Search Results (7,099)

Purpose: Preclinical studies suggest that interleukin-1β (IL-1β) influences tumor behavior in non-small cell lung cancer (NSCLC). While the CANTOS trial demonstrated reduced lung cancer incidence with IL-1β inhibition, the CANOPY trials failed to show survival benefit when combined with chemoimmunotherapy. The role of IL-1β in NSCLC with oncogenic mutations remains unclear. We evaluated the prognostic and predictive significance of IL-1β expression across NSCLC subtypes. Methods: We analyzed 21,698 NSCLC tumors profiled by Caris Life Sciences using DNA and RNA next-generation sequencing. IL-1β expression was stratified into quartiles (Q1: lowest 25%, Q4: highest 25%). Real-world overall survival (OS) and time on treatment (TOT) were obtained from insurance claims. Statistical comparisons used Chi-square, Fisher’s exact, or Mann–Whitney U tests. Survival outcomes were assessed with Cox models. Results: Across unselected NSCLC patients, low IL-1β expression (Q1) was associated with modestly longer OS versus high expression (Q4) (median OS 19.5 vs. 17.4 months; HR 0.94; p < 0.0001). This effect was more pronounced in EGFR-mutant adenocarcinoma (36.7 vs. 27.2 months; HR 0.76; p < 0.001) and ALK fusion-positive NSCLC (53.0 vs. 35.2 months; HR 0.62; p = 0.002). In NSCLC without targetable mutations, IL-1β expression was not prognostic. In KRAS-mutant adenocarcinoma, high IL-1β expression was associated with modestly longer TOT on immunotherapy (7.4 vs. 6.4 months; HR 1.15; p = 0.041), but not OS. High IL-1β expression correlated positively with TP53 mutation, TMB-high, and PD-L1 expression and inversely with EGFR, KRAS, BRAF, ERBB2, KEAP1, and STK11 mutations. Conclusions: IL-1β expression is a potential prognostic and predictive biomarker in NSCLC, associated with survival outcomes in defined molecular subsets. These findings suggest that IL-1β-targeted strategies may be particularly relevant in EGFR- or ALK-altered tumors. Full article

Introduction/aim: N-acetylgalactoseamine-conjugated small interfering RNAs (GalNAc-siRNAs) are an emerging class of drugs possessing an extensive clinical potential because of their high target specificity to the asialoglycoprotein receptor (ASGPR) in hepatocytes. Overall, GalNAc-sRNAs are well-tolerated across species but differences in pharmacokinetic (PK) and pharmacodynamic (PD) properties have been observed. Furthermore, despite GalNAc-siRNA’s high liver specificity, distribution into off-target organs does occur. Through whole-body physiologically based pharmacokinetic (PBPK) modeling, this study seeks to mechanistically address species differences, establish clinical PK-PD relationships, and characterize off-target organ accumulation, ultimately expediting the preclinical-to-clinical translation of GalNAc-sRNAs in drug development. Materials/Methods: For model development, validation, and establishment of species’ translations, three in-house GalNAc-siRNAs with PK data from different biospecimens, as well as downstream effects on mRNA and target proteins in mouse, monkey, and human, were leveraged. A WB-PBPK-PD legacy model, developed as an extension to the generic model for large molecules in the platform Open Systems Pharmacology Suite, was further validated and applied to address the specific aims of this study. Results: The model successfully quantified the PK-PD relationships across species and characterized accumulation in off-target organs. The model further sheds light on species-specific differences, such as liver permeability, subcutaneous absorption rate, as well as PD-related mechanisms. Moreover, the model confirmed previously established compound-specific pharmacokinetic differences and similarities. Conclusions: This PBPK-PD can serve as a framework for future investigations of novel GalNAc-siRNAs across species. Full article

