Human Genomics最新文献

Background: The causal bridge from environmental exposure to endometriosis (Ems) biology remains incompletely defined. Di(2-ethylhexyl) phthalate (DEHP) is repeatedly implicated in elevated Ems risk, yet actionable molecular anchors linking exposure to phenotype are scarce.

Methods: We established a multi-layered pipeline centered on DEHP. Comprehensive in silico target prediction across ChEMBL, PharmMapper, and SwissTargetPrediction yielded 1364 de-duplicated candidate proteins. Three transcriptomic cohorts (GSE51981, GSE6364, GSE7305) were integrated and analyzed using differential expression and Weighted Gene Co-expression Network Analysis (WGCNA) to derive a 229-gene, high-confidence Ems set. The intersection identified 17 overlapping genes, which were contextualized by protein-protein interaction (PPI) networks and Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment. Interpretable machine learning with SHapley Additive exPlanations (SHAP) prioritized a core signature, followed by molecular docking and 100-ns molecular dynamics (MD) simulations to validate binding feasibility and temporal stability.

Results: The 17-gene overlap formed a compact functional subnetwork aligned with a "membrane-lipid homeostasis to vesicular transport to detoxification/de-esterification" axis. Classifiers showed robust discrimination across training and external cohorts (most area under the receiver operating characteristic curve [AUC] > 0.75), while single-gene receiver operating characteristic (ROC) analyses highlighted UGT8 (AUC = 0.869) and EPHX1 (0.853) as highly transferable. SHAP prioritized a seven-gene signature-ELOVL6, LYPLA1, UGT8, SLC1A5, HMGCR, EPHX1, and VAMP2-and revealed non-linear relationships, including ELOVL6-UGT8 synergy, HMGCR-LYPLA1 antagonism, and EPHX1-SLC1A5 context dependence. Docking supported pocket complementarity with ~ 2.2-3.3 Å hydrogen bonds plus extensive hydrophobic/π contacts; MD confirmed stable, compact, and persistent binding for UGT8-DEHP, ELOVL6-DEHP, and HMGCR-DEHP over 100 ns.

Conclusions: This study establishes a comprehensive workflow spanning from chemical exposure identification to target discovery, disease network mapping, interpretable computational modeling, and structural/dynamical validation. We propose a DEHP-Ems regulatory framework underpinned by lipid metabolism, vesicular trafficking, and detoxification pathways. The resulting seven-gene signature provides a clinically applicable panel for diagnostic stratification and highlights potential therapeutic entry points, particularly along the HMGCR axis and via SLC1A5-mediated glutamine uptake. These findings lay the groundwork for future mechanistic studies in primary cell systems, organoid models, in vivo experiments, and prospective clinical validation.

Familial hypercholesterolemia (FH) is a genetic disorder driven in part by mutations in three genes that encode components of the cholesterol pathway: LDLR, APOB, and PCSK9. However, the majority of FH genetics has been performed in individuals of European descent. Here, we leveraged a cohort of 300 patients from the Mexican FH registry to understand how rare, high liability alleles and common variants might contribute to shaping individual risk. Using a combination of whole exome and of short- and long-read whole genome sequencing, we report three key findings. First, we observed that rare pathogenic point mutations and structural variants in all known FH genes, together with variants in APOE, CREB3L3, and PLIN1, contribute to a molecular FH diagnosis in 67% of families, including novel gene-disruptive copy number variants (CNVs) which arose in a native American background. Second, ancestry-adjusted polygenic risk score analysis identified a significant liability for coronary artery disease, hypertension, LDL, HDL, and Type 2 Diabetes. The polygenic signal for LDL was present in patients with rare, pathogenic FH mutations and was more prominent in individuals bereft of a molecular FH diagnosis. Finally, we report both a whole-gene duplication and common, non-coding variants in a novel locus, PDZK1, which contribute to the genetic burden of FH, a finding we replicated in the UK Biobank (UKB). Together, our analyses illustrate the value of genetic studies in non-European populations and reinforce the notion that individual risk to disease can arise from both rare, large effect alleles (alone or in combination across genes) and common variants that increase the mutational burden of a biological system.

