administered CCL5 altered the tumor microenvironment, including by recruiting cytotoxic lymphocytes. However, several intratumoral immune cell subsets have higher expression of CCR5 than CD8 T cells or NK cells (FIG.5A). [00243] To determine if the totality of cells recruited by intratumorally administered CCL5 was able to enhance the efficacy of anti-PD-L1 therapy, the ability of CCL5, alone or in combination with anti-PD-L1 was tested, to limit tumor growth using the same tumor model. While neither CCL5 or 1 mg/kg of anti-PD-L1 alone limited tumor growth, CCL5 in combination with anti-PD-L1 significantly reduced tumor growth relative to all individual arms (p<0.05;FIG.4D, 4E). Mice that received intratumoral CCL5 plus anti-PD-L1 combination therapy also had significantly prolonged survival compared to compared to all individual arms (p<0.02;(FIG.4F). Thus, intratumorally administered CCL5 is able to overcome resistance to anti-PD-L1 therapy. Example 5: In vivo efficacy of intratumoral CCL5, CXCL9, or WARS in a MC38 tumor model [00244] The chemokines CXCL9 and CCL5 correlate to immune infiltration in human tumors and were found to recruit immune cells important for anti-tumor immune responses. For example, CXCL9 is able to recruit cytotoxic T cells, T helper-type 1 (Th1) CD4 T cells, and NK cells, which express the CXCL9 receptor CXCR3. CCL5 was shown to recruit dendritic cells in murine tumor models. Thus, the study herein evaluates i.t. administration of recombinant CXCL9 or CCL5 on tumor growth inhibition (TGI).
[00245] An MC38 syngeneic tumor model was used in order to evaluate anti-tumor activity of intratumorally (i.t.) administered recombinant CCL5, CXCL9, or WARS. [00246] Further, the present inventors hypothesized whether combination therapy with CCL5 and CXCL9 would synergize since recruitment of activated T cells to the tumor microenvironment and result in a productive anti-tumor immune response if anti-tumor T cells are properly primed (i.e. recruiting T cells to the tumor will not induce productive anti- tumor response if no anti-tumor T cells are activated). Productive priming of tumor-specific T cells likely requires that activated dendritic cells pick up antigen in the tumor and traffic back to the lymph node where they can prime these T cells. Thus, combination therapy that both recruits dendritic cells and activated T cells to the tumor may be a powerful combination if it enabled both effective priming of anti-tumor T cells and recruitment of these T cells to the tumor microenvironment. [00247] Thus, the study provided herein evaluates i.t. administration of one or both of these chemokines in improving the anti-tumor response induced by anti-PD-L1 treatment. Study Design [00248] A MC38 syngeneic colorectal tumor model was used in this study. The model included C57BL/6 female mice (Taconic) that implanted between 7.5 and 12 weeks of age. Weight criteria at the initial dosing was at least 18 grams. Pre-dosing: [00249] Pre-study Animals: [00250] Groups 1-10: 120 C57BL/6 mice were injected with 0.1 mL volume containing 5x105 MC38 cells in 1x PBS into the left flank; these animals were used for randomization into groups 1-10 based on tumor volumes. [00251] Group 11: 12 C57BL/6 mice were injected in the left flank with a 100uL mixture containing 5x105 MC38 cells in 1x PBS mixed with 1 ug of recombinant WARS. These 12 animals were placed onto study at the time that groups 1-10 were randomized. [00252] Study Animals: Once sufficient pre-study animals reached an average tumor volume of 50.3 mm3, with a tumor volume range of 37 to 85 mm3, 80 animals were randomized into groups 1 - 10. The tumor volume range for group 11 was 16-68 mm3 at that time point. Treatment
[00253] Table 5 outlines the parameters used for each sample group (sample size, test agent, dosage and volume, route of administration, and frequency of administration). Table 5: Study Design
