Search Results (368)

Genome-wide association studies (GWASs) have mapped many regions affecting cattle production, health and fertility, yet the lead variant is usually a marker for a linkage-disequilibrium block rather than the molecular lesion. This state-of-the-field review examines how those loci are interpreted at different levels. The literature shows both progress and persistent limits. Colocalization may identify a likely effector transcript without establishing mediation, whereas structural variants missing from SNP-based analyses can account for expression, splicing, or complex-trait signals. Earlier reviews have audited proposed causative variants across cattle and pigs, surveyed causal variants across livestock species, or concentrated on structural variation. Here, these lines of evidence are brought together around a narrower question: Why do cattle complex-trait loci remain resolved at such different biological depths? Coding, regulatory, splicing, and structural examples show where inference is persuasive and where alternatives remain. The evidence is organized as a conceptual landscape, not a validated hierarchy or prescriptive pipeline. The available mechanistic evidence is nevertheless concentrated in commercial taurine, particularly dairy populations, which limits the direct transferability of locus-level conclusions to indicine, African taurine, composite and locally adapted cattle. Priorities include clearer causal terminology, multi-signal and multi-breed analyses, better representation of structural variation, tissue- and cell-state-matched molecular data, native bovine experimental systems and transparent reporting of unresolved explanations. Full article

The microtubule-associated protein tau, encoded by the MAPT gene, serves as a major component of the neuronal cytoskeleton, facilitating the assembly, stabilization, and spatial organization of microtubules. Much of the work on tau has focused on the low-molecular-weight (LMW) isoforms abundantly expressed in the central nervous system (CNS) and their pathological aggregation in tauopathies. However, a different variant known as “Big tau”, present in the peripheral nervous system (PNS) and selective CNS regions has distinct structural and functional properties and offers a unique perspective on protein evolution. Big tau is characterized by the inclusion of a large, alternatively spliced insert termed exon 4a, which expands the protein’s projection domain by approximately 250 amino acids and increases the molecular weight to 90–110 kDa. The evolutionary trajectory of exon 4a presents a fascinating enigma that challenges conventional models of protein conservation. Across the vertebrate phylogeny, spanning from fishes, amphibians and birds to mammals, the primary amino acid sequence of exon 4a exhibits extreme divergence, often reaching background levels of identity when comparing distant classes. In contrast, the physical length of this domain remains remarkably stable, hovering around the 250-amino acid mark regardless of the species. This pattern suggests that the selective pressure acting on Big tau is not directed toward specific sequence motifs or functional domains, but rather toward the biophysical properties and physical dimensions of the domain. Here, we posit that exon 4a evolved as an essential molecular spacer optimized for the structural demands of long-projection neurons and high-caliber axons as well as a protective structure for the pathologic aggregation of tau. The paper examines the genomic architecture and biophysical identity underlying the stable-size and low sequence identity of exon 4a, presenting two evolutionary mechanisms as working hypotheses: a Prototype Model of neutral drift of an ancient insert, and an Independent Exonization of convergent recruitment of non-coding DNA by transposable elements or intron retention. Finally, we emphasize the need for additional experimental work in vitro and in vivo to resolve unanswered questions about the structure of the 4a exon, the physiological role Big tau and its potential insight into tauopathies therapeutics. Full article

Lung cancer is characterized by profound molecular and clinical heterogeneity and remains the leading cause of cancer-related mortality worldwide. Its initiation and progression are shaped by complex genetic and epigenetic alterations that perturb key biological processes, including cell proliferation, apoptosis, metabolic reprogramming, invasion, metastasis, and immune evasion. Increasing evidence indicates that dysregulated alternative splicing (AS) represents a critical post-transcriptional regulatory mechanism involved in lung cancer pathogenesis. Although AS abnormalities are not the sole drivers of tumorigenesis, they contribute to malignant transformation, tumor progression, therapeutic resistance, and phenotypic plasticity, providing opportunities for biomarker development and therapeutic targeting. This review summarizes the multifaceted roles of AS in lung cancer biology, highlighting its contributions to tumor evolution, metastatic dissemination, and treatment resistance. Furthermore, subtype-specific AS landscapes between major lung cancer subtypes are discussed to elucidate their distinct molecular mechanisms and therapeutic implications. Representative AS-generated isoforms, including cluster of differentiation 44 variants (CD44v), are further discussed as examples of how aberrant splicing events regulate cancer stemness, tumor progression, and therapeutic responses. The regulatory mechanisms underlying CD44v generation, including upstream splicing factors and downstream signaling pathways, are also summarized. Collectively, this review highlights the emerging role of aberrant AS regulation in lung cancer and emphasizes its potential implications for biomarker discovery and precision therapeutic strategies targeting splicing dysregulation. Full article

