Search Results (297)

Spinocerebellar Ataxia type 2 (SCA2) and Amyotrophic Lateral Sclerosis type 13 (ALS13) are triggered by polyglutamine expansion in Ataxin-2 (ATXN2). To understand these neurodegenerative disorders at the molecular level, the brains of 10-month-old Atxn2-CAG100-knockin mice were analyzed as microglial, astroglial and neuronal fractions via global RNA sequencing. Data were validated by comparison with the spinal cord oligonucleotide microarray profile or filtered by RNA-seq consistency. Here, we show that the mutation causes a massive inflammatory response in microglia and a reciprocal loss of neuronal transcripts in glial fractions, suggesting severe synapse loss. Beyond these general neurodegenerative signs, we identify pathognomonic changes in the machinery for protein translation and RNA splicing. Glial fractions showed upregulation of Gpnmb (to 2082%), Cst7, Clec7a, Axl, Csf1, Lgals3, Lgals3bp, Slc11a1, and Usp18 as an unspecific neuroinflammatory signature, versus downregulation of axonal Nefh (to <19%), and synaptic Scn4b, Camk2b, Rab15, and Grin1 mRNAs correlating with circuit disconnection. In all fractions, reductions in Kif5a, Rph3a, and Cplx1 were noted versus disease-specific inductions of ribosomal subunits, presumably mirroring the partial loss-of-function of ATXN2 as RNA translation modulator. Selective accumulations of embryonic factors Rnu1b2 and Eef1a1 versus downregulation of adult Eef1a2 specify the mutation impact on splicing and translation elongation. As a potential underpinning of toxic gain-of-function, the proteostasis transcript Rnf213 appeared increased in astroglial and microglial fractions. These transcriptome data suggest altered ribosomal and spliceosome machinery, with massive microgliosis versus mild astrogliosis, at the core of SCA2 and ALS13. Full article

Chandipura virus (CHPV) is a neurotropic rhabdovirus associated with recurrent outbreaks of acute encephalitis in children and a high case fatality rate, particularly in India. Despite its public health relevance, the host molecular processes governing CHPV infection and disease progression remain poorly defined. To address this gap, we conducted a time-resolved transcriptomic analysis to characterize host responses to CHPV infection and to explore host-directed therapeutic opportunities. Human HEK293T cells were infected with CHPV, followed by RNA sequencing (RNA-seq) at 6, 12, 18, and 24 h post infection (hpi). Transcriptome profiling revealed a temporally ordered host response. At 6 hpi, CHPV infection was dominated by strong activation of innate immune and inflammatory pathways, including interferon-stimulated genes and cytokine signaling. Antiviral responses persisted at 12 hpi, accompanied by suppression of metabolic and translational processes, indicating a shift in host cellular priorities. By 18 hpi, metabolic reprogramming—particularly involving lipid and sphingolipid metabolism—was observed alongside altered immune signaling, consistent with viral exploitation of host cellular machinery. At 24 hpi, repression of genes involved in chromatin organization, RNA processing, spliceosome assembly, and ribosome biogenesis reflected a global transcriptional shutdown associated with cytopathic effects. Integration of temporal transcriptomic signatures enabled identification of host pathways amenable to pharmacological targeting. Selected host-directed compounds were evaluated in vitro and exhibited antiviral activity against CHPV in a neuronal cell line. Collectively, this study provides the first time-resolved transcriptomic landscape of CHPV infection in human cells and identifies host-targeted strategies relevant for antiviral development. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) arises predominantly from activating KRAS mutations, yet individual genetic variants differ markedly in signaling output and clinical impact. G12D, the most prevalent variant, strongly drives oncogenic programs, whereas G12R signals less efficiently through the AKT and ERK pathways and is associated with longer patient survival than G12D-driven PDAC. Methods: To elucidate how these differences influence early cellular transformation, we expressed a panel of KRAS mutants in non-cancerous pancreatic ductal epithelial cells as a model of early PDAC initiation and profiled transcriptional and phospho-proteomic responses. We next examined whether epigenetic differences translate into mutation-specific changes in nuclear organization using quantitative imaging of G12D- and G12R-expressing nuclei at 24 and 48 h. Results: Each variant established a unique regulatory program enriched for chromatin remodelers, histone modifiers, and nuclear structural factors, indicating that variant-specific KRAS signaling rapidly develops divergent epigenetic states. Integrated transcriptomic and phospho-proteomic analyses identified G12D and G12R as the most divergent variants. G12D induced pronounced nuclear remodeling, including increased nuclear size, irregular morphology, and reorganization of the nucleolus and spliceosome, consistent with extensive chromatin and transcriptional reprogramming. In contrast, G12R elicited a weaker response, with minimal or delayed structural changes. Conclusions: Together, these findings demonstrate that KRAS mutational context in pancreatic ductal epithelial cells shapes early transcriptional reprogramming that actively remodels nuclear architecture and nuclear sub-compartments. This work establishes nuclear structural remodeling as a structural state of KRAS-driven epigenetic dysregulation during PDAC initiation. Full article

