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25 pages, 5818 KiB  
Article
A Multivalent mRNA Therapeutic Vaccine Exhibits Breakthroughs in Immune Tolerance and Virological Suppression of HBV by Stably Presenting the Pre-S Antigen on the Cell Membrane
by Shang Liu, Jie Wang, Yunxuan Li, Muhan Wang, Pei Du, Zhijie Zhang, Wenguo Li, Rongchen Sun, Mingtao Fan, Meijia Yang and Hongping Yin
Pharmaceutics 2025, 17(2), 211; https://doi.org/10.3390/pharmaceutics17020211 - 7 Feb 2025
Viewed by 147
Abstract
Background/Objectives: In chronic hepatitis B infection (CHB), the hepatitis B surface antigen (HBsAg) continuously exhausts the hepatitis B surface antibody (HBsAb), which leads to the formation of immune tolerance. Accordingly, the hepatitis B virus (HBV) infection can be blocked by inhibiting the [...] Read more.
Background/Objectives: In chronic hepatitis B infection (CHB), the hepatitis B surface antigen (HBsAg) continuously exhausts the hepatitis B surface antibody (HBsAb), which leads to the formation of immune tolerance. Accordingly, the hepatitis B virus (HBV) infection can be blocked by inhibiting the binding of the hepatitis B surface pre-S1/pre-S2 antigen to the hepatocyte receptor NTCP, but the clinical cure rate of pre-S-based vaccines for CHB is limited. Methods: In this study, we designed and prepared multivalent hepatitis B therapeutic mRNA vaccines encoding three hepatitis B surface antigen proteins (L, M, and S) at the cell membrane, verified via in vitro transfection and expression experiments. An in vivo immunization experiment in HBV transgenic (Tg) mice was first completed. Subsequently, an adeno-associated virus plasmid vector carrying the HBV1.2-fold genome (pAAV HBV1.2) model and the adeno-associated virus vector carrying HBV1.3-fold genome (rAAV HBV1.3) model were constructed and immunized with mRNA vaccines. The HBV antigen, antibodies, and HBV DNA in serum were detected. Indirect (enzyme-linked immunosorbent assay) ELISA were made to analyze the activated antigen-specific IgG in HBV Tg mice. Antigen-dependent T-cell activation experiments were carried out, as well as the acute toxicity tests in mice. Results: The L protein/pre-S antigens could be stably presented at the cell membrane with the support of the S protein (and M protein). After vaccinations, the vaccines effectively reactivated the production of high levels of HBsAb, disrupted immune tolerance, and activated the production of high-affinity antibodies against structural pre-S antigen in HBV Tg mice. The HBsAg seroconversion and serum HBV DNA clearance were achieved in two HBV mice models. Furthermore, pre-S antigen-dependent T-cell response against HBV infection was confirmed. The therapeutic vaccine also showed safety in mice. Conclusions: A novel therapeutic mRNA vaccine was developed to break through HBsAg-mediated immune tolerance and treat CHB by stably presenting the pre-S antigen at the membrane, and the vaccine has great potential for the functional cure of CHB. Full article
(This article belongs to the Section Gene and Cell Therapy)
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<p>In vitro expression analysis of hepatitis B surface antigen mRNA vaccines. LNP-encapsulated L mRNA, M mRNA, and S mRNA were transfected into 293T cells in different combinations, and the dosage of each single mRNA was 5 μg for each treatment. (<b>a</b>) The proportion of cells expressing pre-S2 antigen or S antigen on the surface was detected by FCM at 48 h and 96 h after transfection, respectively. The results of FCM were showed using density maps. (<b>b</b>) WB analysis of the expression or secretion of the L protein (42 kDa), M protein (31 kDa), and S protein (27 kDa) in the cell membrane or supernatants at 48 h after transfection.</p>
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<p>Humoral immune response analysis of HBV Tg mice immunized with the hepatitis B surface antigen mRNA vaccines. (<b>a</b>) Schematic diagram of the experimental protocol for the immunization of BALB/c HBV Tg mice with different combinations of mRNAs encoding hepatitis B surface antigens or with control vaccines. (<b>b</b>) CLIA detection of serum HBsAb levels in HBV Tg mice at weeks 0–32 of the immunization experiment. (<b>c</b>) Analysis of changes in the serum HBsAb concentration in mice whose HBsAb concentration was consistently less than 2000 IU/L and greater than 0 IU/L. (<b>d</b>) Correlation analysis between the serum levels of HBsAb and reduced HBsAg levels. (<b>e</b>) Indirect ELISA analysis of the binding ability of induced serum IgG to recombinant HBsAg, the pre-S peptide, or the LMS VLP after immunization with different vaccines. (<b>f</b>) Variable slope (four parameters) analysis via nonlinear regression (curve fit) was performed for the pre-S antigen-specific indirect ELISA. Representative results are presented as the means ± standard deviations (SDs).</p>
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<p>Serological and virological response analysis of pAAV HBV1.2 mice immunized with hepatitis B surface antigen mRNA vaccines. (<b>a</b>) Schematic diagram of the experimental protocol for immunization of pAAV HBV1.2 mice with LMS mRNA vaccines, S mRNA, or GFP mRNA. Changes in serum (<b>b</b>) HBsAg, (<b>c</b>) HBsAb, and (<b>d</b>) HBeAg from 0 to 5 weeks after immunization of pAAV HBV-1.2 mice with different vaccines. (<b>e</b>) Q–PCR detection of serum HBV DNA levels in immunized mice at week 0 and week 5. Representative results are presented as the means ± SDs.</p>
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<p>Serological and virological response analysis of rAAV8 HBV1.3 mice immunized with hepatitis B surface antigen mRNA vaccines. (<b>a</b>) Schematic diagram of the experimental protocol for immunization of rAAV8 HBV1.3 (1 × 10<sup>10</sup> vg/mouse) mice with hepatitis B surface antigen mRNA vaccines in different combinations, S mRNA, or GFP mRNA. Changes in serum (<b>b</b>) HBsAg, (<b>c</b>) HBsAb, and (<b>d</b>) HBeAg from 0 to 9 weeks of immunization with different vaccines. (<b>e</b>) Q–PCR detection of serum HBV DNA levels in immunized mice at week 0 and week 9. Representative results are presented as the means ± SDs.</p>
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<p>The analysis of antigen-dependent T-cell responses activated by Hepatitis B surface antigen mRNA vaccines. (<b>a</b>) BALB/3T3 cells were transiently transfected with pD2531.L, pD2531.M, and pD2531.S plasmids (1:1:1 mass ratio) via Lipofectamine 3000, and FCM was performed to detect pre-S2 antigen and S antigen expression on the cell surface. (<b>b</b>) After immunization of BALB/c mice with different hepatitis B surface antigen mRNA vaccines or PBS, splenic CD4<sup>+</sup> T cells were isolated and stimulated with BALB/3T3 cells transiently expressing the LMS antigen. Meanwhile, antigen-incubated T cells from PBS-immunized mice were used as negative control and CD3/CD28 bead-stimulated T cells from PBS-immunized mice were used as positive control. FCM was used to measure the level of IFN-γ in CD4<sup>+</sup> T cells after the addition of brefeldin A.</p>
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<p>Schematic diagram of the mechanism by which the LMS mRNA therapeutic vaccine disrupts HBsAg-mediated immune tolerance and reactivates immune responses against HBV. The numbers 1–6 marked on the membrane structure of L protein represent intracellular structure of S antigen, T cell recognition epitopes of pre-S1 antigen, hepatocyte surface receptor NTCP binding site for pre-S1 antigen, S antigen (highly variable region) with a-antigen determinant, lipid membrane, hepatocyte binding region for pre-S2 antigen, membrane attachment region of HBV-infected hepatocytes, respectively.</p>
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14 pages, 958 KiB  
Article
Immune Checkpoint Inhibitor in Hepatocellular Carcinoma: Response Rates, Adverse Events, and Predictors of Response
by Shekhar Swaroop, Sagnik Biswas, Shubham Mehta, Arnav Aggarwal, Umang Arora, Samagra Agarwal, Amitkumar Chavan, Baibaswata Nayak and Shalimar
J. Clin. Med. 2025, 14(3), 1034; https://doi.org/10.3390/jcm14031034 - 6 Feb 2025
Viewed by 259
Abstract
Background/Objectives: Hepatocellular carcinoma (HCC) is the most common primary hepatic malignancy. Barcelona Clinic Liver Cancer (BCLC) guidelines recommend antiangiogenic agents with immune checkpoint inhibitors as first-line therapy for advanced HCC. We present our experience of treating HCC patients with Atezolizumab–Bevacizumab, their response rates, [...] Read more.