Geographic atrophy (GA) represents the advanced, non-neovascular (dry) form of age-related macular degeneration (AMD), a chronic, progressive, and currently irreversible neurodegenerative disease of the retina. The clinical consequences of GA are severe; it is characterized by the insidious, expanding loss of the retinal pigment epithelium (RPE), the overlying photoreceptors, and the underlying choriocapillaris. This state of complete RPE and outer retinal atrophy (cRORA) permanently destroys the neural architecture required for high-acuity central vision. For decades, the pathophysiological etiology of geographic atrophy was framed principally in terms of cumulative oxidative stress, lipid peroxidation, and cellular senescence. However, the foundational understanding of AMD pathophysiology changed substantially following the landmark genomic discoveries published in 2005. Multiple independent genome-wide association studies (GWAS) linked specific single-nucleotide polymorphisms in the CFH gene to a substantially increased risk of developing AMD. The CFH gene encodes Complement Factor H (FH) and its alternative splice variant, Factor H-like protein 1 (FHL-1), which are the primary soluble regulators of the alternative complement pathway. This genetic discovery established GA not merely as a disease of metabolic wear-and-tear, but fundamentally as an immunologic disorder driven by the chronic dysregulation of the innate immune system. With the rapid emergence and clinical validation of targeted gene-silencing technologies, particularly small interfering RNA (siRNA) and antisense oligonucleotides, there is substantial scientific and pharmaceutical interest in modulating the complement cascade at the post-transcriptional level. This narrative review examines the structural biology, spatial partitioning, and pathophysiological roles of the FHL-1/CFH axis in GA focusing on the possibilities of using siRNA as a new potential therapy for GA. Full article

The MAT1-1-1 and MAT1-2-1 proteins perform essential DNA-binding activities and regulation of the transcription of genes governing sexual reproduction in Ophiocordyceps sinensis. Previous studies have documented differential occurrence, alternative splicing, and transcriptional divergence of MAT1-1-1, MAT1-2-1, and pheromone receptor genes in Hirsutella sinensis (Genotype #1 among 17 genome-independent genotypes of O. sinensis fungi). In the present study, we analyzed the natural pairing patterns of structurally variant MAT1-1-1 and MAT1-2-1 proteins simultaneously produced by each of 20 purportedly homogenous O. sinensis strains, based on AlphaFold-predicted 3D structural models and pairwise structural superposition analyses. The differentially naturally paired mating proteins exhibited distinct heteromorphic stereostructures across strains. Specifically, the MATα_HMGbox domain of MAT1-1-1 and the HMG-box_ROX1-like domain of MAT1-2-1 displayed variable N- and/or C-terminal truncations, 1–4 amino acid substitutions at distinct sites, and concomitant alterations in hydrophobic properties and secondary/tertiary structural configurations. Thus, the differentially naturally paired but structurally divergent mating proteins support heterogeneous fungal origins within the analyzed O. sinensis strains and are inconsistent with a strictly self-fertilization reproductive model. Our findings suggest that O. sinensis adopts a self-sterile reproductive strategy, potentially involving heterothallic mating or hybrid reproduction during the lifecycle of the LEVEL-II protected Cordyceps sinensis insect–fungal complex endemic to the Qinghai-Tibet Plateau. Full article

