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PubMed2025

A multi-modal transformer for cell type-agnostic regulatory predictions.

Sequence-based deep learning models have emerged as powerful tools for deciphering the cis-regulatory grammar of the human genome but cannot generalize to unobserved cellular contexts. Here, we present EpiBERT, a multi-modal transformer that learns generalizable representations of genomic sequence and cell type-specific chromatin accessibility through a masked accessibility-based pre-training objective. Following pre-training, EpiBERT can be fine-tuned for gene expression prediction, achieving accuracy comparable to the sequence-only Enformer model, while also being able to generalize to unobserved cell states. The learned representations are interpretable and useful for predicting chromatin accessibility quantitative trait loci (caQTLs), regulatory motifs, and enhancer-gene links. Our work represents a step toward improving the generalization of sequence-based deep neural networks in regulatory genomics.

Humans↗

PubMed2025

ScGOclust: leveraging gene ontology to find functionally analogous cell types between distant species.

MOTIVATION: Basic biological processes are shared across animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell-type gene expression between species reveals conserved and divergent cellular functions. However, as phylogenetic distance increases, gene-based comparisons become less informative. The gene ontology (GO) knowledgebase offers a solution by serving as the most comprehensive resource of gene functions across a vast diversity of species, providing a bridge for distant species comparisons. RESULTS: Here, we present scGOclust, a computational tool that constructs de novo cellular functional profiles using GO terms, facilitating systematic and robust comparisons within and across species. We applied scGOclust to analyse and compare the heart, gut, and kidney between mouse and fly, and whole-body data from Caenorhabditis elegans and Hydra vulgaris. We show that scGOclust effectively recapitulates the function spectrum of different cell types, characterizes functional similarities between homologous cell types, and reveals functional convergence between unrelated cell types. Additionally, we identified subpopulations within the fly crop that show circadian rhythm-regulated secretory properties and hypothesize an analogy between fly principal cells from different segments and distinct mouse kidney tubules. We envision scGOclust as an effective tool for uncovering functionally analogous cell types or organs across distant species, offering fresh perspectives on evolutionary and functional biology. AVAILABILITY AND IMPLEMENTATION: ScGOclust is publicly available on CRAN: https://cran.r-project.org/web/packages/scGOclust/index.html and development versions are available on GitHub: github.com/Papatheodorou-Group/scGOclust/.

Animals↗

PubMed2026

Multiplex FAD2/FATB Editing Generates Ultra-High-Oleic, Low-Saturate Soybean With Increased Seed Fatty Acid Content.

Oleic acid (18:1), saturated fatty acid (SFA), and polyunsaturated fatty acid (PUFA) levels are important traits for storage stability and edibility. In this study, we aimed to develop high-oleic soybean (Glycine max) by simultaneously targeting fatty acid desaturase 2 (FAD2) and fatty acyl-ACP thioesterase B (FATB) gene families using CRISPR/Cas9. Considering the paleopolyploid genome of soybean, multiple sgRNAs were designed to target GmFAD2-1, GmFAD2-2, and GmFATB genes expressed during seed development. Compared with targeting GmFAD2-1 alone (~83%), additional editing of GmFAD2-2B, GmFAD2-2C, and GmFATB1a increased the 18:1 fatty acid content to over 90%. Editing of GmFATB significantly reduced the SFA content by more than 40% compared with wild-type (WT). Reduced absolute SFA content was also observed in GmFAD2-only edited lines with decreased GmFATB expression. Notably, all evaluated high-oleic genotypes in the Williams82-background showed higher mean total fatty acid (TFA) content than the WT, both per unit seed mass and per seed. Correlation analysis of 805 individual seed profiles from Williams82-background lines further characterized the relationship between 18:1 fatty acid composition and TFA content per unit seed mass. Gene expression analysis revealed no consistent increase in triacylglycerol (TAG) synthesis genes, whereas the expression of sugar-dependent 1 (SDP1) was reduced. In contrast, genes involved in phosphatidic acid (PA) metabolism, including diacylglycerol kinase (DGK) and phospholipase D (PLD), were partially upregulated. These transcriptional changes support a hypothesis that altered lipid turnover may contribute to the higher TFA phenotype. Collectively, this study defines effective multiplex target combinations for ultra-high oleic, low-saturated soybean.

