WGCNA Reveals Key Roles of IL8 and MMP-9 in Progression of Involvement Area in Colon of Patients with Ulcerative Colitis

Selected Cytokines and Metalloproteinases in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a collective term for two diseases: ulcerative colitis (UC) and Crohn's disease (CD). There are many factors, e.g., genetic, environmental and immunological, that increase the likelihood of these diseases. Indicators of IBDs include extracellular matrix metalloproteinases (MMPs). The aim of this review is to present data on the role of selected cytokines and metalloproteinases in IBD. In recent years, more and more transcriptomic studies are emerging. These studies are improving the characterization of the cytokine microenvironment inside inflamed tissue. It is observed that the levels of several cytokines are consistently increased in inflamed tissue in IBD, both in UC and CD. This review shows that MMPs play a major role in the pathology of inflammatory processes, cancer, and IBD. IBD-associated inflammation is associated with increased expression of MMPs and reduced ability of tissue inhibitors of metalloproteinases (TIMPs) to inhibit their action. In IBD patients in tissues that are inflamed, MMPs are produced in excess and TIMP activity is not sufficient to block MMPs. This review is based on our personal selection of the literature that was retrieved by a selective search in PubMed using the terms "Inflammatory bowel disease" and "pathogenesis of Inflammatory bowel diseases" that includes systematic reviews, meta-analyses, and clinical trials. The involvement of the immune system in the pathophysiology of IBD is reviewed in terms of the role of the cytokines and metalloproteinases involved.

The immunomodulatory role of matrix metalloproteinases in colitis-associated cancer

Matrix metalloproteinases (MMPs) are an important class of enzymes in the body that function through the extracellular matrix (ECM). They are involved in diverse pathophysiological processes, such as tumor invasion and metastasis, cardiovascular diseases, arthritis, periodontal disease, osteogenesis imperfecta, and diseases of the central nervous system. MMPs participate in the occurrence and development of numerous cancers and are closely related to immunity. In the present study, we review the immunomodulatory role of MMPs in colitis-associated cancer (CAC) and discuss relevant clinical applications. We analyze more than 300 pharmacological studies retrieved from PubMed and the Web of Science, related to MMPs, cancer, colitis, CAC, and immunomodulation. Key MMPs that interfere with pathological processes in CAC such as MMP-2, MMP-3, MMP-7, MMP-9, MMP-10, MMP-12, and MMP-13, as well as their corresponding mechanisms are elaborated. MMPs are involved in cell proliferation, cell differentiation, angiogenesis, ECM remodeling, and the inflammatory response in CAC. They also affect the immune system by modulating differentiation and immune activity of immune cells, recruitment of macrophages, and recruitment of neutrophils. Herein we describe the immunomodulatory role of MMPs in CAC to facilitate treatment of this special type of colon cancer, which is preceded by detectable inflammatory bowel disease in clinical populations.

Investigating Key Targets of Dajianzhong Decoction for Treating Crohn’s Disease Using Weighted Gene Co-Expression Network

Background: Crohn’s disease (CD) is an inflammatory bowel disease, cases of which have substantially increased in recent years. The classical formula Dajianzhong decoction (DD, Japanese: Daikenchuto) is often used to treat CD, but few studies have evaluated related therapeutic mechanisms. In this study, we investigated the potential targets and mechanisms of DD used for treating CD at the molecular level through the weighted gene co-expression network. Methods: The main chemical components of the three DD herbs (Zanthoxylum bungeanum Maxim., Zingiber officinale (Willd.) Rosc., and Ginseng Radix et Rhizoma) were searched for using the HERB database. The targets for each component were identified using the SwissTargetPrediction and HERB databases, whereas the disease targets for CD were retrieved from the GeneCards and DisGeNET databases. The functional enrichment analysis was performed on the common targets of DD and CD. High-throughput sequencing data for CD patients were retrieved from the Gene Expression Omnibus database, and WGCNA was performed to identify the key targets. The association between the key targets and DD ingredients was verified using molecular docking. Results: By analyzing the interaction targets between DD and CD, 196 overlapping genes were identified. The enrichment results indicated that the PI3K-AKT, TNF, MAPK, and IL-17 signaling pathways influenced the mechanism of action of DD in counteracting CD. Combined with WGCNA, four differentially expressed genes (SLC6A4, NOS2, SHBG, and ABCB1) and their corresponding 24 compounds were closely related to the occurrence of CD. Conclusions: By integrating gene co-expression network analysis, this study preliminarily reveals the internal molecular mechanism of DD in treating CD from a systematic perspective, validated by molecular docking. However, these findings require further validation.