Background/Objectives: Hepatocellular carcinoma (HCC) is the most common primary hepatic malignancy. Barcelona Clinic Liver Cancer (BCLC) guidelines recommend antiangiogenic agents with immune checkpoint inhibitors as first-line therapy for advanced HCC. We present our experience of treating HCC patients with Atezolizumab–Bevacizumab, their response rates, adverse events, survival, and response and survival predictors. Methods: This retrospective analysis included HCC patients diagnosed at All India Institute of Medical Sciences, New Delhi, India between July 2021 and April 2024 and receiving at least one dose of Atezolizumab–Bevacizumab. The primary outcome was overall response rate (ORR), comprising complete response (CR) and partial response (PR), as per mRECIST criteria. Secondary outcomes were overall survival (OS), progression-free survival (PFS), and predictors of response and survival. Results: Sixty-three patients were analyzed {mean age: 56.0 + 12.7 years; 82.5% males}. Forty-three (68.2%) patients had BCLC stage C HCC. Thirty-five (55.5%) patients belonged to Child–Pugh class A and 28 (44.5%) belonged to Child–Pugh class B. At 1 year, OS was 39% and PFS was 27%. Among 43 patients with data for radiological response, ORR was 48.8% (CR—9.3% and PR—39.5%) and DCR was 62.7% with stable disease (SD) in 13.9% of patients. PD occurred in 37.2% of patients. AFP response predicted radiological response, while Child–Pugh class and BCLC stage predicted survival. Adverse events were reported in 49.2% of patients. Conclusions: Our study shows slightly lower survival than previous studies with Child–Pugh class being the most important determinant of survival. AFP response predicts radiological response and not survival. Full article
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<p>Flow chart of the study.</p>
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<p>Kaplan–Meier curve showing a comparison of overall survival and progression-free survival among Child–Pugh classes (<b>a</b>,<b>b</b>), ALBI grades (<b>c</b>,<b>d</b>), those who received prior therapy vs. immunotherapy alone (<b>e</b>,<b>f</b>), and various etiologies of liver disease (<b>g</b>,<b>h</b>).</p>
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24 pages, 4073 KiB  
Article
Thyroid Stimulatory Activity of Houttuynia cordata Thunb. Ethanolic Extract in 6-Propyl-Thiouracil-Induced Hypothyroid and STZ Induced Diabetes Rats: In Vivo and In Silico Studies
by Shaikh Shahinur Rahman, Anuwatchakij Klamrak, Nirmal Chandra Mahat, Md. Rakibul Hasan Rahat, Napapuch Nopkuesuk, Md Kamruzzaman, Piyapon Janpan, Yutthakan Saengkun, Jaran Nabnueangsap, Thananya Soonkum, Padol Sangkudruea, Nisachon Jangpromma, Sirinan Kulchat, Rina Patramanon, Arunrat Chaveerach, Jureerut Daduang and Sakda Daduang
Nutrients 2025, 17(3), 594; https://doi.org/10.3390/nu17030594 - 6 Feb 2025
Viewed by 278
Abstract
Houttuynia cordata Thunb. holds a longstanding reputation as a traditional folk remedy in East Asia, where it has been employed to treat a variety of inflammatory conditions, nephritis, hepatitis and cancer. Despite its extensive use, there exists a paucity of research examining its [...] Read more.
Houttuynia cordata Thunb. holds a longstanding reputation as a traditional folk remedy in East Asia, where it has been employed to treat a variety of inflammatory conditions, nephritis, hepatitis and cancer. Despite its extensive use, there exists a paucity of research examining its efficacy in managing thyroid disorders and diabetes. Moreover, the bioactive components responsible for modulating the molecular pathways remain elusive. Objectives: This research aimed to determine the key bioactive components in the ethanolic extract of H. cordata Thunb. (HCEE) responsible for its thyroid-modifying properties and examine its effects on rats with experimentally induced hypothyroidism and diabetes. Methods: Molecular docking was performed to investigate the possible mechanisms of thyroid regulation of HCEE constituents. Researchers induced hypothyroidism in rats by adding 6-propyl-2-thiouracil to their drinking water for a period of four weeks. To induce diabetes, the rats received an intraperitoneal injection of streptozotocin. The animals were then given daily oral doses of HCEE (500 mg/kg b.w.), levothyroxine (50 mg/kg b.w.), or glibenclamide (5 mg/kg b.w.) for 28 days. Following this treatment, standard methods were employed to measure biochemical parameters in the rats’ serum. Results: The results demonstrate that HCEE ameliorated hypothyroidism by increasing serum T3 (14.38%) and T4 (125.96%) levels and decreasing TSH (p < 0.01; −41.75%) levels. In diabetic rats with induced hypothyroidism, HCEE significantly (p < 0.001) increased T3 (149.51%) and T4 (73.54%) levels with reduced TSH (−64.39%) levels. In silico analysis demonstrated that the identified bioactive compounds from HCEE may enhance thyroid hormone function through interaction with the thyroid hormone receptor protein TRβ1 (PDB:3GWS), similar to the conventional pharmaceuticals levothyroxine and triiodothyronine (T3). Conclusions: HCEE exhibits potential as a natural alternative to synthetic medications in the prevention and treatment of thyroid dysfunctions. Full article
(This article belongs to the Section Phytochemicals and Human Health)
14 pages, 2320 KiB  
Review
Sixty Years at the Rega Institute
by Erik De Clercq
Viruses 2025, 17(2), 222; https://doi.org/10.3390/v17020222 - 5 Feb 2025
Viewed by 356
Abstract
I started my research career (in 1965) on interferon by identifying polyacrylic acid (PAA) as an interferon inducer. Poly(I).poly(C), discovered by Maurice Hilleman’s group, proved to be more potent as an interferon inducer, and through its mRNA, we were able to clone and [...] Read more.
I started my research career (in 1965) on interferon by identifying polyacrylic acid (PAA) as an interferon inducer. Poly(I).poly(C), discovered by Maurice Hilleman’s group, proved to be more potent as an interferon inducer, and through its mRNA, we were able to clone and express human β-interferon. The discovery of the reverse transcriptase (RT) by Temin and Baltimore (in 1970) brought me to the detection of suramin as a powerful RT inhibitor and enabled Sam Broder and his colleagues to identify suramin as the first inhibitor of HIV replication. In this capacity, it was subsequently superseded by AZT and other 2′,3′-dideoxynucleoside (ddN) analogs, including d4T. In collaboration with Antonín Holý, we discovered several acyclic nucleoside phosphonates as potent inhibitors of both HIV and HBV (hepatitis B virus) replication. In collaboration with Paul Janssen, we identified various non-nucleoside RT inhibitors (NNRTIs) of HIV-1 replication. Of the nucleotide RT inhibitors (NtRTTs), tenofovir emerged as the most promising congener. It was derivatized to its oral prodrugs TDF and TAF. To enhance their efficacy, they were combined with other anti-HIV drugs, and two of them were pursued (and found efficacious) in the Pre-Exposure Prophylaxis (PrEP) of HIV infections. Full article
(This article belongs to the Section General Virology)
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<p>Polyacrylic acid (PAA).</p>
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<p>Poly(I).poly(C).</p>
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<p>Suramin.</p>
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<p>Azidothymidine (AZT).</p>
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<p>D4T (2′,3′-didehydro-2′,3′-dideoxy thymidine).</p>
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<p>BVDU [(<span class="html-italic">E</span>)-5-(2-bromovinyl 2′-deoxyuridine)].</p>
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<p>DHPA [(<span class="html-italic">S</span>)-2′,3′-dihydroxypropyladenine].</p>
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<p>(<span class="html-italic">S</span>)-HPMPA [(<span class="html-italic">S</span>)-9(3-hydroxyl-2-phosphonyl methoxy propyl)adenine].</p>
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<p>(<span class="html-italic">S</span>)-HPMPC (cidofovir).</p>
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<p>PMEA [9-(2-phosphonylmethoxyethyl)adenine].</p>
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<p>(<span class="html-italic">R</span>)-PMPA [(<span class="html-italic">R</span>)-9-(2-phosphonylmethoxypropyl)adenine].</p>
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<p>TIBO (tetrahydroimidazobenzodiazepinone).</p>
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<p>HEPT [1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine].</p>
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31 pages, 812 KiB  
Article
Qualitative Analysis of Generalized Power Nonlocal Fractional System with p-Laplacian Operator, Including Symmetric Cases: Application to a Hepatitis B Virus Model
by Mohamed S. Algolam, Mohammed A. Almalahi, Muntasir Suhail, Blgys Muflh, Khaled Aldwoah, Mohammed Hassan and Saeed Islam
Fractal Fract. 2025, 9(2), 92; https://doi.org/10.3390/fractalfract9020092 - 1 Feb 2025
Viewed by 304
Abstract
This paper introduces a novel framework for modeling nonlocal fractional system with a p-Laplacian operator under power nonlocal fractional derivatives (PFDs), a generalization encompassing established derivatives like Caputo–Fabrizio, Atangana–Baleanu, weighted Atangana–Baleanu, and weighted Hattaf. The core methodology involves employing a PFD with a [...] Read more.
This paper introduces a novel framework for modeling nonlocal fractional system with a p-Laplacian operator under power nonlocal fractional derivatives (PFDs), a generalization encompassing established derivatives like Caputo–Fabrizio, Atangana–Baleanu, weighted Atangana–Baleanu, and weighted Hattaf. The core methodology involves employing a PFD with a tunable power parameter within a non-singular kernel, enabling a nuanced representation of memory effects not achievable with traditional fixed-kernel derivatives. This flexible framework is analyzed using fixed-point theory, rigorously establishing the existence and uniqueness of solutions for four symmetric cases under specific conditions. Furthermore, we demonstrate the Hyers–Ulam stability, confirming the robustness of these solutions against small perturbations. The versatility and generalizability of this framework is underscored by its application to an epidemiological model of transmission of Hepatitis B Virus (HBV) and numerical simulations for all four symmetric cases. This study presents findings in both theoretical and applied aspects of fractional calculus, introducing an alternative framework for modeling complex systems with memory processes, offering opportunities for more sophisticated and accurate models and new avenues for research in fractional calculus and its applications. Full article
(This article belongs to the Special Issue Advanced Numerical Methods for Fractional Functional Models)
19 pages, 1210 KiB  
Review
Understanding Heritable Variation Among Hosts in Infectious Diseases Through the Lens of Twin Studies
by Maria K. Smatti, Hadi M. Yassine, Hamdi Mbarek and Dorret I. Boomsma
Genes 2025, 16(2), 177; https://doi.org/10.3390/genes16020177 - 1 Feb 2025
Viewed by 444
Abstract
Genetic factors have been hypothesized to contribute to the heterogeneity in the response to infectious diseases (IDs). The classical twin design provides a powerful tool to estimate the role of genetic contributions to variation in infection outcomes. With this design, the impact of [...] Read more.
