Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)

Platelet-Derived Microvesicles Mediate Cardiomyocyte Ferroptosis by Transferring ACSL1 During Acute Myocardial Infarction

Acute myocardial infarction (AMI) is one of the critical health conditions often caused by the rupture of unstable coronary artery plaque, triggering a series of events, such as platelet activation, thrombus formation, coronary artery blockage, lasted severe ischemia, and hypoxia in cardiomyocytes, and culminating in cell death. Platelet-derived microvesicles (PMVs) act as intermediates for cellular communication. Nevertheless, the role of PMVs in myocardial infarction remains unclear. Initially, AMI-related messenger ribose nucleic acid (mRNA) and micro RNA (miRNA) datasets from the Gene Expression Omnibus (GEO) database were analyzed, specifically focusing on the expressed genes associated with Ferroptosis. Further, a miRNA-mRNA regulatory network specific to AMI was constructed. Then, the effect of PMVs on cardiomyocyte survival was further confirmed through in vitro experiments. High ACSL1 expression was observed in the platelets of AMI patients. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that ACSL1, located in the mitochondria, played a key role in the PPAR signaling pathway. The elevated ACSL1 expression in a co-culture model of PMVs and AC16 cardiomyocytes significantly increased the AC16 cell Ferroptosis. Further, we validated that the platelet ACSL1 expression could be regulated by hsa-miR-449a. Together, these findings suggested that platelet ACSL1 could trigger myocardial cell death via PMV transport. In addition, this research provided a theoretical framework for attenuating myocardial cell Ferroptosis in patients with acute myocardial infarction.

Transcriptomic analysis reveals upregulated host metabolisms and downregulated immune responses or cell death induced by acute African swine fever virus infection

The African swine fever virus is a virulent and communicable viral disease that can be transmitted by infected swine, contaminated pork products, or soft tick vectors. Nonstructural proteins encoded by ASFV regulate viral replication, transcription, and evasion. However, the mechanisms underlying the host response to ASFV infection remain incompletely understood. In order to enhance comprehension of the biology and molecular mechanisms at distinct time intervals (6, 12, 24 h) post infection, transcriptome analyses were executed to discern differentially expressed genes (DEGs) between ASFV and mock-infected PAMs. The transcriptomic analysis unveiled a total of 1,677, 2,122, and 2,945 upregulated DEGs and 933, 1,148, and 1,422 downregulated DEGs in ASFV- and mock-infected groups at 6, 12, and 24 h.p.i.. The results of the transcriptomic analysis demonstrated that the infection of ASFV significantly stimulated host metabolism pathways while concurrently inhibiting the expression of various immune responses and cell death pathways. Our study offers crucial mechanistic insights into the comprehension of ASFV viral pathogenesis and the multifaceted host immune responses. The genes that were dysregulated may serve as potential candidates for further exploration of anti-ASFV strategies.

Transcriptomic analysis of esophageal cancer reveals hub genes and networks involved in cancer progression

Esophageal carcinoma (ESCA) has a 5-year survival rate of fewer than 20%. The study aimed to identify new predictive biomarkers for ESCA through transcriptomics meta-analysis to address the problems of ineffective cancer therapy, lack of efficient diagnostic tools, and costly screening and contribute to developing more efficient cancer screening and treatments by identifying new marker genes. Nine GEO datasets of three kinds of esophageal carcinoma were analyzed, and 20 differentially expressed genes were detected in carcinogenic pathways. Network analysis revealed four hub genes, namely RAR Related Orphan Receptor A (RORA), lysine acetyltransferase 2B (KAT2B), Cell Division Cycle 25B (CDC25B), and Epithelial Cell Transforming 2 (ECT2). Overexpression of RORA, KAT2B, and ECT2 was identified with a bad prognosis. These hub genes modulate immune cell infiltration. These hub genes modulate immune cell infiltration. Although this research needs lab confirmation, we found interesting biomarkers in ESCA that may aid in diagnosis and treatment.

Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data

In this protocol we describe our workflow for analyzing complex, multi-condition quantitative proteomic experiments, with the aim to extract biological insights. The tool we use is an R package, PloGO2, contributed to Bioconductor, which we can optionally precede by running correlation network analysis with WGCNA. We describe the data required and the steps we take, including detailed code examples and outputs explanation. The package was designed to generate gene ontology or pathway summaries for many data subsets at the same time, visualize protein abundance summaries for each biological category examined, help determine enriched protein subsets by comparing them all to a reference set, and suggest key highly correlated hub proteins, if the optional network analysis is employed.

Up-Regulated Proteins Have More Protein-Protein Interactions than Down-Regulated Proteins

Microarray technology has been successfully used in many biology studies to solve the protein–protein interaction (PPI) prediction computationally. For normal tissue, the cell regulation process begins with transcription and ends with the translation process. However, when cell regulation activity goes wrong, cancer occurs. Microarray data can precisely give high accuracy expression levels at normal and cancer-affected cells, which can be useful for the identification of disease-related genes. First, the differentially expressed genes (DEGs) are extracted from the cancer microarray dataset in order to identify the genes that are up-regulated and down-regulated during cancer progression in the human body. Then, proteins corresponding to these genes are collected from NCBI, and then the STRING web server is used to build the PPI network of these proteins. Interestingly, up-regulated proteins have always a higher number of PPIs compared to down-regulated proteins, although, in most of the datasets, the majority of these DEGs are down-regulated. We hope this study will help to build a relevant model to analyze the process of cancer progression in the human body.