* Group 4 test agents were mixed together and dosed as a cocktail ** Group 9 test agents CXCL9 and CCL5 were mixed together and dosed IT as a cocktail, while aPD-L1 (10F.9G2) was dosed separately IP *** Group 11 test agent was mixed with tumor cells on day of tumor implantation (DOI). TIW dosing initiated on Study Day 0. In-Life: [00254] Tumor volumes: Tumor volumes were measured three times weekly and a final tumor volume was measured on the day study reached endpoint. [00255] Animal weights: Animals were weighed three times weekly and a final weight was taken on the day the study reached end point. If any animal exhibited >15% weight loss
when compared to day 0, all mice in that specific group were provided DietGel ad libitum equally for the remainder of the study. Fresh DietGel was supplied once daily. [00256] Clinical observations: Animals were observed daily. [00257] Tumor ulceration: Tumor ulceration was defined as a break in the skin through the basement membrane exposing the dermis and associated vasculature and nerves. Mice with ulceration greater than 50% of the tumor total surface area or impacting the overall health and well-being were euthanized. As antibiotic use is known to affect immuno-oncology drug efficacy, no antibiotic ointment was added to tumors. Study Termination: [00258] Individuals animals were removed from the study as their tumor volumes measured >2000 mm3. Some animals were euthanized and had their tumors collected at our request on day 19 for potential future analysis. Results [00259] Tumor Measurements: [00260] Comparison of tumor volumes (mm3) from mice only treated with chemokines is shown in FIG.15A. Monotherapy treatment with recombinant CCL5 (1 ug/dose) induced TGI when administered intratumorally for MC38 tumors that started at ~50 mm3. [00261] Additionally, it was also found that expression of the gene WARS correlated to immune infiltration in tumors, suggesting that WARS is also able to recruit immune to the tumor leading to an anti-tumor response. [00262] Comparison of tumor volumes (mm3) from mice treated with chemokines and aPD- L1 is shown in FIG.15B. [00263] Body weights (% change). The percent change in body weight for each treatment group is shown in FIG.15C. CCL5 alone and CCL5 in combination with aPDL-1 had the greatest increase in body weight over time. 7. SEQUENCE
8. INCORPORATION BY REFERENCE [00264] All publications, patents, patent applications and other documents cited in this application are hereby incorporated by reference in their entireties for all purposes to the same extent as if each individual publication, patent, patent application or other document were individually indicated to be incorporated by reference for all purposes. 9. EQUIVALENTS [00265] While various specific embodiments have been illustrated and described, the above specification is not restrictive. It will be appreciated that various changes can be made without departing from the spirit and scope of the invention(s). Many variations will become apparent to those skilled in the art upon review of this specification.
Claims
WHAT IS CLAIMED IS: 1. A pharmaceutical composition, comprising: a CCL5 mimetic, or pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
2. The pharmaceutical composition of claim 1, wherein the CCL5 mimetic is a human CCL5 peptide, wherein the CCL5 peptide has a sequence of SEQ ID NO: 1.
3. The pharmaceutical composition of claim 1, wherein the CCL5 mimetic is a CCL5 analog.
4. The pharmaceutical composition of claim 3, wherein the CCL5 analog is a polypeptide having the sequence of SEQ ID NO: 2.
5. The pharmaceutical composition of claim 3, wherein the CCL5 analog comprises an active fragment of a human CCL5 peptide.
6. The pharmaceutical composition of claim 5, wherein the active fragment of human CCL5 comprises amino acids 12-22 of SEQ ID NO: 1.
7. The pharmaceutical composition of claim 5, wherein the active fragment of human CCL5 comprises one or more of the following amino acid residues selected from the group consisting of: P2, Y3, D6, T7, F12, I15, and R17.
8. The pharmaceutical composition of any one of claims 1-7, wherein the CCL5 mimetic comprises a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99%sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2.
9. The pharmaceutical composition of any one of claims 3-8, wherein the CCL5 mimetic is a CCL5 analog having a longer half-life in vivo as compared to CCL5.
