Mammalian Genome最新文献

The HER2 (human epidermal growth factor receptor 2) kinase domain plays a pivotal role in receptor-mediated signaling and is frequently mutated across various cancer types. Variants of uncertain significance (VUS) within this domain pose significant challenges for clinical interpretation. In this study, a comprehensive computational analysis was conducted on 97 HER2 kinase domain variants comprising 25 pathogenic and 72 VUS entries using a panel of 13 predictive algorithms, including PredictSNP, PolyPhen-2, SIFT, and CADD. A subset of 32 variants (11 pathogenic and 21 VUS) was prioritized for in-depth structural and functional evaluation, based on concordant deleterious predictions from ≥ 9 algorithms. Conservation profiling via ConSurf and Align-GVGD revealed that these variants predominantly localize to highly conserved and functionally critical residues, underscoring their potential biological relevance. Thermodynamic stability profiling using I-Mutant indicated that the majority of prioritized variants exerted destabilizing effects on the protein's tertiary structure, consistent with their pathogenic annotations. Extended molecular dynamics simulations (200 ns) revealed noticeable deviations in root mean square displacement (RMSD), root mean square fluctuation (RMSF), and solvent-accessible surface area (SASA), accompanied by reductions in intramolecular hydrogen bonding and global structural compactness, highlighting conformational destabilization. Stereochemical integrity, assessed through Ramachandran plot analysis, was compromised in specific variants. At the same time, perturbations in hydrophobic core interactions and secondary structure elements further underscored disruptions in core packing and local conformational stability. Notably, the R816P variant demonstrated minimal perturbation to structural dynamics, highlighting the necessity of integrating time-resolved simulations with sequence-based pathogenicity predictions.

RAD21, a key cohesin subunit, participates in chromatin regulation and may influence tumor metabolism and immunity. Its role in liver HCC remains unclear. We investigated whether RAD21 regulates PON1 and how this axis integrates metabolic and immune signals in HCC. Multi-omics integration (transcriptomic, ChIP-seq, and scRNA-seq) datasets to identify the RAD21-PON1 regulatory axis, with immune infiltration, metabolic remodeling, and prognostic impact assessed via GSVA, TIDE, and LASSO modeling. RAD21 upregulation inversely correlated with PON1 expression. RAD21 binds the promoter of PON1, impacting metabolic pathway activity and shaping the immune microenvironment. Low PON1 expression was linked to immunosuppressive patterns and poor prognosis. A RAD21-PON1 risk signature robustly stratified survival. Our findings highlight the RAD21-PON1 axis as a central regulator connecting metabolism and immunity in HCC, providing prognostic and therapeutic insights.

Chronic obstructive pulmonary disease (COPD) is a leading global cause of mortality, with alveolar macrophages (AMs) dysfunction implicated in pathogenesis, though key molecular drivers remain unclear. This study integrated multi-omics approaches to identify causal AMs-derived factors in COPD. Single-cell RNA sequencing (scRNA-seq) of human lung tissues revealed a significantly increased proportion of macrophages, particularly enriched AMs clusters (0, 1, 5), in COPD patients versus controls. Two-sample Mendelian randomization (MR) analysis of 1,283 AMs-specific genes identified CXCL16 as having a robust negative causal relationship with COPD risk across European (IVW OR = 0.944, P = 0.039) and East Asian (Weighted median OR = 0.858, P = 0.008) populations. Bulk RNA-seq confirmed decreased CXCL16 expression in COPD lungs. Cell-cell chat analysis indicated that CXCL16 + AMs mediated critical immune interactions via pathways like MIF-CD74/CD44. Critically, CXCL16 deficiency in AMs drives COPD progression by disrupting immune-metabolic homeostasis. These findings establish CXCL16 downregulation in AMs as a novel causal mechanism in COPD and highlight its potential as a therapeutic target for restoring macrophage function and halting disease advancement.

The mouse remains the principal animal model for investigating human diseases due, among other reasons, to its anatomical similarities to humans. Despite its widespread use, the assumption that mouse anatomy is a fully established field with standardized and universally accepted terminology is misleading. Many phenotypic anatomical annotations do not refer to the authority or origin of the terminology used, while others inappropriately adopt outdated or human-centric nomenclature. This inconsistency is further exacerbated by the limited availability of comprehensive anatomical references, often compelling researchers to rely on "do-it-yourself" anatomical interpretations when characterizing disease models-an approach that increases the risk of inaccuracies in the absence of expert anatomical guidance. To address this critical gap, we propose the formation of expert working groups comprising comparative anatomists and disease model developers. These groups would be responsible for systematically reviewing the anatomical literature of each mouse organ system and producing consensus-based terminologies aligned with the Nomina Anatomica Veterinaria (NAV), the authoritative standard for quadrupedal species. Such harmonization efforts would not only improve the consistency and reliability of anatomical descriptions in mouse models but also enhance the integration and interoperability of anatomical data across biomedical ontologies and databases, facilitating more robust data mining and translational research.

