Comparative and Functional Genomics最新文献

Objective: T cell exhaustion (TEX) is a critical determinant of immune resistance. This study was performed to investigate the key genes linked to TEX in cholangiocarcinoma (CCA) and construct a TEX-associated gene signature to forecast the prognosis of patients with CCA.

Methods: Based on the expression data acquired from the E-MTAB-6389 dataset, the TEX-related modules and module genes were identified using weighted coexpression network analysis (WGCNA). Subsequently, a TEX-related prognostic signature was built by using the univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analysis. The immune cell infiltration in each CCA sample was evaluated using the single-sample gene set enrichment analysis (ssGSEA) package, followed by single-cell RNA sequencing (scRNA-seq) analysis. Furthermore, the expression of TEX-related genes in the gene signature was experimentally validated in CCA cells by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and western blot analysis.

Results: A total of 15 TEX-associated modules and 23 module genes were identified. Then, a four-gene signature related to TEX was established, containing Palladin, Cytoskeletal Associated Protein (PALLD), Member RAS Oncogene Family (RAB31), ADAM Metallopeptidase With Thrombospondin Type 1 Motif 2 (ADAMTS2), and WISP1, which could predict prognosis of patients with CCA. Moreover, neutrophils, endothelial cells, B cells, and T cells exhibited significant infiltration in CCA samples, and these four TEX-related genes were both significantly positively correlated with T cells, endothelial cells, and B cells while negatively correlated with neutrophils. Moreover, a total of 13 cell types were annotated after scRNA-seq analysis. Notably, RAB31 was mainly highly expressed in monocytes, macrophages, DC2 (Dendritic Cells 2), and DC3 (Dendritic Cells 3), and PALLD, ADAMTS2, and WISP1 were mainly overexpressed in fibroblasts. Furthermore, experimental validation revealed that the expression levels of PALLD, RAB31, ADAMTS2, and WISP1 were consistent with the trend results of bioinformatics analysis.

Conclusion: A prognostic signature was developed by four TEX-related genes, including PALLD, RAB31, ADAMTS2, and WISP1, which might be a powerful predictor for the prognosis of patients with CCA. These TEX-related genes were related to the infiltration of neutrophils, endothelial cells, B cells, and T cells in CCA.

Taro (Colocasia esculenta (L.) Schott.) is an important edible and economically valuable crop that is also a source of high-quality starch. Its quality is determined by the content and proportion of amylopectin. Based on transcriptome sequencing of corms at different growth stages (T1–T6), 34,603 transcripts and 1727 novel genes with functional annotation were obtained. In total, 11,865 differentially expressed genes (DEGs) were identified among six development stages, with 3836 and 3404 DEGs in T2 versus T3 and T3 versus T4, respectively. The regulatory network of taro starch synthesis was constructed on the DeGNServer. Among three cloned soluble starch synthase (SS) genes, CeSS II might be the key gene responsible for soluble starch synthesis in taro corm. The putative transcription factor CeMyb108 might play a negative role in starch synthesis. Sanger sequencing CeSS II gene revealed a single nucleotide polymorphism (SNP) between two variety groups with high and low starch content. A kompetitive allele-specific PCR (KASP) marker, namely, CeSS II-SNP, was developed and validated in a natural population of 89 taro accessions. The starch content of the C:T group amounts to 517.45 mg/g, which is significantly (22.3%) higher than its counterpart (T:T). This newly developed marker is proved to be effective and would facilitate marker-assisted breeding for taro with high starch content.

Purpose: In 2014, the Society of Gynecologic Oncology (SGO) recommended universal germline testing for all patients with epithelial ovarian cancer (EOC), fallopian tube cancer (FTC), or peritoneal cancer (PC). Despite this position statement, genetic testing (GT) uptake among affected patients remains well below the universal testing goal. The aim of this study is to evaluate the impact of an internal policy change on the GT rate at a single institution.