The Molecular Network behind Volatile Aroma Formation in Pear (Pyrus spp. Panguxiang) Revealed by Transcriptome Profiling via Fatty Acid Metabolic Pathways

Pears are popular table fruits, grown and consumed worldwide for their excellent color, aroma, and taste. Volatile aroma is an important factor affecting fruit quality, and the fatty acid metabolism pathway is important in synthesizing volatile aromas. Most of the white pear varieties cultivated in China are not strongly scented, which significantly affects their overall quality. Panguxiang is a white pear cultivar, but its aroma has unique components and is strong. The study of the mechanisms by which aroma is formed in Panguxiang is, therefore, essential to improving the quality of the fruit. The study analyzed physiological and transcriptome factors to reveal the molecular network behind volatile aroma formation in Panguxiang. The samples of Panguxiang fruit were collected in two (fruit development at 60, 90, 120, and 147 days, and fruit storage at 0, 7, 14, 21, and 28 days) periods. A total of nine sample stages were used for RNA extraction and paired-end sequencing. In addition, RNA quantification and qualification, library preparation and sequencing, data analysis and gene annotation, gene co-expression network analysis, and validation of DEGs through quantitative real-time PCR (qRT-;PCR) were performed in this study. The WGCNA identified yellow functional modules and several biological and metabolic pathways related to fatty acid formation. Finally, we identified seven and eight hub genes in the fatty acid synthesis and fatty acid metabolism pathways, respectively. Further analysis of the co-expression network allowed us to identify several key transcription factors related to the volatile aroma, including AP2/ERF-ERF, C3H, MYB, NAC, C2H2, GRAS, and Trihelix, which may also be involved in the fatty acid synthesis. This study lays a theoretical foundation for studying volatile compounds in pear fruits and provides a theoretical basis for related research in other fruits.

Approaches in Gene Coexpression Analysis in Eukaryotes

Simple Summary

Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. Coexpressed genes are clustered in smaller subnetworks, the predominant biological roles of which can be determined through enrichment analysis. By studying well-annotated gene partners, the attribution of new roles to genes of unknown function or assumption for participation in common metabolic pathways can be achieved, through a guilt-by-association approach. In this review, we present key issues in gene coexpression analysis, as well as the most popular tools that perform it.

Abstract

Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied extensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensible account of the steps required for performing a complete gene coexpression analysis in eukaryotic organisms. We comment on the use of RNA-Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.

The Expression and Role Analysis of Methylation-Regulated Differentially Expressed Gene UBE2C in Pan-Cancer, Especially for HGSOC

Simple Summary

DNA methylation has attracted a great deal of scientific interest as an early biomarker and potential therapeutic target. HGSOC result in high mortality due to the absence of reliable biomarkers for early diagnosis and prognosis. In this study, we performed an integrated bioinformatic analysis and found that UBE2C was hypomethylation and overexpression in ovarian cancer, which was associated with advanced cancer stages and poor prognoses. Meantime, this finding was also confirmed in pan-cancer analysis. Furthermore, the experimental validation of the expression and role of UBE2C was performed on HGSOC tissues and cancer cell lines. Importantly, demethylation could upregulate the expression of UBE2C. Taken together, methylation-regulated UBE2C may be a novel biomarker for diagnosis and prognosis, not only for ovarian cancer but a variety of cancers.

Abstract

High-grade serous ovarian cancer (HGSOC) is the most fatal gynecological malignant tumor. DNA methylation is associated with the occurrence and development of a variety of tumor types, including HGSOC. However, the signatures regarding DNA methylation changes for HGSOC diagnosis and prognosis are less explored. Here, we screened differentially methylated genes and differentially expressed genes in HGSOC through the GEO database. We identified that UBE2C was hypomethylation and overexpression in ovarian cancer, which was associated with more advanced cancer stages and poor prognoses. Additionally, the pan-cancer analysis showed that UBE2C was overexpressed and hypomethylation in almost all cancer types and was related to poor prognoses for various cancers. Next, we established a risk or prognosis model related to UBE2C methylation sites and screened out the three sites (cg03969725, cg02838589, and cg00242976). Furthermore, we experimentally validated the overexpression of UBE2C in HGSOC clinical samples and ovarian cell lines using quantitative real-time PCR, Western blot, and immunohistochemistry. Importantly, we discovered that ovarian cancer cell lines had lower DNA methylation levels of UBE2C than IOSE-80 cells (normal ovarian epithelial cell line) by bisulfite sequencing PCR. Consistently, treatment with 5-Azacytidine (a methylation inhibitor) was able to restore the expression of UBE2C. Taken together, our study may help us to understand the underlying molecular mechanism of UBE2C in pan-cancer tumorigenesis; it may be a useful biomarker for diagnosis, treatment, and monitoring, not only of ovarian cancer but a variety of cancers.