The pathophysiological significance of crotonylation and its metabolomic regulatory circuitry in Parkinson's disease (PD) remains elusive. We utilized Mendelian randomization (MR) frameworks combined with mediation analysis to establish causal links between crotonylation-associated genes and PD, while systematically delineating metabolite-mediated mechanisms. In this study, crotonylation-related genes were selected from the eQTLGen dataset, and their causal relationship with PD was assessed using two-sample MR analysis. Subsequently, we investigated metabolites associated with PD risk. Additionally, two-step MR and MR mediation analyses were applied to explore the mediating effects of crotonylation-related genes, metabolites, and PD. To further interpret cellular heterogeneity, publicly available GEO single-cell transcriptome data were integrated to analyze PD brain tissue dynamics and the regulatory mechanisms of key crotonylation-related genes. We identified 16 crotonylation-associated genes harboring cis-eQTLs, notably SIRT1, GCDH, and HDAC7, which demonstrated significant inverse associations with PD risk (p < 0.05). Through MR analysis, 74 PD-associated metabolites were identified. Mediation analysis further delineated GCDH-mediated PD risk reduction (β_all = -0.054) through downregulation of X-21,471 and tetradecanedioate (C14-DC). Furthermore, single-cell transcriptomic analysis revealed that GCDH is predominantly and specifically highly expressed in astrocytes within PD brain tissues, and its dynamic regulatory pattern is closely linked to cell differentiation processes, suggesting a potential role in regulating PD pathogenesis via the NRG3-ERBB4 signaling axis. Our findings indicate that GCDH and its mediated metabolome critically contribute to PD pathogenesis, with astrocytes emerging as a central regulatory cell type. This study not only elucidates novel molecular landscapes underlying PD pathology but also highlights astrocytes as promising targets for therapeutic intervention.

Rattus norvegicus (a.k.a. laboratory rat or Brown Rat) Mammary carcinoma susceptibility 1b (Mcs1b) is a concordant ortholog of a female breast cancer risk allele at human 5q11.2. Previously, Mcs1b was delimited to a 1.8 Mb interval of RNO2 and Map3k1 along with Mier3 were determined to be Mcs1b-nonminated genes. This conclusion was based on shared synteny with human 5q11.2 and differential gene expression between cancer susceptible and Mcs1b resistant mammary glands. In this study, targeted genome sequencing of cancer susceptible and Mcs1b resistance associated alleles was used to identify three Mcs1b-nominated quantitative trait nucleotides (QTNs) in noncoding DNA. In vitro approaches, luciferase activity and electromobility shift assays, were used to suggest these variants reside in potential gene regulatory elements. One of these variants, UL-A74-SNV-17, resulted in luciferase activities that were 2.6× higher for the susceptibility associated variant compared to the resistance associated variant. These results recapitulated Mcs1b nominated gene transcript level differences between Mcs1b genotypes in mammary epithelial cells (MECs), where Map3k1 and Mier3 were 1.5- to 2.0-fold higher for the susceptible genotype compared to the Mcs1b resistance-associated genotype. Evidence of a chromatin loop in Mcs1b that may position Mcs1b QTNs near distal genes was uncovered using chromosome confirmation capture (3C). Rat Mcs1b was also functionally characterized by determining that Mcs1b genotype had effects on the amount of luminal MECs in adult mammary glands. In conclusion, UL-A74-SNV-17 is a priority candidate Mcs1b QTN with a hypothesized mechanistic role in the differential regulation of Mcs1b nominated genes, Mier3 and Map3k1.

Depigmentation defects in cattle are characterized by the absence of pigment in specific skin regions, increasing susceptibility to health issues and often leading to early culling. In Nellore cattle, depigmentation is primarily observed at the tail tip, mucous membranes, and as small patches across the body. This study aimed to estimate genetic parameters and perform a genome-wide association study (GWAS) for depigmentation in Nellore cattle. Data were sourced from the DeltaGen® breeding program, provided by Gensys®. Phenotypic records included 182,964 Nellore cattle, with a 6.8% incidence of depigmentation. Of these, 28,655 genotyped animals and 385,079 SNPs were available for the analysis. The ultra-fast generalized linear mixed model for binary traits (fastGWA-GLMM) was used for the GWAS, while variance components were estimated using a Bayesian threshold model and single-step methodology. The heritability of depigmentation was estimated at 0.12 on the observed scale and 0.54 on the liability scale. The GWAS identified 1,011 significant SNPs (p < 0.05 after Bonferroni correction) associated with depigmentation defects, located across chromosomes BTA6, BTA12, and BTA22. However, after performing a conditional GWAS to account for the top signal on BTA22, the original signal in the MITF region was no longer detected. In total, 234 genes were identified near the associated SNPs, including 129 protein-coding genes. Functional enrichment highlighted MITF, KIT and EDNRB as biologically relevant candidate genes. The gene ontology analysis highlighted biological processes related to melanogenesis, pigmentation, and hypopigmentation phenotypes, while the QTL enrichment analysis identified significant associations on BTA6 and BTA22. These findings improve our understanding of the genetic basis of depigmentation in Nellore cattle and may contribute to future selection strategies.

