Search Results (7,447)

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are devastating neurodegenerative diseases that, despite the availability of symptomatic and modestly beneficial treatments, still lack therapies capable of halting disease progression. A histopathological hallmark of both diseases is the cytoplasmic deposition of TDP-43 in neurons, which is attributed to both intrinsic (e.g., mutations, aberrant cleavage) and extrinsic factors (e.g., prolonged oxidative stress, impaired clearance pathways). Mutations and certain PTMs (e.g., cysteine oxidation) destabilize RNA binding, promoting monomer misfolding and increasing its half-life. Disruptions to core ubiquitin-proteasome system (UPS) subunits impede efficient processing, contributing to the clearance failure of misfolded TDP-43 monomers. The accumulation of monomers drives phase separation within stress granules, creating nucleation hotspots that eventually bypass the thermodynamic barrier, resulting in exponential growth. This rapid growth then culminates in the failure of the autophagy-lysosome pathway (ALP) to contain the aggregation, resulting in a self-sustaining feed-forward loop. Here, we organize these factors into a conceptual kinetic cascade that links TDP-43 misfolding, phase separation, and clearance failure. Therapeutic strategies must therefore move beyond simple clearance and focus on targeting these kinetic inflection points (e.g., oligomer seeding, PTM modulation). Full article

Spermatogenesis is a tightly coordinated differentiation program that sustains male fertility while transmitting genetic and epigenetic information to the next generation. This review consolidates mechanistic evidence showing how RNA-centered regulation integrates with the epitranscriptome and three-dimensional (3D) genome architecture to orchestrate germ-cell fate transitions from spermatogonial stem cells through meiosis and spermiogenesis. Recent literature is critically surveyed and synthesized, with particular emphasis on human and primate data and on stage-resolved maps generated by single-cell and multi-omics technologies. Collectively, available studies support a layered regulatory model in which RNA-binding proteins and RNA modifications coordinate transcript processing, storage, translation, and decay; small and long noncoding RNAs shape post-transcriptional programs and transposon defense; and dynamic chromatin remodeling and 3D reconfiguration align transcriptional competence with recombination, sex-chromosome silencing, and genome packaging. Convergent nodes implicated in spermatogenic failure are highlighted, including defects in RNA metabolism, piRNA pathway integrity, epigenetic reprogramming, and nuclear architecture, and the potential of these frameworks to refine molecular phenotyping in male infertility is discussed. Finally, key gaps and priorities for causal testing in spatially informed, stage-specific experimental systems are outlined. Full article

Accurately identifying drug off-targets is essential for reducing toxicity and improving the success rate of pharmaceutical discovery pipelines. However, current deep learning approaches often struggle to fuse chemical structure, protein biology, and multi-target context. Here, we introduce HDPC-LGT (Hybrid Dual-Prompt Cross-Attention Ligand–Protein Graph Transformer), a framework designed to predict ligand binding across sixteen human translation-related proteins clinically associated with antibiotic toxicity. HDPC-LGT combines graph-based chemical reasoning with protein language model embeddings and structural priors to capture biologically meaningful ligand–protein interactions. The model was trained on 216,482 experimentally validated ligand–protein pairs from the Chemical Database of Bioactive Molecules (ChEMBL) and the Protein–Ligand Binding Database (BindingDB) and evaluated using scaffold-level, protein-level, and combined holdout strategies. HDPC-LGT achieves a macro receiver operating characteristic–area under the curve (macro ROC–AUC) of 0.996 and a micro F1-score (micro F1) of 0.989, outperforming Deep Drug–Target Affinity Model (DeepDTA), Graph-based Drug–Target Affinity Model (GraphDTA), Molecule–Protein Interaction Transformer (MolTrans), Cross-Attention Transformer for Drug–Target Interaction (CAT–DTI), and Heterogeneous Graph Transformer for Drug–Target Affinity (HGT–DTA) by 3–7%. External validation using the Papyrus universal bioactivity resource (Papyrus), the Protein Data Bank binding subset (PDBbind), and the benchmark Yamanishi dataset confirms strong generalisation to unseen chemotypes and proteins. HDPC-LGT also provides biologically interpretable outputs: cross-attention maps, Integrated Gradients (IG), and Gradient-weighted Class Activation Mapping (Grad-CAM) highlight catalytic residues in aminoacyl-tRNA synthetases (aaRSs), ribosomal tunnel regions, and pharmacophoric interaction patterns, aligning with known biochemical mechanisms. By integrating multimodal biochemical information with deep learning, HDPC-LGT offers a practical tool for off-target toxicity prediction, structure-based lead optimisation, and polypharmacology research, with potential applications in antibiotic development, safety profiling, and rational compound redesign. Full article