Risdiplam is an orally administered small molecule that modifies the mRNA splicing of SMN2 for the treatment of spinal muscular atrophy (SMA). Its use is approved in presymptomatic patients diagnosed by neonatal screening with early and severe forms with two copies of SMN2, but we do not have real data on the evolution of oral treatment in this early phenotype of SMA. We present two cases treated at one month of life with a follow-up of 12 months and discuss their different evolutions and the causes of this. Familial adherence to treatment is important, as discontinuation can convert an early form of presymptomatic SMA to symptomatic. Molecular biomarkers such as plasma monitoring of neurofilament light chain (pNf-L) should be considered in the follow-up of early forms of SMA and may support the decision to change treatment in infants with SMA. Full article

Glutamine (Gln) supplementation during the weaning period can alleviate stress in piglets. However, free Gln has poor stability and low absorption in the small intestine. Glycyl-glutamine (Gly-Gln), a stable dipeptide form of Gln, has been evaluated as a potential alternative in pig nutrition. This study investigated the effects of Gly-Gln at 0, 0.125%, 0.25%, 0.375%, and 0.50%, as well as a Gly + Gln positive control, on growth performance, intestinal morphology, immunity, antioxidant status, and nutrient apparent digestibility in weaned piglets. The results showed that dietary supplementation with 0.25%, 0.375%, or 0.50% Gly-Gln significantly increased average daily gain, average daily feed intake, and final weight (p < 0.05). Linear and quadratic effects (p < 0.05) were observed for growth performance indicators, suggesting that moderate supplementation levels yielded optimal benefits. Dietary Gly-Gln supplementation with 0.25%, 0.375%, or 0.50% Gly-Gln significantly increased serum immunoglobulin (IgG, IgA, and IgM), insulin, insulin growth factor 1, growth hormone, and T4 and T3 contents, and decreased IFN-γ and IL-1β contents (p < 0.05). Diets supplemented with 0.25, 0.375, or 0.50% Gly-Gln increased total antioxidant capacity and superoxide dismutase content in serum and liver, and decreased MDA content (p < 0.05). Compared with the negative control group, dietary supplementation of 0.25%, 0.375%, or 0.50% Gly-Gln significantly increased the mRNA expression of ZO-1, Occludin, and Claudin-1 in the jejunum (p < 0.05). Furthermore, crude protein digestibility was significantly improved in piglets receiving 0.375% and 0.5% Gly-Gln (p < 0.05), with a significant linear relationship between Gly-Gln level and digestibility. In conclusion, 0.25% is the minimum effective dose of Gly-Gln for improving weaning outcomes. Gly-Gln is more effective than equivalent doses of free glycine and glutamine in enhancing growth performance, gut barrier integrity, and nutrient utilization in weaned piglets. Full article

Antihypertensive drugs are widely used for the treatment of hypertension, and the choice of drug and dosage is based on trial and error. The variability in drug response and adverse reactions leads to the poor adherence to treatment. Epigenetic modulation is one of the major mechanisms that may contribute to the variability in drug responses, and microRNAs (miRNAs) can serve as crucial epigenetic regulators and have also been reported to be associated with hypertension pathogenesis. The objective of this study is to investigate the regulatory effects of commonly used antihypertensive drugs on the endothelial miRNome in human aortic endothelial cells. We aim to integrate miRNA expression data with proteomic analyses to elucidate drug-induced molecular mechanisms relevant to hypertension treatment. Whole genome small RNA sequencing was performed, followed by whole proteome analysis using LC-MS/MS comparing between control and treated samples. The treatments induced significant differential regulation of several miRNAs and proteins; among these, a few reflected reverse relationships with miRNA regulation and protein expression. Certain miRNAs and their corresponding target proteins seem to distinguish between good therapeutic outcomes and potential side effects. This study unravels the potential role of drug-induced miRNAs in inducing post-transcriptional modifications to cause the differential expression of certain proteins that may induce not only therapeutic effects or drug side effects but can also indicate the potential for drug-repurposing in other diseases. Full article

