Discover Differentially Expressed Genes Research Articles

RNA-seq and bulk RNA-seq data analysis of cancer-related fibroblasts (CAF) in LUAD to construct a CAF-based risk signature

Angiogenesis, metastasis, and resistance to therapy are all facilitated by cancer-associated fibroblasts (CAFs). A CAF-based risk signature can be used to predict patients’ prognoses for Lung adenocarcinoma (LUAD) based on CAF characteristics. The Gene Expression Omnibus (GEO) database was used to gather signal-cell RNA sequencing (scRNA-seq) data for this investigation. The GEO and TCGA databases were used to gather bulk RNA-seq and microarray data for LUAD. The scRNA-seq data were analyzed using the Seurat R program based on the CAF markers. Our goal was to use differential expression analysis to discover differentially expressed genes (DEGs) across normal and tumor samples in the TCGA dataset. Pearson correlation analysis was utilized to discover prognostic genes related with CAF, followed by univariate Cox regression analysis. Using Lasso regression, a risk signature based on CAF-related prognostic genes was created. A nomogram model was created based on the clinical and pathological aspects. 5 CAF clusters were identified in LUAD, 4 of which were associated with prognosis. From 2811 DEGs, 1002 genes were found to be significantly correlated with CAF clusters, which led to the creation of a risk signature with 8 genes. These 8 genes were primarily connected with 41 pathways, such as antigen paocessing and presentation, apoptosis, and cell cycle. Meanwhile, the risk signature was significantly associated with stromal and immune scores, as well as some immune cells. Multivariate analysis revealed that risk signature was an independent prognostic factor for LUAD, and its value in predicting immunotherapeutic outcomes was confirmed. A novel nomogram integrating the stage and CAF-based risk signature was constructed, which exhibited favorable predictability and reliability in the prognosis prediction of LUAD. CAF-based risk signatures can be effective in predicting the prognosis of LUAD, and they may provide new strategies for cancer treatments by interpreting the response of LUAD to immunotherapy.

Deciphering the role of oxidative stress genes in idiopathic pulmonary fibrosis: a multi-omics mendelian randomization approach.

Oxidative stress (OS) is crucial in idiopathic pulmonary fibrosis (IPF) pathogenesis, with its genes potentially acting as both causes and consequences of the disease. We identified OS-related genes from GeneCards and performed a meta-analysis on pulmonary transcriptome datasets to discover differentially expressed genes (DEGs) related to OS in IPF. We integrated this data with the largest available IPF GWAS summaries, expression quantitative trait loci (eQTLs), and DNA methylation QTLs (mQTLs) from blood. This approach aimed to identify blood OS genes and regulatory elements linked to IPF risk, incorporating the latest pulmonary eQTLs and bronchoalveolar lavage fluid microbial QTLs (bmQTLs) for a comprehensive view of gene-lung microbiota interactions through SMR and colocalization analyses. Sensitivity analyses were conducted using two additional mendelian randomization (MR) methods. Meta-analysis revealed 1090 differentially expressed OS genes between IPF patients and controls. Integration with IPF GWAS, eQTL, and mQTL data identified key genes and regulatory elements involved in IPF pathogenesis, highlighting the role of specific genes such as KCNMA1 and SLC22A5 in modulating IPF risk through epigenetic mechanisms. Colocalization analysis further identified potential interactions between gene expression and lung microbiota. Our findings elucidate the complex interplay between OS genes and IPF, suggesting potential therapeutic targets and highlighting the importance of considering epigenetic and microbial interactions in the disease's etiology and progression.

