Genetics research最新文献

Purpose: The transcriptional regulatory factors binding to the polymorphic site C-1888T in the promoter region of the palate, lung, and nasal epithelium clone (PLUNC) gene were identified to investigate whether the C-1888T polymorphic site affects the transcriptional regulation and function of PLUNC gene. Materials and Methods: Three genotypes of C-1888T polymorphic locus were screened from established nasopharyngeal carcinoma (NPC) cells, and the mRNA expression levels of PLUNC gene in different genotypes were detected. The respective transcription factors that were more likely to bind with A or G in SNP were predicted by biological information and preliminarily verified in vitro by gel electrophoresis migration rate analysis. Ulteriorly, the NPC cell lines were analyzed through chromatin immunoprecipitation combined with PCR amplification to confirm that the transcription factors could bind to the PLUNC gene promoter. Results: The cell lines 5-8F, 6-10B, CNE1, and CNE2 were heterozygous CT type, SUNE1 was homozygous CC type, and C666-1 was homozygous TT type. The expression of PLUNC gene was significantly different among all cell lines (F = 33.844, p < 0.001), and the gene expression level of CC type was significantly lower than TT type (p < 0.001). Gel electrophoresis mobility analysis confirmed that the transcription factors XFD3 and EVI1 could bind to the PLUNC gene promoter when the SNP was A and G, respectively. PCR amplification combined with chromatin immunoprecipitation showed that EVI1 could bind to the DNA fragment of the promoter region of PLUNC gene in SUNE1 NPC cells. Conclusion: The transcription factors XFD3 and EVI1 may be involved in the transcriptional regulation of PLUNC gene, and EVI1 can bind to the promoter region of PLUNC gene in SUNE1 NPC cells, thus associated with the susceptibility/risk of NPC.

Backgrounds: Glioma stands as one of the most formidable brain tumor types, with patient outcomes remaining bleak even in the face of advancements in treatment modalities. FBXW4, a constituent of the F-box and WD repeat domain-containing protein family, is recognized for its participation in diverse cellular activities, including those related to tumor dynamics. Yet, the therapeutic relevance and specific role of FBXW4 in the context of glioma are not well defined. This study aims to elucidate the functional dynamics and significance of FBXW4 in glioma cases.

Methods: This research undertook a comprehensive analysis of FBXW4's expression patterns and clinical relevance in glioma by harnessing data from the TCGA and GTEx databases.

Results: The investigation revealed a distinct downregulation of FBXW4 in glioma tissues compared to normal brain counterparts, with a pronounced correlation between FBXW4 levels and disease severity. Intriguingly, FBXW4 expression inversely related to WHO tumor grades, with the most advanced grade IV gliomas exhibiting the lowest FBXW4 levels, whereas grade II tumors demonstrated the highest. Cases presenting with IDH1/2 mutations or 1p/19q codeletions were also associated with elevated FBXW4 levels. Furthermore, diminished FBXW4 expression aligned with an increased risk of mortality.

Conclusions: The findings suggest that FBXW4 holds promise as a prognostic marker and a potential therapeutic avenue in glioma management. Nonetheless, future research is imperative to decode the intricate signaling pathways involving FBXW4 and to understand its broader clinical ramifications in glioma treatment paradigms.

Background: Clear cell renal cell carcinoma (ccRCC) is a renal cortical malignancy with a complex pathogenesis. Identifying ideal biomarkers to establish more accurate promising prognostic models is crucial for the survival of kidney cancer patients.

Methods: Seurat R package was used for single-cell RNA-sequencing (scRNA-seq) data filtering, dimensionality reduction, clustering, and differentially expressed genes analysis. Gene coexpression network analysis (WGCNA) was performed to identify the cytotoxicity-related module. The independent cytotoxicity-related risk model was established by the survival R package, and Kaplan-Meier (KM) survival analysis and timeROC with area under the curve (AUC) were employed to confirm the prognosis and effectiveness of the risk model. The risk and prognosis in patients suffering from ccRCC were predicted by establishing a nomogram. A comparison of the level of immune infiltration in different risk groups and subtypes using the CIBERSORT, MCP-counter, and TIMER methods, as well as assessment of drug sensitivity to conventional chemotherapeutic agents in risk groups using the pRRophetic package, was made.