Genetic factors have been hypothesized to contribute to the heterogeneity in the response to infectious diseases (IDs). The classical twin design provides a powerful tool to estimate the role of genetic contributions to variation in infection outcomes. With this design, the impact of heritability on the proneness as well as infection- and vaccine-induced immune responses have been documented for multiple infections, including tuberculosis, malaria, leprosy, otitis media, polio, mumps, measles, rubella, influenza, hepatitis B, and human papillomavirus infections, and recently, SARS-CoV-2. The current data show the heritable aspect in nearly all infections considered. In this contribution, we review and discuss human twin studies on the heritability of host characteristics in liability and response to IDs. This review emphasizes the importance of considering factors such as sex, disease stages, and disease presentation when assessing heritability and argues that the classical twin design provides a unique circumstance for exploring the genetic contribution as twins share levels of maternal antibodies, ancestral background, often the dates and number of vaccine doses, differences in vaccines’ manufacturing and storage, age, family environment, and other exposures. Additionally, we highlight the value of twin studies and the usefulness of combining the twin model with contemporary genomics technologies and advanced statistical tools to grasp a comprehensive and nuanced understanding of heritability in IDs. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
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<p>Genetic similarity and twin resemblance in response to infections/vaccinations. This figure demonstrates the association between genetic similarity and the correlation in immune responses in monozygotic (MZ) and dizygotic (DZ) twins. MZ twins, with almost 100% of genetic similarity, exhibit higher resemblance in their immune responses compared to DZ twins, who share 50% of their segregating genes. Low correlations in DZ twins compared to MZ twins suggest that genetic factors play a role in determining the trait, as the environmental influences would affect both twin types equally while similar correlations in MZ and DZ twin pairs indicate that shared environmental factors (e.g., lifestyle, microbiome, and previous infections) play a role in shaping the immune response. A combination of genetic and shared environmental influences as an explanation of resemblance would be indicated when the correlation in MZ pairs is less than twice the DZ correlation. (Figure created using Biorender).</p>
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<p>Heritability of antibody response following vaccination against different infectious diseases. NA: Data not available.</p>
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19 pages, 3063 KiB  
Article
Long-Term Survival of Patients with Unresectable Hepatocellular Carcinoma Treated with Lenvatinib in Real-World Clinical Practice
by Junji Furuse, Namiki Izumi, Kenta Motomura, Yoshitaka Inaba, Yoshio Katamura, Yasuteru Kondo, Kazuhisa Yabushita, Toshiyuki Matsuoka, Katsuaki Motoyoshi and Masatoshi Kudo
Cancers 2025, 17(3), 479; https://doi.org/10.3390/cancers17030479 - 1 Feb 2025
Viewed by 403
Abstract
Background/objectives: The real-world survival of patients with unresectable hepatocellular carcinoma (uHCC) treated with lenvatinib has been explored retrospectively with a small sample size. We conducted a prospective observational 2-year extension study (510 study) of a 1-year observational post-marketing study of lenvatinib (504 study) [...] Read more.
Background/objectives: The real-world survival of patients with unresectable hepatocellular carcinoma (uHCC) treated with lenvatinib has been explored retrospectively with a small sample size. We conducted a prospective observational 2-year extension study (510 study) of a 1-year observational post-marketing study of lenvatinib (504 study) to evaluate the long-term overall survival (OS) of patients with uHCC treated with lenvatinib and associated factors with a large sample size. Methods: Patients with uHCC included (July 2018 to January 2019) in the 504 study and who consented were eligible for the 510 study and were followed for up to 3 years after lenvatinib treatment initiation. Using the data from the 504 study and 510 study of the 504 study analysis set, we estimated the OS, the time from the first lenvatinib dose to all-cause death by the Kaplan–Meier method (ClinicalTrials.Gov Registration ID, 504 study: NCT03663114; 510 study: NCT04008082). Results: The 703 patients included in the analysis were followed for a median period (min, max) of 12.5 months (0.1, 44.8). The median OS (95% confidence interval) was 16.6 months (15.4, 18.5). OS was significantly (p < 0.05) associated with bile duct invasion (hazard ratio [HR]: 1.621), portal vein invasion (HR: 1.365), ≥ 4 intrahepatic lesions (HR: 1.437), extrahepatic lesions (HR: 1.357), Child–Pugh B/C (HR: 1.515), mALBI Grade 2a (HR: 1.331), and Grade ≥ 2b (HR: 1.811). Conclusions: This large-scale, prospective, real-world study demonstrated a long OS, comparable to that reported in the global Phase III REFLECT trial. More advanced-stage tumors and worse hepatic function have been suggested as OS-associated factors, consistent with previous reports. Full article
(This article belongs to the Collection Primary Liver Cancer)
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<p>Flowchart of study registration for 504 and 510 studies. CRF, case report form; max, maximum; min, minimum. <sup>(a)</sup> The 510 study is an extension study of 504 study. <sup>(b)</sup> Patients were not included in the 510 study since their treating institutions were not under contract for the 510 study. <sup>(c)</sup> Patients were not included in the 510 study since they did not consent to participate in the 510 study while their treating institutions were under contract for the study.</p>
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<p>Kaplan–Meier estimates of OS in (<b>A</b>) all patients (<span class="html-italic">n</span> = 703) and (<b>B</b>) by the REFLECT trial eligibility criteria. Patients were classified into subgroups of whether they met (“Yes”) or did not meet (“No”) the eligibility criteria of the REFLECT trial: inclusion criteria of Eastern Cooperative Oncology Group performance status (ECOG PS) 0 or 1, Barcelona Clinic Liver Cancer (BCLC) stage B or C, Child–Pugh class A, and exclusion criteria of a history of chemotherapy, bile duct invasion, or main portal vein invasion. CI, confidence interval; OS, overall survival.</p>
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<p>Kaplan–Meier estimates of OS in (<b>A</b>) all patients (<span class="html-italic">n</span> = 703) and (<b>B</b>) by the REFLECT trial eligibility criteria. Patients were classified into subgroups of whether they met (“Yes”) or did not meet (“No”) the eligibility criteria of the REFLECT trial: inclusion criteria of Eastern Cooperative Oncology Group performance status (ECOG PS) 0 or 1, Barcelona Clinic Liver Cancer (BCLC) stage B or C, Child–Pugh class A, and exclusion criteria of a history of chemotherapy, bile duct invasion, or main portal vein invasion. CI, confidence interval; OS, overall survival.</p>
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<p>Kaplan–Meier estimates of OS by the factors associated with OS: EOCG PS (<b>A</b>), bile duct invasion (<b>B</b>), portal vein invasion (<b>C</b>), number of intrahepatic lesions (<b>D</b>), extrahepatic lesions (<b>E</b>), Child–Pugh class (<b>F</b>), mALBI grade (<b>G</b>), and AFP level (<b>H</b>). AFP, alpha-fetoprotein; ECOG PS, Eastern Cooperative Oncology Group performance status; mALBI, modified albumin–bilirubin; OS, overall survival.</p>
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<p>Kaplan–Meier estimates of OS by the factors associated with OS: EOCG PS (<b>A</b>), bile duct invasion (<b>B</b>), portal vein invasion (<b>C</b>), number of intrahepatic lesions (<b>D</b>), extrahepatic lesions (<b>E</b>), Child–Pugh class (<b>F</b>), mALBI grade (<b>G</b>), and AFP level (<b>H</b>). AFP, alpha-fetoprotein; ECOG PS, Eastern Cooperative Oncology Group performance status; mALBI, modified albumin–bilirubin; OS, overall survival.</p>
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<p>Kaplan–Meier estimates of OS by the factors associated with OS: EOCG PS (<b>A</b>), bile duct invasion (<b>B</b>), portal vein invasion (<b>C</b>), number of intrahepatic lesions (<b>D</b>), extrahepatic lesions (<b>E</b>), Child–Pugh class (<b>F</b>), mALBI grade (<b>G</b>), and AFP level (<b>H</b>). AFP, alpha-fetoprotein; ECOG PS, Eastern Cooperative Oncology Group performance status; mALBI, modified albumin–bilirubin; OS, overall survival.</p>
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<p>Kaplan–Meier estimates of OS by the factors associated with OS: EOCG PS (<b>A</b>), bile duct invasion (<b>B</b>), portal vein invasion (<b>C</b>), number of intrahepatic lesions (<b>D</b>), extrahepatic lesions (<b>E</b>), Child–Pugh class (<b>F</b>), mALBI grade (<b>G</b>), and AFP level (<b>H</b>). AFP, alpha-fetoprotein; ECOG PS, Eastern Cooperative Oncology Group performance status; mALBI, modified albumin–bilirubin; OS, overall survival.</p>
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22 pages, 13356 KiB  
Article
Comparative Genome Sequencing Analysis of Some Novel Feline Infectious Peritonitis Viruses Isolated from Some Feral Cats in Long Island
by Abid Ullah Shah, Blanca Esparza, Oscar Illanes and Maged Gomaa Hemida
Viruses 2025, 17(2), 209; https://doi.org/10.3390/v17020209 - 31 Jan 2025
Viewed by 517
Abstract
Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples [...] Read more.
Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples from two shelter cats submitted to the Pathology Diagnostic Services of the Long Island University College of Veterinary Medicine, with gross and microscopic lesions consistent with those of FIP were processed for virus isolation, molecular characterization and full-length genome decoding. The younger shelter cat, a 1-year-old male (A15) was found dead without previous signs of illness. Postmortem examination revealed gross and microscopic lesions characterized by vasculitis, necrosis, hemorrhage, and pyogranulomatous inflammation confined to the colon and associated lymph nodes. The second cat, a 7-year-old spayed female (A37) had an identical clinical history and similar but widespread lesions, including fibrinous peritoneal effusion, cecal, colonic, renal, and hepatic involvement. The gross and microscopic diagnosis of FIP in these cats was confirmed by immunohistochemistry (IHC) demonstration of feline coronavirus antigen using mouse anti-FIPV3-70 monoclonal antibody. Virus isolation from saved frozen kidney and colon tissue was performed through several subsequent blind passages in MDCK and Vero cell lines. Confirmation of the FIPV isolation was done through qRT-PCR, IFA, western blot using N protein antibodies, and NGS of the full-length genome sequencing. The full-length genome sequences of the virus isolate from the two cats were decoded using next-generation sequencing (NGS) and deposited in the GenBank as accession numbers PQ192636 and PQ202302. The genome size of these isolates was (29355 and 29321) nucleotides (nt) in length, respectively. While their genome organization was consistent with other FIPV genomes as follows (5’UTR-ORF1ab-S-3abc-M-E-7b-3’UTR-3’), marked differential mutations were observed in the ORF1a/b, S, 3Abc, and 7b protein genes of the two FIPV isolates. One notable deletion of 34 nucleotides was observed in the 7b genes of one of these isolates but was absent in the other. We confirmed the potential recombination events during the evolution of those two FIPV field isolates with the potential parent virus as FECoV-US isolated in 1970 and the potential minor parent as the Canine coronavirus. Our results provide a comprehensive molecular analysis of two novel FIPV isolates causing fatal disease in shelter cats from Long Island. Diagnostic surveillance with molecular characterization and sequencing analysis of circulating FIPV strains within animal shelters may help early detect unique emerging clinical and pathological manifestations of the disease and develop more targeted prophylactic and therapeutic approaches to control it. Full article
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<p>Significant necropsy findings in the FIV/A15 infected cat. (<b>A</b>) The descending colon was diffusely thickened due to transmural congestion, edema and inflammation. (<b>B</b>) Microscopically, there was marked expansion of the colonic submucosa by edema and the presence of inflammatory cells, Hematoxylin and Eosin (H&amp;E)-stained section, scale bar: 1000 µm. (<b>C</b>) Inset: Closeup of submucosal venule surrounded by fibrin, necrotic cellular debris and inflammatory cells (fibrino-necrotizing phlebitis and peri-phlebitis). Scale bar 100µm.</p>
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<p>Necropsy findings in the FIPV/A37 infected cat. (<b>A</b>) In addition to peritoneal effusion, thin layers and small fibrin plaques were scattered on the liver, omentum, mesentery, and serosal surface of the intestine. Fibrin deposition on an edematous gall bladder wall resulted in soft adhesions to the adjacent liver lobes (arrow). (<b>B</b>) Slightly raised pale tan foci around blood vessels on the cortical surface of 279 the kidney (circle). (<b>C</b>) H&amp;E-stained section of a focal area of perivascular interstitial nephritis. (<b>D</b>) IHC demonstrates positive immunostaining for FCoV antigen. (<b>E</b>) Phlebitis and peri-phlebitis, within the gall bladder wall, H&amp;E-stained section.</p>
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<p>Results of the IFA on some processed tissues collected from the A15 feral cat. (<b>A</b>) IFA of the kidney samples collected from A15 FIPV-infected cat. (<b>B</b>) IFA of the lymph nodes collected from A15 FIPV-infected cat. The blue color indicates DAPI staining the cell nucleus. The green color indicates the FCoV-N protein. All the images were captured at 10× magnification. The scale represents 100 µm.</p>
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<p>Results of the IFA on some processed tissues collected from the A37 feral cat. (<b>A</b>) IFA of the kidney samples collected from A37 FIPV-infected cat. (<b>B</b>) IFA of the lymph nodes collected from A37 FIPV-infected cat. The blue color indicates DAPI staining the cell nucleus. The green color indicates the FCoV-N protein. All the images were captured at 10× magnification. The scale represents 100 µm.</p>
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<p>Confirmation of the FIPV infection in the tissues collected from infected feral cats: the qRT-PCT was performed on tissue samples collected from two infected feral cats (A15 and A37) for the presence of FIPV. Tissue samples collected from feral cats negative for FIPV were used as sham (control) to normalize the FIPV genome expression. *<span class="html-italic">p</span> &lt; 0.05, **** <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>Morphological changes in the MDCK and Vero cell lines infected with the FIPV field isolates (A15 and A37). (<b>A</b>–<b>D</b>) Morphological changes in the MDCK infected with the sham, FIPV-79-1146, FIPV-A15, and FIPV-A37. (<b>E</b>–<b>H</b>) Morphological changes in the Vero cells infected with the sham, FIPV-79-1146, FIPV-A15, and FIPV-A37.</p>
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<p>Conformation of FIPV infectivity in MDCK cells through immunofluorescence analysis (IFA): (<b>A</b>) the IFA of the MDCK cells infected with FIPV reference strain 79-1146; (<b>B</b>) FIPV-A15; and (<b>C</b>) FIPV-A37. The blue color indicates DAPI staining the cell nucleus. The green color identifies the FCoV-N. The MDCK cells were infected with the specific virus at (MOI = 1), and IFA was performed after 72 hpi.</p>
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<p>Monitoring of the propagation and isolation of the FIPV/A15 and FIPV/A37 field isolates in the MDCK and Vero cell lines by the qRT-PCR: (<b>A</b>) the genome copy numbers of the MDBK cells infected with either the FIPV/A15 or FIPV/A37 field isolates in the MDCK (P-1–P-3) compared to the sham and the FIPV-79-1146 by the qRT-PCR. (<b>B</b>) Results of the genome copy numbers of Vero cells infected with either the FIPV/A15 or FIPV/A37 field isolates in the Vero (P-1–P-3) compared to the sham and the FIPV-79-1146 by the qRT-PCR. *<span class="html-italic">p</span> &lt; 0.05, **** <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>Conformation of expression of the FIPV proteins by the SDS-PAGE and WB analysis: (<b>A</b>) the SDS-PAGE results showing the total proteins in the case of the mock-infected cells: the FIPV 79-1146, the FIPV-A15, and the FIPV-A37 infected MDCK cells. Lane-1 is the ladder; lane-2 represents the mock-infected MDCK cells; lane-3 is MDCK cells infected with FIPV 79-1146; lane-4 is MDCK cells infected with FIPV-A15; and lane-5 represents the total proteins of the MDCK cells infected with FIPV-A37. (<b>B</b>) Western blot analysis of FCoV-nucleocapsid (FCoV-N) protein and β-actin protein expression in MDCK cells infected with sham, FIPV 79-1146, FIPV-A15, and FIPV-A37. MDCK cells were infected with the specific virus at (MOI = 1) for 72 hpi, and the cells were lysed and used for protein deduction.</p>
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<p>A schematic representation of the structure and organization of the newly isolated FIPV-A15 and FIPV-A37 field isolates. (<b>A</b>) The proposed model for the genome structure and organization of the FIPV-A15 and FIPV-A37 isolates using the data of the complete genome sequences. The genome is organized as follows: the 5′UTR; the Gene-1; the spike (S); the non-structural proteins (NSPs) 3a, 3b, and 3c; the envelope (E); the membrane (M); the nucleocapsid (N); the NSP 7a; the SP7b; and the 3′UTR. (<b>B</b>) A model of the organization of the 16 NSPs of the FIPV isolates was reported in this study. (<b>C</b>) A diagram showing the proposed structure of the spike glycoprotein (S) highlighting its relative subunits, sizes, and positions. The S1 subunit and S2 subunit of the spike gene, with the S1/S2 cleavage site, are in between. The S2 cleavage site is shown in red. The S1 subunit or Receptor Binding Domain (RBD) contains an N-terminal domain (NTD) and a C-terminal domain (CTD). The S2 subunit or Fusion Domain contains Linker, Fusion Peptide (FP), Heptad Repeat 1 (HR1), and Heptad Repeat 2 (HR2).</p>
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<p>The phylogenetic analysis using the decoded full-length genome, spike, nucleocapsid, and the NSP-7b genes sequences of the FIPV-A15 and FIPV-A37 field isolates. (<b>A</b>) The complete genome phylogenetic tree showed the highest Log Likelihood of -218,039.81. (<b>B</b>) The tree based on the spike gene sequences showed the highest Log Likelihood of -43,443.84. (<b>C</b>) The tree based on the nucleocapsid gene sequences showed the highest Log Likelihood of -8689.05. (<b>D</b>) The tree based on the NSP-7b gene sequences showed the highest Log Likelihood of -3224.63. The full-length genomes of FIPV-A15 and FIPV-A37 isolates detected in this study are identified with asterisks (*) and black arrowheads. The phylogenetic trees were generated using the maximum likelihood method and the Tamura–Nei model with bootstrap values (1000 replicates) using MEGA 11 software. The tree was generated using the online software iTOL (version 6). The percentage of the tree in which the associated taxa clustered together is shown next to the branches. The genotype distribution of the isolates is shown on the right side of the Figure.</p>
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<p>The pairwise homology analysis of FIPV-A15 and FIPV-A37 with alpha coronaviruses. Comparative pairwise analysis was performed for the complete genome, ORF1ab, spike, 3a, 3b, 3c, envelope, membrane, nucleocapsid, 7a, and 7b between 32 alpha coronaviruses isolates. The dataset includes 13 isolates from the type-II FCoV group, 16 isolates from the type-I FCoV group, as well as reference strains for CCoV, PRCV, and TGEV. The FIPV-A15 was used as a standard for the pairwise comparison. The pairwise homology was calculated using Geneious Prime v11. The heatmap was generated using GraphPad Prism v9 software based on the nucleotide similarity level with a color gradient, as indicated in the figure legend.</p>
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<p>Mapping of some notable deletions and mutations in the FIPV-A37-7b field isolate. The MSA of NSP-7b gene from 24 isolates. The consensus identity at the top represents conserved nucleotide positions across the isolates, with positions labeled based on the NSP-7b gene. Variations are highlighted with distinct colors. The green box indicates the FIPV-A15 and FIPV-A37 isolates generated in the current study. The red box highlights the 34-nucleotide deletion region reported in the FIPV-A37 isolate. The Geneious Prime 2024 Version 11 software was used to generate the MSA.</p>
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12 pages, 969 KiB  
Article
Histopathological Features of Hepatocellular Carcinoma in Patients with Hepatitis B and D Virus Infection: A Single-Institution Study in Mongolia
by Orgil Jargalsaikhan, Wenhua Shao, Mayuko Ichimura-Shimizu, Soichiro Ishimaru, Takaaki Koma, Masako Nomaguchi, Hirohisa Ogawa, Shotaro Tachibana, Battogtokh Chimeddorj, Khongorzul Batchuluun, Anujin Tseveenjav, Battur Magvan, Bayarmaa Enkhbat, Sayamaa Lkhagvadorj, Adilsaikhan Mendjargal, Lkhagvadulam Ganbaatar, Minoru Irahara, Masashi Akaike, Damdindorj Boldbaatar and Koichi Tsuneyama
Cancers 2025, 17(3), 432; https://doi.org/10.3390/cancers17030432 - 27 Jan 2025
Viewed by 734
Abstract
Background: Viral hepatitis, particularly hepatitis B (HBV) and hepatitis C (HCV), is highly prevalent in Mongolia. Moreover, Mongolia has the highest prevalence of hepatitis delta virus (HDV) globally, with over 60% of HBV-infected individuals also co-infected with HDV. Since HBV/HDV infections accelerate [...] Read more.