Patients and Methods: This investigation was an Institutional Review Board (IRB)–approved (#22-00711) retrospective cohort study which took place at a single institution from June 2021 to April 2022. The study assessed GT uptake among patients diagnosed with EOC, FTC, and PC to evaluate the following internal policy change integrating point-of-care (POC) GT.

Results: A total of 272 patients were identified with 47 patients excluded due to nonepithelial tumors. Genetic counseling was documented in 94.2% of eligible patients (212/225) and completed in 90.2% (203/225). Of the 22 (9.8%) who were not genetically tested, 27% (6/22) were offered and declined. Deleterious mutations were identified in 22% (45/205) of patients tested. Of these, 82.2% (37/45) were in BRCA, 6.8% (3/45) in Lynch-associated mutations (MSH2, MSH6, MLH1, and PMS2), 4.4% (2/45) in RAD51, 4.4% (2/45) in BRIP1, and 2.2% (1/45) in an unknown deleterious mutation reportedly diagnosed at a different facility.

Conclusion: Internal policy developed based on analysis of compliance with the SGO position statement and subsequent implementation of POC testing led to a significant increase in GT, indicating improvement in quality medical care. GT rates in this population are markedly higher than reported in the literature.

Purpose: This study is aimed at exploring the role of pyroptosis-related genes in the development, immune infiltration, and clinical features of lung adenocarcinoma.

Method: Pyroptosis-related genes were searched using online databases, including MSigDB, Gene, and GeneCards. We explored pyroptosis-related gene expression patterns in lung adenocarcinoma using the UALCAN database. Functional enrichment analysis of pyroptosis-related genes in lung adenocarcinoma was performed using the Metascape database. A protein–protein interaction network was constructed using the STRING database, and the outcomes were visualized using Cytoscape. The top five core genes were screened utilizing the MCC algorithm with its cytoHubba plugin. The correlation between immune cell infiltration, diagnosis, and prognosis of core genes in lung adenocarcinoma was explored using the TIMER 2.0, TCGA, and Kaplan–Meier plotter databases. A nomogram was constructed to predict the survival of patients with lung adenocarcinoma using Cox regression analysis, and its clinical value was validated. Samples of paraffin-embedded lung adenocarcinoma tissues were collected and subjected to immunohistochemical tests to verify the expression of core genes in lung adenocarcinoma and adjacent tissues.

Results: Overall, 202 genes related to pyroptosis were identified, with 67 upregulated and 60 downregulated in lung adenocarcinomas. The top five core genes—namely, CASP1 (caspase1), PYCARD (PYD and CARD domain-containing protein), NLRP3 (NOD-like receptor protein 3), AIM2 (absent in melanoma 2), and NLRP1 (NOD-like receptor protein 1)—related to lung adenocarcinoma pyroptosis were selected. The correlation analysis of immune cell infiltration showed that CASP1, NLRP3, and AIM2, which showed that pyroptosis was involved in the infiltration of immune cells in the tumor microenvironment and NLRP1 exhibited high diagnostic efficacy, while PYCARD demonstrated poor diagnostic efficacy. High expression of CASP1, NLRP3, and NLRP1 correlated with a better prognosis (p < 0.05), while elevated AIM2 expression was associated with a poor prognosis (p < 0.05). However, PYCARD exhibited no significant correlation with prognosis (p > 0.05). The immunohistochemistry results showed that positive rates of CASP1, NLRP3, AIM2, and NLRP1 were 20%, 15%, 70%, and 10%, respectively, while in adjacent tissues, the positive rates were 60%, 60%, 20%, and70%, indicating high expression of AIM2 and low expression of CASP1, NLRP3, and NLRP1 in lung adenocarcinoma.

Conclusion: CASP1, NLRP3, AIM2, and NLRP1 are core pyroptotic genes in lung adenocarcinoma and exhibit a strong correlation with immune cell infiltration, diagnosis, and prognosis of this condition. These genes may be useful in the clinical diagnosis and treatment of patients with lung adenocarcinoma.