Improved biomarker discovery through a plot twist in transcriptomic data analysis

Background

Transcriptomic analysis is crucial for understanding the functional elements of the genome, with the classic method consisting of screening transcriptomics datasets for differentially expressed genes (DEGs). Additionally, since 2005, weighted gene co-expression network analysis (WGCNA) has emerged as a powerful method to explore relationships between genes. However, an approach combining both methods, i.e., filtering the transcriptome dataset by DEGs or other criteria, followed by WGCNA (DEGs + WGCNA), has become common. This is of concern because such approach can affect the resulting underlying architecture of the network under analysis and lead to wrong conclusions. Here, we explore a plot twist to transcriptome data analysis: applying WGCNA to exploit entire datasets without affecting the topology of the network, followed with the strength and relative simplicity of DEG analysis (WGCNA + DEGs). We tested WGCNA + DEGs against DEGs + WGCNA to publicly available transcriptomics data in one of the most transcriptomically complex tissues and delicate processes: vertebrate gonads undergoing sex differentiation. We further validate the general applicability of our approach through analysis of datasets from three distinct model systems: European sea bass, mouse, and human.

Results

In all cases, WGCNA + DEGs clearly outperformed DEGs + WGCNA. First, the network model fit and node connectivity measures and other network statistics improved. The gene lists filtered by each method were different, the number of modules associated with the trait of interest and key genes retained increased, and GO terms of biological processes provided a more nuanced representation of the biological question under consideration. Lastly, WGCNA + DEGs facilitated biomarker discovery.

Conclusions

We propose that building a co-expression network from an entire dataset, and only thereafter filtering by DEGs, should be the method to use in transcriptomic studies, regardless of biological system, species, or question being considered.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01398-w.

Identification of Key Genes Associated with Endothelial Cell Dysfunction in Atherosclerosis Using Multiple Bioinformatics Tools

Atherosclerosis is the most notable cardiovascular disease, the latter being the main cause of death globally. Endothelial cell dysfunction plays a major role in the pathogenesis of atherosclerosis. However, it is currently unclear which genes are involved between endothelial cell dysfunction and atherosclerosis. This study was aimed at identifying these genes. Based on the GSE83500 dataset, the quantification of endothelial cell function was conducted using single-sample gene set enrichment analysis; the coexpression modules were conducted using weighted correlation network analysis. After building module-trait relationships, tan and yellow modules were regarded as hub modules. 10 hub genes from each hub module were identified by the protein-protein interaction network analysis. The key genes (RAB5A, CTTN, ITGB1, and MMP9) were obtained by comparing the expression differences of the hub gene between atherosclerotic and normal groups from the GSE28829 and GSE43292 datasets, respectively. ROC analysis showed the diagnostic value of key genes. Moreover, the differential expression of key genes in normal and atherosclerotic aortic walls was verified. In vitro, we establish a model of ox-LDL-injured endothelial cells and transfect RAB5A overexpression and shRNA plasmids. The results showed that overexpression of RAB5A ameliorates the proliferation and migration function of ox-LDL-injured endothelial cells, including the ability of tubule formation. It was speculated that the interferon response, Notch signaling pathways, etc. were involved in this function of RAB5A by using gene set variation analysis. With the multiple bioinformatics analysis methods, we detected that yellow and tan modules are related to the abnormal proliferation and migration of endothelial cells associated with atherosclerosis. RAB5A, CTTN, ITGB1, and MMP9 can be used as potential targets for therapy and diagnostic markers. In vitro, overexpression of RAB5A can ameliorate the proliferation and migration function of ox-LDL-injured endothelial cells, and the possible molecules involved in this process were speculated.