Identification of co-expression hub genes for ferroptosis in kidney renal clear cell carcinoma based on weighted gene co-expression network analysis and The Cancer Genome Atlas clinical data

Renal clear cell carcinoma (KIRC) is one of the most common tumors worldwide and has a high mortality rate. Ferroptosis is a major mechanism of tumor occurrence and development, as well as important for prognosis and treatment of KIRC. Here, we conducted bioinformatics analysis to identify KIRC hub genes that target ferroptosis. By Weighted gene co-expression network analysis (WGCNA), 11 co-expression-related genes were screened out. According to Kaplan Meier's survival analysis of the data from the gene expression profile interactive analysis database, it was identified that the expression levels of two genes, PROM2 and PLIN2, are respectively related to prognosis. In conclusion, our findings indicate that PROM2 and PLIN2 may be effective new targets for the treatment and prognosis of KIRC.

Network Analysis of Microarray Data

DNA microarrays are widely used to investigate gene expression. Even though the classical analysis of microarray data is based on the study of differentially expressed genes, it is well known that genes do not act individually. Network analysis can be applied to study association patterns of the genes in a biological system. Moreover, it finds wide application in differential coexpression analysis between different systems. Network based coexpression studies have for example been used in (complex) disease gene prioritization, disease subtyping, and patient stratification.In this chapter we provide an overview of the methods and tools used to create networks from microarray data and describe multiple methods on how to analyze a single network or a group of networks. The described methods range from topological metrics, functional group identification to data integration strategies, topological pathway analysis as well as graphical models.

Transmembrane signaling molecules play a key role in the pathogenesis of IgA nephropathy: a weighted gene co-expression network analysis study

BACKGROUND

Immunoglobulin A nephropathy (IgAN) is one of the most common primary glomerulonephritis and a serious health concern worldwide; though still the underlying molecular mechanisms of IgAN are yet to be known and there is no efficient treatment for this disease. The main goal of this study was to explore the IgAN underlying pathogenic pathways, plus identifying the disease correlated modules and genes using the weighted gene co-expression network analysis (WGCNA) algorithm.

RESULTS

GSE104948 dataset (the expression data from glomerular tissue of IgAN patients) was analyzed and the identified differentially expressed genes (DEGs) were introduced to the WGCNA algorithm for building co-expression modules. Genes were classified into six co-expression modules. Genes of the disease's most correlated module were mainly enriched in the immune system, cell-cell communication and transmembrane cell signaling pathways. The PPI network was constructed by genes in all the modules and after hub-gene identification and validation steps, 11 genes, mostly transmembrane proteins (CD44, TLR1, TLR2, GNG11, CSF1R, TYROBP, ITGB2, PECAM1), as well as DNMT1, CYBB and PSMB9 were identified as potentially key players in the pathogenesis of IgAN. In the constructed regulatory network, hsa-miR-129-2-3p, hsa-miR-34a-5p and hsa-miR-27a-3p, as well as STAT3 were spotted as top molecules orchestrating the regulation of the hub genes.

CONCLUSIONS

The excavated hub genes from the hearts of co-expressed modules and the PPI network were mostly transmembrane signaling molecules. These genes and their upstream regulators could deepen our understanding of IgAN and be considered as potential targets for hindering its progression.

Identification of key genes as predictive biomarkers for osteosarcoma metastasis using translational bioinformatics

Background

Osteosarcoma (OS) metastasis is the most common cause of cancer-related mortality, however, no sufficient clinical biomarkers have been identified. In this study, we identified five genes to help predict metastasis at diagnosis.

Methods

We performed weighted gene co-expression network analysis (WGCNA) to identify the most relevant gene modules associated with OS metastasis. An important machine learning algorithm, the support vector machine (SVM), was employed to predict key genes for classifying the OS metastasis phenotype. Finally, we investigated the clinical significance of key genes and their enriched pathways.

Results

Eighteen modules were identified in WGCNA, among which the pink, red, brown, blue, and turquoise modules demonstrated good preservation. In the five modules, the brown and red modules were highly correlated with OS metastasis. Genes in the two modules closely interacted in protein–protein interaction networks and were therefore chosen for further analysis. Genes in the two modules were primarily enriched in the biological processes associated with tumorigenesis and development. Furthermore, 65 differentially expressed genes were identified as common hub genes in both WGCNA and protein–protein interaction networks. SVM classifiers with the maximum area under the curve were based on 30 and 15 genes in the brown and red modules, respectively. The clinical significance of the 45 hub genes was analyzed. Of the 45 genes, 17 were found to be significantly correlated with survival time. Finally, 5/17 genes, including ADAP2 (P = 0.0094), LCP2 (P = 0.013), ARHGAP25 (P = 0.0049), CD53 (P = 0.016), and TLR7 (P = 0.04) were significantly correlated with the metastatic phenotype. In vitro verification, western blotting, wound healing analyses, transwell invasion assays, proliferation assays, and colony formation assays indicated that ARHGAP25 promoted OS cell migration, invasion, proliferation, and epithelial–mesenchymal transition.

Conclusion

We identified five genes, namely ADAP2, LCP2, ARHGAP25, CD53, and TLR7, as candidate biomarkers for the prediction of OS metastasis; ARHGAP25 inhibits MG63 OS cell growth, migration, and invasion in vitro, indicating that ARHGAP25 can serve as a promising specific and prognostic biomarker for OS metastasis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02308-w.