FAD2↗

PubMed2018

Convergent evolution of gene expression in two high-toothed stickleback populations.

Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus). Are convergently evolved cis and/or trans changes in gene expression associated with convergently evolved morphological evolution? Do cis or trans regulatory changes contribute more to gene expression changes accompanying an evolved morphological gain trait? Transcriptome data from dental tissue of ancestral low-toothed and two independently derived high-toothed stickleback populations revealed significantly shared gene expression changes that have convergently evolved in the two high-toothed populations. Comparing cis and trans regulatory changes using phased gene expression data from F1 hybrids, we found that trans regulatory changes were predominant and more likely to be shared among both high-toothed populations. In contrast, while cis regulatory changes have evolved in both high-toothed populations, overall these changes were distinct and not shared among high-toothed populations. Together these data suggest that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar trans regulatory environments.

Alleles↗

PubMed2026

Chitosan-dsRNA improves tissue stability and delivery for RNAi-mediated Varroa destructor control.

BACKGROUND: Varroa destructor is an ectoparasitic mite and a major threat to honey-bee colony health worldwide. RNA interference (RNAi) offers a potentially species-specific approach for mite control, but practical application is limited by double-stranded RNA (dsRNA) degradation and inefficient delivery to mites. This study evaluated coatomer protein I (COPI) complex subunits as RNAi targets and tested whether chitosan-based dsRNA formulation could improve dsRNA stability, tissue uptake, and delivery from honey-bees to mites. RESULTS: Direct microinjection of dsRNAs targeting COPB, COPD, and COPE significantly reduced target-gene expression and mite survival compared with the double-stranded green fluorescent protein (dsGFP) control, with 72-h survival rates of 8.0%, 12.7%, and 5.3%, respectively, compared with 40.7% in the control group (all log-rank P < 0.0001). Chitosan-conjugated dsRNA remained detectable for longer periods than naked dsRNA in honey-bee tissue fluids, and CNP-Cy3-dsGFP was detected in the honey-bee midgut and fat body. A qualitative fluorescence observation in V. destructor was consistent with host-to-mite dsRNA transfer. Ingestion of COP-targeted chitosan-dsRNAs reduced mite survival, whereas honey-bee survival and expression of honey-bee COP orthologs were not affected. In silico analysis detected no contiguous ≥19-nt matches between Varroa COP dsRNAs and the honey-bee transcriptome or genome. CONCLUSION: COPI subunits are promising RNAi targets in V. destructor, and chitosan formulation may improve dsRNA persistence and uptake while supporting honey-bee-mediated delivery to mites. These laboratory findings support further evaluation of chitosan-formulated dsRNA as a potentially species-selective strategy for Varroa management, while broader safety assessment and field validation remain necessary. © 2026 Society of Chemical Industry.

COPI complex↗

PubMed2026

Sea urchin co-culture boosts abalone growth by reducing environmental stress and remodeling gut microbiota.

Biofouling and microenvironmental deterioration are major bottlenecks restricting the intensive aquaculture of Pacific abalone (Haliotis discus hannai). While co-culturing offers an eco-friendly mitigation strategy, the underlying mechanisms promoting abalone growth remain poorly understood. This study evaluated the growth performance of H. d. hannai co-cultured with varying densities of the sea urchin (Strongylocentrotus intermedius). By employing transcriptome and 16S rRNA sequencing of the abalone gut, we investigated the synergistic responses of host gene expression and gut microbiota. Compared with the monoculture group, the co-culture groups showed significantly less biofouling and greater growth of abalone, with the co-culture (n = 15) exhibiting the best outcomes. Transcriptomic analysis revealed 1444, 760, and 508 DEGs in G5, G10, and G15, respectively, compared with G0. These DEGs were significantly enriched in metabolic pathways, including glycolysis and sterol metabolism, indicating a shift in intestinal energy metabolism from stress defense toward growth under co-culture conditions. Gut microbiota profiling identified Proteobacteria and Firmicutes as the dominant phyla, with specific functional taxa (e.g., Psychrilyobacter and Akkermansia) enriched in a density-dependent manner. Furthermore, correlation analysis demonstrated that growth traits positively correlated with growth-promoting taxa (e.g., the unclassified AB1 lineage), but negatively correlated with potentially opportunistic taxa (e.g., Tabrizicola). These findings provide insights into a potential synergistic mechanism of "environmental stress alleviation-metabolic reprogramming-microecological remodeling" driving abalone growth, providing a theoretical foundation for optimizing co-culture systems and developing growth-associated biomarkers.

