Biochemical Genetics最新文献

Previously using the omics data on allele-asymmetric gene expression (RNA-seq) and allele-asymmetry in the binding of regulatory proteins (ChIP-seq), we have determined rs590352 G→C as a potential regulatory polymorphism. Substitution G→C is situated in the protein-coding region of gene ATXN7L3B and is synonymic. The product of this gene competes with protein ATXN7L3 of the DUB module of transcription coactivator SAGA complex. The goal of our work is to study the effect of single nucleotide substitution G→C on the activity of putative cis-regulatory element in the exon 1 of ATXN7L3B. We use electrophoretic mobility shift assay (EMSA) to demonstrate that the G→C (rs590352) substitution damages the binding sites of certain transcription factors in the region of its localization. Dual luciferase assay demonstrates that this substitution significantly decreases the reporter gene expression when inserting the cassettes of double or triple repeats of the corresponding element upstream of heterologous promoter. The allele-asymmetric in vivo ATXN7L3B expression is lower in the case of allele C as compared with that of allele G. These data are useful for both the understanding of the regulation of poorly studied gene ATXN7L3B and a deeper insight into the functional role of SNPs in gene coding regions.

CD8+ T cells play a pivotal role in Chronic obstructive pulmonary disease(COPD) inflammatory pathogenesis. To elucidate the molecular mechanisms underlying CD8+ T cell involvement in COPD development, this study employed an integrated approach combining bioinformatics analysis with experimental validation to identify CD8+ T cell-associated marker genes, construct a diagnostic model, and evaluate their correlation with pulmonary function in COPD. Lung tissue sequencing data from COPD patients and controls were obtained from the Gene Expression Omnibus(GEO) database. Differential expression analysis was conducted using R on both bulk RNA-seq and single-cell RNA-seq datasets. LASSO regression analysis was subsequently applied to identify hub genes, followed by functional annotation through Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analyses. Linear regression analysis assessed correlations between key genes and pulmonary function parameters, with qRT-PCR validation performed on three lung function-associated genes using clinical samples from COPD patients and healthy controls. Our analyses identified seven CD8+ T cell-related genes (CST7, HSPA8, PXN, YPEL5, PIP4K2A, CDKN1B, PIK3IP1) that collectively formed a highly effective diagnostic model. Among these, HSPA8, PIP4K2A, and YPEL5 demonstrated significant correlations with impaired lung function in COPD patients. qRT-PCR validation confirmed PIP4K2A expression patterns in clinical samples, consistent with microarray data. These findings establish CD8+ T cell-associated biomarkers for COPD, with PIP4K2A expression showing particular relevance to lung function decline, thereby providing new molecular insights into CD8+ T cell-mediated mechanisms in COPD pathogenesis.

Elevated TSH with normal T3 and T4 levels is a sign of subclinical hypothyroidism (SCH), is often linked to autoimmune thyroiditis. Thyroid peroxidase antibodies (anti-TPO) are early markers, but their diagnostic value and genetic associations in Middle Eastern populations are not well understood. This study assessed serum TPO levels and TPO gene polymorphisms in relation to SCH in Duhok, Iraq (September-December 2024). In a case-control design, 78 patients with SCH and 75 age- and gender-matched euthyroid controls were recruited. Serum levels of TSH, T3, T4, Vitamin D, and anti-TPO were measured. Genotyping of the TPO T1936C variant was performed by ARMS-PCR. Two-sided statistical tests were applied. Correlations were assessed using Spearman's ρ, and genotype frequencies were tested for Hardy-Weinberg equilibrium. Diagnostic performance of anti-TPO was evaluated by receiver operating characteristic (ROC) analysis, including area under the curve (AUC), 95% CI, and Youden index. Patients with SCH showed significantly elevated anti-TPO levels compared to controls (107.5 ± 149.6 vs. 39.5 ± 81.6 IU/mL; p = 0.014). ROC analysis identified ≥ 60.4 IU/mL as the optimal anti-TPO cut-off for SCH prediction (AUC = 0.62, 95% CI: 0.52-0.71, sensitivity = 47.44%, specificity = 89.33%). TPO levels correlated positively with TSH (Spearman ρ = 0.174, p = 0.031), but not with T3, T4, or Vitamin D. TPO (T1936C) gene polymorphism analysis revealed no significant association with SCH (AA genotype: 80.77% in cases vs. 77.33% in controls), (GA genotype: 19.23% in cases vs. 22.67% in controls) p = 0.85. The GG genotype was absent in both groups. Anti-TPO antibodies demonstrated high specificity but modest sensitivity as diagnostic markers for SCH. The TPO T1936C variant was not associated with SCH, though this null finding may reflect the study's limited statistical power. These results highlight the role of autoimmune markers in SCH diagnosis within the Kurdish population of Duhok, Iraq.

