Functional & Integrative Genomics最新文献

Breast cancer (BC) remains one of the most prevalent malignancies affecting women worldwide, necessitating ongoing research to improve treatment outcomes and minimize adverse effects associated with chemotherapy. This article explores the role of genetic variations, particularly single nucleotide polymorphisms (SNPs), in influencing the efficacy and toxicity of chemotherapeutic agents used in BC treatment. It highlights the impact of polymorphisms in drug metabolism and transport genes, such as UDP-glucuronosyltransferase 1A1 (UGT1A1), carbonyl reductase 1 (CBR1), and ATP-binding cassette multidrug transporter (ABCB1) on the risk of adverse effects, including cardiotoxicity and hematological toxicities. By identifying specific SNPs associated with drug response and toxicity, this research underscores the potential for personalized medicine approaches to optimize treatment regimens, enhance therapeutic efficacy, and minimize side effects in BC patients. The findings advocate for the integration of genetic screening in clinical practice to improve patient outcomes and tailor chemotherapy based on individual genetic profiles.

Acute respiratory distress syndrome (ARDS) is a life-threatening condition characterized by severe hypoxemia and high mortality. Ferroptosis, a form of regulated cell death driven by iron accumulation and lipid peroxidation, has emerged as a critical mechanism in ARDS pathogenesis. However, the molecular regulators of ferroptosis in ARDS remain unclear. This study integrates multi-omics analysis and experimental validation to identify ferroptosis-related targets in ARDS. Bronchoalveolar lavage fluid (BALF) samples from ARDS patients and healthy controls were subjected to proteomics and metabolomics analysis. Transcriptomic data from the GSE243066 dataset and ferroptosis-related gene databases were integrated to identify key genes. Functional enrichment analyses were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. An LPS-induced ARDS mouse model was established for experimental validation, including Western blotting, histopathology, and ferroptosis-related biochemical assays. Multi-omics analysis identified YWHAE as a ferroptosis-associated gene significantly upregulated in ARDS. Functional enrichment revealed key pathways, including ferroptosis, hypoxia-inducible factor-1 signaling, and oxidative stress responses. Proteomic and transcriptomic integration highlighted 51 overlapping differentially expressed genes, with YWHAE emerging as a central hub in the protein–protein interaction network. Metabolomics analysis further revealed glutathione and cysteine metabolism as critical pathways linked to ferroptosis. In the ARDS mouse model, ferroptosis inhibitor ferrostatin-1 (Fer-1) attenuated LPS-induced lung injury, reduced oxidative stress markers, and downregulated YWHAE expression. This study identifies YWHAE as a novel ferroptosis-related target in ARDS through multi-omics analysis and experimental validation. These findings provide new insights into the molecular mechanisms of ferroptosis in ARDS and highlight YWHAE as a potential therapeutic target for future interventions.

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The notable comorbidity among autoimmune diseases underscores their shared genetic underpinnings, particularly evident in rheumatoid arthritis (RA), type 1 diabetes (T1D), and multiple sclerosis (MS). However, the exact components and mechanisms of this shared genetic structure remain poorly understood. Here we show that ROMO1 is a key shared genetic component among RA, MS, and T1D. Using differential gene expression (DGE) and LASSO regression analyses of bulk RNA-seq data from whole blood tissues, we identified ROMO1 as a potential shared genetic factor. A multi-sample analysis with external Gene Expression Omnibus (GEO) data revealed ROMO1’s consistent association with immune cell patterns across tissues in all three diseases. Single-gene Gene Set Enrichment Analysis (GSEA) suggested ROMO1’s involvement in the reactive oxygen species (ROS) pathway, which was further substantiated by conjoint analysis with 256 ROS pathway-related genes(ROSGs) from Molecular Signatures Database (MSigDB). Single-gene Receiver Operating Characteristic (ROC) analysis highlighted ROMO1’s potential as a disease biomarker. Single-cell RNA sequencing (scRNA-seq) analysis showed significantly altered ROMO1 expression in monocytes and other immune cells compared to healthy control (HC). Immune infiltration analysis revealed ROMO1’s significant association with monocytes across all three diseases. Furthermore, two-sample Mendelian randomization (MR) analysis using genome-wide association studies (GWAS) data demonstrated that ROMO1 could regulate epitopes on monocytes, potentially lowering autoimmune disease risk. Our findings clarify the importance of ROMO1 in the shared genetic architecture of RA, MS, and T1D, and its underlying mechanism in disease development.