Background: Viral hepatitis, particularly hepatitis B (HBV) and hepatitis C (HCV), is highly prevalent in Mongolia. Moreover, Mongolia has the highest prevalence of hepatitis delta virus (HDV) globally, with over 60% of HBV-infected individuals also co-infected with HDV. Since HBV/HDV infections accelerate liver disease progression more compared to HBV infection alone, urgent national health measures are required. Method: This study presents a clinicopathological analysis of 49 hepatocellular carcinoma cases surgically resected at the Mongolia–Japan Hospital of the Mongolian National University of Medical Sciences. Results: HBV infection was found in 27 (55.1%) cases of all HCC cases. Immunohistochemical staining of the liver revealed that 14 (28.6%) cases were HDV antigen-positive in the HCC cases. HDV-positive cases exhibited significantly higher inflammatory activity compared to HDV-negative cases, with lymphocytic infiltrates predominantly composed of CD4-positive cells. Furthermore, HDV-positive cells were spatially distinct from HBs antigen-positive cells, suggesting that HDV-infected cells may interfere with HBV replication. No significant differences in fibrosis or in tumor characteristics were observed between the HDV-positive and negative cases. Early diagnosis of HBV/HDV infections is essential for appropriate treatment and to prevent further domestic transmission of the virus. However, routine testing for HDV infection is rarely conducted in Mongolia. Since HDV-positive cells are morphologically indistinguishable from surrounding HDV-negative cells, routine histopathological analysis may not be sufficient enough to detect HDV infection. Conclusions: Based on this clinicopathological study, CD4 and CD8 immunostaining can be considered an adjunctive diagnostic tool in cases with significant lymphocytic infiltration and hepatocellular damage. Additionally, HDV screening using blood and tissue samples may be recommended to ensure accurate diagnosis. Full article
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<p>The rates of viral hepatitis in HCC patients.</p>
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<p>Pathological features of background liver tissue in HDV-positive HCC patients. (<b>A</b>,<b>B</b>): Representative images of HE staining in HDV-positive patients. (<b>A</b>): Low-power view showing both the tumor and surrounding (background) liver tissue. Small regenerative nodules are visible around the primary encapsulated nodule. The surrounding liver tissue shows significant inflammatory cell infiltration, accompanied by advanced fibrosis. The region enclosed by the rectangle is shown at higher magnification in panel (<b>B</b>). (<b>B</b>): Higher magnification of the background liver tissue. Marked infiltration of lymphocytes is present, particularly at the interface, with clear evidence of hepatocyte damage due to the immune response. (<b>C</b>,<b>D</b>): Comparative analysis of inflammation and fibrosis scores in the background liver of HDV-positive and -negative HBV-infected HCC patients. Inflammatory activity was significantly elevated in HDV-positive patients (<span class="html-italic">p</span> = 0.043). (<b>E</b>,<b>G</b>): HBsAg immunostaining. (<b>F</b>,<b>H</b>): HDV immunostaining. (<b>E</b>,<b>F</b>) represent serial sections of the same case, as do (<b>G</b>,<b>H</b>). In (<b>E</b>,<b>F</b>), only a few HBsAg-positive cells are present, while a large number of HDV-positive cells can be noted. In contrast, (<b>G</b>,<b>H</b>) show clusters of HBsAg-positive cells, but only a few HDV-positive cells. Notably, there is minimal overlap between HBsAg-positive and HDV-positive cells. (<b>I</b>–<b>L</b>): Lymphocytic profile surrounding HDV-positive hepatocytes. (<b>I</b>): HDV immunostaining in the background liver shows widespread HDV-positive hepatocytes. Significant lymphocytic infiltration is observed, particularly at the interface hepatitis regions in portal areas and within fibrous septa. In contrast, HDV-positive cells are nearly absent within the tumor. (<b>J</b>–<b>L</b>): Double immunostaining of lymphocytes (CD4 in brown, CD8 in blue) infiltrating the liver. (<b>J</b>,<b>K</b>): In the background liver, the majority of infiltrating lymphocytes are CD4-positive, with only a few CD8-positive cells. (<b>L</b>): In the tumor, lymphocytic infiltration shows a more balanced ratio of CD4-positive and CD8-positive cells. (<b>M</b>,<b>N</b>); Immunohistochemical detection of HDV antigen in the biliary system. (<b>M</b>): HDV-positive cells were confined to hepatocytes, with no HDV antigen expression observed in the interlobular bile ducts (arrow). (<b>N</b>): In one patient, an HDV antigen was detected in the nuclei of proliferating bile ductules (arrow) located in the interface region with marked inflammation.</p>
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<p>Characteristics of liver tumors in HDV-positive patients. (<b>A</b>,<b>B</b>): Representative images of liver tumors (<b>A</b>): low magnification, (<b>B</b>): high magnification of the tumor center). (<b>C</b>,<b>D</b>): HDV immunohistochemistry. Most hepatocellular carcinomas (HCCs) showed only a small number of HDV-positive cells (<b>C</b>). However, in two patients, the number of HDV-positive cells within tumor tissue exceeded that in surrounding liver tissue (<b>D</b>).</p>
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25 pages, 7657 KiB  
Article
SARS-CoV-2 S, M, and E Structural Glycoproteins Differentially Modulate Endoplasmic Reticulum Stress Responses
by Wejdan Albalawi, Jordan Thomas, Farah Mughal, Aurelia Kotsiri, Kelly J. Roper, Abdullateef Alshehri, Matthew Kelbrick, Georgios Pollakis and William A. Paxton
Int. J. Mol. Sci. 2025, 26(3), 1047; https://doi.org/10.3390/ijms26031047 - 26 Jan 2025
Viewed by 545
Abstract
We have previously shown that the hepatitis C virus (HCV) E1E2 envelope glycoprotein can regulate HIV-1 long-terminal repeat (LTR) activity through disruption to NF-κB activation. This response is associated with upregulation of the endoplasmic reticulum (ER) stress response pathway. Here, we demonstrate that [...] Read more.