PAICS is related to glioma grade and can promote glioma growth and migration

Glioma is a common malignant tumour of the brain. In this study, we aimed to investigate diagnostic biomarkers and its role in glioma. Weighted gene co-expression network analysis (WGCNA) and Cytoscape software were used to screen the marker genes in glioma. RT-qPCR and Western blotting methods were performed to determine the expression of PAICS, ERCC1 and XPA genes in glioma tissues. Expression level of PAICS in different grades of glioma was examined by immunohistochemistry. CCK8 and Colony formation assays were used to detect cell proliferation. Cell adhesion assay was used to detect adhesion ability. Wound healing and transwell tests were used to detect cell migration ability. Flow cytometry was used to detect cell cycle and apoptosis. According to the predicted co-expression network, we identified the hub gene PAICS. Furthermore, we observed that PAICS expression level was up-regulated in glioma tissues compared with normal tissues, and the expression level was correlated with the grade of glioma. Moreover, we found PAICS can promote glioma cells proliferation and migration in vitro. Flow cytometry results showed that si-PAICS cells were stalled at the G1 phase compared with the si-NC cells and knocking down PAICS expression can increase apoptotic rate. PAICS can regulate the mRNA and protein levels of nucleotide excision repair pathway core genes ERCC1 and XPA. l-aspartic acid can affect the expression of PAICS and then inhibit glioma cell proliferation. Our results indicated that PAICS can promote glioma proliferation and migration. PAICS may act as a potential diagnostic marker and a therapeutic target for glioma.

Upregulation of Fecal Epithelial Heparanase mRNA Is Associated with Increased Ulcerative Colitis Activity and Cancerization Risk

BACKGROUND

Heparanase (HPSE) is considered to play an important role in the occurrence, development and carcinogenesis of ulcerative colitis (UC). There are no reports about the detection of HPSE mRNA in feces to predict UC activity and cancerization risk.

AIMS

To explore the feasibility and effectiveness of fecal epithelial HPSE mRNA in monitoring patients' UC activity and predicting cancer risk.

METHODS

The clinical part of the study enrolled 20 patients with UC and 20 controls. Meanwhile, a UC-induced carcinogenesis mouse model was established using a combination treatment of dimethylhydrazine and dextran sulfate sodium. Tissue expression of HPSE protein was detected by immunohistochemistry. RT-qPCR was used to detect the expression of HPSE mRNA in colonic mucosa and feces.

RESULTS

In the human study, the relative expressions of HPSE mRNA in colonic mucosa and feces were positively correlated with the Mayo score (P < 0.05), and with a significant correlation between feces and colonic mucosa (P < 0.05). In the mouse model, the relative expressions of HPSE mRNA in colonic mucosa and feces in the ulcerative colitis-associated colorectal cancer group was significantly higher than that of the UC group and the normal control group (P < 0.05), and with a significant correlation between feces and colonic mucosa (P < 0.05).

CONCLUSIONS

The relative level of HPSE mRNA was positively correlated with UC activity and cancerization. The relative level of HPSE mRNA in feces was correlated with that in colonic mucosa. The detection of HPSE mRNA in feces can be used as a new marker for disease monitoring and cancer risk prediction of UC.

