Comparative and Functional Genomics最新文献

Introduction: Responses to antitubercular drugs like isoniazid (INH) are influenced by genetic polymorphisms in metabolizing enzymes and transporters.

Objectives: This study is aimed at analyzing genetic polymorphisms of NAT2, CYP2E1, and GSTM1 genes in Saudi TB patients, monitoring INH drug levels, and exploring correlations between these genetic variations, drug levels, hepatotoxicity incidence, and clinical outcomes.

Method: This prospective cohort design was conducted at King Abdul-Aziz University Hospital in Jeddah, Saudi Arabia. It followed 50 TB patients undergoing first-line anti-TB treatment for 6 months. Genotyping and INH serum concentration measurements were conducted.

Results: The mean INH plasma drug levels measured in 30 patients were 2.86 ± 2.80. The presence or absence of the GSTM1 does not statistically affect the plasma INH level between the TB patients with no significant association between GSTM1 and clinical response, while high plasma concentration of INH was significantly associated with improved clinical response. The present study demonstrated no NAT2 and CYP2E1 gene variations in Saudi TB patients but has identified a GSTM1 variant in 68% of patients. The presence or absence of the GSTM1 gene variant appears to not affect INH drug level or clinical outcomes.

Conclusion: Clinicians should consider individualized TB treatment based on genetic and demographic factors.

Background: The MTHFR 677C > T polymorphism in women has been associated with an increased risk of deep venous thrombosis and adverse pregnancy outcomes (APOs). However, research concerning its effects in men remains limited.

Methods: This study examined 662 adults with a history of pregnancies affected by chromosomal abnormalities (CAs: 343 females and 319 males), 137 adults with a history of pregnancies affected by cleft lip and palate (CLP: 71 females and 66 males), and 133 adults with a history of biochemical pregnancies (BPs: 65 females and 68 males), forming three case groups. A control group of 339 adults without APOs (221 females and 118 males) was studied. The genotypes of the MTHFR 677C > T polymorphism and Hcy levels were analyzed for all participants.

Results: Elevated Hcy levels were identified as a risk factor for CA, CLP, and BP in both adult females and males. The MTHFR 677C > T polymorphism was a risk factor for CA, CLP, and BP in females, whereas in males, it was a risk factor for CA and BP, but not for CLP. Individuals with the TT genotype exhibited the highest Hcy levels compared to those with CC and CT genotypes, across both genders and all groups. Males exhibited significantly higher Hcy levels and a significantly greater incidence of hyperhomocysteinemia compared to females across all groups.

Conclusions: The MTHFR 677C > T polymorphism was a gender-dependent risk factor for fetal CLP but was gender-independent for BP and fetal CA. Elevated Hcy levels were a gender-independent risk factor for BP, CLP, and CA. Individuals with the MTHFR 677TT genotype were more likely to have elevated Hcy levels, and there were notable gender differences in Hcy levels and hyperhomocysteinemia incidence.

Hepatocellular carcinoma (HCC) remains a major global health challenge, with limited effective treatment options, particularly in advanced-stage patients. The tumor immune microenvironment (TIME) plays a crucial role in HCC progression and treatment response, with tumor-infiltrating lymphocytes (TILs) being key modulators of immune activity. In this study, we investigated the immunosuppressive role of TIL-related genes in NASH-associated HCC (NASH-HCC) and identified their potential as independent prognostic factors. We employed Gene Set Enrichment Analysis (GSEA) and Weighted Gene Coexpression Network Analysis (WGCNA) to explore immune suppression in NASH-HCC and identify TIL-related gene modules. Machine learning approaches were utilized to construct a prognostic model, validated using multiple cohorts from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). The model’s predictive power was assessed using Kaplan–Meier survival analysis and receiver operating characteristic (ROC) curves. Furthermore, single-cell RNA sequencing (scRNA-seq) analysis was performed to examine the role of TIL-related genes in different immune cell populations within TIME. We identified 10 distinct cell types in HCC and demonstrated that T cells exhibited the highest TIL pathway activity, playing a critical role in cellular communication via MIF signaling. Our findings highlight the immunosuppressive nature of TILs in NASH-HCC and provide valuable insights into their prognostic significance, potentially guiding future immunotherapeutic strategies.

Background: Osteosarcoma (OS) is a highly aggressive bone tumor characterized by poor prognosis and frequent metastasis. Despite advances in treatment, the survival rate remains low. This study investigates the role of deubiquitinase (DUB) genes in OS to identify novel prognostic biomarkers and therapeutic targets.

Methods: We analyzed the expression of DUB genes using single-cell RNA sequencing (scRNA-seq) data from OS samples. Bulk RNA sequencing datasets were also assessed for survival correlation. A prognostic model was constructed by integrating DUB gene expression with clinical features using machine learning algorithms, including random forest and support vector machines. Immune cell infiltration in the tumor microenvironment (TME) was evaluated based on correlations between DUB gene expression and immune cell abundance.