Under physiological and pathological conditions, all cells release extracellular vesicles named exosomes, which act as transporters of lipidic, protein, and genetic material from parent to recipient cells. Neoplastic cells can secrete higher number of exosomes to exert pro-tumoral effects such as microenvironmental changes, disease progression, immunosuppression and drug-resistance. This holds true for both organ-specific cancers and hematologic malignancies. One of the most important components of exosomal cargo are microRNAs which can mediate all the abovementioned effects. More specifically, microRNAs are small non-coding RNAs, routinely detected through quantitative real-time PCR, which act as translational suppressors by regulating protein-coding genes. Considering their high stability in all body fluids and viability in circulation, research is currently focusing on this type of RNAs for the so called “liquid biopsy”, a non-invasive tool for disease diagnosis and longitudinal monitoring. However, several issues remain to be solved including the lack of standardized protocols for exosome isolation and miRNA detection. Starting with this premise, our review aims to provide a wide description of the known microRNA panels employed in the prominent hematological malignancies, which will hopefully redefine the approach to these very challenging diseases in the near future. Full article

Background/Objectives: Medium- and long-chain triacylglycerol (MLCT) and 2′-fucosyllactose (2′-FL) are functional ingredients abundant in human milk; however, their effects on small intestinal development and health remain largely unknown, and no research has explored their potential combined effects. Methods: In this study, growing C57BL/6 mice (3 weeks old) were fed diets without or with 2.5 g/100 g of MLCT, 2′-FL, or the combination (MLCT + 2′-FL; 5:1) for 21 days. Body weight, major organ indices, small intestinal morphology-related indicators (small intestinal length, villus height, crypt depth, villus height/crypt depth (V/C) ratio, and epithelial cell proliferation), and intestinal barrier function markers (goblet cell and Paneth cell count, protein expression of ZO-1 and occludin, and levels of sIgA and LPS) were measured. Results: In addition to the shared promotion of epithelial cell proliferation, MLCT intervention raised villus height and crypt depth, while 2′-FL intervention elevated Paneth cell count and sIgA levels. Notably, MLCT + 2′-FL intervention offered additional advantages (increasing the V/C ratio, goblet cell count, and expression of ZO-1 and occludin) without affecting crypt depth. 16S rRNA sequencing analysis of cecal contents revealed that all three interventions mainly affected beta diversity rather than alpha diversity, and enriched differentially abundant bacterial taxa: Erysipelotrichaceae, Faecalibaculum, UBA1819, and Faecalitalea in the MLCT group; Enterobacteriaceae, Escherichia, and Allobaculum in the 2′-FL group; Bifidobacterium, Romboutsia, Clostridia, and several other bacterial taxa in the MLCT + 2′-FL group. Conclusions: These results indicate that MLCT and 2′-FL interventions alone appear to provide different benefits for small intestinal development, and their combination may confer more comprehensive advantages. Full article

Background/Objectives: HNSCC is a highly aggressive malignancy marked by the dysregulation of the cell cycle. In HPV⁻ HNSCC, mutations in the CDKN2A gene frequently result in the loss of the p16 protein, a key inhibitor of the cyclin D1/CDK4/6 complex. This loss results in unchecked G1/S phase progression. The CDK4/6 inhibitor palbociclib has shown therapeutic potential in HPV⁻ HNSCC by inducing G1 phase arrest and reducing cell viability. In this study, we investigated the molecular mechanisms by which palbociclib affects cell viability in HPV⁻ HNSCC. Methods: Four HPV⁻ HNSCC cell lines were treated with palbociclib, and RNA sequencing was performed to assess changes in gene expression. Cell viability was measured using the MTT assay. To further investigate protein localization, interactions, and function, we used immunofluorescence staining, co-immunoprecipitation, small molecule inhibitors, and siRNA-mediated knockdown. Results: We demonstrate that palbociclib downregulates survivin, a protein that plays dual roles in mitosis and apoptosis, thereby inhibiting cell proliferation. We also found that survivin is overexpressed in HPV⁻ HNSCC. Inhibiting survivin dimerization using the compound LQZ-7i significantly reduces cell viability and promotes its export from the nucleus to the cytoplasm. Additionally, we identified USP1, a deubiquitinase, as both a downstream target of CDK4/6 and a key regulator of survivin stability. Inhibiting USP1 activity or silencing its expression significantly reduces survivin levels. Conclusions: Our findings highlight survivin as a critical mediator of cell proliferation in HPV⁻ HNSCC and suggest that targeting the CDK4/6-USP1-survivin axis may offer a promising therapeutic strategy. Full article