Intense broodiness restricts egg production in Zhedong White Geese, with prolactin (PRL) being a key regulator. This study aimed to elucidate the role of PRL gene alternative splice variants in regulating broodiness in Zhedong White Geese. A total of 20 Zhedong White Geese at 400 days of age were selected and divided into two groups of 10 based on their physiological states: the laying period and the brooding period. Through bioinformatics and molecular biology approaches, PRL-L and PRL-S were identified and characterized. The results showed that PRL-S lacked a signal peptide and the first 57 amino acids at the N-terminus, leading to the disappearance of its first α-helix structure. Functional validation demonstrated that the recombinant PRL-S protein, prepared using a prokaryotic expression system, possessed physiological activity, including receptor binding and the activation of downstream signaling pathways. Furthermore, Real-time PCR and Western blot analyses revealed that the expression of both splice variants in the hypothalamic–pituitary–ovarian axis exhibited significant spatiotemporal specificity and was closely associated with reproductive states. This study revealed the molecular characteristics, in vitro functional activity, and expression patterns of PRL-S, providing new insights into the regulatory mechanisms of PRL. Full article

Background/Objectives: Glutamate-gated chloride channels (GluCls) are essential inhibitory neurotransmitter receptors in insects and key targets of several insecticides. In Spodoptera frugiperda (FAW), mutually exclusive alternative splicing (MEAS) of exon 3 in SfGluCl produces three splice variants (SfGluCl 3A, SfGluCl 3B and SfGluCl 3C), yet the cis-regulatory elements involved in this splicing event remain unknown. This study aimed to identify candidate cis-regulatory regions associated with exon 3 MEAS and characterize their effects on exon 3 selection in a Sf9 cell-based minigene system. Methods: Semi-quantitative RT-PCR was used to assess the expression levels of three splice variants of exon 3 in SfGluCl across developmental stages. Comparative sequence analysis, combined with intron-deletion and exon-exchange assays, were performed to identify candidate cis-regulatory regions. A total of 27 constructs (23 intron-deletion and 4 exon-exchange constructs) were generated and analyzed using a minigene splicing assay in Sf9 cells. Results: Three splice variants were consistently detected across all developmental stages. In the Sf9 cell-based minigene system, two candidate cis-regulatory regions affecting SfGluCl 3B inclusion were identified: a 20 bp intronic region spanning nucleotides +13 to +32 downstream of the 5′ splice junction in the intron between exons 3B and 3C, corresponding to the region deleted in ExonB-C (Exon 3B-exon 3C)-Intdel52, and an 11 bp region within exon 3B containing six nucleotide substitutions in Ex3B (Exchanged exon 3B)-SubA2. Deleting the ExonB-C-Intdel52 or modifying the Ex3B-SubA2 significantly increased the SfGluCl 3B inclusion. Conclusions: These candidate intronic and exonic regions can influence exon 3B inclusion in the Sf9 cell-based minigene system. Although their functional effects and in vivo relevance remain to be validated in further study, our findings still provide a basis for future studies of GluCl splice variant regulation, receptor biology, and insecticide response in insects. Full article

Background: Pathogenic variants in the PPP1R12A gene have been associated with a malformation syndrome involving the brain and the genitourinary systems (GUBS, MIM #618820). To date, neither hearing loss (HL) nor inner ear malformations have been reported in affected individuals, and these features are therefore not currently regarded as part of the PPP1R12A-related phenotype. Moreover, functional evidence supporting the pathogenicity of several reported variants remains limited. Methods: We investigated a 12.5-year-old patient presenting with profound bilateral sensorineural hearing loss associated with inner ear malformations, genitourinary and central nervous system abnormalities. The patient underwent comprehensive clinical, audiological and radiological assessments, followed by genetic testing via trio-based whole-exome sequencing (WES). The molecular consequences of the identified variant were evaluated through minigene splicing assay and RT–PCR analysis on RNA extracted from peripheral blood cells. Results: WES identified a novel heterozygous splicing variant (c.792+3A>C) in the PPP1R12A gene (NM_002480.3). Functional studies demonstrated that this variant causes complete skipping of exon 5, resulting in a frameshift and the introduction of a premature termination codon. RT–PCR analysis confirmed the presence of the alternatively spliced transcript lacking exon 5. In addition, an extensive review of the literature indicated that no clear genotype–phenotype correlation has yet been established for PPP1R12A-related disorders and, whereas the majority of previously reported patients share brain and genitourinary malformations our patient additionally presented with profound bilateral sensorineural HL and inner ear malformations. Conclusions: Our findings suggest that PPP1R12A-related disorders may exhibit a broader phenotypic variability than previously recognized and we further propose that HL and inner ear malformations may represent novel features associated with this clinical spectrum. Moreover, our study underscores the importance of functional studies for accurately defining the molecular consequences of novel variants and establishing appropriate clinical correlations. Full article