The treatment options for pancreatic ductal adenocarcinoma (PDAC) remain limited. It is therefore important to explore new therapeutic targets and strategies for better treatment and prognosis for patients with PDAC. NIMA-related kinase 7 (NEK7) is a serine/threonine kinase involved in PDAC development. Moreover, NEK7 was reported to regulate NLRP3 inflammasome and cell pyroptosis. To evaluate the role of NEK7 in PDAC, we performed RNA sequencing analysis in PDAC cells, and a series of bioinformatics analyses were employed to determine the biological function of NEK7 in PDAC. We identified a NEK7-Specific Pyroptosis Gene Set (NEK7-SPGS) by high-throughput transcriptome sequencing combining Gene Set Enrichment Analysis (GSEA). We reveal that NEK7-SPGS is highly associated with T helper cell infiltration and inflammatory response of PDAC. We therefore proposed that NEK7-SPGS might have potential for tumor microenvironment remodeling via T cells induced inflammatory response. Using dataset from TCGA database, we established a NEK7-SPGS-related prognostic signature for patients with PDAC. Subsequently, sensitivity estimation of chemotherapeutic drugs revealed a series of chemotherapy agents according to the NEK7-SPGS-related prognostic signature, including gemcitabine and paclitaxel, drugs that have been used as conventional agents for PDAC therapy. Meanwhile, we showed that the expression of SCAMP1, which is a member of NEK7-SPGS, was involved in the progression of PDAC in vivo and in vitro. We proposed a NEK7-specific pyroptosis gene signature and evaluated its potential in PDAC tumor microenvironment. The NEK7-SPGS-related prognostic signature could act as a prognostic biomarker and serve as therapeutic guidance in clinical application.

Acute pancreatitis (AP) is a common gastrointestinal inflammatory disease that requires hospitalization, with 40–70% of patients in moderate to severe stages potentially developing sepsis, which is closely related to high mortality rates and poor prognosis. Therefore, early identification of AP patients at risk of developing sepsis is crucial for reducing mortality. This study aims to identify core genes associated with sepsis to provide new core genes for early warning and management of patients with acute pancreatitis. The study utilized the GSE54514, GSE57065, GSE95233, and GSE194331 datasets for analysis, employing weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network construction. Six core genes were identified using two machine learning methods and validated with the GSE3644 and GSE28750 datasets. The analysis revealed that the identified core genes (NDUFA1, COX7A2, COX7B, UQCRQ, SNRPG, and NDUFA4) are related to the oxidative phosphorylation (OxPhos) pathway, and significant differences were observed in the immune cell composition between AP and sepsis patients. SNRPG may play a role in the progression from AP to sepsis by regulating NDUFA4, linking it to cellular metabolism and redox balance. The newly identified core genes and their associated molecular mechanisms provide important clinical insights into the progression of acute pancreatitis to sepsis, potentially offering new research directions for future therapeutic strategies. Clinical trial number: This study was approved by the Ethics Committee of (Municipal Hospital affiliated to Taizhou University), in accordance with the Declaration of Helsinki. Approval number: LWSL202400220.

Gastroesophageal junction cancer (GEJ) is typically investigated alongside gastric or esophageal cancers. However, separate molecular profiles and immune cell infiltration of GEJ remain largely unknown. This study screened for hub genes in GEJ, studied their function and regulation in biological processes, and investigated their relationship with the infiltration of immune cells into tumors. Datasets were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus public databases. Molecular profiling revealed significant down-regulated expression of key genes in GEJ and enrichment in pathways related to epithelial cell differentiation and development, and structural constituents of skin epidermis. Prognostic analysis showed that patients with low KRT1, Desmocollin 2, and Envoplakin expression had a worse prognosis. There was a strong correlation between the levels of KRT1 and both the tumor mutational burden and immune cell infiltration. Single gene pathway enrichment analysis and in vitro experiments confirmed that cancer cell proliferation, migration, and invasion were suppressed by KRT1 via the AKT/mTOR pathway. In conclusion, this multi-dimensional study analyzed the molecular alterations and oncological mechanisms underlying the progression of GEJ. KRT1 is a promising candidate biomarker for the molecular and immunological characterization of GEJ and for prognosis prediction.

Cancer diagnostics highlight the critical requirement for sensitive and accurate tools with functional biomarkers for early tumor detection, diagnosis, and treatment. With a high burden of morbidity and mortality among young men worldwide and an increasing prevalence, Testicular cancer (TC) is a significant death-related cancer. Along with patient history, imaging, clinical presentation, and laboratory data, histological analysis of the testicular tissue following orchiectomy is crucial. Although some patients in advanced stages who belong to a poor risk group die from cancer, surgical treatments and chemotherapeutic treatment offer a high possibility of cure in the early stages. Testicular tumors lack useful indicators despite their traditional pathological classification, which highlights the need to find and use blood tumor markers in therapy. Regretfully, the sensitivity and specificity of the currently available biomarkers are restricted. Novel non-coding RNA molecules, microRNAs (miRNAs), have recently been discovered, offering a potential breakthrough as viable biomarkers and diagnostic tools. They act as fundamental gene regulators at the post-transcriptional level, controlling cell proliferation, differentiation, and apoptosis. This article aims to comprehensively explore the role of miRNAs in the pathophysiology, diagnosis, and treatment of TC, with a focus on their regulatory mechanisms within key signaling pathways such as TGF-β, PTEN/AKT/mTOR, EGFR, JAK/STAT, and WNT/β-catenin. By investigating the potential of miRNAs as diagnostic and prognostic biomarkers and therapeutic targets, this study seeks to address challenges such as treatment resistance and evaluate the clinical importance of miRNAs in improving patient outcomes. Additionally, the work aims to explore innovative approaches, including nanoparticle-based delivery systems, to enhance the efficacy of miRNA-based therapies. Ultimately, this research aims to provide insights into future directions for precision medicine in TC, bridging the gap between molecular discoveries and clinical applications.

