Human Genomics最新文献

Background: Oral squamous cell carcinoma (OSCC) is one of the most common oral malignancies, which can occur in any part of the mouth and is highly malignant. DNA Methylation is an epigenetic modification of the genome, which is involved in key cellular processes and has a crucial impact on the occurrence, development, invasion and metastasis of tumors. In this study, we conducted a comprehensive analysis of DNA methylation characteristics in OSCC with the aim of identifying potential diagnostic epigenetic biomarkers and exploring possible mechanisms of methylation's influence on OSCC.

Methods: In this study, genome-wide DNA methylation analysis was performed using Infinium Methylation EPIC arrays, including tumor tissue and adjacent non-tumor tissue from 12 OSCC patients. Differential methylation probes and regions (DMP/DMR) were identified for gene function analysis. Characteristic DMPs and genes were screened according to the specific situation, and OSCC-targeted methylation data from 25 patients in the validation cohort were used to further validate the differential methylation levels of our selected genes. Finally, the expression levels of methylated genes in OSCC were verified by combining RNA-Seq data with quantitative real-time polymerase chain reaction (qRT-PCR).

Results: There were 277,805 DMPs in OSCC tumor tissue. Hypermethylated DMP accounted for 37.4% of all DMPs and hypomethylated DMPs was 62.6%. Functional pathway analysis showed that it was mainly related to passive transmembrane transporter activity, cancer proteoglycan and PI3K-Akt signaling pathway. The methylation level of ZNF880 was emphatically verified in the verification cohort, and the results showed that there was high methylation in ZNF880 in the verification cohort. Subsequently, through RNA-Seq data and qRT-PCR, it was confirmed that the expression of ZNF880 in OSCC tissues was significantly lower than that in normal tissues. This verified the correlation between the high methylation of ZNF880 and gene expression.

Conclusions: This study comprehensively reveals changes in genome-wide DNA methylation patterns in OSCC, indicating that abnormal hypermethylation of the ZNF880 gene plays a catalytic role in the pathogenesis of OSCC.

Background: Patients with congenital heart disease are identified in 1% of live births. Improved surgical intervention means many patients now survive to adulthood, the corollary of which is increased mortality in the over-65-year-old congenital heart disease (CHD) population. In the clinic, genetic sequencing increasingly identifies novel genetic variants in genes related to CHD. Traditional assays for interpreting novel genetic variants are often limited by gene-specificity, whereas animal models are cumbersome and may not accurately reflect human disease. This study investigates CRISPR gene editing in induced pluripotent stem cells and cardiomyocyte-directed differentiation as a human disease model to investigate novel genetic variants identified in association with CHD.

Methods and results: We identified a GATA4 p.Arg284His genetic variant in a paediatric patient. This genetic variant was introduced into induced pluripotent stem cells (iPSCs) using CRISPR gene editing with homology-directed-repair. GATA4 genetic variant and isogenic control iPSCs were selected and differentiated into cardiomyocytes. Expression of the GATA4 p.Arg284His variant resulted in altered calcium transients, indicative of CHD and consistent with the patient's clinical phenotype. Transcriptomics revealed cellular pathway changes in cardiac development, calcium handling, and energy metabolism that contribute to disease aetiology, mechanism and identification of potential treatments.

Conclusion: Directed differentiation of iPSCs harbouring the GATA4 p.Arg284His genetic variant recapitulated the CHD phenotype, indicated disease mechanisms, and pointed to potential sites for targeting with therapy. The study highlights the utility of transcriptomics for the functional interpretation of cardiac genetic variants and is an exemplar for precision medicine approaches for the investigation of CHD.

Background: Family history of colorectal cancer (CRC) and multiple primary CRCs in a single person may indicate inherited CRC predisposition.

Methods: In the present study, we performed whole exome/genome sequencing on germline DNA from at least two CRC cases in 19 families and from family members with a double primary CRC from seven additional families. We used a set of in silico predictions in combination with a STRING protein-protein interaction and pathway analysis to identify the most likely variants predisposing to CRC.

Results: We identified Cell cycle/DNA repair and TGFβ signaling/Focal adhesion/Extracellular matrix organization pathways as highly significant protein-protein interaction networks. Variants in the APCDD1, CYBA, PTK7 and SRC genes were identified in more than one family, and they were shown to dysregulate basic cellular functions, potentially leading to cancer development. Most variants were private to a family, and each family had more than one candidate variant, suggesting a synergistic or polygenic mode of inheritance. This hypothesis, as well as validation of the identified variants and pathways and their functional consequences, need confirmation by other family-based studies.