A bidirectional relationship has been observed between COVID-19 and respiratory disorders, where respiratory comorbidities increase severity, and COVID-19 induces respiratory sequelae. The underlying biological and genetic mechanisms remain unclear. While previous studies have identified overlapping genetic loci, few have systematically disentangled the genetic factors shared between these conditions versus those specific to COVID-19, particularly at a multi-omics level. We developed and applied a unified analytical framework to compare three COVID-19 phenotypes with eight respiratory disorders (including asthma, COPD, IPF, and pneumonia). Utilizing the cofdr method for shared genetic signal analysis and DDx/mtCOJO for differentiation, we integrated genome-wide association statistics with multi-omics data (transcriptome, splicing, and proteome). This approach allowed for the simultaneous identification of shared genetic signals (concordant or discordant) and disease-specific variants across expression (TWAS), alternative splicing (spTWAS), and protein abundance (PWAS). We delineated a comprehensive atlas of 214 differential and numerous shared loci across 24 pairwise comparisons. The shared genetic architecture was characterized by pleiotropic effects in genes such as ATP11A (exhibiting opposing effects in COVID-19 vs. IPF) and GSDMB (shared with COPD). Crucially, differentiation analysis revealed that severe COVID-19 is genetically distinct from other respiratory infections (e.g., pneumonia and influenza) through dysregulated Type I/III interferon signaling and specific defects in alveolar epithelial and macrophage function, as well as GM-CSF/surfactant metabolism pathways. These findings provide human genetic evidence consistent with the therapeutic rationale underlying GM-CSF modulators and interferon-lambda for COVID-19, both of which have entered clinical trials. Furthermore, multi-trait conditional analysis prioritized FYCO1 and HCN3 as potential COVID-19-specific risk genes. Splicing analysis underscored the critical role of alternative splicing in both shared and differential architectures, highlighting IFNAR2 isoform regulation as a key discriminator between COVID-19 and other respiratory traits. This study provides the first genome-wide, multi-omics map revealing the shared and differential genetic landscapes of COVID-19 and other respiratory phenotypes. By uncovering specific molecular mechanisms that distinguish COVID-19 pathology, specifically involving surfactant homeostasis and interferon pathways, our findings offer novel insights for targeted drug repurposing and precision risk stratification. Full article

FOXP3 is the master transcriptional regulator of regulatory T cells (Tregs) and is expressed in humans as two main alternatively spliced isoforms: full-length FOXP3 (FOXP3-FL) and the exon 2-deficient variant (FOXP3-Δ2). While the role of these isoforms has been mainly studied in CD4⁺ T cells, their distribution across peripheral blood leukocyte populations and their relationship with immune checkpoint expression remain incompletely defined. In this study, we used a multiparametric flow cytometry panel allowing isoform-specific detection of FOXP3-FL and FOXP3-Δ2, together with PD-1 and CTLA-4, to analyze peripheral blood samples from six healthy donors under basal conditions. Major leukocyte populations, including CD4⁺CD25⁺ and CD4⁺CD25⁻ T cells, CD8⁺ T cells, monocytes, and neutrophils, were evaluated. FOXP3-FL predominated in CD4⁺CD25⁺ T cells, whereas FOXP3-Δ2 was more frequently detected in CD8⁺ T cells, monocytes, and neutrophils. However, the absolute frequencies of these FOXP3-Δ2-positive populations were low, consistent with the overall low levels of FOXP3 expression observed in these cell types. In CD4⁺ T-cell subsets, PD-1 expression was generally higher than CTLA-4, regardless of FOXP3 isoform, and FOXP3-Δ2⁺ cells showed relatively higher PD-1 expression compared to FOXP3-FL⁺ cells. In contrast, checkpoint expression in non-CD4⁺ populations was limited. The observed FOXP3-FL⁺/FOXP3-Δ2⁺ ratios across immune cell populations were consistent with a predominant role of FOXP3-FL in maintaining immune tolerance under basal conditions; whether these patterns are preserved or altered in pathological settings warrants further investigation. These results provide a descriptive overview of FOXP3 isoform distribution and checkpoint expression across peripheral blood immune cell subsets in healthy individuals, which may serve as a reference for future studies in immune-mediated diseases. Full article