10. The pharmaceutical composition of any one of claims 1-9, wherein the CCL5 mimetic is a conjugate of CCL5 or a CCL5 analog to a conjugate moiety.
11. The pharmaceutical composition of claim 10, wherein the conjugate moiety is selected from polyethylene glycol (PEG) and hyaluronic acid.
12. The pharmaceutical composition of claim 10, wherein the conjugate moiety is selected from the group consisting of HAS, human IgG, scFv, F(ab), F(ab’)2, transferrin, albumin, and an Fc domain of an immunoglobulin.
13. The pharmaceutical composition of claim 10, wherein the conjugate moiety is selected from the group consisting of: XTEN, a proline-alanine-serine polymer
(PAS), a homopolymer of glycine residues (HAP), a gelatin-like protein (GLP), a signal peptide and an elastin-like peptide (ELP).
14. The pharmaceutical composition of any one of claims 1-13, wherein the CCL5 mimetic comprises one or more modified or non-naturally occurring amino acids, selected from the group consisting of: a steric enantiomer (D isomer), a rare amino acid of plant origin, a non-naturally occurring amino acid or amino acid mimetic, or have been modified by any one or more modifications selected from acetylation, acylation, phosphorylation, dephosphorylation, glycosylation, myristollation, amidation, aspartic acid/asparagine hydroxylation, phosphopantethane attachment, methylation, methylthiolation, prensyl group attachment, intein N-/C-terminal splicing, ADP-ribosylation, bromination, citrullination, deamination, dihydroxylation, formylation, geranyl-geranilation, glycation, palmitoylation, Į-methyl-amino acids, CĮ-methyl amino acids, and NĮ- methyl amino acids.
15. The pharmaceutical composition of any one of claims 1-14, wherein the CCL5 mimetic is chemically-synthesized and comprises one or more non-peptide bonds.
16. The pharmaceutical composition of any one of claims 1-15, comprising the pharmaceutically acceptable salt of a CCL5 mimetic, wherein the salt is hydrochloride, trihydrochloride, sulfate, mesylate, or tosylate.
17. The pharmaceutical composition of any one of claims 1-16, formulated for parenteral administration.
18. The pharmaceutical composition of any one of claims 1-16, formulated for intratumoral injection, intravenous injection or subcutaneous injection.
19. A kit for treatment of cancer, comprising: the pharmaceutical composition of any one of claims 1-18, and an additional therapeutic agent.
20. The kit of claim 19, wherein the additional therapeutic agent is an anti-PD-L1 antibody, an anti-PD-1 antibody, or a TGFβ inhibitor.
21. The kit of claim 19, wherein the additional therapeutic agent is a bispecific antibody against PD-L1 and TGFβ or against PD-1 and TGFβ.
22. The kit of claim 19, the additional therapeutic agent comprises an anti-PD-L1 antibody and an anti-TGFβ antibody.
23. The kit of claim 19, the additional therapeutic agent comprises an anti-PD-1 antibody and an anti-TGFβ antibody.
24. The kit of claim 19, the additional therapeutic agent comprises an anti-PD-L1 antibody, wherein the anti-PD-L1 antibody is atezolizumab.
25. The kit of claim 19, wherein the additional therapeutic agent is an anti-CTLA4 antibody, optionally, wherein the anti-CTLA4 antibody is ipilimumab.
26. The kit of claim 19, wherein the additional therapeutic agent comprises a T cell or an NK cell.
27. The kit of claim 26, wherein the T cell is a CAR-T, CAR-NK, CAR- macrophage,TCR-T cell.
28. The kit of claim 19, wherein the additional therapeutic agent is an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof.
29. The kit of claim 19, wherein the additional therapeutic agent is an agent activating NK cell,T cell activity, dendritic cell activity, or a combination thereof.