Identification of shared hub genes and pathways between gastric cancer and Helicobacter pylori infection through bioinformatics analysis

BackgroundGastric cancer (GC), the third leading cause of cancer-related deaths, has become a worldwide health issue. Gastric cancer is causally associated with Helicobacter pylori (H. pylori) infection. This study characterizes functional genes and critical biological pathways involved in GC and H. pylori infection simultaneously by using bioinformatics approaches. Materials and methodsMicroarray datasets of GC and H. pylori infection diseases were selected from the Gene Expression Omnibus (GEO) public database. So as to discover differentially expressed genes (DEGs), datasets from both diseases (GSE13911, GSE54129, and GSE60427) were examined separately using the GEO2R web tool. Shared DEGs among both conditions were utilized for downstream analyses. Afterward, protein-protein interaction (PPI) networks were generated through the STRING database and visualized via Cytoscape. The degree method was used to define the hub genes using Cytoscape's cytoHubba plug-in. Ultimately, interaction networks for the microRNA (miRNA)-hub genes and transcription factor (TF)-hub genes were evaluated, followed by an analysis of drug-hub gene interactions. ResultsIn this current study, a total of 136 overlapped DEGs, including 101 up- and 35 downregulated genes, were screened between GC and H. pylori infection datasets. The PPI network obtained from the STRING database was subjected to analysis by the Cytoscape's cytoHubba plug-in, and 10 hub genes subsequently were determined using the degree method (which included TLR4, MMP9, ICAM1, CXCL10, CCL4, ITGB2, CXCL1, PTGS2, APOE, and CD80). Based on the obtained results, mir-146a-5p was found to have the highest association with the hub genes among the miRNAs, and RELA was recognized as a TF that regulates most of the hub genes among the TFs. Finally, 104 drugs were identified that might have therapeutic effects on both diseases. ConclusionsThis study provides a new perspective on the genetic association, and molecular pathways between GC and H. pylori infection could result in new treatment methods and diagnostic tests. Further experimental examinations are needed to validate critical genes and biological pathways discovered in this work.

RNA ve protein seviyelerinde temel biyobelirteçleri belirlemek için pulmoner arteriyel hipertansiyonun in silico analizi

Pulmonary arterial hypertension (PAH) is a chronic cardiopulmonary disorder marked by a raised hypertension in the pulmonary arteries. There is no remedy for PAH, existing medications can help reduce the disease’s progression. This research aimed to investigate potential protein and RNA biomarkers of PAH by bioinformatic analysis. Two PAH datasets accessed from the publicly available Gene Expression Omnibus (GEO) database were used to discover differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for common DEGs were conducted by the DAVID tool. Cytoscape was used to create the protein-protein interaction (PPI) and pick the top 10 hub genes. The transcription factors (TFs) and microRNAs (miRNAs) that target DEGs and hub genes were investigated using the JASPAR database. Potential therapeutics that target the top hub genes have been discovered. Ten hub genes were discovered to be linked to the pathogenesis of PAH (CCL5, TLR4, TLR1, SPP1, CYBB, HGF, IGF1, SELL, CD163, and POSTN). “Positive regulation of tumor necrosis factor biosynthetic process” and a “toll-like receptor signaling pathway” are the most enriched GO term and KEGG pathway, respectively. “hsa-mir-26b-5p, hsa-mir-146a-5p, hsa-mir-335-5p” and FOXC1, YY1, GATA2 are the top TFs targeting hub genes. 21 drugs targeting ten hub genes have been discovered. Our results would help to discover the pathogenesis of PAH and hub genes, miRNAs and 10 TFs that might serve as potential therapeutic targets at protein and RNA levels for PAH patients.

Bioinformatics analysis of molecular pathways and key candidate biomarkers associated with human bone marrow hematopoietic stem cells (HSCs) micro-array gene expression data