Background: PANoptosis, a recently characterized inflammatory programmed cell death modality orchestrated by the PANoptosome complex, integrates molecular mechanisms of pyroptosis, apoptosis, and necroptosis. Although this pathway potentially mediates tumor progression, its role in lung adenocarcinoma (LUAD) remains largely unexplored.

Methods: Through comprehensive single-cell transcriptomic profiling, we systematically identified critical PANoptosis-associated gene signatures. Prognostic molecular determinants were subsequently delineated via univariate Cox proportional hazards regression analysis. We constructed a PANoptosis-related optimal model (PROM) through the integration of 10 machine learning algorithms. The model was initially developed using The Cancer Genome Atlas (TCGA)-LUAD cohort and subsequently validated across six independent LUAD cohorts. Model performance was evaluated using mean concordance index. Furthermore, we conducted extensive multiomics analyses to delineate differential pathway activation patterns and immune cell infiltration profiles between PROM-stratified risk subgroups.

Results: Cellular populations exhibiting elevated PANoptosis signatures demonstrated enhanced intercellular signaling networks. PROM demonstrated superior prognostic capability across multiple validation cohorts. Receiver operating characteristic curve analyses revealed area under the curve values exceeding 0.7 across all seven cohorts, with several achieving values above 0.8, indicating robust discriminative performance. The model score exhibited significant correlation with immunological parameters. Notably, high PROM scores were associated with attenuated immune responses, suggesting an immunosuppressive tumor microenvironment. Multiomics investigations revealed significant alterations in critical oncogenic pathways and immune landscape between PROM-stratified subgroups.

Conclusion: This investigation establishes PROM as a clinically applicable prognostic tool for LUAD risk stratification. Beyond its predictive utility, PROM elucidates PANoptosis-associated immunological and biological mechanisms underlying LUAD progression. These findings provide novel mechanistic insights into LUAD pathogenesis and may inform the development of targeted therapeutic interventions and personalized treatment strategies to optimize patient outcomes.

Background: Helicobacter pylori (HP) is associated with the development of various stomach diseases, one of the major risk factors for stomach adenocarcinoma (STAD).

Methods: The HP infection score between tumor and normal groups was compared by single-sample gene set enrichment analysis (ssGSEA). The key modules related to HP infection were identified by weighted gene coexpression network analysis (WGCNA), and functional enrichment analysis was conducted on these module genes. Further, the limma package was used to screen the differentially expressed genes (DEGs) between HP-positive and HP-negative STAD. The prognostic genes were obtained to construct the riskscore model, and the performance of the model was validated. The correlation between riskscore and tumor immune microenvironment (TIME) was analyzed by Spearman’s method. The single-cell atlas of HP-positive STAD was delineated. The mRNA expression levels of the prognostic genes were verified using STAD cells, and the migration and invasion capacities of STAD cells were evaluated by using the wound healing assay and transwell assay.

Results: The HP infection score in the tumor group was significantly higher than that in the normal group. The purple and royal blue modules showed higher correlation with HP infection in STAD, and these module genes were enriched in the immune-related pathway. Further, five prognostic genes (CTLA4, CPVL, EMB, CXCR4, and FAM241A) were screened from the HP infection–related DEGs, which were utilized for establishing the riskscore model, with good robustness. Riskscore exhibited strong correlation with TIME in STAD. Single-cell atlas of HP-positive STAD revealed that CXCR4 is highly expressed in Epithelial Cell 1, Epithelial Cell 2, and parietal cells of the tumor group. CPVL, EMB, CTLA4, FAM241A, and CXCR4 showed high expression in STAD cells, and the silencing of CPVL could suppress the migration and invasion of STAD cells.

Conclusion: This study established a riskscore model based on HP infection–related genes, which could provide reference for prognostic prediction and treatment targets of STAD.

Background: Recently, exportin gene family members have been demonstrated to play essential roles in tumor progression. However, research on the clinical significance of exportin gene family members is limited in clear cell renal cell carcinoma (ccRCC).