30. A method of treating cancer, comprising the step of: administering to a subject with the cancer a therapeutically effective amount of an isolated chemokine mimetic, or pharmaceutically acceptable salt thereof.
31. The method of claim 30, wherein the isolated chemokine mimetic is selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof.
32. The method of claim 31, wherein the isolated chemokine mimetic is two or more isolated chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof.
33. The method of claim 30, wherein the isolated chemokine mimetic is a CCL5 mimetic or pharmaceutically acceptable salt thereof.
34. The method of any one of claims 30-33, wherein the isolated chemokine mimetic or pharmaceutically acceptable salt thereof is administered in a pharmaceutical composition further comprising a pharmaceutically acceptable carrier or excipient.
35. The method of any one of claims 30-34, wherein said administering is via intratumoral injection, intravenous injection or subcutaneous injection.
36. The method of claim 35, wherein said administering is via intratumoral injection.
37. The method of any one of claims 30-36, further comprising the step of administering to the subject an anti-PD-L1 antibody or an anti-PD-1 antibody.
38. The method of any one of claims 30-37, further comprising the step of administering to the subject a TGFβ inhibitor.
39. The method of any one of claims 30-36, further comprising the steps of
administering anti-PD-L1 antibody and an anti-TGFβ antibody.
40. The method of any one of claims 30-36, further comprising the step of administering a bi-specific antibody targeting both PD-L1 and TGFβ.
41. The method of any one of claims 30-36, further comprising the step of administering a bi-specific antibody targeting both PD-1 and TGFβ.
42. The method of any one of claims 30-36, further comprising the step of administering to the subject an anti-CTLA4 antibody, optionally, wherein the anti- CTLA4 antibody is ipilimumab.
43. The method of any one of claims 30-36, further comprising the step of administering to the subject a T cell, an NK cell, macrophage, or dendritic cell, optionally wherein the T cell is a CAR-T, CAR-NK, CAR-macrophage, or TCR-T cell.
44. The method of any one of claims 30-36, further comprising the step of administering to the subject an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof.
45. The method of any one of claims 30-36, further comprising the step of administering to the subject an agent activating NK cell, T cell activity, or dendritic cell activity.
46. The method of any one of claims 30-45, wherein the cancer is selected from the group consisting of: multiple myeloma, adrenocortical carcinoma, acute myeloid leukemia, Bladder Urothelial Carcinoma, glioma, breast invasive carcinoma, glioma, Cervical squamous cell carcinoma, endocervical adenocarcinoma, cholangiocarcinoma, chronic myelogenous leukemia, colon adenocarcinoma, esophageal carcinoma, glioblastoma multiforme, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, lymphoid neoplasm diffuse large B-cell lymphoma, mesothelioma, ovarian serous cystadenocarcinoma, pancreatic adenocarcinoma, pheochromocyoma, paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma,sarcoma, skin cutaneous melanoma, stomach adenocarcinoma, testicular germ cell tumors, thyomas, thyroid carcinoma, uterine carcinosarcoma, uterine corps endometrial carcinoma, microsatellite instability-high cancer, basal cell carcinoma, Merkel cell carcinoma, uveal melanoma, and mucosal melanoma.
47. A method of treating cancer, comprising the steps of:
intratumorally administering a therapeutically effective amount of an isolated chemokine mimetic, or pharmaceutically acceptable salt thereof, to a subject who has been determined to have expression levels in a biological sample of one or more genes selected from the group consisting of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, CD8, CD3, TCRȕ, TCR1, CD11c, WARS, NKp46 and NCR1, CD56, CD16, CD7 CD127, Tbet, Eomes, granzymes, and perforin that are lower than or higher than a predetermined threshold level.
48. The method of claim 47, wherein the biological sample is a tumor biopsy or a liquid biopsy.
49. The method of claim 47, wherein the biological sample is a blood sample.
50. The method of claim 47, wherein the biological sample comprises T-cells or NK cells isolated from the subject or a donor.