Weighted gene co expression network analysis (WGCNA) with key pathways and hub-genes related to micro RNAs in ischemic stroke

Ischemic stroke (IS) is one of the major causes of death and disability worldwide. However, the specific mechanism of gene interplay and the biological function in IS are not clear. Therefore, more research into IS is necessary. Dataset GSE110993 including 20 ischemic stroke (IS) and 20 control specimens are used to establish both groups and the raw RNA‐seq data were analysed. Weighted gene co‐expression network analysis (WGCNA) was used to screen the key micro‐RNA modules. The centrality of key genes were determined by module membership (mm) and gene significance (GS). The key pathways were identified by enrichment analysis with Kyoto Protocol Gene and Genome Encyclopedia (KEGG), and the key genes were validated by protein‐protein interactions network. Result: Upon investigation, 1185 up‐ and down‐regulated genes were gathered and distributed into three modules in response to their degree of correlation to clinical traits of IS, among which the turquoise module show a trait‐correlation of 0.77. The top 140 genes were further identified by GS and MM. KEGG analysis showed two pathways may evolve in the progress of IS. Discussion: CXCL12 and EIF2a may be important biomarkers for the accurate diagnosis and treatment in IS.

Metalloproteinases in Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBD) are chronic inflammatory diseases of the gastrointestinal tract, encompassing two main disorders: Crohn's disease (CD) and ulcerative colitis (UC). In both these pathologies, excessive and local immune response against luminal antigens promotes a pathological process leading to various degrees of gut damage. Matrix metalloproteinases (MMPs) are a family of neutral proteases with the ability to degrade all components of extracellular matrix. In physiological conditions, MMPs are produced at very low level and generally in the latent form and are involved in the normal tissue turnover. Their function is inhibited by tissue inhibitors of metalloproteinases (TIMPs). However, in inflamed tissue of IBD patients, MMPs are produced in excess and/or the activity of TIMPs is not sufficient to block MMPs, thereby making a major contribution to the IBD-related mucosal degradation. In this review, we summarize the available evidence on the expression and role of MMPs in IBD.

Dual Functional Eudragit® S100/L30D-55 and PLGA Colon-Targeted Nanoparticles of Iridoid Glycoside for Improved Treatment of Induced Ulcerative Colitis

AIM

Iridoid glycosides (IG) as the major active fraction of Syringa oblata Lindl. has a proven anti-inflammatory effect for ulcerative colitis (UC). However, its current commercial formulations are hampered by low bioavailability and unable to reach inflamed colon. To overcome the limitation, dual functional IG-loaded nanoparticles (DFNPs) were prepared to increase the residence time of IG in colon. The protective mechanism of DFNPs on DSS-induced colonic injury was evaluated in rats.

MATERIALS AND METHODS

We prepared DFNPs using the oil-in-water emulsion method. PLGA was selected as sustained-release polymer, and ES100 and EL30D-55 as pH-responsive polymers. The morphology and size distribution of NPs were measured by SEM and DLS technique. To evaluate colon targeting of DFNPs, DiR, was encapsulated as a fluorescent probe into NPs. Fluorescent distribution of NPs were investigated. The therapeutic potential and in vivo transportation of NPs in gastrointestinal tract were evaluated in a colitis model.

RESULTS

SEM images and zeta data indicated the successful preparation of DFNPs. This formulation exhibited high loading capacity. Drug release results suggested DFNPs released less than 20% at the first 6 h in simulated gastric fluid (pH1.2) and simulated small intestine fluid (pH6.8). A high amount of 84.7% sustained release from NPs in simulated colonic fluid (pH7.4) was beyond 24 h. DiR-loaded NPs demonstrated a much higher colon accumulation, suggesting effective targeting due to functionalization with pH and time-dependent polymers. DFNPs could significantly ameliorate the colonic damage by reducing DAI, macroscopic score, histological damage and cell apoptosis. Our results also proved that the potent anti-inflammatory effect of DFNPs is contributed by decrease of NADPH, gene expression of COX-2 and MMP-9 and the production of TNF-α, IL-17, IL-23 and PGE2.

CONCLUSION

We confirm that DFNPs exert protective effects through inhibiting the inflammatory response, which could be developed as a potential colon-targeted system.