Conclusions: Different types of family-based analyses together with in silico predictions are helpful to identify candidate genes and pathways for CRC predisposition.

Background: Hereditary protein C deficiency (PCD) increases thrombotic risk, but the molecular mechanisms of distinct missense variants remain incompletely defined. Two siblings from a family with recurrent deep vein thrombosis and a strong family history of thrombotic events were found to carry compound heterozygous PROC variants.

Objectives: To elucidate the biosynthetic and functional consequences of two PROC missense variants, c.632G > A (p.Arg211Gln) and c.1099G > A (p.Val367Met), and their combined impact on anticoagulant capacity.

Methods: Two siblings with recurrent deep vein thrombosis were analyzed. Family segregation analysis was performed on multiple heterozygous carriers to support genotype-phenotype correlations. Recombinant protein C variants were expressed in HEK293T cells to assess expression efficiency and intracellular accumulation. Zymogen activation by thrombin-thrombomodulin and APC anticoagulant activity were evaluated using FVa degradation, clotting, and thrombin generation assays. Structural modeling and Na⁺-dependent enzymatic assays were performed to explore variant-specific mechanistic defects.

Results: Both variants exhibited partial expression defects, with p.Val367Met showing significantly increased intracellular accumulation and reduced secretion efficiency. p.Arg211Gln selectively impaired zymogen activation without affecting APC function (type IIa deficiency), whereas p.Val367Met preserved activation but reduced Na⁺-dependent catalytic efficiency (type IIb deficiency). Structural modeling revealed that Arg211 substitution disrupts activation peptide conformation, while Val367Met perturbs the Na⁺-binding loop adjacent to the S1 pocket. Co-inheritance of both resulted in synergistic anticoagulant impairment, leading to markedly elevated thrombin generation.

Conclusions: These findings demonstrate that PCD pathophysiology can arise from combined biosynthetic and functional defects, with distinct structural perturbations differentially affecting zymogen processing and protease activity. Integrated genetic, biochemical, and structural analyses, in the context of family history and clinical phenotype, are essential for accurate variant interpretation. Understanding the specific molecular mechanisms of PROC variants can inform clinical decision-making, guide personalized anticoagulant therapy, and help prevent thrombotic events in affected individuals. Therapeutic strategies targeting zymogen activation or proteostasis may offer potential avenues to mitigate thrombotic risk in hereditary PCD.

Background: Pharmacogenomic (PGx) testing improves treatment outcomes by tailoring therapy to a patient's genetic profile. However, PGx implementation faces global challenges, including costs, reimbursement, and regulations. Initial PGx guidelines exist in the United Arab Emirates (UAE), but insurers' perspectives remain understudied. This study explores insurers' views on policies and strategies to expand PGx adoption and overcome implementation barriers.

Methods: This qualitative study used a semi-structured interview design to explore the perspectives of twelve executive and middle management insurance representatives selected through purposive convenience and snowball sampling. Thematic analysis was conducted inductively, supported by comparative analysis, the Institutional Theory, the TAM, and SWOT analysis to interpret the findings.

Results: Analysis revealed variable awareness of PGx, highlighting both perceived benefits and significant barriers. Key findings included economic constraints, limited physician and public awareness, and policy challenges related to cost-effectiveness and infrastructure. Ethical and privacy concerns were minimal but were noted, with potential implications for insurance premiums. Participants stressed the need for collaborative efforts to align PGx with UAE healthcare goals and highlighted the role of advanced health information systems in facilitating integration. Differences emerged between executive and middle-level management: the former emphasised strategic policies and long-term returns on investment, while the latter focused on practical operational barriers.

Conclusions: Advancing PGx in the UAE requires local cost-effectiveness studies, clear government-led coverage guidelines, and collaborative action among insurers, providers, regulators, and academia. These findings may inform health systems with similar public-private insurance arrangements, where phased adoption strategies and education initiatives are key to sustainable implementation.