Results: Single-cell analysis revealed significant heterogeneity in DUB gene expression across OS cell types, influencing tumor progression and cell–cell communication. The constructed prognostic model stratified OS patients into the high- and low-risk groups with significantly different survival outcomes. High-risk patients exhibited reduced immune cell infiltration and more aggressive clinical characteristics. The model was validated using three independent cohorts (TARGET-OS, GSE16091, and GSE21257), demonstrating high robustness and clinical utility.

Conclusions: DUB genes are critical regulators of OS progression and immune modulation. The developed prognostic model may serve as a promising tool for risk stratification and personalized treatment strategies in OS.

Background: Gastric cancer (GC) is a widespread type of cancer on a global scale, standing as the fifth most frequently occurring malignant disease. Dysregulation of long noncoding RNAs (lncRNAs) due to genomic mutations in noncoding DNA sequences can contribute to the development of tumors. Detecting GC at an early stage can significantly improve the chances of survival and treatment effectiveness. The current study evaluated the expression of lncRNA HCCAT5 in primary gastric tumors as well as in adjacent noncancerous tissues.

Methods: One hundred pairs of GC and adjacent noncancerous tissue samples were acquired from Tabriz International Valiasr Hospital in Iran for the study. Subsequently, RNA extraction was conducted, and this was followed by cDNA synthesis. The expression of HCCAT5 was evaluated using quantitative reverse transcriptase PCR (qRT-PCR). The relationship between clinicopathological characteristics and HCCAT5 expression was analyzed using SPSS software. Furthermore, the predictive value of HCCAT5 in GC was examined via analysis of the receiver operating characteristic (ROC) curve.

Results: HCCAT5 exhibited a significant upregulation in tumor samples in contrast to adjacent noncancerous tissues (p < 0.0001). On the other hand, no significant relationship was detected between the elevated expression of HCCAT5 and the clinicopathological features of the individuals (p > 0.05).

Conclusions: The lncRNA HCCAT5 is implicated in advancing the development of GC. Consequently, it could be considered a potential target for therapeutic interventions and a prognostic biomarker for GC patients.

Kidney renal clear cell carcinoma (KIRC), the most common type of renal cell carcinoma, is an immunobiologically and metabolically distinct tumor. Its clinical management is closely related to the tumor microenvironment (TME). Identifying its potential markers is important for improving prognosis. Therefore, in this study, we successfully constructed a prognostic model of glutathione metabolism–related molecules and screened for GGTLC1 prognostic molecules, while immunohistochemical analysis of the online database HPA and hospital patient specimens showed that GGTLC1 was highly expressed in paracancerous tissues. Taken together, the results of this study suggest that GGTLC1 is a potential prognostic biomarker associated with KIRC.

Trial Registration: Chinese Clinical Trial Registry identifier: LSKY: 2022-112-01

Background: Spinal cord injury (SCI) is a central nervous system disorder characterized by oxidative stress and inflammatory responses. Activating transcription factor 3 (Atf3) is an early-response stress-regulating gene whose abnormal upregulation exacerbates oxidative stress and inflammation. However, despite its known association with oxidative stress, the mechanism of Atf3 in SCI remains incompletely understood. This study aimed to investigate the role and mechanisms of Atf3 in SCI.

Methods: Bioinformatics analysis was performed using multiple GEO datasets to identify hub genes and key signaling pathways associated with post-SCI oxidative stress. The rat SCI model and a lipopolysaccharide (LPS)-induced PC12 cell injury model were established in vivo and in vitro to investigate whether Atf3 could ameliorate SCI progression, neuronal damage, oxidative stress, and inflammation. Chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) and luciferase reporter assays were used to analyze the interaction between Atf3 and NF-κB/p65, as well as the promoter activity of the p65 gene. Finally, the NF-κB signaling pathway was activated to observe the role of Atf3 in neuronal injury and SCI.

Results: Bioinformatics analysis revealed significant enrichment of Atf3 and the NF-κB signaling pathway in SCI datasets. Atf3 primarily colocalized with NeuN but minimally with GFAP or Iba-1. Knockdown of Atf3 significantly alleviated SCI damage, reduced oxidative stress (decreased MDA/MPO and increased SOD/GSH levels), and suppressed inflammation (reduced TNF-α, IL-1β and IL-6 levels) in both SCI rats and LPS-treated PC12 cells. However, activation of NF-κB counteracted these protective effects. ChIP-qPCR and luciferase reporter assays demonstrated that Atf3 overexpression enhanced its binding to the p65 promoter and promoted NF-κB/p65 activation, whereas Atf3 knockdown reversed these effects.

Conclusion: Downregulation of Atf3 mitigates oxidative stress and inflammation in SCI, potentially by regulating neuronal biological functions via the NF-κB pathway. These findings provide a theoretical foundation for understanding SCI pathogenesis and identifying therapeutic targets.