Results: Eleven ccRCC subpopulations were identified by single-cell sequencing data from the GSE224630 dataset. The identified cytotoxicity-related T-cell cluster and module genes defined three cytotoxicity-related molecular subtypes. Six key genes (SOWAHB, SLC16A12, IL20RB, SLC12A8, PLG, and HHLA2) affecting prognosis risk genes were selected for developing a risk model. A nomogram containing the RiskScore and stage revealed that the RiskScore contributed the most and exhibited excellent predicted performance for prognosis in the calibration plots and decision curve analysis (DCA). Notably, high-risk patients with ccRCC demonstrate a poorer prognosis with higher immune infiltration characteristics and TIDE scores, whereas low-risk patients are more likely to benefit from immunotherapy.

Conclusions: A ccRCC survival prognostic model was produced based on the cytotoxicity-related signature, which had important clinical significance and may provide guidance for ccRCC treatment.

Backgroundsand Aims. Colorectal cancer (CRC) represents a major global health challenge, necessitating comprehensive investigations into its underlying molecular mechanisms to enhance diagnostic and therapeutic strategies. This study focuses on elucidating the oncogenic role of Membrane-Associated Ring-CH-Type Finger 9 (MARCHF9), a RING-Type E3 ubiquitin transferase, in CRC. We aim to assess MARCHF9's clinical significance, functional impact on CRC progression, and its potential as a prognostic biomarker. Methods. We leveraged data from the Cancer Genome Atlas (TCGA) cohort to evaluate MARCHF9 expression profiles in CRC. In vitro experiments involved siRNA-mediated MARCHF9 knockdown in COAD cell lines (SW480 and LoVo). Cell proliferation and invasion assays were conducted to investigate MARCHF9's functional relevance. Survival analyses were performed to assess its prognostic role. Results. Our analysis revealed significantly elevated MARCHF9 expression in CRC tissues compared to normal colorectal tissues (P < 0.05). High MARCHF9 expression correlated with advanced clinical stages, distant metastases, and the presence of residual tumors in CRC patients. Survival analyses demonstrated that high MARCHF9 expression predicted unfavorable overall and disease-free survival outcomes (P < 0.05). In vitro experiments further supported its oncogenic potential, with MARCHF9 knockdown inhibiting COAD cell proliferation and invasion. Conclusions. This study unveils the oncogenic role of MARCHF9 in CRC, highlighting its clinical relevance as a potential biomarker and therapeutic target. MARCHF9's association with adverse clinicopathological features and its functional impact on cancer cell behavior underscore its significance in CRC progression. Further research is essential to elucidate precise mechanisms by which MARCHF9 enhances tumorigenesis and to explore its therapeutic potential in CRC management.

Esophageal cancer is a major global health challenge with a poor prognosis. Recent studies underscore the extracellular matrix (ECM) role in cancer progression, but the full impact of ECM-related genes on patient outcomes remains unclear. Our study utilized next-generation sequencing and clinical data from esophageal cancer patients provided by The Cancer Genome Atlas, employing the R package in RStudio for computational analysis. This analysis identified significant associations between patient survival and various ECM-related genes, including IBSP, LINGO4, COL26A1, MMP12, KLK4, RTBDN, TENM1, GDF15, and RUNX1. Consequently, we developed a prognostic model to predict patient outcomes, which demonstrated clear survival differences between high-risk and low-risk patient groups. Our comprehensive review encompassed clinical correlations, biological pathways, and variations in immune response among these risk categories. We also constructed a nomogram integrating clinical information with risk assessment. Focusing on the TENM1 gene, we found it significantly impacts immune response, showing a positive correlation with T helper cells, NK cells, and CD8+ T cells, but a negative correlation with neutrophils and Th17 cells. Gene Set Enrichment Analysis revealed enhanced pathways related to pancreatic beta cells, spermatogenesis, apical junctions, and muscle formation in patients with high TENM1 expression. This research provides new insights into the role of ECM genes in esophageal cancer and informs future research directions.