TAF1A and ZBTB41 serve as novel key genes in cervical cancer identified by integrated approaches

Cervical cancer (CC) is the second most common cancer and the leading cause of cancer mortality in women. Numerous studies have found that the development of CC was associated with multiple genes. However, the mechanisms on gene level are enigmatic, hindering the understanding of its functional roles. This study sought to identify prognostic biomarkers of CC, and explore their biological functions. Here we conducted an integrated analysis to screen potential vital genes. Candidate genes were further tested by experiments in clinical specimens and cancer cell line. Then, molecular modeling was used to predict the three-dimensional structure of candidate genes’ proteins, and the interaction pattern was analyzed by docking simulation technique. Among the potential genes identified, we found that TAF1A and ZBTB41 were highly correlated. Furthermore, there was a definite interaction between the proteins of TAF1A and ZBTB41, which was affected by the activity of the p53 signaling pathway. In conclusion, our findings identified TAF1A and ZBTB41 could serve as biomarkers of CC. We confirmed their biological function and deciphered their interaction for the first time, which may be helpful for developing further researches.

Identification of key gene modules and genes in colorectal cancer by co-expression analysis weighted gene co-expression network analysis

Colorectal cancer (CRC) has been one of the most common malignancies worldwide, which tends to get worse for the growth and aging of the population and westernized lifestyle. However, there is no effective treatment due to the complexity of its etiology. Hence, the pathogenic mechanisms remain to be clearly defined. In the present study, we adopted an advanced analytical method—Weighted Gene Co-expression Network Analysis (WGCNA) to identify the key gene modules and hub genes associated with CRC. In total, five gene co-expression modules were highly associated with CRC, of which, one gene module correlated with CRC significantly positive (R = 0.88). Functional enrichment analysis of genes in primary gene module found metabolic pathways, which might be a potentially important pathway involved in CRC. Further, we identified and verified some hub genes positively correlated with CRC by using Cytoscape software and UALCAN databases, including PAICS, ATR, AASDHPPT, DDX18, NUP107 and TOMM6. The present study discovered key gene modules and hub genes associated with CRC, which provide references to understand the pathogenesis of CRC and may be novel candidate target genes of CRC.

Big data in IBD: big progress for clinical practice

IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation sequencing, high-throughput omics data generation and molecular networks have catalysed IBD research. The advent of artificial intelligence, in particular, machine learning, and systems biology has opened the avenue for the efficient integration and interpretation of big datasets for discovering clinically translatable knowledge. In this narrative review, we discuss how big data integration and machine learning have been applied to translational IBD research. Approaches such as machine learning may enable patient stratification, prediction of disease progression and therapy responses for fine-tuning treatment options with positive impacts on cost, health and safety. We also outline the challenges and opportunities presented by machine learning and big data in clinical IBD research.

Carboxypeptidase A6 was identified and validated as a novel potential biomarker for predicting the occurrence of active ulcerative colitis

Ulcerative colitis (UC) is a chronic, highly heterogeneous intestinal inflammation with changes in epithelial function and tissue damage. However, the pathogenesis is still unclear between active UC and inactive UC. Herein, weighted gene co‐expression network analysis was applied to explore the gene modules related to active UC. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to further investigate the underlying mechanism of selected genes. We found that in the blue module (r = −.72), carboxypeptidase A6 (CPA6) was chosen to validate because of its high intra‐modular connectivity and module membership. In the test sets, the expression level of CPA6 was down‐regulated in active UC compared with inactive UC and normal colon. Furthermore, CPA6 expression was decreased primarily in the descending colon and only in mucosa affected by active UC. The receiver operating characteristic curve indicated that CPA6 expression had a performed well in diagnosing active UC from inactive UC (area under the curve = 0.99). Importantly, anti‐tumour necrosis factor (TNF) treatment (infliximab and golimumab) significantly increased the CPA6 expression. Finally, GSEA and GSVA found that extracellular matrix receptor, inflammatory response and epithelial‐mesenchymal transition were highly enriched in active UC with low CPA6 expression. In conclusion, CPA6 was identified and validated as a novel potential biomarker for predicting the occurrence of active UC, probably through regulating extracellular matrix or immune response.

