Search Results (501)

Background: Retinol-binding protein 4 (RBP4) is primarily recognized for its role in retinoid transport, but has recently been implicated in cancer progression and prognosis. However, a comprehensive pan-cancer analysis of RBP4’s expression, prognostic significance, and functional associations across various cancers is lacking. Methods: We conducted a pan-cancer analysis of RBP4 using data from public databases. RBP4 expression levels were examined in 33 tumor types, and correlations with clinical outcomes, immune cell infiltration, DNA methylation, and gene mutations were assessed. Enrichment analyses of RBP4 and its co-expressed genes were performed to explore associated biological pathways. Additionally, in vitro experiments were conducted to assess the effects of RBP4 on cell migration and proliferation. Results: RBP4 showed differential expression between tumor and normal tissues, with downregulation in 21 cancer types and upregulation in 6. High expression levels of RBP4 were associated with poor overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in specific cancers, notably in BRCA, HNSC, and STAD, whereas it was a favorable prognostic factor in cancers such as KIRP and MESO. RBP4 expression was also associated with immune cell infiltration, particularly with CD4+ Th2 cells and immune checkpoint genes. DNA methylation analysis suggested that the methylation of RBP4 may play a role in its regulatory mechanisms across cancer types. Enrichment analyses revealed that RBP4 and its co-expressed genes are involved in metabolism-related pathways and immune regulation. Functional assays indicated that RBP4 knockdown promoted tumor cell migration and proliferation. Conclusions: This study provides a comprehensive pan-cancer analysis of RBP4, identifying its prognostic potential and possible involvement in tumor immunity and metabolism. Our findings suggest that RBP4 could serve as a novel biomarker and therapeutic target in cancer, although further experimental studies are required to elucidate its precise mechanisms in specific cancer types. Full article

Breast, colon, and lung carcinomas are classified as aggressive tumors with poor relapse-free survival (RFS), progression-free survival (PF), and poor hazard ratios (HRs) despite extensive therapy. Therefore, it is essential to identify a gene expression signature that correlates with RFS/PF and HR status in order to predict treatment efficiency. RNA-binding proteins (RBPs) play critical roles in RNA metabolism, including RNA transcription, maturation, and post-translational regulation. However, their involvement in cancer is not yet fully understood. In this study, we used computational bioinformatics to classify the functions and correlations of RBPs in solid cancers. We aimed to identify molecular biomarkers that could help predict disease prognosis and improve the therapeutic efficiency in treated patients. Intersection analysis summarized more than 1659 RBPs across three recently updated RNA databases. Bioinformatics analysis showed that 58 RBPs were common in breast, colon, and lung cancers, with HR values < 1 and >1 and a significant Q-value < 0.0001. RBP gene clusters were identified based on RFS/PF, HR, p-value, and fold induction. To define union RBPs, common genes were subjected to hierarchical clustering and were classified into two groups. Poor survival was associated with high genes expression, including CDKN2A, MEX3A, RPL39L, VARS, GSPT1, SNRPE, SSR1, and TIA1 in breast and colon cancer but not with lung cancer; and poor survival was associated with low genes expression, including PPARGC1B, EIF4E3, and SMAD9 in breast, colon, and lung cancer. This study highlights the significant contribution of PPARGC1B, EIF4E3, and SMAD9 out of 11 RBP genes as prognostic predictors in patients with breast, colon, and lung cancers and their potential application in personalized therapy. Full article

Background: Phage tail-like bacteriocins, or tailocins, provide a competitive advantage to producer cells by killing closely related bacteria. Morphologically similar to headless phages, their narrow target specificity is determined by receptor-binding proteins (RBPs). While RBP engineering has been used to alter the target range of a selected R2 tailocin from Pseudomonas aeruginosa, the process is labor-intensive, limiting broader application. Methods: We introduce a VersaTile-driven R2 tailocin engineering and screening platform to scale up RBP grafting. Results: This platform achieved three key milestones: (I) engineering R2 tailocins specific to Escherichia coli serogroups O26, O103, O104, O111, O145, O146, and O157; (II) reprogramming R2 tailocins to target, for the first time, the capsule and a new species, specifically the capsular serotype K1 of E. coli and K11 and K63 of Klebsiella pneumoniae; (III) creating the first bivalent tailocin with a branched RBP and cross-species activity, effective against both E. coli K1 and K. pneumoniae K11. Over 90% of engineered tailocins were effective, with clear pathways for further optimization identified. Conclusions: This work lays the groundwork for a scalable platform for the development of engineered tailocins, marking an important step towards making R2 tailocins a practical therapeutic tool for targeted bacterial infections. Full article