Flagellogenesis in mammalian sperm is essential for sperm motility and successful egg fertilization. Multiple morphological abnormalities of the sperm flagella (MMAF) represent a condition characterized by various structural defects in the flagellum. While CFAP57 has been identified as a factor in the pathogenic mechanisms of MMAF, the precise molecular regulation underlying this process remains unclear. Here, we report novel biallelic mutations in the CFAP57 gene identified in two infertile males from two unrelated families. The first patient carried a homozygous nonsense mutation in CFAP57 [NM_001195831.2: c.3250 C > T (p.R1084X)], while the second was compound heterozygous for two missense mutations c.1340T > C (p.V447A) and c.1856G > A (p.R619H). CRISPR-Cas9-generated CFAP57 mutant mice recapitulated human MMAF phenotypes, exhibiting structural flagellar defects and complete infertility. Using immunoprecipitation-mass spectrometry (IP-MS), we identified MYH10, a non-muscle myosin II isoform, as an interaction partner of CFAP57. Immunofluorescence analysis confirmed that both MYH10 and CFAP57 localize to the sperm flagella. We further examined the precise localization of MYH10 at the ultrastructural level using immunoelectron microscopy. Gold particles conjugated to the MYH10 antibody were predominantly detected in the sperm flagella. In sperm with CFAP57 mutations, MYH10 was mislocalized to the mid-piece region while being notably absent from the principal and end pieces. This mislocalization affected the expression of IFT88, a key component of the intraflagellar transport (IFT) system that plays a critical role in mammalian flagellar assembly. Fortunately, ICSI can overcome CFAP57-associated male infertility. Together, our findings establish CFAP57 as an important mediator of sperm flagellogenesis that orchestrates MYH10 and IFT88 positioning and intraflagellar transport dynamics to maintain flagellar integrity, providing molecular insights into MMAF-associated male infertility.

Background: Hepatocellular carcinoma (HCC) is often diagnosed in the late stage, with limited effectiveness of traditional treatments and a low overall survival rate. The underlying molecular mechanisms of HCC require further study.

Methods: Differential and survival analyses evaluated IGF2BP3 expression and prognosis. CCK8 and colony formation assays assessed the impact of IGF2BP3 on tumor malignancy. GEO data screened potential substrates modified by IGF2BP3. RIP-qPCR validated N6-methyladenosine (m6A) modification, while animal models confirmed the tumor-promoting effects of IGF2BP3.

Results: Abnormally high expression of IGF2BP3 is associated with poor prognosis in HCC. IGF2BP3 activates the JAK2-STAT3 pathway through m6a modification of IL4R mRNA in HCC. Then, STAT3 regulates the nuclear localization of METTL3 through WTAP.

Conclusion: In this study, we show that IGF2BP3 binds to and stabilizes IL4R mRNA, activating the JAK2/STAT3 pathway. STAT3 enhances METTL3's nuclear retention via WTAP, coordinating the m6A modification of IGF2BP3 in HCC.

Background: The accurate identification of complex kinship relationships remains a significant challenge in forensic practice. Traditional kinship identification methods, which primarily rely on length polymorphisms of short tandem repeats (STRs), often face difficulty in achieving sufficient discriminatory power for complex relationships due to the limited genetic information they provide. While next-generation sequencing (NGS) enables the detection of allelic sequence polymorphisms within STRs, its practical value for different kinship analyses in specific populations requires comprehensive evaluation. To this end, the present study investigated the genetic polymorphisms of 52 STRs, with a focus on both length and sequence variations, aiming to evaluate the system efficacy and forensic application value of the amplification system in the forensic identification of complex kinship analyses.

Results: The 52 STRs were highly polymorphic in the studied Baoan group. The acquisition of sequence polymorphism information significantly enhanced the genetic polymorphisms of STRs, and the number of alleles increased by 61.00% compared to length-based polymorphisms alone. Kinship performance was evaluated by simulating 1,000 kinship pairs and 1,000 unrelated individual pairs on the basis of the allele frequencies of 52 STRs, and the influence of different combinations of STR loci on the identification efficacies of different kinship was assessed by using the likelihood ratio (LR) method and identical by state (IBS) method, respectively. When the LR was greater than 10,000 or less than 0.0001 as the judgment threshold, the system efficacy of the 52 STR loci based on sequence polymorphisms for forensic identifications of full siblings and unrelated individuals was 99.85%, and those of half-siblings, grandparents-grandchildren, uncle-nephews and unrelated individuals were 61.50%, 60.95%, and 61.00%, respectively.

Conclusions: The availability of sequence polymorphism data and the increased number of STR loci could enhance the efficacy of the detection systems for kinship identifications to a certain extent. These results highlight the potential of combining length and sequence polymorphisms of STRs in forensic practice, offering a valuable tool for addressing the challenge of complex kinship identification. Future research should validate these thresholds in casework samples and expand the number of STR loci to enhance the detection efficacy for distant relationships.