An identification of the molecular properties of glioma stem cells (GSCs) has led studies in clinical use, stem cell identification, and highly-effective usage. The GSE32719 contains a total expression of 54,676 genes of healthy human bone marrow HSCs in 14 young (20–31 years), 5 middle (42–61 years), and a lot of old (65–85 years) age groups. The researchers of this study described age-related changes in the human HSC population, using the gene expression profile of significance analysis to discover differentially expressed genes (DEGs) between each age group. The DEGs were subjected to significantly enriched biological processing that decoded the increase and functional decline in the HSC population. The GSE dataset analysis was conducted by the GEOquery package in Bioconductor. Using the Biobase and gplots packages, 453 DEGs were screened. DEGs analyses were conducted by gene ontology (GO) pathway enrichment and Kyoto Encylopedia of Genes and Genomes (KEGG) enrichment analysis. The Hippo signaling pathway was observed to be significant using the GO pathway enrichment analysis, which was previously reported as an effective pathway in cancers, including AML. A protein-protein interaction (PPI) network was constructed; then based on that, a subnetwork module analysis for the Hippo signaling pathway was made. Additionally, the GO pathway enrichment analysis revealed ‘cellular process’, ‘cellular metabolic process’, ‘metabolic process’, ‘biogenesis’, and ‘vasculogenesis biological processes’, which are involved in a wide of biological activities such as metabolic regulation, cell growth, and proliferation. Our findings offer silico evidence for candidate genes, such as the UBC, PTK2, and TCF7L2, that may be promising biomarkers for the translation approach associated with HSC population age-related diseases.

Transcriptomic characterization of tissues from patients and subsequent pathway analyses reveal biological pathways that are implicated in spastic ataxia

BackgroundSpastic ataxias (SAs) encompass a group of rare and severe neurodegenerative diseases, characterized by an overlap between ataxia and spastic paraplegia clinical features. They have been associated with pathogenic variants in a number of genes, including GBA2. This gene codes for the non-lysososomal β-glucosylceramidase, which is involved in sphingolipid metabolism through its catalytic role in the degradation of glucosylceramide. However, the mechanism by which GBA2 variants lead to the development of SA is still unclear.MethodsIn this work, we perform next-generation RNA-sequencing (RNA-seq), in an attempt to discover differentially expressed genes (DEGs) in lymphoblastoid, fibroblast cell lines and induced pluripotent stem cell-derived neurons derived from patients with SA, homozygous for the GBA2 c.1780G > C missense variant. We further exploit DEGs in pathway analyses in order to elucidate candidate molecular mechanisms that are implicated in the development of the GBA2 gene-associated SA.ResultsOur data reveal a total of 5217 genes with significantly altered expression between patient and control tested tissues. Furthermore, the most significant extracted pathways are presented and discussed for their possible role in the pathogenesis of the disease. Among them are the oxidative stress, neuroinflammation, sphingolipid signaling and metabolism, PI3K-Akt and MAPK signaling pathways.ConclusionsOverall, our work examines for the first time the transcriptome profiles of GBA2-associated SA patients and suggests pathways and pathway synergies that could possibly have a role in SA pathogenesis. Lastly, it provides a list of DEGs and pathways that could be further validated towards the discovery of disease biomarkers.

Identification of Six Prognostic Genes in EGFR-Mutant Lung Adenocarcinoma Using Structure Network Algorithms.

This study aims to determine hub genes related to the incidence and prognosis of EGFR-mutant (MT) lung adenocarcinoma (LUAD) with weighted gene coexpression network analysis (WGCNA). From The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we used 253 EGFR-MT LUAD samples and 38 normal lung tissue samples. At the same time, GSE19188 was additionally included to verify the accuracy of the predicted gene. To discover differentially expressed genes (DEGs), the R package “limma” was used. The R packages “WGCNA” and “survival” were used to perform WGCNA and survival analyses, respectively. The functional analysis was carried out with the R package “clusterProfiler.” In total, 1450 EGFR-MT–specific DEGs were found, and 7 tumor-related modules were marked with WGCNA. We found 6 hub genes in DEGs that overlapped with the tumor-related modules, and the overexpression level of B3GNT3 was significantly associated with the worse OS (overall survival) of the EGFR-MT LUAD patients (p < 0.05). Functional analysis of the hub genes showed the metabolism and protein synthesis–related terms added value. In conclusion, we used WGCNA to identify hub genes in the development of EGFR-MT LUAD. The established prognostic factors could be used as clinical biomarkers. To confirm the mechanism of those genes in EGFR-MT LUAD, further molecular research is required.