Identification of specific modules and hub genes associated with the progression of gastric cancer

Gastric cancer (GC) has high morbidity and mortality rates worldwide. Abundant literature has reported several individual genes and their related pathways intimately involved in tumor progression. However, little is known about GC progression at the gene network level. Therefore, understanding the underlying mechanisms of pathological transition from early stage to late stage is urgently needed. This study aims to identify potential vital genes and modules involved in the progression of GC. To understand the gene regulatory network of GC progression, we analyzed micro RNAs and messenger RNA s expression profiles by using a couple of bioinformatics tools. miR-205 was identified by differentially expressed analysis and was further confirmed through using multiple kernel learning-based Kronecker regularized least squares. Using weighted gene co-expression network analysis, the gastric cancer progression-related module, which has the highest correlation value with cancer progression, was obtained. Kyoto Encyclopedia of Genes and Genomes pathways and biological processes of the GCPR module genes were related to cell adhesion. Meanwhile, large-scale genes of GCPR module were found to be targeted by miR-205, including two hub genes SORBS1 and LPAR1. In brief, through multiple analytical methods, we found that miR-205 and the GCPR module play critical roles in GC progression. In addition, miR-205 might maintain cell adhesion by regulating SORBS1 and LPAR1. To screen the potential drug candidates, the gene expression profile of the GCPR module was mapped connectivity map (Cmap), and the mTOR inhibitor (Sirolimus) was found to be the most promising candidate. We further confirmed that Sirolimus can suppress cell proliferation of GC cell in vitro.

IL-8 and LYPD8 expression levels are associated with the inflammatory response in the colon of patients with ulcerative colitis

Ulcerative colitis (UC) is an idiopathic chronic inflammatory disorder affecting the large intestine, which may involve mucosal degeneration. Glycoproteins, mucin2 (MUC2) and the LY6/PLAUR domain containing 8 (LYPD8) are present on the mucous layer of the colon and can hinder the invasion of bacteria, thus contributing to the prevention of colitis. The present study investigated the expression levels of interleukin-8 (IL-8), MUC2 and LYPD8 on the mucous membranes of patients with UC. A total of 18 patients with UC (6 females and 12 males) were examined. Biopsies of the lesions as well as matching normal membranes were obtained and the mRNA expression levels of IL-8, MUC2 and LYPD8 were compared. LYPD8 expression was downregulated in the lesions and the relapsing-remitting subtype of lesions was associated with higher levels of MUC2 expression compared with single attack and chronic lesions subtypes. A positive correlation between Matts' histopathological grade and IL-8, as well as a negative correlation between Matts' histopathological grade and LYPD8 were observed. The expression levels of LYPD8 were lower in highly active lesions and these levels decreased according to the intensity of the mucosal inflammation. Conversely, an increase in MUC2 expression levels may reflect the recovery of the outer mucus layer in the remission phase. Therefore, the examination of MUC2 and LYPD8 expression levels may be useful indicators of mucosal healing in patients with UC.

Identification of genes and functional coexpression modules closely related to ulcerative colitis by gene datasets analysis

Background

Ulcerative colitis is a type of inflammatory bowel disease posing a great threat to the public health worldwide. Previously, gene expression studies of mucosal colonic biopsies have provided some insight into the pathophysiological mechanisms in ulcerative colitis; however, the exact pathogenesis is unclear. The purpose of this study is to identify the most related genes and pathways of UC by bioinformatics, so as to reveal the core of the pathogenesis.

Methods

Genome-wide gene expression datasets involving ulcerative colitis patients were collected from gene expression omnibus database. To identify most close genes, an integrated analysis of gene expression signature was performed by employing robust rank aggregation method. We used weighted gene co-expression network analysis to explore the functional modules involved in ulcerative colitis pathogenesis. Besides, biological process and pathways analysis of co-expression modules were figured out by gene ontology enrichment analysis using Metascape.