We have previously shown that the hepatitis C virus (HCV) E1E2 envelope glycoprotein can regulate HIV-1 long-terminal repeat (LTR) activity through disruption to NF-κB activation. This response is associated with upregulation of the endoplasmic reticulum (ER) stress response pathway. Here, we demonstrate that the SARS-CoV-2 S, M, and E but not the N structural protein can perform similar downmodulation of HIV-1 LTR activation, and in a dose-dependent manner, in both HEK293 and lung BEAS-2B cell lines. This effect is highest with the SARS-CoV-2 Wuhan S strain and decreases over time for the subsequent emerging variants of concern (VOC), with Omicron providing the weakest effect. We developed pseudo-typed viral particle (PVP) viral tools that allowed for the generation of cell lines constitutively expressing the four SARS-CoV-2 structural proteins and utilising the VSV-g envelope protein to deliver the integrated gene construct. Differential gene expression analysis (DGEA) was performed on cells expressing S, E, M, or N to determine cell activation status. Gene expression differences were found in a number of interferon-stimulated genes (ISGs), including IF16, IFIT1, IFIT2, and ISG15, as well as for a number of heat shock protein (HSP) genes, including HSPH1, HSPA6, and HSPBP1, with all four SARS-CoV-2 structural proteins. There were also differences observed in expression patterns of transcription factors, with both SP1 and MAVS upregulated in the presence of S, M, and E but not the N protein. Collectively, the results indicate that gene expression patterns associated with ER stress pathways can be activated by SARS-CoV-2 envelope glycoprotein expression. The results suggest the SARS-CoV-2 infection can modulate an array of cell pathways, resulting in disruption to NF-κB signalling, hence providing alterations to multiple physiological responses of SARS-CoV-2-infected cells. Full article
(This article belongs to the Section Molecular Microbiology)
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<p>SARS-CoV-2 glycoproteins downmodulate HIV-1 LTR activity. HIV-1 LTR subtype B activation in the presence of varying concentrations of SARS-CoV-2 proteins. (<b>A</b>) Effect of SARS-CoV-2 Env glycoproteins on HEK293T cells. (<b>B</b>) Effect on BEAS-2B cells. (<b>C</b>) Effect on HEK293T ACE2-expressing cells. (<b>D</b>) Effect of combined SARS-CoV-2 S, E, and M proteins on HIV-1 LTR activity. Each LTR and Tat was transfected alone as a control for overall LTR activity. Statistical analysis was performed using Kruskal–Wallis and Dunn’s tests to compare the control (LTR + Tat) with each concentration of the SARS-CoV-2 proteins. Significance: * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001; ns: not significant (<span class="html-italic">p</span> &gt; 0.05). The figure illustrates the results of a single experiment, which was conducted in triplicate for validation.</p>
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<p>The impact of spike protein mutations on the ability to downmodulate HIV-1 LTR activity. (<b>A</b>) Activation of HIV-1 LTR subtype B when co-transfected with varying concentrations of the SARS-CoV-2 Wuhan spike protein, including Alpha, Beta, Gamma, Delta, and Omicron variants. Each LTR and Tat was transfected alone as a control for overall LTR activity. Kruskal–Wallis and Dunn’s tests were used to perform a statistical comparison between the control (LTR + Tat) and each concentration of SARS-CoV-2 spike variant protein. The <span class="html-italic">p</span>-value for the concentration of 12ng of SARS-CoV-2 spike and Alpha variants was found to be (* <span class="html-italic">p</span> &lt; 0.05). (<b>B</b>) Comparative sequence alignment of spike protein amino acid sequences among SARS-CoV-2 wild-type and Alpha, Beta, Delta, Gamma, and Omicron variants. The alignment highlights the positions where variation has occurred in the spike protein when compared to the sequence from the strain (MN908947_Hu.1) first isolated in humans in Wuhan/China. The numbering above indicates the amino acid position within the full-length spike protein, spanning from 1 to 1275. The green highlights indicate the variant amino acid positions within the receptor-binding domain (RBD) region (* <span class="html-italic">p</span> &lt; 0.05).</p>
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<p>Ribbon representations of AlphaFold predicted structures of the SARS-CoV-2 spike protein of strains: (<b>A</b>) Wuhan (pTM = 0.79) and (<b>B</b>) Omicron (pTM = 0.81). The residual colour indicates the confidence in the protein structure based on a per-residue measure of local confidence (pLDDT): blue (very high pLDDT &gt; 90), light blue (confident pLDDT 90–70), yellow (low pLDDT 70–50), Orange (very low pLDDT &lt; 50). (<b>C</b>) Protein alignment of Wuhan (green) and Omicron (pink), indicating the high similarity between the spike protein structures of the two strains (RMSD = 1.867). The receptor-binding domain (RBD; residue 320–520) is indicated by the dashed rectangle, with further images (C: i, ii, and iii) showing the domain from three angles, highlighting the similarity of the spike protein RBD between the Wuhan and Omicron strains.</p>
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<p>Volcano plots of differential gene expression analysis in SARS-CoV-2 transcriptomics. (<b>A</b>–<b>D</b>) correspond to specific viral structural proteins: (<b>A</b>) spike, (<b>B</b>) membrane, (<b>C</b>) envelope, and (<b>D</b>) nucleocapsid. Volcano plot displaying -Log2 adjusted <span class="html-italic">p</span>-value versus Log2 fold change for each gene. Dashed lines indicate the thresholds, with a <span class="html-italic">p</span>-value greater than 1.3 -Log10 and a fold change greater than 1 or less than −1. The gene names of the most substantially differentially expressed genes are annotated.</p>
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<p>Expression levels of genes associated with interferon-stimulated genes (ISGs) in the presence or absence of SARS-CoV-2 proteins. The normalised counts, expressed as counts per million (CPM), are plotted for each sample group, including mock (n = 3), SARS-CoV-2 S (n = 3), SARS-CoV-2 M (n = 3), SARS-CoV-2 E (n = 3), and SARS-CoV-2 N (n = 3). (<b>A</b>) presents the comparison of CPM for IFI16, panel (<b>B</b>) for IFIT1, panel (<b>C</b>) for IFIT2, (<b>D</b>) for ISG15. The statistical significance of differential gene expression was determined using the Voom/Limma analysis, and the results were indicated as ns (not significant), *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>Expression levels of genes associated with heat shock proteins (HSPs) in the presence or absence of SARS-CoV-2 proteins. The normalised counts, expressed as counts per million (CPM), are plotted for each sample group, including mock (n = 3), SARS-CoV-2 S (n = 3), SARS-CoV-2 M (n = 3), SARS-CoV-2 E (n = 3), and SARS-CoV-2 N (n = 3). Panel (<b>A</b>) displays the comparison of CPM for HSPA1B, panel (<b>B</b>) for HSPH1, panel (<b>C</b>) for HSPA6, panel (<b>D</b>) for HSPBP1. The statistical significance of differential gene expression was determined using the Voom/Limma analysis, and the results were indicated as ns (not significant), * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, or *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>Expression levels of genes associated with long non-coding RNAs (lncRNAs) in the presence or absence of SARS-CoV-2 structural proteins. The normalised counts, expressed as counts per million (CPM), are plotted for each sample group, including mock (n = 3), SARS-CoV-2 S (n = 3), SARS-CoV-2 M (n = 3), SARS-CoV-2 E (n = 3), and SARS-CoV-2 N (n = 3). (<b>A</b>) displays the comparison of CPM for SNHG1, (<b>B</b>) for SNHG32, (<b>C</b>) for EPB4IL4A-AS1, and (<b>D</b>) for MALAT1. The statistical significance of differential gene expression was determined using the Voom/Limma analysis, and the results were indicated as ns (not significant), *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>Expression of viral transcription factors in the presence or absence of SARS-CoV-2 proteins. Normalised counts for each gene, expressed as counts per million (CPM), are plotted for each sample group (mock n = 4, SARS-CoV-2 n = 3). (<b>A</b>) comparison of CPM for NF-κB1, (<b>B</b>) NF-κBIB, (<b>C</b>) SP1, and (<b>D</b>) MAVS. The statistical significance of differential gene expression was determined using the Voom/Limma analysis, and the results were indicated as ns (not significant), *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>Gene ontology (GO) enrichment analysis for upregulation of DGEs in SARS-CoV-2 spike, membrane, envelope, and nucleocapsid transcriptome. GO annotations show the top 10 terms for significant enrichment of three main categories (biological process, cellular component, and molecular function) with the adjusted <span class="html-italic">p</span>-value &lt; 0.05. (<b>A</b>) SARS-CoV-2 S, (<b>B</b>), SARS-CoV-2 M, (<b>C</b>) SARS-CoV-2 E, (<b>D</b>) SARS-CoV-2 N.</p>
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<p>Gene ontology (GO) enrichment analysis for downregulation of DGEs in SARS-CoV-2 spike, membrane, envelope, and nucleocapsid transcriptome. Top 10 terms were plotted for biological process, molecular function, and cellular component in SARS-CoV-2 S (<b>A</b>), SARS-CoV-2 M (<b>B</b>), SARS-CoV-2 E (<b>C</b>), and SARS-CoV-2 N (<b>D</b>).</p>
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29 pages, 9729 KiB  
Article
Sexually Dimorphic Effects of CYP2B6 in the Development of Fasting-Mediated Steatosis in Mice: Role of the Oxylipin Products 9-HODE and 9-HOTrE
by Jazmine A. Eccles-Miller, Tyler D. Johnson and William S. Baldwin
Biomedicines 2025, 13(2), 295; https://doi.org/10.3390/biomedicines13020295 - 25 Jan 2025
Viewed by 381
Abstract
Background: Cytochrome P450 2B6 (CYP2B6) is a sexually dimorphic, anti-obesity CYP enzyme responsible for the metabolism of xeno- and endobiotics, including the metabolism of polyunsaturated fatty acids (PUFAs) into 9-hydroxyoctadecadienoic acid (9-HODE) and 9-hydroxyoctadecatrienoic acid (9-HOTrE). However, humanized CYP2B6 transgenic (hCYP2B6-Tg) mice [...] Read more.
