Functional & Integrative Genomics最新文献

Indigenous sheep genetic resources are important for breeding improvement and germplasm conservation. Baerchuke (BECK) sheep, an indigenous breed from Xinjiang, China, is valued for its meat quality and environmental adaptability, but its genomic characteristics remain poorly understood. Here, 343 BECK sheep were genotyped using a 50 K SNP chip and integrated with genomic data from six indigenous Xinjiang sheep populations. Population genetic analyses revealed moderate genetic diversity and close genetic affinity between BECK and Bayinbuluke sheep. Selection signature analyses identified 26 candidate genes, including ZNF385B, TSHZ2, and FCHSD2, with potential roles in growth and muscle-related biological processes. In addition, the HITSNP approach identified 343 breed-informative SNP markers with high informativeness and low redundancy that effectively differentiated BECK from the other populations examined. This study provides the first systematic genome-wide characterization of BECK sheep and provides genomic resources for germplasm conservation, breed identification, and future marker-assisted breeding.

The construction of gene regulatory networks based on single-cell transcriptomics (scRNA-seq) data provides crucial technical support for decoding cell fate determination mechanisms at the single-cell level, elucidating molecular mechanisms underlying disease progression, and developing targeted therapeutics. Existing methods for constructing GRNs often rely excessively on gene expression features, struggling to achieve an effective balance between local direct regulatory signals and global multi-step regulatory pathways. This imbalance results in insufficient utilization of topological information within the network structure. Therefore, this study proposes a heuristic graph neural network-based GRN inference model (scHGNN). scHGNN integrates multi-order neighbor topological information into learnable weights through unified heuristic matrix and link prediction modules, thereby balancing local and global regulatory relationships. This approach effectively fuses gene expression features with network structural information to achieve precise inference of latent regulatory links within gene regulatory networks. Across GRN inference tasks using benchmark networks of varying gene scales and diverse origins, scHGNN consistently outperforms existing mainstream methods on key evaluation metrics. Furthermore, in target gene prediction cases for key transcription factors such as TP53, OTX2, and FOXP1, the model achieved validation rates as high as 76%–84% in the hTFtarget database. This not only supports its accuracy in identifying known regulatory relationships but also indicates its potential to identify high-confidence candidate regulatory interactions for further biological investigation. Collectively, these results demonstrate that scHGNN holds significant application value in elucidating gene regulatory mechanisms and exploring the molecular basis of related diseases.

Mycobacterium abscessus (Mab) is a rapidly growing non-tuberculous mycobacterium that causes opportunistic infections and exhibits extensive intrinsic antibiotic resistance. The proline-glutamate (PE) and proline-proline-glutamate (PPE) protein families are mycobacteria-specific virulence factors implicated in immune modulation, antigenic variation, and persistence. While Mycobacterium tuberculosis (Mtb) harbors approximately 170 PE/PPE members, the repertoire of PE/PPE genes in Mab remains largely uncharacterized. Here, we performed a genome-wide survey of PE/PPE genes in Mab ATCC 19,977 and identified 18 candidate family members, representing a relatively small fraction of the genome compared with slow-growing mycobacteria. Most predicted proteins harbor canonical PE or PPE domains and display acidic physicochemical properties. Phylogenetic analysis resolved the proteins into three subfamilies: PE, PPE, and PE-PPE, revealing moderate structural diversity but limited family expansion. Motif and gene structure analyses supported the evolutionary conservation. Notably, no PE_polymorphic GC-rich repetitive sequence (PE_PGRS) or PPE_major polymorphic tandem repeat (PPE_MPTR) members were detected, suggesting lineage-specific genomic reduction relative to other pathogenic mycobacteria. AlphaFold predictions revealed conserved N-terminal folds and variable C-terminal regions, which may contribute to functional diversification. Subcellular localization predictions indicated that most proteins are extracellular. Synteny analysis revealed no detectable collinearity among these genes. Transcriptomic analyses revealed condition-dependent expression of PE/PPE genes during amoeba and macrophage infection and under artificial sputum medium and metal ion stress, suggesting roles in environmental adaptation and host interaction. This study provides the first systematic overview of PE/PPE gene repertoire in Mab and lays the groundwork for elucidating their roles in intracellular survival, host interaction, and antimicrobial resistance.