Background: Thyroid eye disease (TED) is an autoimmune disorder characterized by persistent inflammation around the periphery and within the orbit, potentially driven by hypoxic conditions. Effective biomarkers and precise predictive models are still lacking for the early diagnosis of TED.

Methods: Bulk RNA sequencing was conducted on peripheral blood samples from TED patients, Graves' hyperthyroidism (GH) patients without ocular involvement, and healthy controls (HC). Differentially expressed genes between TED and HC, hypoxia-related genes and genes identified through weighted gene co-expression network analysis (WGCNA) were intersected to identify candidate biomarkers. Subsequently, nine machine learning algorithms were applied to screen for critical hypoxia-related TED diagnostic genes (HRTDGs). A diagnostic model based on HRTDG score (HRTDGS) was constructed using logistic regression analyses and then evaluated. TED patients were categorized into high and low HRTDGS groups based on the median score. Distinct immunological profiles and underlying pathological functions were investigated between two groups. Single cell RNA sequencing (scRNA-seq) data further explored HRTDGs' roles at cellular level.

Results: Hypoxia was identified as a prominent feature of TED. Among all machine learning algorithms, random forest achieved the highest area under curve (AUC) and was used to identify three key HRTDGs: EGFR, PIK3CB, and CREBBP. The HRTDGS model was then established and found to be an independent predictive factor for TED diagnosis (odds ratio (OR): 2.656, 95% confidence interval (CI): 1.735-4.324, p < 0.001). The model demonstrated high diagnostic accuracy in distinguishing TED from both HC (AUC = 0.785 in training set and 0.905 in testing set) and GH (AUC = 0.935). TED patients with higher HRTDGS exhibited elevated levels of thyrotropin receptor antibodies (TRAb) and abnormal free thyroxine (fT4), along with greater infiltration by activated CD4 + T cells and natural killer (NK) cells. ScRNA-seq revealed elevated expression of HRTDGs in fibroblasts, NK and CD4 + T cells, with enriched EGFR signaling pathway between T/NK cells and fibroblasts in TED compared to HC.

Conclusions: This study presents a novel hypoxia biomarkers-based diagnostic model for TED, facilitating early detection and offering valuable insights into potential therapeutic targets.

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as the most prevalent type of chronic liver disease, posing a significant threat to human health. Protein kinase AMP-activated catalytic subunit alpha 2 (PRKAA2) plays a pivotal role in regulating metabolic diseases. Nevertheless, the underlying molecular mechanisms by which PRKAA2 influences the pathogenesis of MASLD remain unclear.

Method: Bioinformatics analysis of public datasets identified the potential role of PRKAA2 in MASLD, verified its immune cells correlation, and constructed its competitive endogenous RNA (ceRNA) network. We assessed the mRNA and protein expression of PRKAA2, along with phosphatidylinositol 3-kinase (PI3K) and protein kinase B (AKT) phosphorylation levels after PRKAA2 knockdown. Pro-inflammatory cytokines were quantified by Enzyme-linked immunosorbent assay (ELISA), and lipid species were profiled using Liquid chromatography-mass spectrometry (LC-MS). In vivo, hepatic morphology and lipid deposition were evaluated by Hematoxylin-eosin (H&E) staining. Immunofluorescence measured PRKAA2, phospho-PI3K (p-PI3K) and phospho-AKT (p-AKT) expression. The regulatory interaction between PRKAA2 and its upstream miRNA was confirmed by dual-luciferase reporter assay.