Basonuclin 2 (BNC2) is a highly conserved cysteine–histidine (C2H2)-type zinc-finger nuclear regulatory protein characterized by three pairs of zinc-finger domains, a putative nuclear localization signal, a serine-rich region, broad tissue distribution, and remarkable transcript diversity generated through alternative promoter usage, alternative splicing, and polyadenylation. Increasing evidence from human genetics, animal models, functional genomics, and transcriptomic studies indicates that BNC2 links nuclear regulatory mechanisms to tissue-specific developmental and disease phenotypes. In the nervous system, BNC2-positive neuronal populations and BNC2-derived circular RNAs have been implicated in energy-balance circuits and neuroinflammatory regulation. In the skeletal system, BNC2 contributes to osteochondral development, periosteal stem-cell activation, chromatin remodeling, fracture repair, and genetic susceptibility to adolescent idiopathic scoliosis. BNC2 variants have also been associated with congenital lower urinary tract obstruction, whereas its expression and regulatory landscape are closely related to germ-cell development, epithelial ovarian cancer susceptibility, pigmentation traits, fibrosis, and several tumor contexts. Mechanistically, BNC2-associated phenotypes appear to involve cysteine–histidine zinc-finger-mediated transcriptional regulation, non-coding enhancer activity, epigenetic alterations, RNA-processing-associated nuclear functions, and chromatin-remodeling-dependent control of cell proliferation, differentiation, and stromal activation. This review integrates current evidence on the molecular architecture and regulatory functions of BNC2, critically discusses its context-dependent roles across development and disease, and highlights unresolved questions regarding isoform-specific activity, cell-type-specific regulation, downstream target networks, and clinical translation. A clearer understanding of these mechanisms may support the future evaluation of BNC2 as a biomarker, genetic susceptibility locus, molecular stratification factor, and potential therapeutic regulatory node. Full article

Holotrichia parallela is a globally distributed soil-dwelling pest that poses a major threat to peanut cultivation in China. Neuropeptides, as critical signaling molecules, regulate multiple physiological and behavioral processes in insects and represent highly promising targets for pest management. To date, the functional characteristics of neuropeptides in H. parallela remain unreported. In this study, we isolated and cloned one NPF and one NPFR gene, respectively. Bioinformatics analysis revealed that alternative splicing of the NPF gene produces two transcript variants, NPFa (255 bp) and NPFb (369 bp). The NPFR gene spans a length of 1188 bp, encoding 395 amino acids that contain seven α-helical transmembrane domains, indicating that it belongs to the family A G protein-coupled receptor (GPCR) family. Spatiotemporal expression profiles demonstrated that NPF was most abundant in the adult brain, whereas NPFR was highly enriched in the brain and antennae. NPF expression peaked in second-to-third-instar larvae, while NPFR was highly expressed in eggs. Starvation stress significantly upregulated the expression of both genes. RNA interference (RNAi)-mediated silencing of NPF and NPFR significantly reduced food intake, female fecundity, and glycogen content in adults. These findings enhance our understanding of insect neuropeptides signaling networks and support the development of behavior-based pest control strategies. Full article

Primary sclerosing cholangitis (PSC) and ulcerative colitis (UC) exhibit a striking clinical comorbidity, with 60–80% of PSC patients concurrently harboring UC, yet the shared immunogenetic mechanisms remain poorly understood. Here, we constructed a multi-omics integrative framework to systematically dissect the cellular and molecular basis of this comorbidity. GWAS meta-analyses were performed for each disease, followed by tissue-level enrichment assessment using QTLEnrich, MAGMA, and gsMap spatial mapping. Single-cell transcriptomic atlases were constructed, and cell-type prioritization was conducted using four complementary methods. Core genes were identified through cross-validation of five algorithms, with subsequent genomic fine-mapping via FUMA and GCTA-COJO. Tissue-level analyses consistently identified the intestine and immune-related tissues as commonly affected. Multi-dimensional evidence integration prioritized natural killer (NK) cells as the core effector cell type for both diseases, supported principally by CELLECT (Cell-type Expression-specific Integration for Complex Traits) heritability enrichment and single-cell differential analysis. Convergence of five gene-level algorithms pinpointed STAT3 as the sole high-confidence comorbidity gene, broadly expressed across immune cell populations and exhibiting tissue-differential alternative splicing. Colocalization identified a high-risk variant (rs3736161) within the STAT3 locus, with conditional analysis revealing 35 additional independent signals. These findings identify the NK cell–STAT3 axis as a central immunogenetic hub connecting PSC and UC, offering potential therapeutic targets for comorbidity management. Full article