We carried out limited enzymatic hydrolysis with trypsin on rice bran protein (RBP) pretreated by high hydrostatic pressure (HHP) in this study. The effects of the degree of hydrolysis (DH) on the structural and emulsifying properties were investigated. The results indicated that the molecular structure of RBP changed after limited enzymatic hydrolysis. The rice bran protein hydrolysate (RBPH, DH8) exhibited a better molecular distribution, a smaller particle size (200.4 nm), a better emulsifying activity index (31.82 m²/g), and an improved emulsifying stability index (24.69 min). RBPH emulsions with different DH (0–12) values were prepared. The interfacial properties, such as particle size, the ζ-potential, and the interfacial tension of the emulsions, were measured. Compared to the control, the interfacial properties of the RBPH emulsions were significantly improved after limited enzymatic hydrolysis. The RBPH emulsion at DH8 showed better stability with a smaller emulsion droplet size (2.31 μm), a lower ζ-potential (−25.56 mV), and a lower interfacial tension. This study can provide a theoretical basis for the application of RBP as the plant protein-based emulsifier in the beverage industry. Full article

Currently, the use of recycled aggregates (RA) in new concrete is allowed by several international regulations, although their replacement is limited to low percentages of the coarse fraction. In order to increase the percentage of RA, several authors have studied different processes to improve the microstructure of its surface. Therefore, it is necessary to analyze whether the current standards simulate the structural behavior of concretes with high percentages of RA. For this purpose, beams with 0%, 50% and 100% RA replacement coated with recycled binder paste (RBP) were made and their behavior was compared with the equations of the Eurocode 2 and ACI 318-19 code. As a result, we found that when 100% coated RA was used, the reduction in compressive strength was only 12.73%, with similar cracking patterns observed in RA beams across all series. In addition, the load capacity of the beams with RA was higher than the theoretical values provided by the codes. Finally, the experimental critical deflection was higher than that calculated by the code equations. Thus, it is recommended that these higher deflections be taken into account at the time of design. Full article

RNA-binding proteins (RBPs) are cellular factors involved in every step of RNA metabolism. During HIV-1 infection, these proteins are key players in the fine-tuning of viral and host cellular and molecular pathways, including (but not limited to) viral entry, transcription, splicing, RNA modification, translation, decay, assembly, and packaging, as well as the modulation of the antiviral response. Targeted studies have been of paramount importance in identifying and understanding the role of RNA-binding proteins that bind to HIV-1 RNAs. However, novel approaches aimed at identifying all the proteins bound to specific RNAs (RBPome), such as RNA interactome capture, have also contributed to expanding our understanding of the HIV-1 replication cycle, allowing the identification of RBPs with functions not only in viral RNA metabolism but also in cellular metabolism. Strikingly, several of the RBPs found through interactome capture are not canonical RBPs, meaning that they do not have conventional RNA-binding domains and are therefore not readily predicted as being RBPs. Further studies on the different cellular targets of HIV-1, such as subtypes of T cells or myeloid cells, or on the context (active replication versus reactivation from latency) are needed to fully elucidate the host RBPome bound to the viral RNA, which will allow researchers and clinicians to discover new therapeutic targets during active replication and provirus reactivation from latency. Full article