Background/Objectives: Cancer-associated fibroblasts (CAFs) play a pivotal role in the tumor microenvironment. We conducted an analysis using RNA sequencing to identify specific markers for CAFs compared to normal fibroblasts (NFs) in non-small-cell carcinoma (NSCLC). Methods: CAFs and NFs were isolated and cultured from tumor tissues (primary tumor or metastatic lymph nodes) and matched non-tumor tissues, respectively. Bulk RNA sequencing was conducted on isolated CAFs and normal fibroblast NFs. Differential expressions, gene set enrichment, and CAF subpopulation prediction analyses were performed. Results: During the study period, 27 CAFs and 12 NFs were isolated and cultured from tumor and non-tumor tissues in patients with treatment-naïve NSCLC. Among them, 22 CAFs and 11 NFs were included in the RNA sequencing analysis. The 22 CAF samples consisted of 12 adenocarcinomas and 10 squamous cell carcinomas (SqCC), with 16 samples from the lungs and 6 samples from the lymph nodes. Notably, COL11A1, GREM1, CD36, and GAS6 showed a higher expression in CAFs than in NFs, whereas TNC and CXCL2 were more abundantly expressed in NFs. CD36 levels were elevated in CAFs from lymph nodes (LN-CAFs) compared with those from lung specimens (Lung-CAFs) and NFs. COL11A1 levels in Lung-CAFs surpassed those in LN-CAFs and NFs. Both GREM1 and GAS6 showed a strong expression in Lung-CAFs and LN-CAFs relative to NFs. CAFs exhibited features of the myofibroblast CAF subpopulation, whereas NFs displayed traits of the antigen-presenting CAF subtype. In the co-culture model of CAFs and THP-1 cells, the knockdown of GREM1 or GAS6 in CAFs significantly decreased the M2 marker expression in macrophages. Conclusions: In NSCLC, GREM1 and GAS6 can be valuable diagnostic targets for CAFs from primary tumors and metastatic sites; they warrant further study. Full article

Extracellular vesicles (EVs) are mediators of intercellular communication and serve as promising tools for drug discovery and targeted therapies. These lipid bilayer-bound nanovesicles facilitate the transfer of functional proteins, RNAs, lipids, and other biomolecules between cells, thereby influencing various physiological and pathological processes. This review outlines the molecular mechanisms governing EV biogenesis and cargo sorting, emphasizing the role of key regulatory proteins in modulating selective protein packaging. We explore the critical involvement of EVs in various disease microenvironments, including cancer progression, neurodegeneration, and immunological modulation. Their ability to cross biological barriers and deliver bioactive cargo makes them desirable candidates for precise drug delivery systems, especially in neurological and oncological disorders. Moreover, this review highlights advances in engineering EVs for the delivery of RNA therapeutics, CRISPR-Cas systems, and targeted small molecules. The utility of EVs as diagnostic tools in liquid biopsies and their integration into personalized medicine and companion diagnostics are also discussed. Patient-derived EVs offer dynamic insights into disease states and enable real-time treatment stratification. Despite their potential, challenges such as scalable isolation, cargo heterogeneity, and regulatory ambiguity remain significant hurdles. Recent studies have reported novel pharmacological approaches targeting EV biogenesis, secretion, and uptake pathways, with emerging regulators showing promise as drug targets for modulating EV cargo. Future directions include the standardization of EV analytics, scalable biomanufacturing, and the classification of EV-based therapeutics under evolving regulatory frameworks. This review emphasizes the multifaceted roles of EVs and their transformative potential as therapeutic platforms and biomarker reservoirs in next-generation precision medicine. Full article