From innate to adaptive immunity: Abomasal transcriptomic responses of merino sheep to Haemonchus contortus infection

Although many important mediators and critical pathways are found to be involved in host immune responses to Haemonchus contortus infection, the initial responses to infection in the naïve and in the previously exposed state have not been compared at the transcriptional level. To further understand the development of adaptive immunity to H. contortus infection, we compared the early abomasal gene expression patterns between a primary and a tertiary challenge for four lines of sheep to discover differentially expressed genes (DEGs). The sheep were from the resistant (R) and susceptible (S) lines of two flocks of sheep selected for divergent responses to gastro-intestinal parasites (HSF and TSF). The flocks have separate origins and were initiated using two different strains of Merino sheep. One of the DEGs, mast cell proteinase 1, had significantly lower expression in tertiary compared to primary infections for all four lines of sheep. This gene was not identified in previous studies where resistant and susceptible sheep samples were compared within infection time points. Comparing the differentially expressed genes (DEGs) for the two R lines reveals that responses differed very little between the primary and tertiary challenges for HSFR and only two genes were identified, in contrast to the TSFR where there were 134 genes identified including the two identified using the HSFR animals. Similarly, comparing the primary and tertiary challenges for HSFS identified 15 DEGs, whilst for TSFS there were 128 DEGs identified. It is surprising that so few genes respond similarly between the two challenge regimes across the four lines of sheep, and suggests significant differences in immune mechanisms between the two flocks (across the lines) and also between the lines within flocks. Our results offer a quantitative snapshot comparing the transcriptome in the ovine abomasum between primary and tertiary infections with H. contortus in both genetically resistant and susceptible sheep.

Identification of critical pathways and potential therapeutic targets in poorly differentiated duodenal papilla adenocarcinoma

BackgroundDuodenal papilla carcinoma (DPC) is a rare malignancy of the gastrointestinal tract with high recurrence rate, and the pathogenesis of this highly malignant neoplasm is yet to be fully elucidated. This study aims to identify key genes to further understand the biology and pathogenesis underlying the molecular alterations driving DPC, which could be potential diagnostic or therapeutic targets.MethodsTumor samples of three DPC patients were collected and integrating RNA-seq analysis of tumor tissues and matched normal tissues were performed to discover differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were carried out to understand the potential bio-functions of the DPC differentially expressed genes (DEGs). Protein–protein interaction (PPI) network was constructed for functional modules analysis and identification of hub genes. qRT-PCR of clinical samples was conducted to validate the expression level of the hub genes.ResultsA total of 110 DEGs were identified from our RNA-seq data, GO and KEGG analyses showed that the DEGs were mainly enriched in multiple cancer-related functions and pathways, such as cell proliferation, IL-17signaling pathway, Jak-STAT signaling pathway, PPAR signaling pathway. The PPI network screened out five hub genes including IL-6, LCN2, FABP4, LEP and MMP1, which were identified as core genes in the network and the expression value were validated by qRT-PCR. The hub genes identified in this work were suggested to be potential therapeutic targets of DPC.DiscussionThe current study may provide new insight into the exploration of DPC pathogenesis and the screened hub genes may serve as potential diagnostic indicator and novel therapeutic target.

Key Molecules and Pathways Underlying Sporadic Amyotrophic Lateral Sclerosis: Integrated Analysis on Gene Expression Profiles of Motor Neurons.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by progressive loss of motor neurons. The complex mechanisms underlying ALS are yet to be elucidated, while the lack of disease biomarkers and therapeutic options are associated with the poor prognosis of ALS patients. In this study, we performed bioinformatics analysis to clarify potential mechanisms in sporadic ALS (sALS). We compared three gene expression profiles (GSE18920, GSE56500, and GSE68605) of motor neurons obtained from sALS patients and healthy controls to discover differentially expressed genes (DEGs), and then performed integrated bioinformatics analyses to identify key molecules and pathways underlying sALS. We found that these DEGs were mainly enriched in the structure and functions of extracellular matrix (ECM), while functional enrichment in blood vessel morphogenesis was less correlated with motor neurons. The clustered subnetworks of the constructed protein-protein interaction network for DEGs and the group of selected hub genes were more significantly involved in the organization of collagen-containing ECM. The transcriptional factors database proposed RelA and NF-κB1 from NF-κB family as the key regulators of these hub genes. These results mainly demonstrated the alternations in ECM-related gene expression in motor neurons and suggested the role of NF-κB regulatory pathway in the pathogenesis of sALS.