Animals↗

PubMed2026

Liver transcriptome analysis revealed multiple immune processes and lipid metabolism pathways involved in the defense response of the turbot (Scophthalmus maximus) against Aeromonas salmonicida.

Aeromonas salmonicida is a significant pathogen causing notable economic losses in Scophthalmus maximus aquaculture. This study utilized Illumina sequencing technology to examine the transcriptional response characteristics of S. maximus liver at 24 h following A. salmonicida infection. A total of 2363 differentially expressed genes (DEGs) were identified when compared to the negative control group. The immunity-related Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, as well as metabolism-related PPAR signaling pathway and insulin signaling pathway, were notably enriched. Significant differences exist in the expression of key genes within the PPAR pathway, particularly cd36, acsl4a, pparαa, and plin2, all of which mediate the interaction between lipid metabolism and the immune response. These results offer valuable insights into the immunometabolic regulatory mechanism of S. maximus response to A. salmonicida infection.

Animals↗

PubMed2025

Cholesterol Metabolism-related Characteristics Predict Therapeutic Response and Survival in Esophageal Cancer.

INTRODUCTION: Cholesterol homeostasis has been identified as an essential downstream pathway of mutations in TP53. Esophageal cancer is one of the most prevalent malignancies exhibiting the mutation. OBJECTIVES: To explore the significance of cholesterol metabolism-related characteristics in tumor phenotype and treatment outcomes of esophageal cancer. METHODS: We established a cholesterol metabolism-related gene set (CMGs) and performed Lasso-Cox analysis to identify prognostic signatures. Nomogram-based risk scores and clinical stages afterwards were constructed and evaluated. We simultaneously identified two metabolic subtypes based on the distinct features of the CMGs. We annotated the functional and pathway characteristics of differentially expressed genes between the clusters and compared the differences in clinical and immune characteristics. Finally, we assessed the prognostic value of signatures in the GSE53625 and two clinical cohorts using whole-exon sequencing and multiplex immunofluorescence. RESULTS: Our study identified five cholesterol prognosis-related genes (CRGs) that demonstrated superior prognostic efficacy in the training set compared to clinical staging, validated in independent public databases and two clinical cohorts. According to the different expression patterns of the signatures, patients were divided into two subtypes. The C1 group demonstrated poorer overall survival, response to immunotherapy, and downregulation of the p53 pathway. In the immune correlation analysis, we found that the risk score based on 5-signature model was significantly positively correlated with the abundance of suppressive immune cells and the immune checkpoints. Finally, we explored the impact of expression and genomic polymorphism of the signatures on the prognosis at the pan-cancer level. CONCLUSIONS: Our findings underscore the distinct expression patterns of CRGs in esophageal cancer. These signatures are efficient to serve as prognostic indicators and assess the effectiveness of immunotherapy. They may also represent promising targets in other TP53 mutant malignancies.

Humans↗

PubMed2026

Investigation of pmrCAB and mcr associated resistance in colistin-resistant A. baumannii isolates.