Background/Objectives: Drug discovery is a lengthy and expensive process, taking an average of 10 years and more than USD 2 billion from target discovery to drug approval. It is even more challenging in complex diseases due to disease heterogeneity and limited knowledge about the underlying mechanisms. We present a novel computational framework that integrates network analysis, statistical mediation, and deep learning to identify causal target genes and repurposable small-molecule candidates. Methods: We applied weighted gene co-expression network analysis (WGCNA) and bidirectional mediation analysis (causal WGCNA) to transcriptomic data from idiopathic pulmonary fibrosis (IPF) patients to identify genes causally linked to the disease phenotype. These genes were used as a phenotypic signature for deep learning-based compound screening using the DeepCE model. Results: Using RNA-seq data from 103 IPF patients and 103 controls, we identified seven significantly correlated modules and 145 causal genes. Five of these genes (ITM2C, PRTFDC1, CRABP2, CPNE7, and NMNAT2) were predictive of disease severity in IPF. Our compound screening identified several promising candidates, such as Telaglenastat (GLS1 inhibitor), Merestinib (MET kinase inhibitor), and Cilostazol (PDE3 inhibitor), with significant inverse correlation with the IPF-specific gene signature. Conclusions: This study demonstrates the utility of combining causal inference and deep learning for drug discovery. Our framework identified novel gene targets and therapeutic candidates for IPF, offering a scalable strategy for phenotype-driven drug discovery and repurposing. Full article

Human methyltransferase-like protein 16 (METTL16) installs N⁶-methyladenosine on U6 small nuclear RNA (snRNA) and other RNAs. Multiple X-ray crystal structures of METTL16 have been published; however, we do not yet fully understand the structure–function relationships of specific residues. We designed 38 mutants, including seven cancer-associated mutants, and used electrophoretic mobility shift assays and single-turnover kinetic assays to better understand the functional roles of specific domains and amino acid residues in binding to U6 snRNA, formation of the METTL16•U6 snRNA•S-adenosylmethionine (SAM) complex, and the rate of methylation. While point mutations in the methyltransferase domain mildly weaken the binding of METTL16 to U6 snRNA, the C-terminal vertebrate conserved regions (VCRs), particularly the arginine-rich region (R382 to R388), mediate cooperative binding and contribute more to RNA binding. All METTL16 K-loop mutants displayed tighter SAM binding, suggesting that the K-loop blocks SAM binding. In addition, residues E133 and F227 are critical for stabilizing SAM binding. Mutations in the ₁₈₄NPPF₁₈₇ catalytic core and R282A abolished methyltransferase activity. Two METTL16 somatic cancer-associated mutants (G110C and R241Dfs*2) displayed reduced methylation activity. This mutational analysis expands our understanding of how specific domains and residues contribute to substrate-binding activity and methylation of U6 snRNA catalyzed by METTL16. Full article

Background: Collabieae is a medium-sized group within the orchid subfamily Epidendroideae that is distributed primarily across tropical Asia. Most Collabieae species are known for their considerable ornamental and medicinal merits. However, habitat destruction and overharvesting have led to severe decline in their wild populations. Chloroplast (cp) genomes are highly valued in evolutionary studies, due to comparative conservation and accumulation of genomic variations. Elucidating the structure of chloroplast genome is instrumental in conserving genetic diversity within the Collabieae. Methods: we explored the chloroplast genome characteristics of Collabieae. We incorporated three newly sequenced genomes from species (Acanthophippium sylhetense, Eriodes barbata, and Spathoglottis plicata), along with seven related species. Results: all analyzed cp genomes displayed a typical quadripartite circular structure. The total lengths ranged from 157,036 bp to 158,321 bp. Each genome contained 136 genes: 88 protein-coding genes, 38 tRNA genes, eight rRNA genes, and two pseudogenes. Across the ten Collabieae species, gene number, order, orientation, GC content, and codon usage bias were highly consistent, indicative of strong sequence conservation. However, notable structural divergence was observed at the plastome junctions, alongside variations in SSR and repetitive element frequencies. Moreover, six hypervariable regions were identified. Noncoding regions exhibited higher variability compared to protein-coding regions. Phylogenetic analysis indicated that E. barbata forms a distinct, small branch sister to the rest of the Collabieae members. Genera Acanthophippium and Spathoglottis were sister to the remaining groups within the tribe. Conclusions: this overall phylogenetic framework aligns well with previous findings. Our study provides valuable cp genomic resources and advances evolutionary research in Collabieae. Full article

