Human Genomics最新文献

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.

Background: Prenatal presentation of polycystic kidney disease (PKD), characterized by bilateral renal cysts and enlarged echogenic kidneys on ultrasound, often results in perinatal death. Prenatal manifestations of PKD are generally associated with autosomal recessive PKD, most commonly a result of pathogenic variants in PKHD1, but in rare cases can also be driven by bi-allelic inheritance of pathogenic variants in genes more commonly associated with autosomal dominant PKD such as PKD1. Diagnosing the underlying cause of prenatal PKD can be complicated by atypical histology, and/or a prenatal phenotype that does not align with family history. In this study, five cases of prenatal PKD with atypical or inconclusive features identified during post-mortem investigations underwent trio exome or genome sequencing, termed a genomic autopsy.

Results: Genomic autopsy was able to delineate the genetic basis of prenatal PKD in all five families.

Conclusion: Our findings demonstrate the diagnostic utility of a genomic autopsy in providing a genetic diagnosis for fetal PKD cases post-mortem, particularly in atypical presentations. A genetic diagnosis is highly beneficial for future family planning, including the use of reproductive technologies, as well as identifying presymptomatic parents who are likely to develop PKD in the future.

Background: Non-invasive prenatal testing (NIPT)-derived total cell-free DNA (cfDNA) and fetal fractions (FFs) are potential indicators of placental dysfunction, a hallmark of preeclampsia (PE). However, their clinical utility in PE risk stratification, particularly in twin pregnancies, remains underexplored. This study evaluated the association between total cfDNA levels and the incidence of PE and assessed mediation by FFs.

Methods: This retrospective cohort study included 2,366 pregnant women who underwent NIPT at 12-22 weeks of gestation at a tertiary hospital. Total cfDNA levels and FFs were extracted from the NIPT data, and PE diagnoses were confirmed via medical records. Logistic regression and mediation analyses were used to assess associations and mediating effects.

Results: PE prevalence was 3.51% (83/2,366). Elevated total cfDNA tertiles (T2/T3 vs. T1) were associated with increased rates of PE (T2: OR = 2.36, 95% CI: 1.16-4.80; T3: OR = 3.00, 95% CI: 1.51-5.97). Each 1 µg/L increase in total cfDNA was associated with a 12% increase in PE odds (OR = 1.12, 95% CI: 1.05-1.20). Lower FFs were associated with PE risk (T1 vs. T3: OR = 2.70, 95% CI: 1.45-5.00; per 1% decrease: OR = 1.15, 95% CI: 1.07-1.23). In singleton pregnancies, total cfDNA levels ≤ 4.41 µg/L were significantly associated with increased PE risk (OR = 2.89, 95% CI: 1.32-6.29, P = 0.008) with a validated threshold effect [log-likelihood ratio test (LRT, P = 0.005)], while FF ≤ 8.86% showed a protective trend (OR = 0.81, 95% CI: 0.68-0.97, P = 0.021) despite a nonsignificant LRT (P = 0.192). In twin pregnancies, total cfDNA showed no significant threshold or linear association with PE risk (OR = 1.06, P = 0.382; LRT, P = 0.215), while FFs exhibited a stronger inverse linear association (OR = 0.77, 95% CI: 0.65-0.92, P = 0.003) with no significant threshold effect (LRT, P = 0.270). Total cfDNA was inversely correlated with FFs (T3 vs. T1: β=-2.96, 95% CI: -3.34 to -2.59). Mediation analyses showed FFs partially explained 24.4% and 32.5% of the total cfDNA-PE relationship in singleton pregnancies and all pregnancies, respectively.

Conclusion: This study observed that elevated total cfDNA levels during NIPT were associated with an increased risk of PE, with FFs acting as partial mediators. These findings warrant further investigation into total cfDNA and FFs as potential biomarkers for early PE risk stratification, even in high-risk settings such as twin pregnancies, to determine whether their use in screening could contribute to the development of strategies aimed at improving maternal-fetal health.