In plants, the transition from heterotrophic to autotrophic growth is a critical developmental shift, tightly coupled to the establishment of photosynthesis. This process demands a precise interplay between the nucleus and chloroplasts, with communication schemes providing essential checkpoints to synchronize gene expression during seedling greening and establishment. While light response and photomorphogenesis are known to rely on transcriptional networks, recent evidence highlights a key role for alternative pre-mRNA splicing in facilitating plant adaptation to new light regimes, thereby enhancing transcriptome diversity. LEFKOTHEA, a dual-localized nuclear and chloroplast protein, has emerged as a potential integrator of these processes; it mediates the splicing of both chloroplast group II introns and nuclear introns via interactions with spliceosomal proteins. Here, we demonstrate that LEFKOTHEA is an active component of early light response signaling, regulating gene expression both transcriptionally and post-transcriptionally. Transcriptomic analysis reveals that LEFKOTHEA shapes the transcriptome both quantitatively and qualitatively by modulating alternative splicing, a mechanism essential for plant plasticity and adaptation. Furthermore, we show that the dynamic subcellular localization of LEFKOTHEA underpins its role in establishing a nucleus–chloroplast communication network that guides plant development. Full article

Multiple myeloma (MM) is characterised by the clonal expansion of plasma cells in the bone marrow followed by end-organ damage. Despite a significant increase in the five-year survival rate in recent years, MM is still considered an incurable disease as patients will repeatedly relapse and develop resistance to standard-of-care therapies. A central theme for the personalization of MM therapy is understanding the biological mechanisms of drug resistance and identifying clinically relevant biomarkers of therapeutic response. Highly effective protocols for the enrichment of phosphorylated peptides followed by high-resolution mass spectrometry makes possible the quantitation of thousands of site-specific phosphorylation events, principally on serine, threonine or tyrosine residues. In this study, phosphoproteomic analysis of 20 MM patient cell lysates was performed, stratified based on their ex vivo drug response profiles to Bortezomib and Lenalidomide, two of the most foundational therapeutic agents in the management of MM. In this study, patients who are highly sensitive to these drugs show increased phosphorylation of proteins concerned with translation and RNA processing including the spliceosome, RNA transport and RNA binding pathways, while highly resistant patients demonstrated an increased phosphorylation of proteins involved with tight junctions, the Rap1 signalling pathway and the phosphatidylinositol signalling system. This study has established a phosphoproteomic dataset displaying unique phosphorylation signatures associated with drug sensitivity in MM patient plasma cells. The identification of phosphorylation signatures associated with drug resistance provides the foundation for further exploration of these mechanisms and associated signalling pathways to further characterise drug resistance mechanisms in MM and identify promising biomarkers of therapeutic response and targets for drug re-sensitization in MM. Full article

Splicing defects represent a significant class of human genetic disorders, yet strategies to directly correct aberrant splice-site recognition remain limited. The small nuclear RNA (snRNA) U1 plays a critical role in pre-messenger RNA splicing by base-pairing with the conserved 5′ splice-site ‘GU’ dinucleotide. Disruption of this interaction can lead to abnormal splicing or frameshift mutations, contributing to disease pathology. Extracellular vesicles (EVs) can transport small molecules to cells for therapeutic applications. Here, U1 snRNA-overexpressing HEK293T cells were used to generate approximately 120 nm-diameter U1 snRNA-enriched EVs, whose purity and content were confirmed by exosomal marker Western blots and reverse transcription–quantitative PCR. When HeLa cells expressing a β-globin minigene bearing a β-thalassaemia-like 5′ splice-site mutation were treated with U1-snRNA-enriched EVs, they corrected up to sixty percent of normal exon–intron junction recognition in a dose-dependent manner. Recovery was abolished by heat or RNase treatment, suggesting that intact vesicular RNA cargo was essential for activity. These findings provide the first demonstration that EVs can transport spliceosomal snRNAs capable of reconstituting splice-site recognition in recipient cells and introduce a novel class of RNA-based therapeutics that exploit the natural cargo-shuttling capacity of EVs to correct splicing defects associated with genetic disease. Full article