The clinical significance and fibrogenic mechanisms of long non-coding RNA LINC00657 in atrial fibrillation (AF) remain unclear. This study aimed to elucidate whether LINC00657 served as a mechanistic driver of atrial fibrogenesis in AF via modulation of the microRNA-144-3p (miR-144-3p)/Rho-associated coiled-coil containing protein kinase 1 (ROCK1) axis. LINC00657 expression was quantified in peripheral blood from 150 AF patients and 150 matched controls. Angiotensin II (Ang II)-stimulated primary rat cardiac fibroblasts and continuously infused C57BL/6 mice served as in vitro and in vivo fibrosis models, respectively. Functional assays (cell counting kit-8 (CCK-8), flow cytometry, enzyme-linked immunosorbent assay (ELISA), western blot) and mechanistic experiments (subcellular fractionation, RNA pull-down, RNA immunoprecipitation (RIP), dual-luciferase reporter) were conducted to dissect the LINC00657/miR-144-3p/ROCK1 competing endogenous RNA (ceRNA) axis. Clinically, elevated circulating LINC00657 discriminated AF patients from controls and independently predicted AF risk, correlating positively with high-sensitivity cardiac troponin I (hs-cTnI) and high-sensitivity C-reactive protein (hs-CRP). In vitro, Ang II induced LINC00657 upregulation; silencing LINC00657 suppressed cardiac fibroblast proliferation, attenuated the release of inflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α), reduced the expression of fibrotic markers including type I/III collagen and transforming growth factor-beta (TGF-β), and promoted apoptosis. In vivo, knockdown of LINC00657 significantly attenuated Ang II-mediated atrial fibrosis in mice. Electrocardiogram (ECG) monitoring and transesophageal atrial pacing further revealed that silencing LINC00657 significantly restored the atrial effective refractory period (AERP) and markedly decreased both the inducibility and duration of AF. Mechanistically, LINC00657 was predominantly localized to the cytoplasm and functioned as a ceRNA to sponge miR-144-3p, with ROCK1 identified as a direct downstream target of miR-144-3p. Both AF patients and model mice exhibited decreased miR-144-3p and increased ROCK1 expression, which negatively and positively correlated with LINC00657 levels, respectively. Rescue experiments demonstrated that miR-144-3p inhibitors partially reversed the anti-fibrotic effects of LINC00657 silencing, whereas further ROCK1 knockdown abrogated this reversal. Mechanistically, dissection of ROCK1 downstream signaling revealed that the LINC00657/miR-144-3p/ROCK1 axis specifically activated the ROCK1/myosin light chain 2 phosphorylation pathway, enhancing actomyosin contractility and stress fiber formation to drive the fibrotic cascade. The LINC00657/miR-144-3p/ROCK1 regulatory axis contributed to atrial fibrosis in AF.

m5C, an important RNA modification, is closely associated with breast cancer; however, their causal relationship is unknown. We examined the relationship between m5C regulation and breast cancer. Genome-wide association study breast cancer data and expression quantitative trait loci of m5C regulatory factor genes in blood were collected. We explored the causal relationship among m5C regulatory genes, breast cancer susceptibility, and prognosis through Mendelian randomization. Single-cell RNA sequencing data from peripheral blood mononuclear cells of patients with breast cancer and healthy controls were used to determine the differential expression of key genes among different cellular subpopulations. The effects of these genes on specific cellular subpopulations were further explored in single-cell RNAseq data from primary breast cancer using cellular communication, metabolic and cellular function analyses and validated the findings using flow cytometry. We validated the prognostic value of specific cellular subpopulations expressing key genes and assessed the impact of antitumor immunity using spatial transcriptomics, bulk transcriptomics, and immunofluorescence analysis of tissue microarray (120 patients). Mendelian randomization analysis indicated that the expression of the m5C writer tRNA aspartate methyltransferase 1 (TRDMT1) in blood was associated with breast cancer prognosis. TRDMT1 expression in T cells was decreased in patients with breast cancer. TRDMT1 was closely related to T-cell function. Moreover, it may modulate the antitumor immune effects of CD8⁺ T cells by influencing cellular communication and metabolism, impacting the prognosis and immunotherapeutic response of patients with breast cancer. We confirmed the immunotherapy predict value and prognostic value of measuring TRDMT1 levels in CD8⁺ T cells, provided insights into enhancing CD8⁺ T-cell function, and identified potential targets to improve breast cancer prognosis and immunotherapy. Our research may help guide breast cancer treatment decisions and provide a prognostic evaluation option for future breast cancer treatment.