51. The method of any one of claims 47-49, further comprising the prior step of determining the expression levels of one or more genes selected from the group consisting of CCL5, CXCL9, CXCL13, CXCL10, CXCL11, CD8, CD3, TCRȕ, TCR1, CD11c, WARS, NKp46, NCR1, CD11B, FcRs, collagen genes, CTLA4, CD56, CD16, CD7 CD127, Tbet, Eomes, granzymes, and perforin in the biological sample.
52. The method of any one of claims 47-51, further comprising the prior step of detecting CD8+ T cells, NK cells, mature NK cells, lymphocytes, fibroblasts, Tregs, or dendritic cells in the biological sample.
53. The method of claim 52, wherein the CD8+ T cells, NK cells, lymphocytes, or dendritic cells are detected by immune histochemistry.
54. The method of any one of claims 47-53, wherein the chemokine mimetic is selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof.
55. The method of claim 54, wherein the chemokine mimetic is two or more chemokine mimetics selected from the group consisting of: CCL5, CXCL9, CXCL13, CXCL10, CXCL11, WARS, XCL-1, and an analog thereof.
56. The method of any one of claims 47-51, wherein the chemokine mimetic is a CCL5 mimetic or pharmaceutically acceptable salt thereof.
57. The method of claim 56, wherein the chemokine mimetic is CCL5 or a CCL5 analog.
58. The method of any one of claims 47-57, wherein the chemokine mimetic or
pharmaceutically acceptable salt thereof is administered in a pharmaceutical composition further comprising a pharmaceutically acceptable carrier or excipient.
59. The method of any one of claims 47-58, wherein said administering is via intratumoral injection, intravenous injection or subcutaneous injection.
60. The method of any one of claims 47-58, further comprising the step of administering to the subject an anti-PD-L1 antibody or an anti-PD-1 antibody.
61. The method of claim 47-60, furthercomprising the step of administering to the subject a TGFβ inhibitor.
62. The method of any one of claims 47-58, further comprising the step of administering an anti-PD-L1 antibody and a TGFβ antibody.
63. The method of any one of claims 47-58, further comprising the step of administering a bi-specific antibody targeting both PD-L1 and TGFβ.
64. The method of any one of claims 47-58, further comprising the step of administering a bi-specific antibody targeting both PD-1 and TGFβ.
65. The method of any one of claims 47-58, further comprising the step of administering to the subject an anti-CTLA4 antibody, optionally, wherein the anti- CTLA4 antibody is ipilimumab.
66. The method of any one of claims 47-58, further comprising the step of administering to the subject a T cell or an NK cell, optionally wherein the T cell is a CAR-T, CAR-NK cell, CAR-macrophage, or TCR-T cell.
67. The method of any one of claims 47-58, further comprising the step of administering to the subject an IL-15, IL-15 complex, IL-2, IL-7, or a variant thereof.
68. The method of any one of claims 47-58, further comprising the step of administering to the subject an agent activating NK cell or T cell activity.
69. The method of any one of claims 47-68, wherein the cancer is selected from the group consisting of: multiple myeloma, adrenocortical carcinoma, acute myeloid leukemia, Bladder Urothelial Carcinoma, glioma, breast invasive carcinoma, glioma, Cervical squamous cell carcinoma, endocervical adenocarcinoma, cholangiocarcinoma, chronic myelogenous leukemia, colon adenocarcinoma, esophageal carcinoma, glioblasoma multiforme, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, lymphoid neoplasm diffuse large B-cell
lymphoma, mesothelioma, ovarian serous cystadenocarcinoma, pancreatic adenocarcinoma, pheochromocyoma, paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma,sarcoma, skin cutaneous melanoma, stomach adenocarcinoma, testicular germ cell tumors, thyomas, thyroid carcinoma, uterine carcinosarcoma, uterine corps endometrial carcinoma, microsatellite instability- high cancer, basal cell carcinoma, Merkel cell carcinoma, uveal melanoma, and mucosal melanoma.