Alternative splicing of pre-mRNA is a crucial mechanism in gene expression regulation. As a core component of the spliceosome, the biological function of the Skip protein in Aspergillus flavus remains unknown. Quantitative real-time PCR (qPCR) analysis revealed the presence of two skip gene copies in A. flavus. Single-copy deletion of Skip resulted in slowed growth, reduced conidiation, abolished sclerotial formation, increased aflatoxin biosynthesis, and diminished crop colonization. Meanwhile, Skip was found to regulate the oxidative stress response by modulating the alternative splicing of yapA. Subsequently, immunoprecipitation and Western blot analyses identified lysine 325 (K325) as the benzoylated site on the Skip protein, which catalyzed by the acyltransferase EsaA. Mutation of benzoylated site K325 directly impaired fungal morphogenesis, pathogenicity, and stress adaptation. These findings established the crucial role of Skip and its benzoylation in A. flavus and suggested a potential target for controlling its infection in important crops. Full article

Neuroinflammation plays a dual role in brain health supporting defense and repair, but causes neurotoxicity when persistent. Microglia and astrocytes coordinate these responses through cytokine signaling and extracellular vesicles (EVs), though their vesicle-mediated communication remains unclear. This study investigated whether EVs from activated microglia (ABEVs) influence astrocyte polarization and inflammatory signaling. BV-2 microglial cells were activated with lipopolysaccharide (LPS), and microvesicle (ABMVs) and exosome (ABEXs) EVs were isolated via sequential ultracentrifugation. Primary mouse astrocytes were treated with LPS, ABMVs, or ABEXs, and expression of reactive astrocyte markers (C3, Serpina3n, S100a10, Sphk1) and inflammatory mediators (Lcn2, Il-1β, Ccl2, Ccl5, Cxcl10) was quantified, and EV protein cargo was analyzed by mass spectrometry and proteomics. LPS-treated astrocytes exhibited increased C3 and Serpina3n and decreased S100a10, consistent with reactive polarization. ABEXs mimicked this effect, significantly inducing C3, Serpina3n, and Sphk1, whereas ABMVs had a weaker influence. ABEXs also upregulated Lcn2 and Il-1β, partially reproducing microglial inflammatory effects. Proteomic profiling revealed marked cargo differences: ABEXs exhibited 16 upregulated proteins linked to NOD-like receptor signaling compared to non-activated BEXs, and 165 proteins associated with ribosome biogenesis and spliceosome pathways compared to ABMVs, indicating subtype-specific signaling potential. Collectively, our findings demonstrate that microglia-derived EVs modulate astrocytic polarization and cytokine profiles in a cargo-dependent manner, emphasizing their importance in interglial communication and revealing novel targets for neuroinflammatory modulation. Full article

Prader–Willi (PWS) and Angelman (AS) syndromes were the first examples in humans with errors in genomic imprinting, usually from de novo 15q11-q13 deletions of different parent origin (paternal in PWS and maternal in AS). Dozens of genes and transcripts are found in the 15q11-q13 region, and may play a role in PWS, specifically paternally expressed SNURF-SNRPN and MAGEL2 genes, while AS is due to the maternally expressed UBE3A gene. These three causative genes, including their encoding proteins, were targeted. This review article summarizes and illustrates the current understanding and cause of both PWS and AS using strategies to include the literature sources of key words and searchable web-based programs with databases for integrated gene and protein interactions, biological processes, and molecular mechanisms available for the two imprinting disorders. The SNURF-SNRPN gene is key in developing complex spliceosomal snRNP assemblies required for mRNA processing, cellular events, splicing, and binding required for detailed protein production and variation, neurodevelopment, immunodeficiency, and cell migration. The MAGEL2 gene is involved with the regulation of retrograde transport and promotion of endosomal assembly, oxytocin and reproduction, as well as circadian rhythm, transcriptional activity control, and appetite. The UBE3A gene encodes a key enzyme for the ubiquitin protein degradation system, apoptosis, tumor suppression, cell adhesion, and targeting proteins for degradation, autophagy, signaling pathways, and circadian rhythm. PWS is characterized early with infantile hypotonia, a poor suck, and failure to thrive with hypogenitalism/hypogonadism. Later, growth and other hormone deficiencies, developmental delays, and behavioral problems are noted with hyperphagia and morbid obesity, if not externally controlled. AS is characterized by seizures, lack of speech, severe learning disabilities, inappropriate laughter, and ataxia. This review captures the clinical presentation, natural history, causes with genetics, mechanisms, and description of established laboratory testing for genetic confirmation of each disorder. Three separate searchable web-based programs and databases that included information from the updated literature and other sources were used to identify and examine integrated genetic findings with predicted gene and protein interactions, molecular mechanisms and functions, biological processes, pathways, and gene-disease associations for candidate or causative genes per disorder. The natural history, review of pathophysiology, clinical presentation, genetics, and genetic-phenotypic findings were described along with computational biology, molecular mechanisms, genetic testing approaches, and status for each disorder, management and treatment options, clinical trial experiences, and future strategies. Conclusions and limitations were discussed to improve understanding, clinical care, genetics, diagnostic protocols, therapeutic agents, and genetic counseling for those with these genomic imprinting disorders. Full article