Results: Our bioinformatics analysis identified PRKAA2 as a significantly upregulated gene in MASLD. Both in vitro and in vivo experiments consistently revealed markedly elevated PRKAA2 expression levels in MASLD models. Knockdown of PRKAA2 significantly reduced lipid accumulation, suppressed production of pro-inflammatory cytokines and attenuated the phosphorylation ratios of PI3K and AKT. Further mechanistic investigations confirmed that hsa-let-7b-5p directly targets PRKAA2 by binding to its wild-type (WT) 3'UTR, establishing this miRNA as a key upstream regulator of PRKAA2 in MASLD pathogenesis.

Conclusions: Our findings collectively demonstrated that PRKAA2 serves as a crucial mediator in MASLD pathogenesis, functioning through a novel regulatory axis involving the upstream hsa-let-7b-5p and the downstream activation of the PI3K/AKT pathway.

Background: Increasing evidence suggests that ferroptosis plays a pivotal role in Staphylococcus aureus (S. aureus)-induced osteomyelitis. However, the regulatory mechanisms underlying ferroptosis-related genes (FRGs) in osteomyelitis remain poorly understood. This study aimed to identify key FRGs and elucidate their regulatory roles in osteomyelitis.

Methods: Key FRGs were identified using least absolute shrinkage and selection operator (LASSO) logistic regression and support vector machine-recursive feature elimination (SVM-RFE) algorithms based on transcriptomic data from the Gene Expression Omnibus (GEO) database. Bone marrow mesenchymal stromal cells (BMSCs) were isolated, characterized, and infected with S. aureus protein A (SpA) to construct an in vitro model. Cell viability, osteogenic differentiation, inflammation, and gene expression were assessed using Cell Counting Kit-8 (CCK-8), Alizarin Red S staining, enzyme-linked immunosorbent assay (ELISA), and quantitative reverse transcription polymerase chain reaction (qRT-PCR). In vivo, a mouse model of S. aureus-induced osteomyelitis was established, and the role of KLF2 was examined by micro-computed tomography (micro-CT), ELISA, histological staining, immunohistochemistry, immunofluorescence, and qRT-PCR.

Results: A total of 683 differentially expressed FRGs were identified. Ten candidate biomarkers were screened using LASSO and SVM-RFE, of which TXN, KLF2, HSPA8, CCT3, and AKR1C3 were consistently validated across training and validation datasets. These genes were associated with immune regulation, protein synthesis, and multiple ribosome- and metabolism-related pathways. In vitro, SpA treatment increased inflammation response, reduced BMSC proliferation and osteogenic differentiation, upregulated HSPA8, TXN, and CCT3, and downregulated KLF2 and its putative downstream target GPX4. In vivo, KLF2 overexpression alleviated S. aureus-induced bone loss, inflammation, and ferroptosis, while promoting angiogenesis and osteogenesis, in part through modulation of GPX4.

Conclusion: This study highlights KLF2 as a potential protective factor in S. aureus-induced osteomyelitis, possibly by regulating GPX4 and ferroptosis.

Background: Single nucleotide polymorphism array (SNP-array) has been introduced for prenatal diagnosis. This study aims to evaluate the clinical utility of SNP-array in the prenatal central nervous system (CNS) malformations.

Methods: A retrospective study was conducted on 437 prenatal cases involving CNS malformations and other structural abnormalities detected by ultrasound. Samples were categorized into three groups: Single CNS malformation, Multiple CNS malformations, and CNS malformations with multiple system malformations. SNP-array and karyotype analysis were simultaneously performed on the Fetal samples. Comparative analysis of data was conducted using SPSS (χ2).