Parathyroid hormone-related protein (PTHrP) and retinol-binding protein 4 (RBP4) have been associated with a worse prognosis of kidney disease. Recently, the direct interconnection between PTHrP and the peroxisome proliferator-activated receptor gamma (PPARγ), a nuclear receptor whose activation is nephroprotective, has been discovered. The aim of this study was to analyze the relationship between PTHrP, PPARγ, and RBP4. For this purpose, we analyzed the levels of these proteins, which were studied in the kidneys of five experimental groups of mice at 6 weeks of age: controls, diabetics, insulin-treated diabetics, transgenic mice overexpressing PTHrP at the renal level, and the latter mice that were also induced with diabetes. In addition, we also analyzed the expression levels of these molecules in two mouse podocyte cell lines, controls and PPARγKO, subjected to a lipotoxic insult by palmitic acid. We found that RBP4 and PTHrP are increased in the kidney in pathological conditions and that insulin and PPARγ act regulating PTHrP and RBP4 expression, suggesting that the regulation of this system is critical for the maintenance of renal homeostasis and how it becomes imbalanced in different pathophysiological conditions. Full article

The protein therapeutics market, including antibody and fusion proteins, has experienced steady growth over the past decade, underscoring the importance of optimizing amino acid sequences. In our previous study, we developed a fusion protein, R31, which combines retinol-binding protein (RBP) with albumin domains IIIA and IB, linked by a sequence (AAAA), and includes an additional disulfide bond (N227C-V254C) in IIIA. This fusion protein effectively inhibited hepatic stellate cell activation. In this study, we further optimized the sequence. The G176K mutation at the C-terminus of RBP altered the initiation site of the first α-helix in domain IIIA, shifting it from P182 to K176, and promoted polar interactions between K176 and adjacent residues, enhancing the rigidity of the RBP/IIIA interface. The introduction of an additional disulfide bond (V231C/Y250C) connecting helices 3 and 4 in IIIA resulted in a three-fold increase in productivity and a 2 °C improvement in thermal stability compared to R31. Furthermore, combining the G176K mutation with V231C/Y250C further enhanced both productivity and anti-fibrotic activity. These findings suggest that the enhanced stability of domain IIIA, conferred by V231C/Y250C, along with the increased rigidity of the RBP/IIIA interface, optimizes interdomain distance and alignment, facilitating proper protein folding. Full article

Small nucleolar RNAs (snoRNAs) are non-coding RNAs (ncRNAs) that regulate many cellular processes. Changes in the profiles of cellular ncRNAs and those secreted in exosomes are observed during viral infection. In our study, we analysed differences in expression profiles of snoRNAs isolated from exosomes of influenza (IAV)-infected and non-infected MDCK cells using high-throughput sequencing. The analysis revealed 133 significantly differentially regulated snoRNAs (131 upregulated and 2 downregulated), including 93 SNORD, 38 SNORA, and 2 SCARNA. The most upregulated was SNORD58 (log2FoldChange = 9.61), while the only downregulated snoRNAs were SNORD3 (log2FC = −2.98) and SNORA74 (log2FC = −2.67). Several snoRNAs previously described as involved in viral infections were upregulated, including SNORD27, SNORD28, SNORD29, SNORD58, and SNORD44. In total, 533 interactors of dysregulated snoRNAs were identified using the RNAinter database with an assigned confidence score ≥ 0.25. The main groups of predicted interactors were transcription factors (TFs, 169 interactors) and RNA-binding proteins (RBPs, 130 interactors). Among the most important were pioneer TFs such as POU5F1, SOX2, CEBPB, and MYC, while in the RBP category, notable interactors included Polr2a, TNRC6A, IGF2BP3, and FMRP. Our results suggest that snoRNAs are involved in pro-viral activity, although follow-up studies including experimental validation would be beneficial. Full article