Background: Retinitis pigmentosa (RP) encompasses a group of inherited retinal disorders characterized by progressive degeneration of rod and cone photoreceptors, leading to vision loss. Among RP subtypes, RP11 is linked to mutations in PRPF31, a key spliceosome component, resulting in retinal cell dysfunction. Although PRPF31 is ubiquitously expressed, its mutations predominantly impact retinal cells, leading to the progressive loss of photoreceptors. Despite significant progress, studies have focused on photoreceptor and retinal pigment epithelium dysfunction in late disease stages, leaving early molecular events and the involvement of other retinal cell types unresolved. Moreover, comprehensive single-cell analyses capturing dynamic transcriptional changes across all retinal populations at early and late differentiation stages are still lacking. Methods: Using patient-derived retinal organoids (ROs), this study investigates the impact of PRPF31-RP11 mutation through a series of morphological, functional, molecular, and transcriptomics analyses. Results:. Single-cell RNA sequencing revealed dynamic gene expression related to early Müller glia activation, retinal ganglion cell distress, and progressive photoreceptor degeneration. Findings identify dysregulated molecular pathways associated with phototransduction, oxidative stress, and inflammation. Conclusions: Our results support a specific RO model of RP11 in which PRPF31 mutation recapitulate in vitro key features of RP, while simultaneously eliciting compensatory or modulatory responses in other retinal cell types. Full article

Microinflammation serves as a central mechanism linking metabolic diseases and cancer. This study integrates gene expression profiles from irritable bowel syndrome (IBS), obesity, type 2 diabetes (T2D), colorectal cancer (CRC), renal cell carcinoma (RCC), and pancreatic cancer (PC) to identify shared molecular drivers of inflammation-mediated pathology. Weighted gene co-expression network analysis (WGCNA) revealed three highly preserved modules (blue, brown, turquoise) enriched in RNA processing, spliceosome assembly, ribosome biogenesis, and proteostasis regulation. Key hub genes, along with regulatory miRNAs have interconnected networks that modulate transcription, mRNA maturation, protein synthesis, and inflammatory signaling. Although classical inflammatory pathways were not directly enriched, their activity appears to be indirectly shaped by disruptions in RNA-processing and proteostasis machinery. Additionally, gut microbiota-derived products and altered metabolic states may further reinforce these transcriptional and post-transcriptional imbalances. Collectively, these findings reveal conserved molecular signatures that bridge microinflammation, metabolic disease, and oncogenesis, and highlight potential diagnostic and therapeutic targets centered on RNA regulation, proteostasis, and miRNA-mediated control Full article

Feline herpesvirus-1 (FHV-1) is taxonomically classified within the family Herpesviridae, subfamily Alphaherpesvirinae, genus Varicellovirus, and species Felid alphaherpesvirus 1. The genome of FHV-1 is 135,797 bp in length and encodes 74 proteins. Among these proteins, serine/threonine protein kinase (pK) and thymidine kinase (TK) have been identified as potential virulence factors in alphaherpesviruses, although these kinases are dispensable for viral replication. As kinases, regulating phosphorylation modification is one of their functions, while the mechanism by which phosphorylation modification affects cell physiological functions and thereby influences viral replication remains unclear. In this study, we generated pK- and TK-deficient FHV-1 mutants by CRISPR/Cas9-mediated homologous recombination. The pK-deficient virus produced significantly smaller plaques than the TK-deficient virus. The replication kinetics of the pK-deficient virus were attenuated in multistep growth compared to the TK-deficient virus. These results indicate that deletion of the pK gene markedly reduces the replicative capacity of FHV-1. We applied data-independent acquisition (DIA) quantitative proteomics to profile changes in global protein expression and phosphorylation in F81 cells upon infection with TK⁻, pK^−, and wild-type FHV-1 strain. The pK-deficient virus exhibited 3632 differentially phosphorylated proteins containing 11,936 modification sites; the TK-deficient virus showed 4529 differentially phosphorylated proteins with 19,225 phosphorylation sites. Functional characterization through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses identified significant involvement of phosphoproteins in spliceosome pathways in pK-deficient virus and ATP-dependent chromatin remodeling pathway in TK-deficient virus. Notably, several splicing regulators—including Ess-2 and CDK13, which modulate host spliceosomal function—displayed significantly reduced phosphorylation levels in pK-deficient viruses. A significant enrichment of ATP-dependent factors, such as SMARCA5 and RSF1, was observed in the TK-deficient virus. To our knowledge, this is the first investigation into the effects of FHV-1 infection on the host cell phosphoproteome. These data offer new insights into the phosphoregulatory circuits and signaling networks triggered by FHV-1 and may enhance our understanding of the FHV-1 replication mechanism. Full article