Bladder cancer has recently seen an alarming increase in global diagnoses, ascending as a predominant cause of cancer-related mortalities. Given this pressing scenario, there is a burgeoning need to identify effective biomarkers for both the diagnosis and therapeutic guidance of bladder cancer. This study focuses on evaluating the potential of high-definition computed tomography (CT) imagery coupled with RNA-sequencing analysis to accurately predict bladder tumor stages, utilizing deep residual networks. Data for this study, including CT images and RNA-Seq datasets for 82 high-grade bladder cancer patients, were sourced from the TCIA and TCGA databases. We employed Cox and lasso regression analyses to determine radiomics and gene signatures, leading to the identification of a three-factor radiomics signature and a four-gene signature in our bladder cancer cohort. ROC curve analyses underscored the strong predictive capacities of both these signatures. Furthermore, we formulated a nomogram integrating clinical features, radiomics, and gene signatures. This nomogram's AUC scores stood at 0.870, 0.873, and 0.971 for 1-year, 3-year, and 5-year predictions, respectively. Our model, leveraging radiomics and gene signatures, presents significant promise for enhancing diagnostic precision in bladder cancer prognosis, advocating for its clinical adoption.

Materials and methods: This study included 66 patients with CLL, diagnosed between 2020 and 2022, and 100 healthy controls. HLA class I and class II genes (HLA-A/B/C, HLA-DQA1/DQB1/DPA1/DPB1, and HLA-DRB1/3/4/5) were investigated using next-generation sequencing technology.

Results: Several HLA alleles were strongly associated with CLL. The most important finding was that HLA-DRB1^∗04:02:01 (p=0.001, OR = 1.05) and HLA-DRB3^∗02:01:01 (p=0.009, OR = 1.03) have a predisposing role in CLL development. Moreover, we identified that HLA-A^∗24:02:01 0.01 (p=0.01, OR = 0.38), HLA-DQA1^∗05:05:01 (p=0.01, OR = 0.56), HLA-DQB1^∗03:02:01 (p=0.03, OR = 0.40), and HLA-DRB4^∗01:03:01 (p=0.03, OR = 0.54 alleles have protective roles. Correlations between HLA expression and gender showed that women had a higher expression of protective HLA alleles when compared to men.

Conclusions: Our data are the first to indicate that in Romanian patients with CLL, the HLA-A^∗24:02:01 and HLA-DQA1^∗05:05:01 alleles have a protective role against CLL development, whereas HLA-DRB1^∗04:02:01 and HLA-DRB3^∗02:01:01alleles are positively associated with CLL.

Despite much attention given to the history of goat evolution in Kenya, information on the origin, demographic history, dispersal route, and genetic diversity of Galla goats remains unclear. Here, we examined the genetic background, diversity, demographic history, and population genetic variation of Galla goats using mtDNA D-loop and HSP70 single-nucleotide polymorphism markers. The results revealed 90 segregating sites and 68 haplotypes in a 600-bp mtDNA D-loop sequence. The overall mean mitochondrial haplotype diversity was 0.993. The haplotype diversities ranged between 0.8939 ± 0.0777 and 1.0000 ± 0.0221 in all populations supporting high genetic diversity. Mitochondrial phylogenetic analysis revealed three Galla goat haplogroups (A, G, and D), supporting multiple maternal ancestries, of which haplogroup A was the most predominant. Analysis of molecular variance (AMOVA) showed considerable variation within populations at 94.39%, evidence of high genetic diversity. Bimodal mismatch distribution patterns were observed while most populations recorded negative results for Tajima and Fu's Fs neutrality tests supporting population expansion. Genetic variation among populations was also confirmed using HSP70 gene fragment sequences, where six polymorphic sites which defined 21 haplotypes were discovered. Analysis of molecular variance revealed a significant FST index value of 0.134 and a high FIS index value of 0.746, an indication of inbreeding. This information will pave the way for conservation strategies and informed breeding to improve Galla or other goat breeds for climate-smart agriculture.