Background: Cytochrome P450 2B6 (CYP2B6) is a sexually dimorphic, anti-obesity CYP enzyme responsible for the metabolism of xeno- and endobiotics, including the metabolism of polyunsaturated fatty acids (PUFAs) into 9-hydroxyoctadecadienoic acid (9-HODE) and 9-hydroxyoctadecatrienoic acid (9-HOTrE). However, humanized CYP2B6 transgenic (hCYP2B6-Tg) mice are sensitive to diet-induced hepatic steatosis despite their resistance to obesity. The purpose of this study was to determine if 9-HODE, 9-HOTrE, or other factors contribute to the sexually dimorphic steatosis observed in hCYP2B6-Tg mice. Results: Cyp2b9/10/13-null (Cyp2b-null) mice were injected with either 9-HODE or 9-HOTrE for 2 days and were then subjected to a fasting period of 20 h to induce steatosis. Serum lipids were moderately increased, especially in females, after 9-HODE (triglycerides (TGs), very low-density lipoproteins (VLDLs)) and 9-HOTrE (high-density lipoproteins (HDLs), low-density lipoproteins (LDLs), cholesterol) treatment. No change in hepatic lipids and few changes in hepatic gene expression were observed in mice treated with either oxylipin, suggesting that these oxylipins had minimal to moderate effects. Therefore, to further investigate CYP2B6’s role in steatosis, hCYP2B6-Tg and Cyp2b-null mice were subjected to a 20 h fast and compared. Both male and female hCYP2B6-Tg mice exhibited increased steatosis compared to Cyp2b-null mice. Serum cholesterol, triglycerides, HDLs, and VLDLs were increased in hCYP2B6-Tg males. Serum triglycerides and VLDLs were decreased in hCYP2B6-Tg females, suggesting the greater hepatic retention of lipids in females. Hepatic oxylipin profiles revealed eight perturbed oxylipins in female hCYP2B6-Tg mice and only one in males when compared to Cyp2b-null mice. RNA-seq also demonstrated greater effects in females in terms of the number of genes and gene ontology (GO) terms perturbed. There were only a few overlapping GO terms between sexes, and lipid metabolic processes were enriched in hCYP2B6-Tg male mice but were repressed in hCYP2B6-Tg females compared to Cyp2b-nulls. Conclusions: hCYP2B6-Tg mice are sensitive to fasting-mediated steatosis in males and females, although the responses are different. In addition, the oxylipins 9-HODE and 9-HOTrE are unlikely to be the primary cause of CYP2B6’s pro-steatotic effects. Full article
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<p>Quantification of liver triglycerides in 9-HODE- and 9-HOTrE-treated mice. (<b>A</b>) Quantification of male and female liver triglycerides colorimetrically after 9-HODE treatment. (<b>B</b>) Quantification of male and female liver triglycerides via Oil Red O staining of liver sections after 9-HODE treatment. (<b>C</b>) Quantification of male and female liver triglycerides colorimetrically after 9-HOTrE treatment. (<b>D</b>) Quantification of male and female liver triglycerides via Oil Red O staining of liver sections after 9-HOTrE treatment. Data are presented at mean ± SEM. Statistical significance was determined by unpaired <span class="html-italic">t</span>-tests using GraphPad Prism 7.0. No differences were observed.</p>
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<p>Hierarchical clustering of DEG and serum and liver lipids from male or female mice treated with 9-HODE. (<b>A</b>) Clustering of male data showed few associations of DEG with serum or liver lipid content. (<b>B</b>) Clustering of female data showed no associations between DEG and lipid content.</p>
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<p>Hierarchical clustering of DEG and serum and liver lipids in male or female mice treated with 9-HOTrE. (<b>A</b>) Clustering of male data showed no close associations of gene expression changes and alterations in serum or liver lipids. (<b>B</b>) Clustering of female data showed associations between serum HDLs (S-HDLs) and LDLs (S-LDLs) with several genes.</p>
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<p>Increased hepatic triglyceride content in hCYP2B6-Tg mice. (<b>A</b>) Both male and female hCYP2B6-Tg mice show a significant increase in liver triglycerides measured colorimetrically. Quantification (<b>C</b>) of Oil Red-O-stained histological sections of liver (<b>B</b>) showed significance only in female hCYP2B6-Tg mice. Data are represented as mean ± SEM. Statistical significance determined by unpaired <span class="html-italic">t</span>-tests on GraphPad Prism 7.0. * <span class="html-italic">p</span>-value &lt; 0.05.</p>
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<p>Gene ontology (GO) terms in the Biological Processes category enriched in either hCYP2B6-Tg mice or Cyp2b-null mice. (<b>A</b>) GO terms enriched in hCYP2B6-Tg male mice. (<b>B</b>) GO terms enriched in Cyp2b-null male mice. (<b>C</b>) GO terms enriched in hCYP2B6-Tg female mice. (<b>D</b>) GO terms enriched in Cyp2b-null female mice. GO terms were included if they had an FDR (adjusted <span class="html-italic">p</span>-value) of &lt;0.05. Larger dots indicating greater number of genes and darker colors (reds) indicates greater statistical significance.</p>
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<p>Visualization of GO terms shared between male and female DEG analysis. Significant DEG were used to generate GO term lists across sexes that were not dysregulated in an opposing manner. (<b>A</b>) GO terms enriched in hCYP2B6-Tg mice. (<b>B</b>) GO terms enriched in Cyp2b-null mice. Shared GO terms were identified within these lists then visualized using Revigo. GO terms included have a <span class="html-italic">p</span>-value of &lt;0.05. Larger dots indicating greater number of genes and darker colors (reds) indicates greater statistical significance.</p>
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<p>Oxylipin profiles in Cyp2b-null vs. gCYP2B6-Tg mice. (<b>A</b>) Profiles showed increased concentrations of only one oxylipin in livers of hCYP2B6-Tg male mice. (<b>B</b>) Profiles showed increased concentrations of eight oxylipins in livers of in hCYP2B6-Tg female mice. Multiple <span class="html-italic">t</span>-tests. Mean ± SEM. * <span class="html-italic">p</span> value &lt; 0.05, ** <span class="html-italic">p</span> value &lt; 0.01.</p>
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<p>Hierarchical clustering of DEG, oxylipins, serum, and liver lipids. (<b>A</b>) Hierarchical clustering of differential gene expression data and oxylipins/lipids in male Cyp2b-null and hCYP2B6-Tg mice showed minimal co-clustering. (<b>B</b>) Hierarchical clustering of differential gene expression data and oxylipins/lipids comparing female Cyp2b-null and hCYP2B6-Tg mice showed that some oxylipins and serum lipids clustered with DEG.</p>
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<p>Summary of proposed sexually dimorphic lipid metabolic alterations caused by CYP2B6 in fasting-mediated steatosis. Comparisons of Cyp2b-null to hCYP2B6-Tg mice after a 20 h period of fasting indicated that male hCYP2B6-Tg mice appear to increase lipid synthesis in the liver and transport of lipids out of the liver while decreasing lipid metabolism, leading to increased steatosis and increased serum lipids. Female hCYP2B6-Tg mice in comparison to Cyp2b-null mice appear to increase lipid synthesis in the liver but decrease lipid metabolism and transport of lipids out of the liver, leading to increased steatosis but decreased serum lipids. Example genes are provided over the green (up-regulated pathways) and red arrows (down-regulated pathways). Figure created using <a href="http://BioRender.com" target="_blank">BioRender.com</a>.</p>
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18 pages, 1345 KiB  
Article
Hepatitis C Virus Resistance-Associated Substitutions in Mexico
by Alexis Jose-Abrego, Saul Laguna-Meraz, Sonia Roman, Irene M. Mariscal-Martinez and Arturo Panduro
Viruses 2025, 17(2), 169; https://doi.org/10.3390/v17020169 - 25 Jan 2025
Viewed by 375
Abstract
Hepatitis C virus (HCV) is susceptible to resistance-associated substitutions (RASs) in the NS3, NS5A, and NS5B nonstructural genes, key targets of the direct-acting antivirals (DAAs). This study aimed to assess the prevalence and distribution of RASs across different HCV subtypes in Mexico. A [...] Read more.
Hepatitis C virus (HCV) is susceptible to resistance-associated substitutions (RASs) in the NS3, NS5A, and NS5B nonstructural genes, key targets of the direct-acting antivirals (DAAs). This study aimed to assess the prevalence and distribution of RASs across different HCV subtypes in Mexico. A Genbank dataset of 566 HCV sequences was analyzed. Most sequences were from Mexico City (49.1%, 278/566) and Jalisco (39.4%, 223/566). The NS5B region was the most sequenced (59.7%, 338/566). The most frequent HCV subtypes were 1a (44.0%, 249/566), 1b (28.6%, 162/566), 2b (9.5%, 54/566), and 3a (6.2%, 35/566). Subtypes 1a (57.4%, 128/223) and 3a (12.6%, 28/223) were significantly higher in Jalisco than in Mexico City (34.2%, 95/278 and 2.5%, 7/278), whereas subtype 1b was higher in Mexico City (34.5%, 96/278 vs. 14.8%, 33/223). Subtype 1a increased from 2019 to 2024, representing 49.4% (123/249) of all reported cases. RASs were detected in NS3 (6.7%, 1/15), NS5A (2.9%, 3/102), and NS5B (0.3%, 1/349), with the most frequent mutations being Q80K, Y93H, and S282T, respectively, and detected in subtypes 1b (n = 3), 1a (n = 1), and 2a (n = 1). In conclusion, Mexico’s HCV sequencing-based surveillance is limited. Subtype 1a predominated, but frequencies varied across states. The prevalence of RASs varied by gene from 0.3% to 6.7%. Establishing regional sequencing centers for NS3, NS5A, and NS5B is crucial to monitoring Mexico’s DAA-resistant mutations and HCV subtype genetic diversity. Full article
(This article belongs to the Special Issue Hepatitis C Virus 2024)
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<p>Data collection strategy for analyzing HCV genotypes and antiviral resistance in Mexico.</p>
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<p>Epidemiology of HCV in Mexico based on GenBank sequences. Geographic distribution of reported HCV sequences (<b>A</b>). Frequency of HCV genomic regions sequenced (<b>B</b>) and distribution of HCV subtypes (<b>C</b>). Temporal trends in HCV subtype prevalence from 2010 to 2024 (<b>D</b>). Q-CG: Quasi-complete genome, NA: Not available, 2k/2m refers to the recombinant HCV subtype.</p>
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<p>Frequency of resistance and reduced susceptibility mutations to antiviral drugs by HCV subtype based on NS3 (<b>A</b>), NS5A (<b>B</b>), and NS5B (<b>C</b>) regions.</p>
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21 pages, 1491 KiB  
Review
Role of Kynurenine and Its Derivatives in Liver Diseases: Recent Advances and Future Clinical Perspectives
by Qiwen Tan, Shenghe Deng and Lijuan Xiong
Int. J. Mol. Sci. 2025, 26(3), 968; https://doi.org/10.3390/ijms26030968 - 24 Jan 2025
Viewed by 416
Abstract
Liver health is integral to overall human well-being and the pathogenesis of various diseases. In recent years, kynurenine and its derivatives have gradually been recognized for their involvement in various pathophysiological processes, especially in the regulation of liver diseases, such as acute liver [...] Read more.