Tumor-adjacent mucosa is commonly used as a normal reference in colorectal cancer (CRC) transcriptomic studies, but its relationship with distant normal mucosa and tumor tissue remains unclear. Here, we performed bulk RNA sequencing of paired distant normal, adjacent, and tumor tissues from 25 patients with CRC and used these three tissue states to construct an ordered normal–adjacent–tumor (N-A-T) expression continuum. Although adjacent mucosa was globally closer to distant normal mucosa and showed no significant differential expression by pairwise analysis, a limma-based linear trend model identified widespread monotonic transcriptional changes along the N-A-T continuum. Tumor-directed genes were enriched in translation, RNA processing, cell-cycle activity, and proliferation-related pathways, whereas genes decreasing along this axis were associated with oxidative metabolism and epithelial homeostasis. A trend gene-based N-A-T score positioned adjacent mucosa between normal and tumor tissues in external bulk cohorts and was associated with proliferative and immune-low molecular states in CRC. Single-cell RNA-seq analysis localized this signal mainly to epithelial cells and associated higher scores with proliferative and stem-like epithelial states. In conclusion, CRC-adjacent mucosa is not fully equivalent to distant normal mucosa but carries coordinated tumor-directed transcriptional changes mainly associated with epithelial-cell programs.

Transcript-derived metabolic representations connect gene expression with pathway state, but interpretation depends on sampling unit, endpoint, cohort, and validation evidence. NeuroMetBench is a patient-aware methodology that keeps target quantity, independent unit, endpoint mapping, coverage, uncertainty, transport, numerical diagnostics, and provenance separate rather than collapsing them into a universal score. A frozen three-gene serine score showed RNA-protein rank concordance in 89 lung squamous cell carcinoma (LSCC) patients (Spearman (rho =0.9071), 95% confidence interval (CI) 0.8496 to 0.9388) and in a patient-disjoint 90-patient central nervous system/high-grade-glioma (CNS/HGG) cohort ((rho =0.6266), 95% CI 0.4697 to 0.7507). Reviewer-driven age/sex sensitivities remained positive in complete cases (LSCC (n=86), partial (rho =0.9118); CNS/HGG (n=69), partial (rho =0.7058)), but CNS/HGG complete-case selection was associated with the frozen RNA-score distribution and cannot rule out demographic confounding. A preanalysis-frozen Tel Aviv glioblastoma test was NOT RUN because public RNA/proteomics deposits yielded zero source-documented patient cross-matches (minimum (n=10)). A separately frozen Sun Yat-sen University Cancer Center (SYSUCC) analysis found 20 exact RNA/protein-matched glioblastomas and positive concordance ((rho =0.5984), 95% CI 0.1252 to 0.9101; permutation (p=0.00637)). By contrast, RNA score correspondence with measured L-serine in 75 same-cohort patients was weak and uncertain ((rho =0.1534), 95% CI -0.0803 to 0.3737; permutation (p=0.1853)). Evidence strength is therefore axis-specific: cross-modal proxy concordance does not establish metabolic flux, biochemical validation, universal method superiority, framework-wide external validation, or calibration.

Polyploidization serves as a major driver of plant genome evolution and functional innovation. However, how it influences genome structural remodeling and functional divergence remains unclear. In this study, we selected six species with different ploidy levels in the genus Panax as research materials. By integrating pan-genome and gene duplication analyses, we systematically evaluated the evolutionary patterns under distinct ploidy backgrounds. The results showed that, under their respective ploidy-specific pan-genome frameworks, tetraploid species had a higher proportion of core genes than diploid species. This compositional difference, combined with extensive gene family remodeling in tetraploid lineages, suggests that polyploidization was accompanied by systematic genome structural reorganization, likely driven by distinct selective pressures corresponding to different modes of gene duplication. The composition of duplication types differed extremely significantly among ploidy levels, and WGD as well as TRD were significantly elevated in tetraploid species. Further analysis revealed that WGD contributed predominantly to core genes, whereas DSD and TRD were more involved in the formation of dispensable and private genes. Functional analysis indicated that duplicated genes in tetraploids were involved in a broader range of metabolic and cellular processes, among which private genes derived from DSD were significantly enriched in DNA replication and repair pathways. These findings suggest that polyploidization promotes functional diversification while maintaining core functional stability by regulating different duplication mechanisms, thereby driving genome structural reorganization and adaptive evolution in Panax. These findings provide a genomic framework for understanding the diversity of bioactive compounds and may support future breeding and quality improvement of Panax medicinal resources.