Background: Long noncoding RNA (lncRNA) CASC, crucial in colorectal cancer (CRC) progression, remains largely unexplored despite its potential.

Methods: The CRC data comes from The Cancer Genome Atlas (TCGA) database. The limma package was used to screen differentially expressed genes (DEGs), intersecting with CASC genes that yielded key hub lncRNAs. Next, the lncRNA–protein interaction network was developed applying Cytoscape software. The association between immune cell infiltration and lncRNAs was calculated using the ESTIMATE package, CIBERSORT package, and ssGSEA. Based on the survminer package to assess the correlation between hub gene expression levels and clinicopathologic features of CRC patients, cellular models were utilized to assess the mRNA expression levels and potential biological functions of the screened markers.

Results: We filtered 2326 DEGs that were notably enriched in pathways related to metastasis, cell growth, and EMT. This study found six hub lncRNAs (CASC15, CASC16, CASC8, CASC9, CASC19, and CASC18) showed a high diagnostic accuracy, with the area under the curve (AUC) values all exceeding 0.7. There were 44 proteins in the lncRNA–protein interaction network that interact with hub lncRNAs, among which both LIN28B and IGF2BP2 interact with six hub lncRNAs. Immune infiltration analysis indicated that the six hub lncRNAs were significantly correlated with the multiple types of immune cells. Pathological analysis demonstrated that the expression of CASC15 elevated with the progression of TNM staging. Cellular assays had revealed that all are significantly associated with CRC; particularly, CASC15 knockdown repressed the in vitro metastasis of CRC cells.

Conclusion: We constructed and validated a robust signature of six lncRNA CASC for predicting survival of CRC patients and characterizing the immune infiltration landscape. These results reveal that the CASC gene family could be a therapeutic target for CRC patients.

Introduction: Muscular dystrophy (MD) refers to a group of hereditary disorders characterized by progressive muscle degeneration, often caused by a deficiency or insufficient levels of glycoproteins in muscle cell membranes. Mutations in various genes lead to different types of MD, each with distinct clinical manifestations and inheritance patterns. The genetic heterogeneity of MD complicates the identification of the causative genes.

Materials and Methods: This research was conducted to identify the genetic basis of MD in an Iranian family with three affected members. Whole exome sequencing (WES) was performed on a proband who had initially been misdiagnosed with polymyositis. Following the identification of the disease-causing variant via WES, cosegregation analysis was carried out among two affected siblings, the asymptomatic parents, and one unaffected sibling.

Results: WES identified a homozygous nonsense variant (c.6001C>T, p.Gln2001Ter) in Exon 53 of the DYSF gene, which encodes dysferlin, a transmembrane protein essential for membrane protection and repair following damage. This stop-gain mutation results in a nonfunctional truncated protein lacking the transmembrane helix, preventing its anchorage to the membrane. Dysfunction of dysferlin is associated with limb–girdle muscular dystrophy 2B (LGMD2B) and Miyoshi myopathy.

Discussion: Bioinformatics analyses and clinical findings confirmed the pathogenicity of this variant in a homozygous state, consistent with autosomal recessive inheritance. Furthermore, structural modeling suggested that the mutation significantly disrupts the tertiary structure of dysferlin. Since the disorder onset in the proband and his two affected sisters began in the proximal limb muscles, the condition was classified as LGMD. The study highlights the diagnostic value of WES in accurately identifying disease-causing variants, offering substantial improvements in time and cost efficiency over conventional diagnostic procedures.

Background: Pituitary adenomas (PAs) are common intracranial tumors, and their aggressive phenotype exhibits a poor prognosis. We aimed to explore the aggressive feature of PAs and discover novel diagnostic markers.

Method: The datasets of GSE260487 and GSE169498, which contained invasive and noninvasive samples, were downloaded from the Gene Expression Omnibus (GEO) database. Aggressive phenotype-related gene modules were classified using the “WGCNA” package. Differentially expressed genes (DEGs) in each module were identified by the “limma” package. Next, a protein–protein interaction (PPI) network was used in the construction and identification process of key genes, and the CytoHubba tool was utilized to analyze the subnetwork and select the top 10 genes. Diagnostic markers were selected using two machine learning algorithms: support vector machine (SVM) and Lasso. Finally, the ESTIMATE and “GSVA” were applied for immune infiltration assessment.

Results: WGCNA showed that the turquoise module was closely associated with the aggressive phenotype and enriched in neural differentiation and cell migration pathways. A total of 521 DEGs were intersected with the turquoise module genes to obtain 187 overlapping genes, from which 10 hub genes related to tumor proliferation were selected to develop a PPI network. Next, we determined MYH7 as an accurate diagnostic marker, and the immune infiltration analysis revealed that MYH7 expression was negatively correlated with stromal score and immune score but positively correlated with the infiltration of antitumor cells.

Conclusion: We developed a novel marker with a strong diagnostic performance for PAs, providing novel insights for the detection and individualized treatment of PAs.