BACKGROUND & OBJECTIVES: Colistin is one of the last-resort antibiotics for multidrug-resistant Acinetobacter baumannii. Increasing resistance to colistin limits treatment options, particularly in intensive care units (ICUs). The aim of this study was to compare the expression levels of pmrC, pmrA, and pmrB, among colistin-resistant and colistin-susceptible clinical A. baumannii isolates, to investigate the presence of plasmid-mediated mcr-1-5 genes, and to determine clonal relationships among colistin-resistant isolates. METHODS: A total of 110 A. baumannii isolates recovered from ICU patients in 2020 were included. Colistin minimum inhibitory concentrations were determined using the broth microdilution method. Expression levels of pmrC, pmrA, and pmrB were analyzed by RT-qPCR and compared with the reference strain A. baumannii ATCC 19606. Colistin-resistant isolates (Group 1) were compared with 10 randomly selected colistin-susceptible isolates (Group 2). Detection of mcr-1-5 genes was performed by in-house multiplex PCR. Clonal relationships among resistant isolates were assessed by PFGE. RESULTS: Colistin resistance was detected in 15.45% (17/110) of isolates. The median relative expression levels of pmrC, pmrB, and pmrA in colistin-resistant isolates were 47.84-fold (IQR: 19.29-67.18), 14.72-fold (IQR: 10.13-16.68), and 8.57-fold (IQR: 5.17-12.82), respectively. In colistin-susceptible isolates, the corresponding median expression levels were 5.32-fold (IQR: 3.60-7.97), 3.29-fold (IQR: 0.85-5.95), and 3.31-fold (IQR: 2.58-6.55). Expression levels were significantly higher in colistin-resistant isolates for pmrC (p < 0.001), pmrB (p = 0.002), and pmrA (p = 0.024). None of the resistant isolates carried mcr-1-5 genes. PFGE analysis revealed 12 distinct genotypes among 17 resistant isolates. INTERPRETATION & CONCLUSIONS: Colistin-resistant A. baumannii isolates exhibited significantly higher expression levels of the pmrC, pmrA, and pmrB genes compared to colistin-susceptible isolates. Among the genes evaluated, pmrC showed the largest effect size and the strongest association with the colistin-resistant phenotype. No changes were found in the mcr-1-5 genes among the isolates studied. Further studies, including genomic and functional analyses, are needed to elucidate the underlying mechanisms of these expression changes and their contribution to colistin resistance.

Journal Article↗

PubMed2017

Systemic and Persistent Muscle Gene Expression in Rhesus Monkeys with a Liver De-Targeted Adeno-Associated Virus Vector.

The liver is a major off-target organ in gene therapy approaches for cardiac and musculoskeletal disorders. Intravenous administration of most of the naturally occurring adeno-associated virus (AAV) strains invariably results in vector genome sequestration within the liver. In the current study, we compared the muscle tropism and transduction efficiency of a liver de-targeted AAV variant to AAV9 following systemic administration in newborn rhesus monkeys. In vivo bioluminescence imaging was performed to monitor transgene expression (firefly luciferase) post administration. Results indicated comparable and sustained levels of systemic firefly luciferase gene expression in skeletal muscle over a period of two years. Quantitation of vector biodistribution in harvested tissues post-administration revealed widespread recovery of vector genomes delivered by AAV9 but markedly decreased levels in major systemic organs from the AAV variant. These studies validate the translational potential and safety of liver de-targeted AAV strains for gene therapy of muscle-related diseases.

Animals↗

PubMed2026

Evaluation of the subtype-specific epigenetic prognostic association of HELLS in non-small cell lung cancer: integrated clinical and molecular insights.

BACKGROUND: Helicase, lymphoid-specific (HELLS) is an epigenetic chromatin remodeler implicated in several cancers, but its prognostic role in non-small cell lung cancer (NSCLC) subtypes remains unclear. We investigated the expression, prognostic significance, and subtype-specific associations of HELLS in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). METHODS: The Cancer Genome Atlas (TCGA) and independent Gene Expression Omnibus (GEO) datasets were analyzed. HELLS expression was compared between tumor and normal tissues, survival was evaluated separately in LUAD and LUSC, and gene set enrichment analysis (GSEA) was performed. Multivariable analyses were used to assess associations between HELLS and selected oncogenic and immune-related genes after adjustment for clinical variables. RESULTS: HELLS was significantly upregulated in both LUAD and LUSC compared with normal lung tissues (P<0.001). High HELLS expression was associated with shorter overall survival (OS) in LUAD (log-rank P=0.001) and in the TCGA-LUSC cohort (log-rank P=0.002); however, external validation in GSE42127 (LUSC, n=43) was not significant [log-rank P=0.12; hazard ratio (HR) =0.49, 95% confidence interval (CI): 0.20-1.22, P=0.13]. HELLS-high LUAD tumors showed enrichment trends enriched in proliferation-related pathways, whereas HELLS-low LUSC tumors were enriched in inflammatory and apoptotic pathways. HELLS expression remained associated with KRAS, BRAF, and CD274 in LUAD after adjustment for age, sex, and stage, while only limited associations were observed in LUSC. CONCLUSIONS: HELLS shows a subtype-dependent prognostic and molecular association in NSCLC, with the strongest and most reproducible signal in LUAD; however, its prognostic value is attenuated after multivariable adjustment and is not consistently reproduced across external cohorts.