Water-Pipe Smoking Exposure Deregulates a Set of Genes Associated with Human Head and Neck Cancer Development and Prognosis.

Water-pipe smoking (WPS) is becoming the most popular form of tobacco use among the youth, especially in the Middle East, replacing cigarettes rapidly and becoming a major risk of tobacco addiction worldwide. Smoke from WPS contains similar toxins as those present in cigarette smoke and is linked directly with different types of cancers including lung and head and neck (HN) carcinomas. However, the underlying molecular pathways and/or target genes responsible for the carcinogenic process are still unknown. In this study, human normal oral epithelial (HNOE) cells, NanoString PanCancer Pathways panel of 770 gene transcripts and quantitative real-time polymerase chain reaction (qRT-PCR) analysis were applied to discover differentially expressed genes (DEG) modulated by WPS. In silico analysis was performed to analyze the impact of these genes in HN cancer patient’s biology and outcome. We found that WPS can induce the epithelial–mesenchymal transition (EMT: hallmark of cancer progression) of HNOE cells. More significantly, our analysis of NanoString revealed 23 genes deregulated under the effect of WPS, responsible for the modulation of cell cycle, proliferation, migration/invasion, apoptosis, signal transduction, and inflammatory response. Further analysis was performed using qRT-PCR of HNOE WPS-exposed and unexposed cells supported the reliability of our NanoString data. Moreover, we demonstrate those DEG to be upregulated in cancer compared with normal tissue. Using the Kaplan–Meier analysis, we observed a significant association between WPS-deregulated genes and relapse-free survival/overall survival in HN cancer patients. Our findings imply that WPS can modulate EMT as well as a set of genes that are directly involved in human HN carcinogenesis, thereby affecting HN cancer patients’ survival.

A transcriptomics-based analysis of toxicity mechanisms of zebrafish embryos and larvae following parental Bisphenol A exposure

BackgroundBisphenol A (BPA) is a well-known xenobiotic endocrine disrupting chemical, with estrogenic activity and many other potential biological effects. Although multiple toxicities have been reported for BPA, molecular mechanisms underlying the transgenerational toxic effects of BPA are still underestimated. MethodsParental F0 fish were exposed to 1.0 μM BPA or control (0.1% DMSO, v/v) for 7 days. Eggs (F1) were collected and kept in control medium until 4.5 or 120 h post fertilization (hpf). RNA sequencing (RNA-seq) was conducted on embryos and larvae, to discover differentially expressed genes (DEGs), and then KEGG pathway, GO enrichment and GSEA were performed to interpret functional ontology. Histopathology was performed to explore the morphological and structural alterations in liver tissues of zebrafish larvae (120 hpf) after parental BPA exposure. ResultsParental BPA exposure induced global transcriptomic changes in zebrafish embryos and larvae. For embryos, epigenetic regulation genes were decidedly affected, highlighted epigenotoxicity might involve in the transgenerational effects during embryogenesis and early development. By further investigation on its delayed effects, our RNA-Seq data of larvae suggested ROS metabolic process, apoptosis, p53 and MAPK signaling pathway were concentrated, indicating defensive cellular processes still involved in protecting against BPA toxicity. Furthermore, parental BPA-treated larvae manifested hepatic injury by histopathological analysis. ConclusionsParental BPA exposure led to global transcriptomic changes involved in epigenetic regulation, oxidative stress, apoptosis and DNA damage of offspring. These findings advanced the field of the parental-mediated subsequent generational toxic effects of BPA.