Identifying critical genes associated with aneurysmal subarachnoid hemorrhage by weighted gene co-expression network analysis

Aneurysmal subarachnoid hemorrhage (aSAH) is a life-threatening medical condition with a high mortality and disability rate. aSAH has an unclear pathogenesis, and limited treatment options are available. Here, we aimed to identify critical genes involved in aSAH pathogenesis using peripheral blood gene expression data of 43 patients with aSAH due to ruptured intracranial aneurysms and 18 controls with headache, downloaded from Gene Expression Omnibus. These data were used to construct a co-expression network using weighted gene co-expression network analysis (WGCNA). The biological functions of the hub genes were explored, and critical genes were selected by combining with differentially expressed genes analysis. Fourteen modules were identified by WGCNA. Among those modules, red, blue, brown and cyan modules were closely associated with aSAH. Moreover, 364 hub genes in the significant modules were found to play important roles in aSAH. Biological function analysis suggested that protein biosynthesis-related processes and inflammatory responses-related processes were involved in the pathology of aSAH pathology. Combined with differentially expressed genes analysis and validation in 35 clinical samples, seven gene (CD27, ANXA3, ACSL1, PGLYRP1, ALPL, ARG1, and TPST1) were identified as potential biomarkers for aSAH, and three genes (ANXA3, ALPL, and ARG1) were changed with disease development, that may provide new insights into potential molecular mechanisms for aSAH.

Cell-specific gene association network construction from single-cell RNA sequence

The recent development of a high throughput single-cell RNA sequence devises the opportunity to study entire transcriptomes in the smallest detail. It also leads to the characterization of molecules and subtypes of a cell. Cancer epigenetics induced not only from individual molecules but also from the dysfunction of the system and the coupling effect of genes. While rapid advances are being made in the development of tools for single-cell RNA-seq data analysis, few slants are noticed in the potential advantages of single-cell network construction.Here, we used network perturbation theory with significant analysis to develop a cell-specific network that provides an insight into gene-gene association based on molecular expressions in a single-cell resolution. Besides, using this method, we can characterize each cell by inspecting how genes are connected and can identify the hub genes using network degree theory. Pathway & Gene enrichment analysis of the identified cell-specific high network degree genes supported the effectiveness of this method. This method could be beneficial for personalized drug design and even therapeutics.

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.

Identification of hub genes in colorectal cancer based on weighted gene co-expression network analysis and clinical data from The Cancer Genome Atlas

Colorectal cancer (CRC) is one of the most common tumors worldwide and is associated with high mortality. Here we performed bioinformatics analysis, which we validated using immunohistochemistry in order to search for hub genes that might serve as biomarkers or therapeutic targets in CRC. Based on data from The Cancer Genome Atlas (TCGA), we identified 4832 genes differentially expressed between CRC and normal samples (1562 up-regulated and 3270 down-regulated in CRC). Gene ontology (GO) analysis showed that up-regulated genes were enriched mainly in organelle fission, cell cycle regulation, and DNA replication; down-regulated genes were enriched primarily in the regulation of ion transmembrane transport and ion homeostasis. Weighted gene co-expression network analysis (WGCNA) identified eight gene modules that were associated with clinical characteristics of CRC patients, including brown and blue modules that were associated with cancer onset. Analysis of the latter two hub modules revealed the following six hub genes: adhesion G protein-coupled receptor B3 (BAI3, also known as ADGRB3), cyclin F (CCNF), cytoskeleton-associated protein 2 like (CKAP2L), diaphanous-related formin 3 (DIAPH3), oxysterol binding protein-like 3 (OSBPL3), and RERG-like protein (RERGL). Expression levels of these hub genes were associated with prognosis, based on Kaplan–Meier survival analysis of data from the Gene Expression Profiling Interactive Analysis database. Immunohistochemistry of CRC tumor tissues confirmed that OSBPL3 is up-regulated in CRC. Our findings suggest that CCNF, DIAPH3, OSBPL3, and RERGL may be useful as therapeutic targets against CRC. BAI3 and CKAP2L may be novel biomarkers of the disease.

Development of a novel gene signature to predict prognosis and response to PD-1 blockade in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common kidney malignancy characterized by a poor prognosis. The treatment efficacy of immune checkpoint inhibitors (ICIs) also varies widely in advanced ccRCC. We aim to construct a robust gene signature to improve the prognostic discrimination and prediction of ICIs for ccRCC patients. In this study, adopting differentially expressed genes from seven ccRCC datasets in GEO (Gene Expression Omnibus), a novel signature (FOXM1&TOP2A) was constructed in TCGA (The Cancer Genome Atlas) database by LASSO and Cox regression. Survival and time-dependent ROC analysis revealed the strong predictive ability of our signature in discovery set, two online validation sets and one tissue microarray (TMA) from our institution. High-risk group based on the signature comprises more high-grade (G3&G4) and advanced pathologic stage (stageIII/IV) tumors and presents hyperactivation of cell cycle process according to the functional analysis. Meanwhile, high-risk tumors demonstrate an immunosuppressive phenotype with more infiltrations of regulatory T cells (Tregs), macrophages and high expressions of genes negatively regulating anti-tumor immunity. Low-risk tumors have an improved response to anti-PD-1 therapy and the predictive ability of our signature is better than other recognized biomarkers in ccRCC. A nomogram containing this signature showed a high predictive accuracy with AUCs of 0.90 and 0.84 at 3 and 5 years. Overall, this robust signature could predict prognosis, evaluate immune microenvironment and response to anti-PD-1 therapy in ccRCC, which is very promising in clinical promotion.