Helicase, lymphoid-specific (HELLS)↗

PubMed2026

Comprehensive transcriptomic analysis of BjGL1-knockout Brassica juncea: novel insights into leaf trichome formation.

Brassica juncea is a common cruciferous crop, which can be used not only for oil extraction but also as condiments and medicinal materials. It is regarded by both traditional medicine and modern nutrition science as a food with combined dietary and health promoting value. Leaf trichomes are hair-like structures differentiated from epidermal cells and constitute an important barrier against biotic and abiotic stresses, playing a crucial role in enhancing plant resistance and thus possessing significant scientific relevance. In this study, the phenotype and gene editing site of BjA06.GL1 and BjB02.GL1 knockout mustard T1 generation plants were identified. Then, RNA sequencing was performed to compare the leaf transcriptome profiles between gene-edited lines and wild-type plants, with the aim of elucidating the molecular regulatory mechanisms by which BjGL1 controls leaf trichome development and associated biological processes in mustard. The sequencing data showed that, on average, 90.64% of the reads uniquely aligned to the Brassica juncea (Xuecai) reference genome. A total of 4,604 differentially expressed genes were identified in this study. Compared with the gene knockout mutant, 1,831 genes were significantly upregulated and 2,773 genes were downregulated in mustard leaves with trichomes. The differentially expressed genes were mainly enriched in pathways related to cytochrome P450 (CYP), transporters, environmental adaptation, and plant-pathogen interactions. These pathways are closely associated with secondary metabolite biosynthesis, transmembrane transport, and responses to abiotic stress and pathogen defense. qRT-PCR validation confirmed consistent expression trends of trichome regulatory genes screened from transcriptome data. This study provides an important theoretical basis for elucidating molecular mechanisms potentially contributing to trichome formation in mustard.

Mustard Plant↗

PubMed2026

Functional analysis of stem-loop structures within the SARS-CoV-2 5' untranslated region using a plasmid-based reporter system.

The 5' untranslated region (5'UTR) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains highly conserved stem-loop structures that regulate viral gene expression. This study investigated the functional contributions of selected 5'UTR stem-loop elements to reporter gene expression using a plasmid-based mammalian expression system. Five constructs were tested using a non-integrating plasmid: the wild-type (WT) 5'UTR fused to GFP under the CMV promoter, and four deletion variants (ΔB, ΔC, ΔD, and ΔE) corresponding to deletions of stem-loop 4 (SL4), SL4.5, SL5, and SL5a, respectively. Following transfection into HEK293 cells, GFP fluorescence was quantified using a fluorescence microplate reader, and relative GFP transcript abundance was assessed by RT-qPCR. Deletion of SL4 (ΔB) resulted in marked reduction in both fluorescence and relative transcript abundance compared to WT construct, indicating substantially reduced reporter gene expression. In contrast, deletion of SL4.5, SL5, or SL5a did not produce the pronounced reduction observed for ΔB, although descriptive RT-qPCR analysis indicated differences in relative transcript abundance among these variants. Statistical analysis of fluorescence data demonstrated significant differences among constructs (one-way ANOVA, p < 0.05). Because the reporter assay was based on plasmid expression, the observed differences likely reflect combined contributions from transcription, transcript abundance, RNA stability, and translation rather than translation alone. These findings demonstrate that the SL4 region contributes substantially to reporter gene expression in this experimental system, whereas the remaining stem-loop regions examined exert comparatively modest effects. This study provides additional insight into the functional organization of the SARS-CoV-2 5'UTR and establishes a framework for future investigations aimed at distinguished the transcriptional, post-transcriptional, and translational contributions of individual RNA structural elements.