Background: Myocardial fibrosis, a central pathological process leading to heart failure, lacks specific mechanism-based therapies. Although the anti-inflammatory activity of the natural compound protocatechuic acid is recognized, its direct anti-fibrotic mechanism, particularly concerning the critical role of endothelial–mesenchymal transition (EndMT), remains unexplored. This study aimed to investigate the protective effects and underlying mechanisms of protocatechuic acid. Methods: The study employed both in vivo and in vitro models. For in vivo evaluation, a rat model of myocardial fibrosis was induced by isoproterenol hydrochloride (ISO). For in vitro analysis, human umbilical vein endothelial cells (HUVECs) were stimulated with angiotensin II (Ang II) and subjected to siRNA-mediated histone deacetylase 1 (HDAC1) knockdown, alongside a co-culture model involving HUVECs and the AC16 human cardiomyocyte cells. Additionally, molecular docking and dynamics simulations were performed to evaluate the binding affinity and stability of protocatechuic acid with the target protein, HDAC1. Results: In vivo, protocatechuic acid significantly improved cardiac function, attenuated pathological injury, and reduced collagen deposition in ISO-induced fibrotic rats. It also potently suppressed inflammatory responses and inhibited the EndMT process. These beneficial effects were associated with decreased HDAC1 and increased GATA binding protein 4 (GATA4) expression in perivascular regions, which suggests the modulation of the HDAC1/GATA4 pathway. In vitro, protocatechuic acid suppressed Ang II-induced endothelial inflammation in HUVECs. This effect was replicated by HDAC1 knockdown, thus confirming that the HDAC1/GATA4 pathway mediates its anti-inflammatory action at the cellular level. Furthermore, molecular docking and dynamics simulations indicated that protocatechuic acid stably binds to a key target, HDAC1. Conclusions: Protocatechuic acid alleviates inflammation and EndMT by inhibiting the HDAC1/GATA4 signaling pathway, thereby preserving cardiac function and retarding the progression of myocardial fibrosis. These findings provide a theoretical and experimental foundation for the potential application of protocatechuic acid in treating cardiovascular diseases. Full article

CRISPR-Cas9 systems have enabled unprecedented advances in genome engineering, particularly in developing treatments for human diseases, like cancer. Despite potential applications, limitations of Cas9 include its relatively large size and strict targeting requirements. Cas12j2, a variant ofCasΦ-2, shows promise for overcoming these limitations. However, its effectiveness in mammalian cells remains relatively unexplored. This study sought to develop an optimized CRISPR-Cas12j2 system for targeted knockout of the E6 oncogene in HPV-associated cancers. A combination of computational tools (ColabFold, CCTop, Cas-OFFinder, HADDOCK2.4, and Amber for Molecular Dynamics) was utilized to investigate the impact of engineered modifications on structural integrity and gRNA binding of Cas12j2 fusion constructs, in potential intracellular conditions. Cas12j2_F2, a Cas12j2 variant designed and evaluated in this study, behaves similarly to the wild-type Cas12j2 structure in terms of RMSD/RMSF profiles, compact Rg values, and minimal electrostatic perturbation. The computationally validated Cas12j2 variant was incorporated into a custom expression vector, co-expressing the engineered construct along with a dual gRNA for packaging into a viral vector for targeted knockout of HPV-associated cancers. This study provides a structural and computational foundation for the rational design of Cas12j2 fusion constructs with enhanced stability and functionality, supporting their potential application for precise genome editing in mammalian cells. Full article