Inhibition of KIF20A by transcription factor IRF6 affects the progression of renal clear cell carcinoma

Background

Renal clear cell carcinoma (ccRCC) is one of the most common malignant tumors, whose incidence is increasing year by year. IRF6 plays an important role in the occurrence of tumors, although there is yet no report on its expression in ccRCC.

Methods

The expression of IRF6 and KIF20A in ccRCC was predicted by GEPIA and HAP databases. In addition, GEPIA database predicted the relationship between IRF6 and KIF20A expressions and the pathological staging, overall survival, and disease-free survival of ccRCC. The possible binding sites of IRF6 and KIF20A promoters were predicted by JASPAR database and verified by luciferase and ChIP assays. The specific effects of IRF6 on ccRCC cell proliferation, invasion and apoptosis were subsequently examined at both cellular level and animal level.

Results

The database predicted down-regulated IRF6 expression in renal carcinoma tissues and its correlation with poor prognosis. IRF6 overexpression inhibited cRCC cell proliferation, invasion and migration. In addition, up-regulated KIF20A expression in renal carcinoma tissues and its association with prognosis were also predicted. Interference with KIF20A inhibited the proliferation, invasion, and migration of ccRCC cells. Finally, we confirmed that KIF20A is a functional target of IRF6 and can partially reverse the effects of IRF6 on the proliferation, invasion and migration of ccRCC cells. Conclusion: Inhibition of KIF20A by transcription factor IRF6 affects cell proliferation, invasion and migration in renal clear cell carcinoma.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-01879-y.

Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19

Current coronavirus disease-2019 (COVID-19) pandemic has caused massive loss of lives. Clinical trials of vaccines and drugs are currently being conducted around the world; however, till now no effective drug is available for COVID-19. Identification of key genes and perturbed pathways in COVID-19 may uncover potential drug targets and biomarkers. We aimed to identify key gene modules and hub targets involved in COVID-19. We have analyzed SARS-CoV-2 infected peripheral blood mononuclear cell (PBMC) transcriptomic data through gene coexpression analysis. We identified 1520 and 1733 differentially expressed genes (DEGs) from the GSE152418 and CRA002390 PBMC datasets, respectively (FDR < 0.05). We found four key gene modules and hub gene signature based on module membership (MMhub) statistics and protein-protein interaction (PPI) networks (PPIhub). Functional annotation by enrichment analysis of the genes of these modules demonstrated immune and inflammatory response biological processes enriched by the DEGs. The pathway analysis revealed the hub genes were enriched with the IL-17 signaling pathway, cytokine-cytokine receptor interaction pathways. Then, we demonstrated the classification performance of hub genes (PLK1, AURKB, AURKA, CDK1, CDC20, KIF11, CCNB1, KIF2C, DTL and CDC6) with accuracy >0.90 suggesting the biomarker potential of the hub genes. The regulatory network analysis showed transcription factors and microRNAs that target these hub genes. Finally, drug-gene interactions analysis suggests amsacrine, BRD-K68548958, naproxol, palbociclib and teniposide as the top-scored repurposed drugs. The identified biomarkers and pathways might be therapeutic targets to the COVID-19.

Machine learning-based investigation of the cancer protein secretory pathway

Deregulation of the protein secretory pathway (PSP) is linked to many hallmarks of cancer, such as promoting tissue invasion and modulating cell-cell signaling. The collection of secreted proteins processed by the PSP, known as the secretome, is often studied due to its potential as a reservoir of tumor biomarkers. However, there has been less focus on the protein components of the secretory machinery itself. We therefore investigated the expression changes in secretory pathway components across many different cancer types. Specifically, we implemented a dual approach involving differential expression analysis and machine learning to identify PSP genes whose expression was associated with key tumor characteristics: mutation of p53, cancer status, and tumor stage. Eight different machine learning algorithms were included in the analysis to enable comparison between methods and to focus on signals that were robust to algorithm type. The machine learning approach was validated by identifying PSP genes known to be regulated by p53, and even outperformed the differential expression analysis approach. Among the different analysis methods and cancer types, the kinesin family members KIF20A and KIF23 were consistently among the top genes associated with malignant transformation or tumor stage. However, unlike most cancer types which exhibited elevated KIF20A expression that remained relatively constant across tumor stages, renal carcinomas displayed a more gradual increase that continued with increasing disease severity. Collectively, our study demonstrates the complementary nature of a combined differential expression and machine learning approach for analyzing gene expression data, and highlights key PSP components relevant to features of tumor pathophysiology that may constitute potential therapeutic targets.