70. A method of treating cancer, comprising: intratumorally administering to a subject with cancer a therapeutically effective amount of an TGFβ inhibitor; and systemically administering to the subject a therapeutically effective amount of an anti-PD-L1 antibody.
71. The method of claim 70, wherein the TGFβ inhibitor is an anti-TGFβ antibody.
72. The method of any one of claims 70-71, wherein the anti-PD-L1 antibody is administered at least once a day, at least once a week, or at least once every two weeks; and the TGFβ inhibitor is administered at least once a day, at least once a week, or at least once every two weeks.
73. The method of any one of claims 70-71, wherein the anti-PD-L1 antibody is administered at least twice a day, at least twice a week, or at least twice every two weeks; and the TGFβ inhibitor is administered at least twice a day, at least twice a week, or at least twice every two weeks.
74. The method of any one of claims 70-71, wherein the anti-PD-L1 antibody is administered at least two times a week for at least 2 weeks or at least two times a week for at least 3 weeks; and the TGFβ inhibitor is administered at least two times a week for at least 2 weeks or at least two times a week for at least 3 weeks.
75. The method of any one of claims 70-74, wherein the cancer is selected from the group consisting of: multiple myeloma, adrenocortical carcinoma, acute myeloid leukemia, Bladder Urothelial Carcinoma, glioma, breast invasive carcinoma, glioma, Cervical squamous cell carcinoma, endocervical adenocarcinoma, cholangiocarcinoma, chronic myelogenous leukemia, colon adenocarcinoma, esophageal carcinoma, glioblastoma multiforme, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, lymphoid neoplasm diffuse large B-cell lymphoma,
mesothelioma, ovarian serous cystadenocarcinoma, pancreatic adenocarcinoma, pheochromocyoma, paraganglioma, prostate adenocarcinoma, rectum adenocarcinoma,sarcoma, skin cutaneous melanoma, stomach adenocarcinoma, testicular germ cell tumors, thyomas, thyroid carcinoma, uterine carcinosarcoma, uterine corps endometrial carcinoma, microsatellite instability-high cancer, basal cell carcinoma, Merkel cell carcinoma, uveal melanoma, and mucosal melanoma.
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WO2023172948A1 (en) * | 2022-03-08 | 2023-09-14 | Ohio State Innovation Foundation | Ccl5 mrna nanoparticle and methods of use thereof |
WO2023226788A1 (en) * | 2022-05-27 | 2023-11-30 | 苏州大学 | Medicament for combined immunization, thermo-responsive gel composition, chemokine particle, and use thereof |
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US7091310B2 (en) * | 2002-09-13 | 2006-08-15 | Chemokine Therapeutics Corporation | Chemokine analogs for the treatment of human disease |
ES2666206T3 (en) * | 2007-10-02 | 2018-05-03 | Universität Zu Köln | Novel marker genes for human blood regulatory T lymphocytes |
US20140017227A1 (en) * | 2011-01-14 | 2014-01-16 | Suk Peng Chew | Gene signatures for use with hepatocellular carcinoma |
WO2017058896A1 (en) * | 2015-09-28 | 2017-04-06 | Sanford Burnham Prebys Medical Discovery Institute | Targets for treatment of hepatocellular carcinoma cancer and methods related thereto |
CA3101556A1 (en) * | 2018-05-28 | 2019-12-05 | ORION Biotechnology Switzerland Sarl | Ccr5 inhibitor for use in treating cancer |
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WO2023172948A1 (en) * | 2022-03-08 | 2023-09-14 | Ohio State Innovation Foundation | Ccl5 mrna nanoparticle and methods of use thereof |
WO2023226788A1 (en) * | 2022-05-27 | 2023-11-30 | 苏州大学 | Medicament for combined immunization, thermo-responsive gel composition, chemokine particle, and use thereof |
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