Results

A total of 328 ulcerative colitis patients and 138 healthy controls were from 14 datasets. The 150 most significant differentially expressed genes are likely to include causative genes of disease, and further studies are needed to demonstrate this. Seven main functional modules were identified, which pathway enrichment analysis indicated were associated with many biological processes. Pathways such as ‘extracellular matrix, immune inflammatory response, cell cycle, material metabolism’ are consistent with the core mechanism of ulcerative colitis. However, ‘defense response to virus’ and ‘herpes simplex infection’ suggest that viral infection is one of the aetiological agents. Besides, ‘Signaling by Receptor Tyrosine Kinases’ and ‘pathway in cancer’ provide new clues for the study of the risk and process of ulcerative colitis cancerization.

Gene and lncRNA co-expression network analysis reveals novel ceRNA network for triple-negative breast cancer

Breast cancer is the most frequently diagnosed malignancy among women, and triple-negative breast cancer (TNBC) is a highly aggressive subtype. Increasing evidence has shown that lncRNAs are involved in tumor growth, cell-cycle, and apoptosis through interactions with miRNAs or mRNAs. However, there is still limited data on ceRNAs involved in the molecular mechanisms underlying TNBC. In this study, we applied the weighted gene co-expression network analysis to the existing microarray mRNA and lncRNA expression data obtained from the breast tissues of TNBC patients to find the hub genes and lncRNAs involved in TNBC. Functional enrichment was performed on the module that correlated with Ki-67 status the most (Turquoise module). The hub genes in the Turquoise module were found to be associated with DNA repair, cell proliferation, and the p53 signaling pathway. We performed co-expression analysis of the protein-coding and lncRNA hub genes in the Turquoise module. Analysis of the RNA-seq data obtained from The Cancer Genome Atlas database revealed that the protein-coding genes and lncRNAs that were co-expressed were also differentially expressed in the TNBC tissues compared with the normal mammary tissues. On the basis of establishing the ceRNA network, two mRNAs (RAD51AP1 and TYMS) were found to be correlated with overall survival in TNBC. These results suggest that TNBC-specific mRNA and lncRNAs may participate in a complex ceRNA network, which represents a potential therapeutic target for the treatment of TNBC.

Identification of key genes and pathways associated with Crohn's disease by bioinformatics analysis

Aims: Crohn's disease (CD) is a type of inflammatory bowel disease. The present study aimed to identify key genes and significant signaling pathways associated with CD by bioinformatics analysis. A total of 179 CD patients and 94 healthy controls from nine genome-wide gene expression datasets were included.Results: MMP1 and CLDN8 were two key genes screened from the differentially expressed genes. Connectivity Map predicted several small molecules as possible adjuvant drugs to treat CD. Besides, we used weighted gene coexpression network analysis to explore the functional modules involved in CD pathogenesis. Seven main functional modules were identified, of which black module showed the highest correlation with CD. The genes in black module mainly enriched in interferon signaling and defense response to virus. Blue module was another important module and enriched in several signaling pathways, including extracellular matrix organization, inflammatory response and blood vessel development.Conclusions: This study identified a number of key genes and pathways involved in CD and potential drugs to combat it, which might offer insights into CD pathogenesis and provide a clue to potential treatments.

Identification of potential biomarkers and pathways in ulcerative colitis with combined public mRNA and miRNA expression microarray data analysis

Background

Ulcerative colitis (UC) is a chronic, relapsing and non-specific inflammatory disease, involving various genes and pathways in their pathogenesis. Increasing evidences have showed that microRNAs (miRNAs) act as key post-transcriptional regulators of gene expression in UC. This current study aimed to identify key miRNAs, potential target genes, and relevant pathways involved in UC to uncover their underlying molecular mechanisms by using bioinformatics analysis.