5' Untranslated Regions↗

PubMed2026

Genome-wide identification and comparative analysis of Leucine-Rich Repeat Containing (LRRC) gene and their expression responses to Vibrio alginolyticus infection in the Manila clam (Ruditapes philippinarum).

Leucine-rich repeat (LRR) domains are important components of many pattern recognition receptors (PRRs). Previous studies have demonstrated that LRR domain-containing immune receptors, such as nucleotide-binding oligomerization domain-like receptors (NLRs) and Toll-like receptors (TLRs), play important roles in innate immunity in aquatic animals. In addition to these well-characterized LRR-containing receptors, also possesses a group of LRR-containing proteins. These proteins were collectively referred to as leucine-rich repeat-containing (LRRC) proteins in this study, and their genomic characteristics, evolutionary relationships, were systematically analyzed. In this study, a genome-wide identification and characterization of LRRC genes were performed in the Manila clam. A total of 97 unclassified LRR genes were identified and designated as RpLRRCs.. Expression profiling indicated that RpLRRCs are predominantly expressed in the labial palps, digestive gland, and gills, increasing from the blastula stage and peaking at the juvenile stage during development, based on the transcriptome results from V. alginolyticus, V. anguillarum and V. parahaemolyticus, some RpLRRCs were involved in the response to different Vibrio stress. The qPCR analysis following V. alginolyticus challenge demonstrated that different RpLRRC members exhibit diverse response patterns to Vibrio infection. These results suggest that RpLRRCs may play critical roles in immune regulation. The RpLRRC gene family exhibits diverse structural characteristics and regulatory mechanisms and likely plays important roles in the growth, development, and immune response of R. philippinarum.

Immune response↗

PubMed2026

Uncovering hub genes and key pathways responsive to drought stress in rice via meta-analysis of transcriptomic data.

Drought stress presents a formidable threat to global rice cultivation, triggering complex molecular responses that impact plant growth and productivity. To decipher the underlying gene expression dynamics, we performed a comprehensive meta-analysis of transcriptomic datasets derived from drought-tolerant rice genotypes. Via microarray data from three independent studies, we identified a set of consistently expressed differentially expressed genes (DEGs) under drought conditions. Integration of functional annotation tools, including GO and KEGG pathway enrichment, revealed key biological processes and signaling cascades involved in stress mitigation, such as ABA signaling, protein folding, and photosynthesis suppression. Protein-protein interaction (PPI) network construction, followed by hub gene identification via maximal clique centrality (MCC), highlighted pivotal regulators including LEA proteins, dehydrins, HSP70, and several transcription factors. Machine learning approaches further prioritize potential biomarkers, with Random Forest models achieving high classification accuracy and pinpointing key predictive genes. Chromosomal localization analysis provided spatial insights into the distribution of these hub genes, whose expression patterns were further compared against qRT-PCR data from previously published studies. This integrative approach identifies candidate genomic markers and mechanistic insights that may support future breeding strategies for drought-tolerant rice, pending experimental validation.

Cytoscape↗

PubMed1979

Gene expression in vitro of colicin El plasmid.

Among eighteen polypeptides synthesized in vitro from colicin El plasmid, one of the major products with a molecular weight of 59,000 was identified as colicin El by its immunological property, molecular size, and biological activity. In addition to this polypeptide, seven other polypeptides reacted with colicin El antiserum. Using EcoRI-cleaved colicin El DNA, a 56,000 dalton polypeptide of truncated colicin El was synthesized, but no polypeptide that reacted with colicin El antiserum was produced from SmaI-cleaved colicin El DNA. This fact indicates that the direction of transcription of colicin El structural gene is from SmaI site to EcoRI site in vitro. The immunity protein of a molecular weight of 14,300 and a component of relaxation proteins of a molecular weight of 64,000 were deduced by comparing the results of the gene expression in vitro of one-half (pAO100) and a quarter (pAO2) of colicin El plasmid. The directions of transcription-translation in the genes on the plasmid were discussed. The colicin El plasmid appears to have at least three transcriptional units.