African swine fever virus (ASFV) causes a highly fatal disease in domestic pigs, resulting in substantial economic losses to the global swine industry. Vaccine development continues to be hindered by limited characterization of viral proteins and their functional redundancies. In this study, we employ combined experimental and computational approaches to characterize the ASFV I73R protein (pI73R), which contains a Z-DNA binding domain and plays a critical role in ASFV virulence and pathogenesis. We demonstrate that pI73R shares significant structural similarity with transcription factors of the forkhead box (FOX) protein family. Overexpression of pI73R results in downregulation of Crooked neck-like protein 1 (CRNKL1), a core spliceosome component, suggesting a potential mechanism by which pI73R modulates host protein synthesis. Using high-resolution mass spectrometry, we map the pI73R interactome and identify the host protein Guanine nucleotide-binding protein subunit beta-1 (GNB1) as a novel direct interactor of pI73R which may facilitate its nuclear transport. Furthermore, we show that pI73R exhibits consistent oligomerization and expression across different ASFV genotypes, highlighting its functional importance. Taken together, these results provide new insights into pI73R function, ASFV–host dynamics, and offer promising directions for antiviral strategy development. Full article

Small Cajal body-associated RNAs (scaRNAs) are essential for biochemical modification of spliceosomal RNAs and spliceosome function. Changes in scaRNA expression level have been associated with developmental issues, including cancer and congenital heart defects (CHDs), although the mechanism remains unclear. Small Cajal body-associated RNA 1 (scaRNA1) guides pseudouridylation at uridine 89 (Ψ89) of the spliceosomal RNA U2, a highly conserved modification that may be critical for spliceosome function. To investigate the role of scaRNA1 in splicing regulation, CRISPR-Cas9 genome editing was used to introduce targeted deletions in the scaRNA1 locus in HEK293T cells. Edited clones were identified by T7 endonuclease I assay and confirmed by Sanger sequencing. Pseudouridylation at Ψ89 was quantified using CMC-based reverse transcription followed by quantitative PCR, and global mRNA splicing alterations were assessed by RNA sequencing. Clones harboring scaRNA1 disruptions exhibited a significant reduction in Ψ89 pseudouridylation, consistent with impaired scaRNA1 function. Transcriptome analysis (of mRNA from two clones) revealed >300 protein coding genes with significant changes in transcript isoform level, including >100 genes related to RNA-binding activity. These results indicate that scaRNA1 disruption alters spliceosomal function and leads to substantial changes in mRNA splicing. The dysregulated splicing of RNA-binding proteins may impair RNA processing and gene expression programs required for normal development, providing new insight into how noncoding RNA dysfunction may contribute to developmental pathogenesis. Full article

Retinitis pigmentosa (RP) represents a genetically heterogeneous group of inherited retinal dystrophies characterized by progressive photoreceptor degeneration and irreversible vision loss. Among the diverse pathogenic mechanisms, dysregulation of alternative splicing has emerged as a pivotal driver, particularly in RP cases caused by mutations in splicing factors or cis-regulatory elements. Alternative splicing governs transcript diversity and fine-tunes gene expression, with more than 95% of human multi-exon genes undergoing this process. Disruption of precise splicing patterns in the retina—an organ with exceptionally high transcriptional complexity—leads to widespread mis-splicing of photoreceptor-specific genes, triggering retinal dysfunction and cell death. This review synthesizes current understanding of alternative splicing-related mechanisms in RP, integrating molecular insights from splicing-factor mutations, retina-specific splice isoforms, and their downstream cellular consequences. We also evaluate therapeutic strategies targeting splicing dysregulation, including antisense oligonucleotides (ASOs), modified U1 snRNA, spliceosome-mediated RNA trans-splicing (SMaRT), and genome editing, emphasizing translational potential and clinical challenges. Finally, we highlight key research gaps and propose future directions for splicing-centered precision medicine in RP. Full article