Background/Objectives: Transfer RNA-derived fragments (tRFs) are small non-coding RNAs increasingly implicated in gene regulation and disease, yet their target specificity and disease relevance remain poorly understood. This is an exploratory study that investigates the phenomenon of identical tRF sequences reported in distinct disease contexts and evaluates the consistency between experimental findings and predictions from both target-based and abundance-based tRF databases. Methods: Five tRFs with identical sequences across at least two peer-reviewed disease studies were selected from a recent systematic review. Their validated targets and disease associations were extracted from the literature. Motifs and predicted targets were cross-referenced using three target-oriented databases: tatDB, tRFTar, and tsRFun. In parallel, the abundance enrichment of cancer-associated tRFs was assessed in OncotRF and MINTbase using TCGA-based abundance data. Results: Among the five tRFs, only LeuAAG-001-N-3p-68-85 showed complete alignment between experimental data and both tatDB and tRFTar predictions. Most of the other four displayed at least partial overlaps in motif/binding regions with some of validated targets. tRF abundance data from MINTbase and OncotRF showed inconsistent enrichment, with only AlaAGC-002-N-3p-58-75 exhibiting concordance with its experimentally validated cancer type. Most functionally relevant tRFs were not strongly represented in abundance-only databases. Conclusions: Given the limited number of tRFs analyzed, this study serves primarily as a pilot analysis designed to generate hypotheses and guide future in-depth research, rather than offering comprehensive conclusions. We did, however, illustrate how the analysis of tRFs can benefit from utilizing currently available databases. Target-based databases more closely reflected experimental evidence for mechanistic details when a tRF or a motif match is found. Yet all database types are incomplete, including the abundance-focused tools, which often fail to capture disease-specific regulatory roles of tRFs. These findings underscore the importance of using integrated data sources for tRF annotation. As a pilot analysis, the study provides insights into how identical tRF sequences might function differently across disease contexts, highlighting areas for further investigation while pointing out the limitations of relying on expression data alone to infer functional relevance. Full article

Circular RNAs (circRNAs) are increasingly recognized as regulators of gene expression, although their roles in hematopoietic differentiation remain relatively understudied. This study compares circRNA expression profiles between erythroblasts derived from human fetal liver and bone marrow CD34⁺ hematopoietic stem cells using publicly available RNA-seq datasets (GEO: GSE90878). Twelve samples from each developmental source were analyzed. Differential expression analysis was performed, and circAtlas 3.0 was employed to predict interactions between circRNAs, microRNAs (miRNAs), and RNA-binding proteins. Differentially expressed miRNAs were curated from miRNA-seq data (GEO: GSE110936) profiling the same cell types. Principal component analysis of circRNA expression profiles demonstrated clear separation between erythroblasts from fetal liver and bone marrow, which was statistically confirmed by PERMANOVA (p = 0.001); though this effect size is small (R² = 0.065). One circRNA, circALS2(4).1, was significantly upregulated in bone marrow-derived erythroblasts (adjusted p < 0.05), and ten additional circRNAs showed suggestive evidence for differential expression (adjusted p < 0.1). The resulting interaction networks reveal distinct circRNA landscapes and suggest regulatory circuits that may contribute to developmental differences in human erythropoiesis, indicating that the functions of circRNAs in hematopoietic development remain to be further elucidated. Full article