Tuberous sclerosis complex (TSC) is a rare genetic disorder with an autosomal dominant inheritance pattern, affecting roughly 1 in 6,000 to 1 in 10,000 live births. The genetic mutations in the TSC1 or TSC2 genes lead to this condition, while TSC2 mutations tend to produce more severe symptoms at an earlier age. The research uses exome sequencing (ES) and molecular dynamics (MD) simulations to detect and study a novel pathogenic TSC2 frameshift deletion variant and its structural and functional consequences. The causative variant was identified by ES and then confirmed by Sanger sequencing and cosegregation analysis. MD simulations with GROMACS software were used to investigate the structural and functional impacts of the variant on the tuberin protein. The American College of Medical Genetics and Genomics (ACMG) guidelines were followed for the variant interpretation. We identified a novel de novo frameshift deletion variant, c.3647_3651del (p.Leu1216Profs*16), in the TSC2 gene in a 12-year-old boy with skin lesions, seizures, and autistic behaviors. A frameshift deletion variant was detected in the 31st exon of TSC2. It fulfills the pathogenic criteria established by ACMG guidelines. The structural modeling and molecular dynamics simulations show that the mutation causes three main effects: it eliminates the GAP domain while breaking intramolecular hydrogen bonds. It decreases solvent exposure, which results in decreased stability and modified conformational movements of tuberin. This study highlights the effective use of ES for TSC diagnosis and genetic counseling. Our computational analysis provides predictive molecular insights into the potential mechanisms driving TSC pathology. The combined approach could aid in developing new therapeutic and management strategies for TSC. These findings suggest that such variants could be amenable to therapeutic modulation of the mTOR pathway, for example, through mTOR inhibitors.

A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) protease family involves a critical member ADAMTS6, which is implicated in the pathogenesis of various cancers. This study explores the function of ADAMTS6 in tumor growth and angiogenesis in gastric carcinoma (GC). Using the TCGA-STAD dataset, key genes closely associated with GC prognosis were screened, and their correlation with the angiogenesis pathway was evaluated. In vitro, a GC cell model with ADAMTS6 knockdown was established, and cell proliferation, migration, invasion, and apoptosis were systematically assessed. The regulatory effect of ADAMTS6 on the angiogenic capacity of human umbilical vein endothelial cells (HUVECs) was determined via tube formation assay. In vivo, a GC xenograft mouse model was established to monitor tumor growth, and the effects of ADAMTS6 knockdown on tumor proliferation, apoptosis, and angiogenesis were comprehensively evaluated using immunohistochemistry, TUNEL staining, immunofluorescence, and Western blot analysis. ADAMTS6 was highly expressed in GC tissues and cell lines, and its expression was positively correlated with poor prognosis and tumor angiogenesis. Silencing ADAMTS6 significantly inhibited GC cell proliferation, migration, and invasion, while inducing apoptosis and attenuating the pro-angiogenic effect on HUVECs in vitro. Consistently, in vivo experiments confirmed that ADAMTS6 knockdown markedly suppressed tumor growth, as evidenced by reduced tumor volume and weight. Moreover, the expression of angiogenesis-related markers was downregulated following ADAMTS6 silencing. ADAMTS6 facilitates tumor growth and angiogenesis in GC and might act as a valuable biomarker for prognosis and a candidate target for anti-angiogenic therapeutic approaches.

Breast cancer (BC) remains the most prevalent malignancy among women and a leading cause of cancer-related mortality worldwide. Despite significant advances in recent decades, the molecular mechanisms underlying BC pathogenesis are not yet fully elucidated. Emerging evidence indicates that more than half of the members of the tripartite motif (TRIM) protein superfamily, the majority of which exhibit E3 ubiquitin ligase activity, contribute to BC initiation, progression, and metastasis by exerting functions as either oncoproteins or tumor suppressors. TRIM proteins participate in diverse cellular processes and signaling pathways. In this review, we discuss the specific molecular mechanisms by which TRIM proteins influence BC development, including post-transcriptional modifications, regulation of apoptosis and autophagy, cell cycle control, and metabolic reprogramming of glucose and lipid pathways. A notable feature of TRIM proteins is their engagement in diverse cellular processes and signaling pathways, coupled with their ability to play opposing roles - either promoting or inhibiting BC development - thus reflecting a 'yin and yang' paradigm. Collectively, current data suggest that TRIM genes and their protein products represent promising targets for therapeutic intervention and potential biomarkers for BC prognosis and disease progression.