Methods

The mRNA and miRNA expression profiles were retrieved and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by using the R software package.

Results

A total of 79 DEGs and 47 DEMIs were obtained. And a panel of miRNAs and their target mRNAs were identified. It showed that miR-1231 may be a key regulator for DUOX2 and TFF1. CCL11 may be potentially targeted by miR-625. MMP1 may play vital roles in the development of UC by regulating the miR-1228/PPAR signaling pathway. In addition, we validated the most significantly up/down-expressed miRNAs (miR-92b, miR-625) and two of their corresponding target mRNAs (AQP8 and TAGAP, CCL11 and CHI3L1) in colon tissues of UC models preliminarily. The results were consistent with the microarray analysis.

Conclusions

These findings may provide new insights into representing key mechanisms associated with the development of UC.

Identification of key modules and prognostic markers in adrenocortical carcinoma by weighted gene co-expression network analysis

Adrenocortical carcinoma (ACC) is a rare and aggressive cancer with a high relapse rate and limited treatment options. Therefore, the identification of potential prognostic markers in patients with ACC may improve early detection, survival rates and may additionally provide novel insights into the early detection of recurrence. In the present study, clinical traits and RNA-seq data of 79 patients with ACC were obtained from The Cancer Genome Atlas (TCGA). Weighted gene co-expression network analysis was carried out and 17 distinct co-expression modules were built to examine the association between the modules and the clinical traits. Of the 17 modules, two co-expression modules, which contained 214 and 168 genes, were significantly correlated with two clinical traits, tumor stage and vital status. Functional enrichment analysis was performed on the selected modules. The results showed that one of the modules was primarily enriched in cell division and the other module was enriched in metabolic pathways, suggesting their involvement in tumor progression. Furthermore, cyclin dependent kinase 1 (CDK1) and ubiquitin C (UBC) were identified as hub genes in both modules. Survival analysis revealed that the high expression of the hub genes significantly correlated with the poor survival rate of patients, suggesting that CDK1 and UBC have vital roles in the progression of ACC. In the present study, a co-expression gene module of ACC was provided and the prognostic genes that may serve as new diagnostic markers in the future were defined.

Joint bioinformatics analysis of underlying potential functions of hsa-let-7b-5p and core genes in human glioma

BACKGROUND

Glioma accounts for a large proportion of cancer, and an effective treatment for this disease is still lacking because of the absence of specific driver molecules. Current challenges in the treatment of glioma are the accurate and timely diagnosis of brain glioma and targeted treatment plans. To investigate the diagnostic biomarkers and prospective role of miRNAs in the tumorigenesis and progression of glioma, we analyzed the expression of miRNAs and key genes in glioma based on The Cancer Genome Atlas database.

METHODS

Of the 701 cases that were downloaded, five were normal and 696 were glioma. Then, 1626 differentially expressed genes were identified, and 173 aberrantly expressed miRNAs were calculated by edgeR. GO and KEGG pathway enrichment analyses were performed using Cytoscape software. A coexpression network was built by weighted correlation network analysis (WGCNA). A cell scratch test and transwell, cell apoptosis and cell cycle assays were performed to validate the function of hsa-let-7b-5p.

RESULTS

Based on crosstalk genes in the KEGG, PPI network, and WGCNA analyses, PLK1, CCNA2, cyclin B2 (CCNB2), and AURKA were screened as candidate diagnostic marker genes. The survival analysis revealed that high mRNA expression of PLK1, CCNA2, and AURKA was significantly associated with poor overall survival. Furthermore, hsa-let-7b-5p was identified as a core miRNA in the regulation of candidate genes involved in glioma development. We confirmed that hsa-let-7b-5p could inhibit the migration, invasion, and cell cycle of glioma cells.

CONCLUSIONS

This study provides four potential biomarkers for the diagnosis of glioma, offers a potential explanation of its pathogenesis, and proposes hsa-let-7b-5p as a therapeutic target.