Results: SNP-array analysis of 437 samples revealed an overall abnormality detection rate of 19.0%, which was significantly higher than the 11.7% positive rate detected by karyotype analysis in 427 samples (χ2 = 8.797, P = 0.003). The positivity rates detected by SNP-array were 11.4%, 43.3%, and 63.0% in the above three groups, respectively, and these differences were statistically significant (χ2 = 83.247, P = 8.379×10^- 19). The detection rate of clinically significant copy number variants (CNVs) (pathogenic/likely pathogenic, P/LP) was also statistically significant among the three groups (χ2 = 42.000, P = 9.127×10^- 11). In pathogenic CNVs, dose-sensitive regions or genes that occur more frequently include the 4p16.3 terminal region, the 17p13.3 region, the 22q11.2 recurrent region, and DLL1, TGIF1, EBF3. We also did an analysis for pregnancy data of advanced maternal age (AMA) and found that the ratio of chromosomal abnormalities in samples was 18.8% tested by SNP-array. The postnatal follow-up data were analyzed. Compared to the group with normal chromosomal microarray analysis (CMA) result and isolated CNS malformation, the proportions of termination of pregnancy (TOP)/perinatal mortality/spontaneous abortion (27.2% vs. 69.6%, P < 0.0001), liveborn infants requiring medical attention (6.3% vs. 21.7%, P < 0.01), infants being alive and well at birth (66.5% vs. 8.7%, P < 0.0001) were all statistically significant in the group with normal CMA result and non-isolated CNS malformation. The proportions of TOP/perinatal mortality/spontaneous abortion (27.2% vs. 76.7%, P < 0.0001), infants being alive and well at birth (66.5% vs. 23.3%, P < 0.0001) were also statistically significant in the group with abnormal CMA result and isolated CNS malformation compared to the same group mentioned above.

Conclusions: This study evaluated the application of SNP-array in the prenatal CNS malformations in terms of detection of positive rates, advantages in prenatal diagnosis, AMA, genotype-phenotype correlations, pregnancy outcomes and follow-up data, which could assist in the clinical diagnosis and assessment of fetal CNS malformations.

Background: Mandibular hypoplasia, Deafness, Progeroid features, and Lipodystrophy (MDPL) syndrome is a very rare genetic disorder linked to variants in the POLD1 gene, which encodes the catalytic subunit of DNA polymerase delta, a key enzyme involved in DNA replication and repair. Most patients carry a recurrent in frame deletion (p.Ser605del) within the active site of the p125 subunit. Despite its rarity, understanding the functional consequences of the Ser605del variant has broad implications for aging-related diseases and genome stability.

Methods: We combined structural modelling, molecular dynamics simulations, and protein-protein interaction (PPIs) analyses to evaluate the impact of Ser605del in the catalytic activity of DNA polymerase delta. Bioinformatic tools were applied to characterize its interaction network. RT-q PCR and Western Blot were performed to assess expression levels of POLD1, TRF1, and PARP1 in human dermal fibroblasts (HDFs) of three MDPL patients of different ages. Cells were monitored at different passages, both in basal condition and after damage by X irradiation. POLD1/TRF1 interaction was confirmed by immunoprecipitation analyses.

Results: Using molecular docking, molecular dynamics simulations and thermodynamic analyses, we found that Ser605del affects the DNA-binding site, impairing dTTP binding. The deletion alters short linear motifs involved in protein-protein interactions (PPIs), allowing the acquisition of a F/Y-X-L-X-P (FSLYP) consensus sequence with TRF1, a telomeric protein. In silico analyses highlighted a stronger interaction between the Ser605del POLD1 variant and TRF1. Experiments on MDPL fibroblasts confirmed a stronger POLD1-TRF1 binding and revealed dysregulation of PARP1, involved in telomere maintenance. Following X-ray irradiation, aimed at exacerbating the cellular phenotype, we observed a decreasing trend in these markers, which reached statistical significance particularly in one older patient.

Conclusions: We identified a novel short linear motif (FSLYP) in the Ser605del POLD1 protein that mediates abnormal interaction with TRF1, revealing a structural and functional link between POLD1 and telomere biology, contributing to premature aging phenotypes. This work provides new insights into MDPL pathogenesis and lays the foundation for future research into aging-related therapies.