The secretory pathway is a series of intracellular compartments and enzymes that process and export proteins from the cell to its surrounding environment. Dysfunction of the secretory pathway is associated with many diseases, including cancer, and therefore constitutes a potential target for novel therapeutic strategies. The large number of interacting components that comprise the secretory pathway pose a challenge when attempting to identify where the dysfunction originates or how to restore healthy function. To improve our understanding of how the secretory pathway is changed within tumors, we used gene expression data from normal tissue and tumor samples from thousands of individuals which included many different types of cancers. The data was analyzed using different machine learning algorithms which we trained to predict sample characteristics, such as disease severity. This training quantified the relative degree to which each gene was associated with the tumor characteristic, allowing us to predict which secretory pathway components were important for processes such as tumor progression—both within specific cancer types and across many different cancer types. The machine learning-based approach demonstrated excellent performance compared to traditional gene expression analysis methods and identified several secretory pathway components with strong evidence of involvement in tumor development.

The clinical significance of <em>UBE2C</em> gene in progression of renal cell carcinoma

Renal cell carcinoma (RCC), with high morbidity and mortality, is one of the top ten serious cancers. Due to limited therapies and little knowledge about the mechanism underlying RCC, overall survival of RCC patients is poor. UBE2C is a member of ubiquitin modification system and promotes carcinogenesis in cancer, but its role in RCC is unknown. Based on the TCGA (The Cancer Genome Atlas) data, UBE2C was over-expressed in a total of 525 RCC tissues and displayed higher expression in advanced tissues (stage IV vs stage I, p<0.05). RT-qPCR and IHC analysis confirmed over-expression of UBE2C in 90 of clinical RCC tissues. Further, UBE2C was associated with clinical factors including TNM stage, gender, and pathological stage. And higher UBE2C expression predicted shorter overall survival and progression-free survival. Both univariate and multivariate COX analysis suggested UBE2C as a critical gene in RCC. Then GO and KEGG analysis showed that cell cycle and DNA replication pathways were two top signaling pathways affected by UBE2C. In vitro assay showed that knockdown of UBE2C in 786-O cells inhibited proliferation and migration significantly. Therefore, this study proves that UBE2C is an important gene in RCC and is essential to proliferation and migration of RCC.

Integrated Protein-Protein Interaction and Weighted Gene Co-expression Network Analysis Uncover Three Key Genes in Hepatoblastoma

Hepatoblastoma (HB) is the most common liver tumor in the pediatric population, with typically poor outcomes for advanced-stage or chemotherapy-refractory HB patients. The objective of this study was to identify genes involved in HB pathogenesis via microarray analysis and subsequent experimental validation. We identified 856 differentially expressed genes (DEGs) between HB and normal liver tissue based on two publicly available microarray datasets (GSE131329 and GSE75271) after data merging and batch effect correction. Protein–protein interaction (PPI) analysis and weighted gene co-expression network analysis (WGCNA) were conducted to explore HB-related critical modules and hub genes. Subsequently, Gene Ontology (GO) analysis was used to reveal critical biological functions in the initiation and progression of HB. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that genes involved in cell cycle phase transition and the PI3K/AKT signaling were associated with HB. The intersection of hub genes identified by both PPI and WGCNA analyses revealed five potential candidate genes. Based on receiver operating characteristic (ROC) curve analysis and reports in the literature, we selected CCNA2, CDK1, and CDC20 as key genes of interest to validate experimentally. CCNA2, CDK1, or CDC20 small interfering RNA (siRNA) knockdown inhibited aggressive biological properties of both HepG2 and HuH-6 cell lines in vitro. In conclusion, we identified CCNA2, CDK1, and CDC20 as new potential therapeutic biomarkers for HB, providing novel insights into important and viable targets in future HB treatment.

Identification of tumor-associated antigens of lung cancer: SEREX combined with bioinformatics analysis

The aim of this study is to identify novel tumor-associated antigens (TAAs) of lung cancer by using serological analysis of recombinant cDNA expression library (SEREX) and bioinformatics analysis as well as to explore their humoral immune response. SEREX and pathway enrichment analysis were used to immunoscreen TAAs of lung cancer and elaborate their function in biological pathways, respectively. Subsequently, the sera level of autoantibodies against the selected TAAs (TOP2A, TRIM37, HSP90AB1, EEF1G and TPP1) was detected by immunoserological analysis to explore the immune response of these antigens. The Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) database were applied to explore the mRNA and protein expression level of TOP2A, TRIM37 and HSP90AB1 in tissues, respectively. Seventy positive clones were identified by SEREX which contain 63 different genes, and 35 genes of them have been reported. These 35 genes were mainly related to regulation of different transcription factor and performed enrichment in legionellosis, RNA transport, IL-17 signaling pathway via enrichment analysis. Additionally, the positive rate of autoantibodies against TOP2A, TRIM37 and HSP90AB1 in lung cancer patients were typically higher than normal control (NC; P < 0.05). Moreover, the combination of the autoantibodies against TOP2A, TRIM37 and HSP90AB1 possessed an excellent diagnostic performance with sensitivity of 84% and specificity of 60%. The mRNA expression level of TOP2A was obviously unregulated in squamous cell carcinoma (SCC) tissues and adenocarcinoma (ADC) tissues compared to normal tissues (P < 0.05). In addition, TRIM37 and HSP90AB1 also showed a significant difference between SCC and NC at the mRNA expression level (P < 0.05). This study combining comprehensive autoantibody and gene expression assays has added to the growing list of lung cancer antigens, which may aid the development of diagnostic and immunotherapeutic targets for lung cancer patients.

ComHub: Community predictions of hubs in gene regulatory networks

BACKGROUND

Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expression data, few methods focus on inferring these hubs.