Parental exposure to bisphenol A affects pharyngeal cartilage development and causes global transcriptomic changes in zebrafish (Danio rerio) offspring

BackgroundAs one of the most common endocrine-disrupting chemicals (EDCs), bisphenol A (BPA) is a threat to aquatic ecosystems. Despite a rich literature addressing the adverse effects of BPA on various systems in fish models, the potential impact of parental BPA exposure on offspring pharyngeal cartilage development is poorly understood. MethodsAdult zebrafish (F0) were exposed to BPA (1.0 μM) or control for 7 days. Eggs (F1) were collected and exposed to BPA (control, 0.05, 0.1, 1, 10 μM) until 120 h post-fertilization. Histomorphometrical essay was used to quantitatively and qualitatively assess the effects of BPA on pharyngeal cartilage development. RNA sequencing (RNA-seq) was used to discover differentially expressed genes (DEGs), and KEGG pathway and GO enrichment analysis were performed to interpret functional ontology. ResultsParental BPA exposure affected hatchability and heart rates of F1 progeny. By pathology analysis, parental BPA exposure caused craniofacial deformity, characterized by wider angles of cartilage elements, disrupted pharyngeal chondrocytes and promoted apoptosis and elongation of head length. RNA-seq suggested that many DEGs were involved in multiple biological processes and signaling pathways; defense responses, reactive oxygen species metabolic process, apoptosis, p53 signaling pathway and MAPK signaling pathway were closely associated with the toxicity of parental BPA exposure. ConclusionsParental BPA exposure affected chondrogenesis in the viscerocranium of zebrafish offspring and led to global transcriptomic changes involved in apoptosis, hyperplasia and oxidative stress. These newly identified gene expression patterns, pathways and gene networks of zebrafish eleutheroembryos after early-life waterborne BPA exposure, may lead to severe and permanent morphological and functional consequences.

Genetic polymorphisms and transcription profiles associated with intracranial aneurysm: a key role for NOTCH3.

Intracranial aneurysm (IA) incidence is about 1~2%. However, the specific mechanisms of IA onset and development need further study. Our objective was to discover novel IA-related genes to determine possible etiologies further. We performed next-generation sequencing on nineteen Chinese patients with familial IA and one patient with sporadic IA. We obtained mRNA expression data of 129 samples from Gene Expression Omnibus (GEO) and made statistical computing to discover differentially expressed genes (DEGs). The screened IA-related gene NOTCH3 was determined by bioinformatic data mining. We verified the IA-related indicators of NOTCH3. Association was found between IA and the NOTCH3 SNPs rs779314594, rs200504060 and rs2285981. Levels of NOTCH3 mRNA were lower in IA tissue than in control tissue, but higher in peripheral blood neutrophils from IA patients than in neutrophils from controls. Levels of NOTCH3 protein were lower in IA tissue than in cerebral artery tissue. NOTCH3 also decreased the expression of angiogenesis factors in human umbilical vein endothelial cells. Variation in NOTCH3 and alteration of its expression in cerebral artery or neutrophils may contribute to IA. Our findings also describe a bioinformatic-experimental approach that may prove useful for probing the pathophysiology of other complex diseases.

Genome-scale analysis identifies NEK2, DLGAP5 and ECT2 as promising diagnostic and prognostic biomarkers in human lung cancer

This study aims to identify promising biomarkers for the early detection of lung cancer and evaluate the prognosis of lung cancer patients. Genome-wide mRNA expression data obtained from the Gene Expression Omnibus (GSE19188, GSE18842 and GSE40791), including 231 primary tumor samples and 210 normal samples, were used to discover differentially expressed genes (DEGs). NEK2, DLGAP5 and ECT2 were found to be highly expressed in tumor samples. These results were experimentally confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The elevated expression of the three candidate genes was also validated using the Cancer Genome Atlas (TCGA) datasets, which consist of 349 tumor and 58 normal tissues. Furthermore, we performed receiver operating characteristics (ROC) analysis to assess the diagnostic value of these lung cancer biomarkers, and the results suggested that NEK2, DLGAP5 and ECT2 expression levels could robustly distinguish lung cancer patients from normal subjects. Finally, Kaplan-Meier analysis revealed that elevated NEK2, DLGAP5 and ECT2 expression was negatively correlated with both overall survival (OS) and relapse-free survival (RFS). Taken together, these findings indicate that these three genes might be used as promising biomarkers for the early detection of lung cancer, as well as predicting the prognosis of lung cancer patients.