Feline calicivirus (FCV) is a highly variable RNA virus that infects domestic cats and circulates endemically within feline populations, causing a wide spectrum of clinical manifestations, from asymptomatic infections to severe disease. Genomic analysis of 69 FCV strains revealed a high prevalence of the virus across multiple provinces in China. In vitro infection of CRFK cells with laboratory isolates FCV-BJ616 and FCV-BJDX40 resulted in significant cytotoxic effects. Serum proteomic analysis identified 221 upregulated and 123 downregulated proteins following infection with FCV-BJ616, and 233 upregulated and 165 downregulated proteins following infection with FCV-BJDX40. Among these, 215 proteins exhibited shared differential expression. Functional analyses revealed enriched pathways, including TNF signaling and ferroptosis. Notably, upregulation of Acyl-CoA Synthetase Long-Chain Family Member 4 (ACSL4) was correlated with lung injury, while downregulation of S100 Calcium Binding Protein A2 (S100A2) was associated with poor prognosis in FCV-associated oral disease. The differential expression of ACSL4 and S100A2 was further validated through Western blot analysis. These results suggest that ACSL4 and S100A2 are promising candidate biomarkers for monitoring FCV infection and disease progression, laying a foundation for future diagnostic and prognostic applications. Full article

The presence of an extra DNA segment in a genome could indicate a transposon or another repetitive element on the move. In Neurospora crassa, a surveillance mechanism called meiotic silencing by unpaired DNA (MSUD) is maintained to monitor these selfish elements. MSUD utilizes common RNA interference (RNAi) factors, including the SMS-2 Argonaute, to target mRNAs from genes lacking a pairing partner during meiosis. In eukaryotes, an mRNA transcript is typically bound at the 5′ cap by the cap-binding complex (CBC), which assists in its nuclear export. Previously, we discovered that CBC and its interactor NCBP3 mediate MSUD, possibly by guiding the perinuclear SMS-2 to effectively recognize exported mRNAs. Here, we report that ARS2, a CBC cofactor, is involved in MSUD. ARS2 interacts with both CBC and NCBP3, and it may help bring them together. In addition to its role in silencing, ARS2 also contributes to vegetative growth and sexual sporulation. Full article

Cells are continuously exposed to physiological and environmental stressors that disrupt homeostasis, triggering adaptive mechanisms such as the integrated stress response (ISR). A central feature of ISR is the selective translation of activating transcription factor 4 (ATF4), which orchestrates gene programs essential for metabolic adaptation and survival. Stress-induced acute ATF4 expression occurs in diverse mammalian cell types and is typically protective; however, chronic activation contributes to pathologies including cancer and neurodegeneration. Canonical ISR (c-ISR) is initiated by phosphorylation of eIF2α in response to stressors such as endoplasmic reticulum or mitochondrial dysfunction, hypoxia, nutrient deprivation, and infections. This modification suppresses global protein synthesis while promoting ATF4 translation through upstream open reading frames (uORFs) in its 5′UTR. Recently, an alternative pathway, split ISR (s-ISR), enabling ATF4 translation independently of eIF2α phosphorylation, was identified in mice, suggesting ISR adaptability, though its relevance in humans remains unclear. Under normal conditions, cap-dependent translation predominates, mediated by the eIF4F complex and requiring the activity of eIF2B at its initial steps. During translational stress, eIF2α phosphorylation inhibits eIF2B activity, resulting in the formation of stalled initiation complexes, which can aggregate into stress granules (SGs). SGs sequester mRNAs and translation initiation factors, further repressing global translation, while ATF4 mRNA largely escapes sequestration, enabling selective translation. This partitioning highlights a finely tuned regulatory mechanism balancing ATF4 expression during stress. Recent advances reveal that, beyond cis-regulatory uORFs, trans-acting factors such as translation initiation factors and associated RNA-binding proteins critically influence ATF4 translation. Understanding these mechanisms provides insight into ISR plasticity and its implications for development, aging, and disease. Full article