RESULTS

We have developed ComHub, a tool to predict hubs in GRNs. ComHub makes a community prediction of hubs by averaging over predictions by a compendium of network inference methods. Benchmarking ComHub against the DREAM5 challenge data and two independent gene expression datasets showed a robust performance of ComHub over all datasets.

CONCLUSIONS

In contrast to other evaluated methods, ComHub consistently scored among the top performing methods on data from different sources. Lastly, we implemented ComHub to work with both predefined networks and to perform stand-alone network inference, which will make the method generally applicable.

Identification of Core Genes Involved in the Metastasis of Clear Cell Renal Cell Carcinoma

Introduction

Renal cell carcinoma (RCC) is one of the most common malignancies globally, among which clear cell carcinoma (ccRCC) accounts for 85–90% of all pathological types. This study aims to screen out potential genes in metastatic ccRCC so as to provide novel insights for ccRCC treatment.

Methods

GSE53757 and GSE84546 datasets in the Gene Expression Omnibus (GEO) were profiled to identify differentially expressed genes (DEGs) from ccRCC samples with or without metastasis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene ontology (GO) analysis were performed to analyze pathway enrichment and functional annotation of DEGs. Protein–protein interaction (PPI) network was constructed, and survival analysis was conducted to evaluate the clinical values of the identified hub genes. In vitro loss-of-function assays were performed to explore the biological roles of these genes.

Results

The bioinformatic analysis indicated that 312 DEGs were identified, including 148 upregulated genes and 164 downregulated ones. Using PPI and Cytoscape, 10 hub genes were selected (C3, CXCR4, CCl4, ACKR3, KIF20A, CCNB2, CDCA8, CCL28, S1PR5, and CCL20) from DEGs which might be closely related with ccRCC metastasis. In Kaplan–Meier analysis, three potential prognostic biomarkers (KIF20A, CCNB2 and CDCA8) were identified. Finally, cell proliferative and invasive assays further verified that KIF20A, CCNB2 and CDCA8 were associated with the proliferation and invasion of ccRCC cells.

Conclusion

Our results demonstrated that metastatic ccRCC was partially attributed to the aberrant expression of KIF20A, CCNB2 and CDCA8, and more personalized therapeutic approaches should be explored targeting these hub genes.

Influence of gene expression on survival of clear cell renal cell carcinoma

Approximately 10%‐20% of patients with clinically localized clear cell renal cell carcinoma (ccRCC) at time of surgery will subsequently experience metastatic progression. Although considerable progression was seen in the systemic treatment of metastatic ccRCC in last 20 years, once ccRCC spreads beyond the confines of the kidney, 5‐year survival is less than 10%. Therefore, significant clinical advances are urgently needed to improve overall survival and patient care to manage the growing number of patients with localized ccRCC. We comprehensively evaluated expression of 388 candidate genes related with survival of ccRCC by using TCGA RNAseq (n = 515), Total Cancer Care (TCC) expression array data (n = 298), and a well characterized Moffitt RCC cohort (n = 248). We initially evaluated all 388 genes for association with overall survival using TCGA and TCC data. Eighty‐one genes were selected for further analysis and tested on Moffitt RCC cohort using NanoString expression analysis. Expression of nine genes (AURKA, AURKB, BIRC5, CCNE1, MK167, MMP9, PLOD2, SAA1, and TOP2A) was validated as being associated with poor survival. Survival prognostic models showed that expression of the nine genes and clinical factors predicted the survival in ccRCC patients with AUC value: 0.776, 0.821 and 0.873 for TCGA, TCC and Moffitt data set, respectively. Some of these genes have not been previously implicated in ccRCC survival and thus potentially offer insight into novel therapeutic targets. Future studies are warranted to validate these identified genes, determine their biological mechanisms and evaluate their therapeutic potential in preclinical studies.

Identification of Hub Genes Associated with Hypertension and Their Interaction with miRNA Based on Weighted Gene Coexpression Network Analysis (WGCNA) Analysis

Background

Hypertension is one of the most widespread health conditions in the world, and the molecular mechanism of it is still unclear. In this study, we identified the hub genes (hub miRNA genes) associated with hypertension and explored the relationship between hypertension miRNA-gene by constructing a mRNA co-expression network and a miRNA co-expression network, which can help to reveal the mechanism and predict the prognosis of hypertension progression.

Material/Methods

Based on gene expression profile data of hypertensive samples from the Gene Expression Omnibus database, WGCNA was used to detect hypertension-related biomarkers and key mRNA and miRNA modules. Then, DAVID was used to perform gene-annotation enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) and miRPath were used for pathway analysis of mRNA and miRNAs genes.