Chitin synthase (CHS) catalyzes the final polymerization step in chitin biosynthesis and is therefore central to cuticle formation in arthropods. In this study, a chitin synthase gene from the swimming crab Portunus trituberculatus (PtCHS) was identified and functionally characterized in relation to epidermal formation and molting. The open reading frame of PtCHS was 4731 bp and encoded a predicted protein of 1576 amino acids belonging to glycosyltransferase family 2. Domain prediction revealed multiple transmembrane helices, a conserved chitin-synthase catalytic region, a coiled-coil region, and the diagnostic EDR, QRRRW, and SWGTRE motifs. Phylogenetic analysis assigned PtCHS to the class A/CHS1 chitin synthase lineage, and two alternative splice variants, designated PtCHS1a and PtCHS1b were detected. PtCHS transcripts were broadly distributed across examined tissues, with comparatively high abundance in the Y-organ, midgut, ovary, and epidermis. During the molting cycle, epidermal PtCHS expression increased during premolt, reached its highest level in postmolt stages, and declined during intermolt. During embryonic development, PtCHS expression remained relatively stable until late embryogenesis and then increased sharply before hatching. RNA interference-mediated knockdown of PtCHS reduced the expression of key chitin-biosynthesis genes, decreased epidermal chitin content, prolonged the molting interval, and was associated with molting failure and increased mortality. Conversely, unilateral eyestalk ablation induced PtCHS and molting-related genes, increased epidermal chitin content, shortened the molting interval, and promoted histological features consistent with enhanced extracellular matrix deposition and epidermal biosynthesis. These findings indicate that PtCHS is indispensable for epidermal chitin deposition and successful molting in P. trituberculatus, and provide a molecular basis for understanding molting regulation in economically important portunid crabs. Full article

Physical inactivity contributes to type 2 diabetes (T2D), but the molecular links between exercise and metabolic improvement remain incompletely understood. We meta-analyzed genome-wide association studies of vigorous physical activity and T2D (combined n ≈ 1.95 million) and integrated eQTL/sQTL maps with single-cell and spatial transcriptomic datasets to connect genetic risk with tissues, cell types, and regulatory programs. Tissue and cell-type enrichment, colocalization, and network analyses were performed. Computational findings were further examined in male 10-week-old C57BL/6J mice with high-fat diet-induced diabetes. After 1 week of acclimatization, mice were randomly assigned to normal chow, high-fat diet, or high-fat diet plus exercise groups (n = 6 per group; high-fat diet with 60% of total energy from fat). The exercise intervention consisted of treadmill running (10 m/min for 50 min per day, 5 days per week, total 16 weeks), followed by metabolic phenotyping, skeletal muscle histology, bulk RNA sequencing, alternative splicing analysis, and RT-qPCR of Mau2 isoforms. Exercise- and T2D-associated variants showed joint enrichment in skeletal muscle and adipose eQTL/sQTL signals. Integrated single-cell analyses prioritized fibro-adipogenic progenitors and endothelial cells, and identified an extracellular matrix- and collagen-related module in fibro-adipogenic progenitors associated with both exercise and T2D. Mau2 emerged as a shared candidate gene with tissue-specific splicing signals. In diabetic mice, exercise improved glucose homeostasis and muscle fiber structure, and reduced Mau2 intron retention in skeletal muscle without changing total Mau2 expression. These findings support a multiscale framework linking exercise-responsive regulation to T2D-related tissue remodeling and splicing plasticity. Full article