Using construction and demolition (C&D) waste in concrete production is a promising step toward environmental resilience amid the construction industry’s ecological footprint. The extensive history of using bricks in the construction of buildings has resulted in a considerable amount of waste associated with this commonly used material. This study aimed to assess the quality of concrete by examining the effect of replacing cement with varying percentages of recycled brick powder (RBP—0% to 50%). The primary objectives include evaluating the mechanical properties of concrete and establishing the feasibility of using RBP as a partial cement substitute. The investigation of target concrete can be divided into two phases: (i) laboratory investigation, and (ii) numerical investigation. In the laboratory phase, the performance of concrete with RBP was assessed under short-term dynamic and various static loads. The drop-weight test recommended by the ACI 544 committee was used to assess the short-term dynamic behavior (352 concrete discs). Furthermore, the behavior under static load was analyzed through compressive, flexural, and tensile strength tests. During the numerical phase, artificial neural network models (ANN) and fuzzy logic models (FL) were used to predict the results of 28-day compressive strength. The impact life with different failure probabilities was predicted based on the impact resistance results, by combining the Weibull distribution model. Additionally, an impact damage evolution equation was presented for mixtures containing RBP. The results show that the use of RBP up to 15% caused a slight decrease in compressive, flexural, and tensile strength (about 3–5%). Also, by replacing RBP up to 15%, the first crack strength decreased by 7.15% and the failure strength decreased by 6.46%. The average error for predicting 28-day compressive strength by FL and ANN models was recorded as 4.66% and 0.87%, respectively. In addition, the results indicate that the impact data follow the two-parameter Weibull distribution, and the R² value for different mixtures was higher than 0.9275. The findings suggest that incorporating RBP in concrete can contribute to sustainable construction practices by reducing the reliance on cement and utilizing waste materials. This approach not only addresses environmental concerns but also enhances the quality assessment of concrete, offering potential cost savings and resource efficiency for the construction industry. Real-world applications include using RBP-enhanced concrete in non-structural elements, such as pavements, walkways, and landscaping features, where high strength is not the primary requirement. Full article

Background/Objectives: Breast cancer is the second most common malignancy worldwide and poses a significant threat to women’s health. However, the prognostic biomarkers and therapeutic targets of breast cancer are unclear. A prognostic model can help in identifying biomarkers and targets for breast cancer. In this study, a novel prognostic model was developed to optimize treatment, improve clinical prognosis, and screen potential phosphoglycerate kinase 1 (PGK1) inhibitors for breast cancer treatment. Methods: Using data from the Gene Expression Omnibus (GEO) database, differentially expressed genes (DEGs) were identified in normal individuals and breast cancer patients. The biological functions of the DEGs were examined using bioinformatics analysis. A novel prognostic model was then constructed using the DEGs through LASSO and multivariate Cox regression analyses. The relationship between the prognostic model, survival, and immunity was also evaluated. In addition, virtual screening was conducted based on the risk genes to identify novel small molecule inhibitors of PGK1 from Chemdiv and Targetmol libraries. The effects of the potential inhibitors were confirmed through cell experiments. Results: A total of 230 up- and 325 down-regulated DEGs were identified in HER2, LumA, LumB, and TN breast cancer subtypes. A new prognostic model was constructed using ten risk genes. The analysis from The Cancer Genome Atlas (TCGA) indicated that the prognosis was poorer in the high-risk group compared to the low-risk group. The accuracy of the model was confirmed using the ROC curve. Furthermore, functional enrichment analyses indicated that the DEGs between low- and high-risk groups were linked to the immune response. The risk score was also correlated with tumor immune infiltrates. Moreover, four compounds with the highest score and the lowest affinity energy were identified. Notably, D231-0058 showed better inhibitory activity against breast cancer cells. Conclusions: Ten genes (ACSS2, C2CD2, CXCL9, KRT15, MRPL13, NR3C2, PGK1, PIGR, RBP4, and SORBS1) were identified as prognostic signatures for breast cancer. Additionally, results showed that D231-0058 (2-((((4-(2-methyl-1H-indol-3-yl)-1,3-thiazol-2-yl)carbamoyl)methyl)sulfanyl)acetic acid) may be a novel candidate for treating breast cancer. Full article

T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein (RBP) that plays a multifunctional role in RNA metabolism. TIA1 has three RNA-Recognition Motifs (RRMs) and a prion-like carboxyl C-terminal domain (LCD) with intrinsically disordered regions (IDR) implicated in the dynamics (i.e., formation, assembly, and disassembly) of transient RNA-protein aggregates known as stress granules (SGs). A protein related to TIA1 is its paralog TIA1-related/like protein (TIAR/TIAL1), whose amino acid sequence, structural organisation, and molecular and cellular functions are highly conserved with TIA1. Both proteins are the main components of SGs, which are non-membranous RNA-protein condensates formed under stress to promote cell survival. Welander distal myopathy (WDM) is a late-onset muscular dystrophy that has been linked to a single-nucleotide substitution (c.1362G>A; p.E384K) in the gene encoding the TIA1 protein, which impacts TIA1-dependent SGs dynamics. Herein, we have analysed cellular and molecular aspects by targeting mutagenesis to position 384 to understand its molecular grammar in an amino acid/proteinogenic-dependent or -independent manner under oxidative stress. The observations suggest differential, even opposing, behaviours between TIA1 and TIAR in the presence of specific amino acids with negative and positive charges, and also uncharged acids, at equivalent positions of TIA1 and TIAR, respectively. Collectively, these findings illustrate a characteristic molecular grammar of TIAR- and TIA1-dependent SGs under oxidative conditions, suggesting a gain of versatility between two structurally and functionally highly conserved/related proteins. Full article