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article

The application of nanotechnology in medicine has garnered significant interest, particularly in the development of advanced drug delivery systems. Graphene oxide (GO) shows promise as a carrier for delivering microRNA (miRNA) mimics or antisense constructs. miRNAs play a crucial role in regulating gene expression, and their dysregulation is associated with various diseases, including cancer. This study aimed to evaluate the impact of graphene oxide on cellular signaling pathways and its potential as a platform for gene delivery by developing a GO–antisense miRNA-21 nanosystem in HepG2 liver cancer cells. A colloidal dispersion of GO was used to prepare GO-antisense miRNA-21 nanosystems via self-assembly. The nanosystem was characterized in terms of ultrastructure, size distribution, surface composition and binding by TEM, DLS, ATR-FTIR and UV-Vis spectra. Zeta potential measurements were conducted to evaluate nanosystem stability by assessing the release kinetics of antisense miRNA-21. The efficiency of the GO nanosystem in delivering antisense miRNA-21 into HepG2 cells was analyzed using confocal microscopy and flow cytometry. Given the central role of miRNA-21 in inflammatory and oncogenic pathways, we first assessed its expression following GO exposure. In line with previous studies reporting high miRNA-21 expression in hepatocellular carcinoma cells, GO treatment further increased miRNA-21 levels in HepG2 cells compared with untreated controls. Changes in the expression levels of IL-8, MCP-1, ICAM-1, TIMP-2, and NF-kB were quantified by qPCR analysis. The ultrastructural analysis confirmed a strong affinity between GO and antisense miRNA-21. Transfection results demonstrate that the GO-based nanosystem effectively delivered antisense miRNA-21 into HepG2 cells, leading to a reduction in the expression of key pro-inflammatory genes. These findings suggest that GO-based nanocarriers may offer a promising strategy for delivering localized intratumoral miRNA-based therapies that target gene regulation in hepatocellular carcinoma. Full article

Extracellular vesicles (EVs) are emerging as key factors in maintaining cellular homeostasis, critical mediators of intercellular communication, potential biomarkers, and therapeutic tools. While small EVs have been extensively characterized, the molecular signatures of large EVs (including those generated during regulated cell death pathways) remain poorly defined. Here, we investigated the characteristics of large EVs released during apoptosis and pyroptosis by human monocytic cell lines (THP-1 and U937). Apoptosis was induced by staurosporine and blocked using the pan-caspase inhibitor Q-VD-OPh, whereas pyroptosis was triggered by LPS/nigericin and inhibited with a selective NLRP3 inhibitor. We found that both forms of regulated cell death markedly enhanced the release of large EVs. Both apoptotic and pyroptotic large EVs showed increased Annexin V binding and decreased CD9 expression compared with those released by healthy cells. Large EVs derived from apoptotic and pyroptotic cells exhibited distinct proteomic profiles. Pyroptotic large EVs carried interacting protein networks of RNA-binding proteins and chromatin-associated proteins many of which are known damage-associated molecular patterns or alarmins. In contrast, we found that a subpopulation of apoptotic large EVs was characterized by the presence of dsDNA, and active caspase-3/7. Together, our data shed light on the specific protein cargo of large EVs released by cells during apoptosis and pyroptosis. This study identifies candidate markers of large EVs released by dying cells and may enhance our understanding of the role of EVs in regulated cell death. Full article

Norovirus is associated with vomiting and diarrhea and, in severe cases, can result in death. Currently, there is no effective treatment or vaccine for this virus. Bilateral interactions have been reported between gut microbiota and viral infection. Our laboratory has been studying the Surface layer protein A (SlpA) of a human isolate of Lactobacillus acidophilus. Previously, we reported that SlpA induces a variety of antiviral genes in human dendritic cells, suggesting it may prevent viral replication. SlpA binds to its cognate receptor SIGNR3-expressed on limited dendritic cells. To achieve a homogenous expression of the gene, we modified murine macrophage RAW 264.7 (RAW) cells by transducing SIGNR3-expressing lentivirus, resulting in RAWS cells. These cells and wild-type RAW cells were pretreated with SlpA for one hour and infected with 1 MOI of murine norovirus (MNV). We report that RAWS cells, when treated with SlpA, enhance the antiviral program to prevent viral replication, as determined by quantitative real-time PCR and viral titer. RNA isolated from MNV-infected cells revealed an elevation in two critical antiviral genes, Iigp1 and Ifit1, in SlpA-treated RAWS cells, potentially preventing viral replication. Full article