Membrane-bound O-acyltransferase domain-containing member 7 (MBOAT7) plays an irreplaceable role in lipogenesis and neural development. Over the past decade, a few variants in MBOAT7 have been associated with intellectual disability (ID), and a spectrum of clinical symptoms, including seizures, autism spectrum disorders (ASD), and speech impairment. DNA samples from two of the three affected members of a large Iranian Azeri family with moderate ID and no major dysmorphic features were investigated by whole exome sequencing (WES). Bioinformatic tools were used to identify and evaluate the pathogenicity of the candidate variants. The most likely causative variant was pursued by Sanger sequencing in patients and their relatives. ACMG guidelines and in silico analysis, including molecular modeling, were used to validate the identified variant of uncertain significance (VUS). An in-frame deletion, NM_024298.5: c.37_39 del (p.Leu13del) in the MBOAT7 gene, which had not been previously reported with homozygous genotype, was identified as a possible cause of the clinical conditions in patients. Sanger analysis confirmed the recessive inheritance pattern of this variant in probands and 14 relatives. In-silico modeling of the mutant protein revealed structural changes resulting from removing a highly conserved amino acid. The current study has expanded the MBOAT7 gene variant spectrum and clarified variable phenotypic features to the associated ID criteria. Meanwhile, we have provided insights into the importance of the MBOAT7 protein's first alpha helix in terms of its functionality and solid evidence regarding a VUS's pathogenicity. Additionally, this study presents the oldest recorded case of MBOAT7-related ID in a 51-year-old female to date.

German chamomile (Matricaria chamomilla) is a medicinal herb that promotes improved digestion and reduces insomnia. Although it is widely used worldwide, the mechanism of induction of drug-metabolizing enzymes is unknown. We found that German chamomile extracts induced cytochrome P450 expression at the transcriptional stage. Cyp3a11 expression is decreased at night in wild-type mice, but German chamomile extract induced nocturnal Cyp3a11 and Cyp1a2 expression. German chamomile extract increased the nuclear protein expression of the clock gene BMAL1, which drives and abolishes the rhythm of Cyp3a11 expression. By contrast, German chamomile extract did not significantly alter clock gene expression in the suprachiasmatic nucleus (SCN). Similarly, it did not affect the mRNA expression of the clock genes in the kidneys. Because it did not induce the mRNA expression of ATP-binding cassette (ABC) transporters (Abcb1a, Abcc2, Abcc4, and Abcg2) in the kidney, German chamomile extract had no effect on the transcription of pharmacokinetics-related molecules other than CYPs. German chamomile extract promoted liver-selective nuclear transfer rhythm changes in clock genes and induced the expression of CYPs. This study may help to explain the mechanism of drug interactions associated with chronic German chamomile extract consumption.

Schizophrenia (SCZ) is a deleterious neuropsychological disorder with a worldwide incidence of 1% and unknown etiology. Understanding the role of genetic variants in disease development would enable us to explain the disorder's molecular mechanism and find a more effective prognostic approach. Several studies in various European and East Asian populations have displayed the association of schizophrenia with functional polymorphisms such as rs16944 and rs1143634 that lie within inflammatory pathway genes. This study aimed to evaluate the association of Interleukin-1 beta (IL1B) variants (rs16944, rs1143634) with schizophrenia in the Iranian population for the first time. 565 individuals (240 cases and 325 controls) were recruited. Genotyping was conducted for IL1B single nucleotide polymorphisms (SNPs) (rs16944 and rs1143634) using polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP). In addition, the haplotype analysis was conducted. All statistical analysis was performed using SPSS version 26. Regarding rs1143634 (C > T), T carrier genotypes (CT, TT) compared to CC homozygous genotypes showed a significantly more protective effect (p-value < 0.001). Similarly, concerning the co-dominant model, CT heterozygous genotypes in comparison with homozygous genotypes (CC, TT) illustrated a protective impact regarding schizophrenia (p-value < 0.001). Findings showed a significant difference between cases and healthy controls regarding the rs1143634 (C > T) allele frequency (p-value = 0.025), whereas it determined no considerable difference given rs16944 (p-value = 0.41). Furthermore, in the case of rs16944 (T > C), we found no significant association between case and control groups (p-value = 0.69). Haplotype analysis demonstrated that the C-C (rs1143634-rs16944) haplotype was significantly associated with the risk of schizophrenia (p-value = 0.013). The findings suggest that IL1B rs1143634 (C > T) is significantly associated with SCZ in the Iranian population.