Background. Variant 3′UTRs provide mRNAs with different binding sites for miRNAs or RNA-binding proteins (RBPs) allowing the establishment of new regulatory environments. Regulation of 3′UTR length impacts on the control of gene expression by regulating accessibility of miRNAs or RBPs to homologous sequences in mRNAs. Objective. Studying the dynamics of mRNA length variations in atherosclerosis (ATS) progression and reversion in ApoE-deficient mice exposed to a high-fat diet and treated with an αCD40-specific siRNA or with a sequence-scrambled siRNA as control. Methods. We gathered microarray mRNA expression data from the aortas of mice after 2 or 16 weeks of treatments, and used these data in a Bioinformatics analysis. Results. Here, we report the lengthening of the 5′UTR/3′UTRs and the shortening of the CDS in downregulated mRNAs during ATS progression. Furthermore, treatment with the αCD40-specific siRNA resulted in the partial reversion of the 3′UTR lengthening. Exon analysis showed that these length variations were actually due to changes in the number of exons embedded in mRNAs, and the further examination of transcripts co-expressed at weeks 2 and 16 in mice treated with the control siRNA revealed a process of mRNA isoform switching in which transcript variants differed in the patterns of alternative splicing or activated latent/cryptic splice sites. Conclusion. We document length variations in the 5′UTR/3′UTR and CDS of mRNAs downregulated during atherosclerosis progression and suggest a role for mRNA splicing reprogramming and transcript isoform switching in the generation of disease-related mRNA sequence diversity and variability. Full article

Hepatobiliary cancers, such as hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are among the deadliest malignancies worldwide, leading to a significant number of cancer-related deaths. While bone metastases from these cancers are rare, they are highly aggressive and linked to poor prognosis. This review focuses on RNA-based molecular mechanisms that contribute to bone metastasis from hepatobiliary cancers. Specifically, the role of two key factors, microRNAs (miRNAs) and RNA-binding proteins (RBPs), which have not been extensively studied in the context of HCC and CCA, is discussed. These molecules often exhibit abnormal expression in hepatobiliary tumors, influencing cancer cell spread and metastasis by disrupting bone homeostasis, thereby aiding tumor cell migration and survival in the bone microenvironment. This review also discusses potential therapeutic strategies targeting these RNA-based pathways to reduce bone metastasis and improve patient outcomes. Further research is crucial for developing effective miRNA- and RBP-based diagnostic and prognostic biomarkers and treatments to prevent bone metastases in hepatobiliary cancers. Full article

This paper presents a systematic overview of the applications of RBP as a substitute for cement. Initially, the fundamental properties of RBP, including physical properties, chemical compositions, and morphology, are discussed. Subsequently, the effects of RBP on various aspects of cement-based materials, such as fresh properties, shrinkage behavior, hydration, microstructure, strength development, and durability, are thoroughly reviewed. The findings of this study reveal that waste brick powder exhibits pozzolanic activity and can be used to partially replace cement in concrete formulations. However, its relatively high water absorption and irregular shape increase the water demand and, thus, reduce the rheological properties. The incorporation of RBP with 10–20% or finer particle sizes can refine the pore structure and promote the formation of hydration products. However, replacements of RBP greater than 25% can lead to adverse effects on the mechanical properties, frost resistance, and carbonation resistance of cementitious composites. Therefore, to enhance the effectiveness of RBP, measures such as improving fineness, incorporating mineral admixtures, adjusting curing conditions, and applying nano- or chemical modifications are necessary. This study provides valuable technical support for promoting the sustainable preparation of construction materials, which holds important environmental and economic implications. Full article