Colicins↗

PubMed2025

Tensor decomposition of multi-dimensional splicing events across multiple tissues to identify splicing-mediated risk genes associated with complex traits.

Identifying risk genes associated with complex traits remains challenging. Integrating gene expression data with Genome-Wide Association Study (GWAS) through Transcriptome-Wide Association Study (TWAS) methods has discovered candidate risk genes for various complex traits. Splicing, which explains a comparable heritability of complex traits as gene expression, is under-explored due to its multidimensionality. To leverage multiple splicing events in a gene and shared splicing across tissues, we develop Multi-tissue Splicing Gene (MTSG), which employs tensor decomposition and sparse Canonical Correlation Analysis (sCCA) to extract meaningful information from high-dimensional multiple splicing events across multiple tissues. We build MTSG models using GTEx data and apply them to GWAS summary statistics of Alzheimer's disease (AD) (111,326 cases and 677,663 controls) and schizophrenia (SCZ) (36,989 cases and 113,075 controls). We identify 174 and 497 significant splicing-mediated risk genes for AD and SCZ, respectively, at Bonferroni correction. For AD, our results demonstrate significant enrichment of AD related pathways and identify additional AD risk genes not detected in the single-tissue analysis, while preserving most top genes identified in the brain frontal cortex. Consistently, for SCZ, genes identified by our brain-wide MTSG model, built from a cluster of 13 brain tissues, exhibit stronger enrichment in SCZ-relevant genes and MTSG identifies unique SCZ risk genes compared to single-tissue models. These results showcase that our MTSG models capture distinctive splicing events across tissues, which might be overlooked when using single tissue alone. Our MTSG models can be applied to other complex traits to help identify splicing-mediated disease risk genes.

Humans↗

PubMed2025

Distinct spatial transcriptomic patterns of substantia Nigra in Parkinson disease and Parkinsonian subtype of multiple system atrophy.

To investigate transcriptomic signatures of Parkinson's disease (PD) and the Parkinsonian subtype of Multiple System Atrophy (MSA-P) in substantia nigra pars compacta (SNpc), we conducted transcriptome analysis using in-situ hybridization on paraffin-embedded SNpc tissues from post-mortem brains. The study included 2 MSA-P patients, 2 PD patients, and 2 healthy controls (HC), with 12 regions of interest (ROIs) selected from the dorsal to ventral and medial to lateral aspects of the SNpc. A total of 72 ROIs from 6 participants were analyzed, and differentially expressed genes (DEGs) were identified by comparing MSA-P, PD and HC groups. The MSA-P group showed 88 upregulated DEGs and 326 downregulated DEGs (adjusted 𝑝<0.05) compared to HC. The downregulated DEGs were significantly enriched in pathways related to ribosomal translation, immune processes, mitochondrial function, and autophagy. Notably, the dorsomedial quadrant was uniquely linked to antigen presentation, while other quadrants showed downregulation of protein synthesis. The PD group exhibited 165 upregulated DEGs and 350 downregulated DEGs (adjusted 𝑝<0.05) compared to HC, with downregulated DEGs associated with ribosomal translation, mitochondrial function, and the ubiquitin-proteasome system. In both MSA-P and PD, the upregulated DEGs were not associated with any pathways or biological process in gene enrichment analysis. In network propagation analysis, amyloid precursor protein was the most significant network hub among DEGs in both MSA-P and PD. Comparing the transcriptomic signatures of SNpc between MSA-P and PD, we found immune/inflammation, mitochondrial function and neural signaling related genes were significantly downregulated in MSA-P compared to PD. Overall, the transcriptomic signature of the SNpc in MSA-P and PD revealed overlapping but distinct features, including alterations in protein synthesis, immune processes, mitochondrial function, and protein degradation systems. Future studies with larger cohorts and functional validation are needed to further elucidate these findings.

Humans↗