Methods: Pan-cancer data, ccRCC multiomics data, and single-cell sequence were included to analyze the differences in DNA methylation modification, single nucleotide variations (SNVs), copy number variations (CNVs), and expression levels of exportin gene family members. Non-negative matrix factorization was used to identify molecular subtypes based on exportin gene family members, and the prognostic and biological differences of different molecular subtypes were compared across multiple dimensions.

Results: Exportin gene family members were upregulated in pan-cancer expression, and their aberrant expression was significantly influenced by DNA methylation, SNV, and CNV, particularly in ccRCC. Based on the expression matrix of exportin gene family members, two molecular subtypes, exportin famliy genes (XPO)–based subtype 1 (XPS1) and exportin famliy genes (XPO)–based subtype 2 (XPS2), were identified. The expression levels of exportin gene family members in the XPS2 subtype were significantly higher than those in XPS1, and the prognosis was poorer. The XPS2 subtype had lower immune component abundance and higher immune exhaustion scores. Its response rate to immunotherapy was significantly lower than that of the XPS1 subtype, but it was more sensitive to small molecules, including mercaptopurine and nutlin. Among them, exportin-1 (XPO1) is a potential diagnostic and therapeutic target for ccRCC, which can promote renal cancer progression by activating the PI3K-AKT-mTOR (phosphatidylinositol 3-kinase (PI3K)/AKT serine/threonine kinase (AKT)/mechanistic target of rapamycin (MTOR)) and interferon alpha pathways.

Conclusion: This study analyzed the variations of exportin gene family members at the pan-cancer level and identified two distinct ccRCC subtypes, which can guide personalized management of patients.

Red raspberry (Rubus idaeus L.), which is an important nutritional source for human health, belongs to fruit crops of the Rosaceae family. Here, we used Pacific Biosciences single-molecule real-time (SMRT) sequencing and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to assemble genomes and reported a high-quality Rubus idaeus L. (DNS-1) genome with 321.29 Mb assembled into seven chromosomes. The LAI score of the DNS-1 genome assembly was 21.32, belonging to gold quality. Approximately 52.3% of the assembly sequences were annotated as repetitive sequences, and 24.15% were composed of long terminal repeat elements. A total of 29,814 protein-coding genes and 2474 pseudogenes were predicted in DNS-1. We characterized the complete genomes of DNS-1 and compared them to those of seven other species. We found that 652 gene families were unique to DNS-1 and they were shaped from an ancestor. There were 1000 and 5193 gene families that expanded and contracted in the DNS-1 genome. The Rubus idaeus L. genome can be used to understand the structure and evolution of Rosaceae genomes and can be developed to identify genes controlling important traits and improve breeding work.

Circular RNA (circRNA) serves as a competitive endogenous RNA (ceRNA) that plays a pivotal role in the initiation and progression of breast cancer (BC). However, compared to other noncoding RNAs (ncRNAs), research on circRNA in BC is still in its infancy. Through the analysis of circRNA datasets in the GEO database, hsa_circ_0001314, which is upregulated in BC, was selected as the focus of this study. RT-qPCR analysis showed that hsa_circ_0001314 was significantly upregulated in BC tissues and cells. Subsequently, the biological functions of hsa_circ_0001314 in BC cells were examined through CCK-8, wound healing, transwell invasion, and flow cytometry analyses. The research demonstrated that knocking down the expression level of hsa_circ_0001314 significantly inhibited cell proliferation, migration, and invasion abilities while notably promoting cell apoptosis. Bioinformatics methods were used to predict downstream miRNAs and mRNAs that may interact with hsa_circ_0001314, constructing a ceRNA regulatory network related to hsa_circ_0001314. RT-qPCR confirmed that hsa_circ_0001314 functions as a sponge for hsa-miR-548aj-3p, competitively binding to hsa-miR-548aj-3p to activate the MAPK signaling pathway and regulate the expression of MAPK8 and MAP3K1. The findings uncover the potential of hsa_circ_0001314 as a novel prognostic biomarker and therapeutic target for BC patients.