Mucopolysaccharidosis-plus syndrome (MPS plus or MPSPS) is an ultrarare inherited metabolic disease, caused by mutations in the VPS33A gene. Like in different types of mucopolysaccharidosis (MPS), glycosaminoglycan (GAG) storage in cells of patients is evident. However, unlike MPS, the genetic defects in MPSPS cause impairment in the VPS33A protein level rather than inactivation of lysosomal hydrolases responsible for GAG degradation. Recent works demonstrated that low abundance of mutated VPS33A causes defective endosomal trafficking, resulting in poor delivery of GAGs (and perhaps also other compounds) to lysosomes, preventing their effective turnover. Here, we tested the hypothesis that impairment of protein degradation machineries, proteasomes by genistein (5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-1-benzopyran-4-one) and endoplasmic-reticulum-associated protein degradation (ERAD) by ambroxol (4-((2-amino-3,5-dibromophenyl)methylamino) cyclohexan-1-ol), might result in elevation of levels of the mutated, partially active VPS33A and improvement of cellular functions. Using a line of MPSPS patient-derived fibroblasts, we demonstrated that treatment with genistein and ambroxol resulted in elevation of the mutant VPS33A protein level, as well as in improvement or correction of various previously reported cellular defects, including GAG levels, endosomal markers, and cytoskeleton elements. In the light of these results, and since both genistein and ambroxol were previously demonstrated to be safe when used in relatively high amounts, we suggest that the use of these compounds, and especially their combination, might be considered as a potential therapeutic approach in MPSPS, which is currently an incurable disease.

Poststroke depression (PSD) presents with persistent depressive symptoms and cognitive dysfunction. This study explored the regulatory mechanism of E2F2 in hippocampal neurogenesis in PSD. In a PSD rat model established by MCAO and CUMS, depressive behaviors (reduced sucrose preference, prolonged immobility time) and impaired hippocampal neurogenesis (decreased NeuN-positive cells and BDNF protein) were observed. BDNF, E2F2, CBR1, and miR-1290 were measured by WB and RT-qPCR. E2F2 enrichment on the miR-1290 promoter was assessed by Ch-IP assay. The bindings of E2F2 to the miR-1290 promoter and miR-1290 to the CBR1 3'-UTRwere validated using dual-luciferase reporter assays. Molecular analyses revealed that E2F2 was upregulated in PSD rats, and E2F2 knockdown alleviated depressive symptoms and neurogenesis deficits. Mechanistically, E2F2 bound to the miR-1290 promoter and enhance miR-1290 transcription, while miR-1290 targeted the 3'-UTR of CBR1 and suppress its expression. Rescue experiments confirmed that miR-1290 overexpression or CBR1 inhibition counteracted the neurogenesis-promoting effects of E2F2 knockdown. In conclusion, E2F2 inhibits hippocampal neurogenesis in PSD via the miR-1290/CBR1 axis, providing a potential therapeutic target for treating PSD.

Italy hosts a remarkable ovine biodiversity shaped by centuries of history, regional traditions, and environmental heterogeneity. This diversity sustains agricultural production as well as ecosystem services and cultural heritage. Yet, many local breeds are undergoing severe demographic decline. To explore these dynamics, we analyzed census data from all registered Italian sheep, which revealed highly variable situations across breeds but confirmed that most are currently at risk of extinction. To complement this picture, we genotyped 34 Italian sheep populations using the Ovine50K BeadChip and compared them with foreign breeds with recognized herd books in Italy. Genomic analyses of diversity (including inbreeding and effective population size), population structure, and genomic background provided insights into the state of genetic variation and relationships among breeds, including patterns of introgression. By comparing these results with data from populations sampled twenty years ago, we assessed temporal changes in diversity, genomic background, and selection signatures. Fst analyses highlighted genomic regions that have undergone the most marked shifts, allowing us to explore associated genes and QTLs. Correlations between Fst and environmental changes across 20 variables further emphasized the role of local adaptation in shaping genomic landscapes. In addition, local ancestry inference in two breeds (Gentile di Puglia and Nera di Arbus) with evidence of recent admixture identified genomic regions influenced by gene flow. Overall, our study illustrates the complex evolutionary dynamics of Italian sheep breeds and underscores the importance of integrating demographic analyses with genomic tools to guide their conservation and sustainable management.