Liver health is integral to overall human well-being and the pathogenesis of various diseases. In recent years, kynurenine and its derivatives have gradually been recognized for their involvement in various pathophysiological processes, especially in the regulation of liver diseases, such as acute liver injury, non-alcoholic fatty liver disease, cirrhosis, and liver cancer. Kynurenine and its derivatives are derived from tryptophan, which is broken down by the enzymes indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO), converting the essential amino acid tryptophan into kynurenine (KYN) and other downstream metabolites, such as kynurenic acid (KYNA), 3-hydroxykynurenine (3-HK), xanthurenic acid (XA), and quinolinic acid (QA). In liver diseases, kynurenine and its derivatives can promote the activity of the transcription factor aryl hydrocarbon receptor (AhR), suppress T cell activity for immune modulation, inhibit the activation of inflammatory signaling pathways, such as NF-κB for anti-inflammatory effects, and inhibit the activation of hepatic stellate cells to slow down fibrosis progression. Additionally, kynurenine and other downstream metabolites can influence the progression of liver diseases by modulating the gut microbiota. Therefore, in this review, we summarize and explore the mechanisms by which kynurenine and its derivatives regulate liver diseases to help develop new diagnostic or prognostic biomarkers and effective therapies targeting the kynurenine pathway for liver disease treatment. Full article
(This article belongs to the Section Biochemistry)
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<p>Overview of the kynurenine pathway (KP). This figure shows the main metabolites and enzymes of the KP. Abbreviations: NAD+, nicotinamide adenine dinucleotide; IDO, indoleamine 2,3-dioxygenase; TDO, Tryptophan 2,3-dioxygenase; KMO, kynurenine 3-monooxygenase; KAT, kynurenine aminotransferases; KMO, kynurenine 3-monooxygenase; 3-HAO, 3-hydroxyanthranilate 3,4-dioxygenase; QPRT, quinolinic acid phosphoribosyl transferase.</p>
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<p>The interaction between the gut and liver. Tryptophan is partially absorbed in the gut, while the rest is metabolized by gut microbiota through the indole pathway into various beneficial or harmful metabolites like IPA, IAA, indole, SCFAs, etc., which then enter the portal vein system and reach the liver, modulating the kynurenine pathway. On the other hand, kynurenine metabolites, such as KYN, KYNA, 3-HKK, IDO, etc., are also capable of returning to the gut to exert regulatory effects. Abbreviations: KYNA, kynurenic acid; NAD+, nicotinamide adenine dinucleotide; 3-HK, 3-hydrokynurenine; Trp, tryptophan; IPA, indole-3-propionic acid; IAA, indole-3-acetic acid; SCFAs, short-chain fatty acids.</p>
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<p>Molecular mechanisms of kynurenine pathway in liver diseases. (<b>a</b>) In acute liver injury, the metabolic migration of kynurenine pathway from kynurenine (Kyn) to nicotinamide adenine dinucleotide leads to endoplasmic reticulum stress and activation of NF-κB signaling pathway to induce hepatocyte apoptosis. (<b>b</b>) In metabolic dysfunction-associated steatotic liver disease, the kynurenine pathway activates Gpr35 and RGS to increase energy expenditure, regulate fatty acid metabolism, and improve inflammation. (<b>c</b>) In liver cirrhosis, IDO-1 can inhibit hepatic stellate cell activation and scavenge free radicals to reduce oxidative damage by decreasing nuclear factor E2-related factor 2 (Nrf2). (<b>d</b>) The kynurenine pathway activates AHR, thereby inhibiting tumor initiation and progression and promoting tumor cell apoptosis. Abbreviations: Trp, tryptophan; KYN, kynurenine; KYNA, kynurenic acid; 3-HAA, 3-hydroxyanthranilic acid; ROS, reactive oxygen species; NF-κB, nuclear factor-κB; NAD+, nicotinamide adenine dinucleotide; IDO, indoleamine 2,3-dioxygenase; TDO, tryptophan 2,3-dioxygenase; KMO, kynurenine 3-monooxygenase; RGS, regulator of G protein; GPR35, G protein-coupled receptor 35; AhR, aryl hydrocarbon receptor; CYP1A1, cytochrome P450, family 1, subfamily A, polypeptide 1.</p>
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20 pages, 2992 KiB  
Review
Evaluating the Efficacy of Repurposed Antiretrovirals in Hepatitis B Virus Treatment: A Narrative Review of the Pros and Cons
by Samuel Chima Ugbaja, Simon Achi Omerigwe, Saziso Malusi Zephirinus Ndlovu, Mlungisi Ngcobo and Nceba Gqaleni
Int. J. Mol. Sci. 2025, 26(3), 925; https://doi.org/10.3390/ijms26030925 - 23 Jan 2025
Viewed by 780
Abstract
Human immunodeficiency virus (HIV) and hepatitis B virus (HBV) continue to be global public health issues. Globally, about 39.9 million persons live with HIV in 2023, according to the Joint United Nations Programme on HIV/AIDS (UNAIDS) 2024 Fact Sheet. Consequently, the World Health [...] Read more.
Human immunodeficiency virus (HIV) and hepatitis B virus (HBV) continue to be global public health issues. Globally, about 39.9 million persons live with HIV in 2023, according to the Joint United Nations Programme on HIV/AIDS (UNAIDS) 2024 Fact Sheet. Consequently, the World Health Organisation (WHO) reported that about 1.5 million new cases of HBV occur, with approximately 820 thousand mortalities yearly. Conversely, the lower percentage of HBV (30%) cases that receive a diagnosis is a setback in achieving the WHO 2030 target for zero HBV globally. This has necessitated a public health concern to repurpose antiretroviral (ARV) drugs for the treatment of HBV diseases. This review provides an introductory background, including the pros and cons of repurposing antiretrovirals (ARVs) for HBV treatment. We examine the similarities in replication mechanisms between HIV and HBV. We further investigate some clinical studies and trials of co-infected and mono-infected patients with HIV–HBV. The topical keywords including repurposing ARV drugs, repurposing antiretroviral therapy, Hepatitis B drugs, HBV therapy, title, and abstracts are searched in PubMed, Web of Science, and Google Scholar. The advanced search includes the search period 2014–2024, full text, clinical trials, randomized control trials, and review. The search results filtered from 361 to 51 relevant articles. The investigations revealed that HIV and HBV replicate via a common route known as ‘reverse transcription’. Clinical trial results indicate that an early initiation of ARVs, particularly with tenofovir disoproxil fumarate (TDF) as part of a regimen, significantly reduced the HBV viral load in co-infected patients. In mono-infected HBV, timely and correct precise medication is essential for HBV viral load reduction. Therefore, genetic profiling is pivotal for successful ARV drug repurposing in HBV treatment. Pharmacogenetics enables the prediction of the right dosages, specific individual responses, and reactions. This study uniquely explores the intersection of pharmacogenetics and drug repurposing for optimized HBV therapy. Additional in vivo, clinical trials, and in silico research are important for validation of the potency, optimum dosage, and safety of repurposed antiretrovirals in HBV therapy. Furthermore, a prioritization of research collaborations comprising of regulators and funders to foster clinically adopting and incorporating repurposed ARVs for HBV therapy is recommended. Full article
(This article belongs to the Section Molecular Microbiology)
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<p>HIV replication cycle highlighting the key stages targeted by antiretrovirals for HIV treatment, redrawn with a bio-render as adapted from source [<a href="#B32-ijms-26-00925" class="html-bibr">32</a>].</p>
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<p>HBV replication cycle highlighting the key stages targeted by the antiretrovirals repurposed for HBV treatment, redrawn with a bio-render as adapted from source [<a href="#B33-ijms-26-00925" class="html-bibr">33</a>].</p>
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22 pages, 762 KiB  
Review
Clinical Applications of Artificial Intelligence (AI) in Human Cancer: Is It Time to Update the Diagnostic and Predictive Models in Managing Hepatocellular Carcinoma (HCC)?
by Mario Romeo, Marcello Dallio, Carmine Napolitano, Claudio Basile, Fiammetta Di Nardo, Paolo Vaia, Patrizia Iodice and Alessandro Federico
Diagnostics 2025, 15(3), 252; https://doi.org/10.3390/diagnostics15030252 - 22 Jan 2025
Viewed by 558
Abstract
In recent years, novel findings have progressively and promisingly supported the potential role of Artificial intelligence (AI) in transforming the management of various neoplasms, including hepatocellular carcinoma (HCC). HCC represents the most common primary liver cancer. Alarmingly, the HCC incidence is dramatically increasing [...] Read more.
In recent years, novel findings have progressively and promisingly supported the potential role of Artificial intelligence (AI) in transforming the management of various neoplasms, including hepatocellular carcinoma (HCC). HCC represents the most common primary liver cancer. Alarmingly, the HCC incidence is dramatically increasing worldwide due to the simultaneous “pandemic” spreading of metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD currently constitutes the leading cause of chronic hepatic damage (steatosis and steatohepatitis), fibrosis, and liver cirrhosis, configuring a scenario where an HCC onset has been reported even in the early disease stage. On the other hand, HCC represents a serious plague, significantly burdening the outcomes of chronic hepatitis B (HBV) and hepatitis C (HCV) virus-infected patients. Despite the recent progress in the management of this cancer, the overall prognosis for advanced-stage HCC patients continues to be poor, suggesting the absolute need to develop personalized healthcare strategies further. In this “cold war”, machine learning techniques and neural networks are emerging as weapons, able to identify the patterns and biomarkers that would have normally escaped human observation. Using advanced algorithms, AI can analyze large volumes of clinical data and medical images (including routinely obtained ultrasound data) with an elevated accuracy, facilitating early diagnosis, improving the performance of predictive models, and supporting the multidisciplinary (oncologist, gastroenterologist, surgeon, radiologist) team in opting for the best “tailored” individual treatment. Additionally, AI can significantly contribute to enhancing the effectiveness of metabolomics–radiomics-based models, promoting the identification of specific HCC-pathogenetic molecules as new targets for realizing novel therapeutic regimens. In the era of precision medicine, integrating AI into routine clinical practice appears as a promising frontier, opening new avenues for liver cancer research and treatment. Full article
(This article belongs to the Special Issue Artificial Intelligence in Clinical Medical Imaging: 2nd Edition)
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<p>Potential AI contribution to developing tailored HCC surveillance models according to chronic liver disease etiologies. HBV: Hepatitis B virus; HCV: Hepatitis C virus; MASLD: Metabolic dysfunction-associated steatotic liver disease; EMR: Electronic medical record; alfa: alpha-fetoprotein; GGT: gamma-glutamyl transferase; BMI: body mass index; AST: aspartate aminotransferase; RNN: recurrent neural network; RSF: random survival forest; TDF: tenofovir; ETV: entecavir; PLT: platelet count; HBsAg: HBV-surface antigen; FIB-4: Fibrosis 4 score; GB: gradient-boosting.</p>
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