Myopathy, Lactic Acidosis, and Sideroblastic Anemia type 2 (MLASA2) is a rare mitochondrial disorder caused by pathogenic variants (PVs) in the YARS2 gene (which encodes the Mt-TyrRS protein. We performed a comprehensive clinical–molecular synthesis by integrating a systematic review and meta-analysis of all published MLASA2 cases with survival modeling and three-dimensional structural mapping. Across the aggregated cohort, anemia (88.6%), sideroblastic phenotype (85.7%), and lactic acidosis (82.9%) were the most prevalent phenotypes. Fifteen PVs were identified, dominated by p.(Phe52Leu) (29.4%). Survival estimates were 94.1% at 10 years, 70.7% at 30 years, and 42.4% at 50 years; cardiomyopathy and diagnosis before age 10 were associated with decreased survival. We generated the first 3D structural map of all reported Mt-TyrRS PVs, identifying nine spatial hotspots across catalytic, anticodon-binding, and tRNA-binding domains. An integrated framework combining structural density, clinical severity, in silico predictions, and ΔΔG destabilization classified three clusters as High-risk, three as Medium-risk, and three as Low-risk. Among them, cluster 3, a large catalytic hotspot encompassing 44 residues and including nearly half of all MLASA2 cases, showed the strongest pathogenic convergence. This clinical–structural integration provides new insights for a better comprehension of MLASA2, enhancing variant interpretation and improving diagnostic and prognostic precision. Full article

The origin of life embodies two fundamental questions: how and when did life begin? It is commonly conjectured that life began on Earth around 4 billion years ago. This requires that the complex organization of RNA, DNA, triplet codon, protein, and lipid membrane (RDTPM) architecture was easy to establish between the time the Earth cooled enough for liquid water and the time when early microorganisms appeared. These bracketing events create a narrow window of time to construct a completely operational self-replicating organic system of very high complexity. Another conjecture is that life did not begin on Earth but was seeded from life-bearing space objects (e.g., asteroids, comets, space dust), commonly referred to as panspermia. The second conjecture implies that life formed somewhere else and was part of the solar nebula, originating from an earlier generation star where there was more time available for the development of life. In this paper, the goal is to provide a hypothetical perspective related to the timing for the origin of pre-biotic chemistry and life itself. Using a form of complexity growth, biological features spanning from the present day back to early life on Earth were examined for trends across time. Genome sizes, gene number, protein–protein binding sites, energy for cell construction, mass of individual cells, the rate of cell mass growth, and a molecular complexity measure all yield highly significant regressions of linearly increasing complexity when plotted over the last 4 Gyr (billion years). When extrapolated back in time, intersections with simple complexities associated with each variable yield a mean value of 8.6 Gyr before the present time. This era coincides with the peak of star and planet formation in the universe. This speculative analysis is consistent with the second conjecture for the origin of life. The major assumptions of such an analysis are presented and discussed. Full article

Cannabinoids can bind to several cannabinoid receptors and modulate cellular signaling and gene expression relevant to inflammation and lipid homeostasis. Likewise, several vitamin E analogs can modulate inflammatory signaling and foam cell formation in macrophages by antioxidant and non-antioxidant mechanisms. We analyzed the regulatory effects on the expression of genes involved in cellular lipid homeostasis (e.g., CD36/FAT cluster of differentiation/fatty acid transporter and scavenger receptor SR-B1) and inflammation (e.g., inflammatory cytokines, TNFα, IL1β) by cannabinoids (cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC)) in human THP-1 macrophages with/without co-treatment with natural alpha-tocopherol (RRR-αT), natural RRR-αTA (αTAn), and synthetic racemic all-rac-αTA (αTAr). In general, αTAr inhibited both lipid accumulation and the inflammatory response (TNFα, IL6, IL1β) more efficiently compared to αTAn. Our results suggest that induction of CD36/FAT mRNA expression after treatment with THC can be prevented, albeit incompletely, by αTA (either αTAn or αTAr) or CBD. A similar response pattern was observed with genes involved in lipid efflux (ABCA1, less with SR-B1), suggesting an imbalance between uptake, metabolism, and efflux of lipids/αTA, increasing macrophage foam cell formation. THC increased reactive oxygen species (ROS), and co-treatment with αTAn or αTAr only partially prevented this. To study the mechanisms by which inflammatory and lipid-related genes are modulated, HEK293 cells overexpressing cannabinoid receptors (CB1 or TRPV-1) were transfected with luciferase reporter plasmids containing the human CD36 promoter or response elements for transcription factors involved in its regulation (e.g., LXR and NFκB). In cells overexpressing CB1, we observed activation of NFκB by THC that was inhibited by αTAr. Full article