Human EXO1 is a 5' → 3' exonuclease that plays a critical role in regulating cell cycle checkpoints, maintaining replication forks and participating in post-replication DNA repair pathways. Previous studies have highlighted the importance of EXO1 in cancers such as liver and breast cancer. However, there is a gap in the comprehensive analysis of EXO1 in a wide range of cancers, and its precise role in cancer patient prognosis and immune response remains unclear. This study aims to systematically investigate the potential associations between EXO1, immune infiltration and prognostic value in different cancer types and to gain a deeper understanding of its mechanisms of action.We conducted a comprehensive investigation into the overarching role of EXO1 across various cancers by utilizing multiple databases. Our analysis encompassed scrutinizing EXO1 expression and evaluating its correlation with clinical survival, immune checkpoints, Tumor Stemness Score, Prognostic Value, immunomodulators, genomic profiles, immunological characteristics, immunotherapy, and functional enrichment. EXO1 is expressed in various normal tissues and at significantly higher levels in most tumors compared to non-tumor tissues. High EXO1 expression is associated with poor prognosis in certain cancers. Genetic mutations and RNA modifications of EXO1 were also investigated, as well as its correlation with tumor immunity and genomic stability. We investigated the potential role of EXO1 in immunotherapy and identified differing drug responses based on EXO1 expression levels in Skin Cutaneous Melanoma (SKCM), which holds promise for personalized treatment. Furthermore, we analyzed EXO1-related genes and pathways, revealing its potential involvement in crucial biological processes such as DNA repair and cell cycle regulation. These findings provide a comprehensive understanding of the role of EXO1 in cancer initiation and progression, offering valuable insights for personalized cancer therapy and precision medicine. This study highlights the diverse functions of EXO1 in cancer, including its involvement in cancer initiation, prognosis, immune regulation, and response to immunotherapy. These findings provide valuable insights into the potential of EXO1 as a biomarker and therapeutic target, as well as its role in determining treatment response in cancer management. This information is crucial for guiding personalized cancer therapy and precision medicine.

In 2023, the Global Initiative for Chronic Obstructive Lung Disease (GOLD) introduced a provision regarding preserved ratio-impaired spirometry (PRISm), a presumed pre-stage of Chronic Obstructive Pulmonary Disease (COPD), into the COPD guidelines. However, further research in this area is needed. Our study aimed to investigate the epigenetic differences between PRISm and COPD. EWAS (n = 572) and RNA-sequencing (n = 60) were performed on blood samples from the COPD registry, and EWAS was replicated in the KoGES cohort data (n = 98). Our findings revealed significant epigenetic differences between patients with PRISm and COPD. 39,980 CpG-sites displayed differential methylation between PRISm and COPD. Seven gene regions—EEF1A2, EMP2, EPCAM, MTSS1L, ARHGEF10, HYDIN, and FADS2 were not only differentially methylated but also exhibited differential expression. The consistency of differential methylation of CpG sites in five genes, excluding ARHGEF10 and MTSS1L, was replicated in the KoGES study, affirming the distinction between COPD and PRISm. Our research identified seven gene regions as critical contributors related to the modulation of gene expression, including CpG sites that differentiate COPD from PRISm. These results highlight the significance of DNA methylation changes in distinguishing PRISm from COPD and shed light on potential mechanisms by which methylation alterations impact lung function.

Obesity, characterized by the excessive accumulation of white adipose tissue, is a significant global health burden and a major risk factor for a range of diseases, including malignancies and metabolic disorders. Individuals with high visceral fat content are particularly susceptible to severe complications such as type 2 diabetes, cardiovascular diseases, and liver disorders. However, the pathogenesis of obesity-related metabolic diseases extends beyond simple adiposity. Chronic obesity triggers a prolonged inflammatory response, which leads to tissue fibrosis and sustained organ damage, contributing to multi-organ dysfunction. This review explores the autoimmune mechanisms and inflammatory pathways underlying obesity-induced type 2 diabetes, atherosclerosis, and non-alcoholic fatty liver disease, with an emphasis on their interrelated pathophysiology and the potential for therapeutic interventions.