Results

We identified 3 key modules relating to hypertension, 2 mRNA modules named M_saddlebrown and M_greenyellow and 1 miRNA module named M_salmon. In addition, 12 hub genes (RPL21, RPS28, LOC442727/PTGAP10, LOC100129599/RPS29P14, TBXAS1, FCER1G, CFP, FURIN, PECAM1, IGSF6, NCF1C, and LOC285296/UNC93B3) and 7 hub miRNAs (hsa-miR-1268a/b, hsa-miR-513c-3p, hsa-miR-4799-5p, hsa-miR-296-3p, hsa-miR-5195-5p, hsa-miR-219-2-3p, and hsa-miR-548d-5p) relating to hypertension were identified. HIF-1 signaling pathway and insulin signaling pathway were closely related to the 3 key modules. We also discovered 4 miRNAs (hsa-miR-548am-3p, hsa-miR-513c-3p, hsa-miR-182-5p, and hsa-miR-548d-5p) and 6 genes (IGF1R, GSK3B, FOXO1, PRKAR2B, HIF1A, and PIK3R1) were the core nodes in the hypertension-related miRNA-gene network, and hsa-miR-548am-3p was at the center of the network.

Conclusions

These findings will help improve the understanding of the pathogenesis of hypertension, and the discovered genes can serve as signatures for early diagnosis of hypertension.

Co-expression Network Analysis Identifies Fourteen Hub Genes Associated with Prognosis in Clear Cell Renal Cell Carcinoma

Renal cancer is a common genitourinary malignance, of which clear cell renal cell carcinoma (ccRCC) has high aggressiveness and leads to most cancer-related deaths. Identification of sensitive and reliable biomarkers for predicting tumorigenesis and progression has great significance in guiding the diagnosis and treatment of ccRCC. Here, we identified 2397 common differentially expressed genes (DEGs) using paired normal and tumor ccRCC tissues from GSE53757 and The Cancer Genome Atlas (TCGA). Then, we performed weighted gene co-expression network analysis and protein-protein interaction network analysis, 17 candidate hub genes were identified. These candidate hub genes were further validated in GSE36895 and Oncomine database and 14 real hub genes were identified. All the hub genes were up-regulated and significantly positively correlated with pathological stage and histologic grade of ccRCC. Survival analysis showed that the higher expression level of each hub gene tended to predict a worse clinical outcome. ROC analysis showed that all the hub genes can accurately distinguish between tumor and normal samples, and between early stage and advanced stage ccRCC. Moreover, all the hub genes were positively associated with distant metastasis, lymph node infiltration, tumor recurrence and the expression of MKi67, suggesting these genes might promote tumor proliferation, invasion and metastasis. Furthermore, the functional annotation demonstrated that most genes were enriched in cell-cycle related biological function. In summary, our study identified 14 potential biomarkers for predicting tumorigenesis and progression, which might contribute to early diagnosis, prognosis prediction and therapeutic intervention.

Identification of KIF18B as a Hub Candidate Gene in the Metastasis of Clear Cell Renal Cell Carcinoma by Weighted Gene Co-expression Network Analysis

Background

Clear cell renal cell carcinoma (ccRCC) is a common type of fatal malignancy in the urinary system. As the therapeutic strategies of ccRCC are severely limited at present, the prognosis of patients with metastatic carcinoma is usually not promising. Revealing the pathogenesis and identifying hub candidate genes for prognosis prediction and precise treatment are urgently needed in metastatic ccRCC.

Methods

In the present study, we conducted a series of bioinformatics studies with the gene expression profiles of ccRCC samples from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) database for identifying and validating the hub gene of metastatic ccRCC. We constructed a co-expression network, divided genes into co-expression modules, and identified ccRCC-related modules by weighted gene co-expression network analysis (WGCNA) with data from GEO. Then, we investigated the functions of genes in the ccRCC-related modules by enrichment analyses and built a sub-network accordingly. A hub candidate gene of the metastatic ccRCC was identified by maximal clique centrality (MCC) method. We validate the hub gene by differentially expressed gene analysis, overall survival analysis, and correlation analysis with clinical traits with the external dataset (TCGA). Finally, we explored the function of the hub gene by correlation analysis with targets of precise therapies and single-gene gene set enrichment analysis.

Results

We conducted WGCNA with the expression profiles of GSE73731 from GEO and divided all genes into 8 meaningful co-expression modules. One module is proved to be positively correlated with pathological stage and tumor grade of ccRCC. Genes in the ccRCC-related module were mainly enriched in functions of mitotic cell division and several proverbial tumor related signal pathways. We then identified KIF18B as a hub gene of the metastasis of ccRCC. Validating analyses in external dataset observed the up-regulation of KIF18B in ccRCC and its correlation with worse outcomes. Further analyses found that the expression of KIF18B is related to that of targets of precise therapies.

Conclusion

Our study proposed KIF18B as a hub candidate gene of ccRCC for the first time. Our conclusion may provide a brand-new clue for prognosis evaluating and precise treatment for ccRCC in the future.

Weighted Gene Coexpression Network Analysis Reveals the Dynamic Transcriptome Regulation and Prognostic Biomarkers of Hepatocellular Carcinoma

This study was aimed at revealing the dynamic regulation of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in hepatocellular carcinoma (HCC) and to identify HCC biomarkers capable of predicting prognosis. Differentially expressed mRNAs (DEmRNAs), lncRNAs, and miRNAs were acquired by comparing expression profiles of HCC with normal samples, using an expression data set from The Cancer Genome Atlas. Altered biological functions and pathways in HCC were analyzed by subjecting DEmRNAs to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Gene modules significantly associated with disease status were identified by weighted gene coexpression network analysis. An lncRNA-mRNA and an miRNA-mRNA coexpression network were constructed for genes in disease-related modules, followed by the identification of prognostic biomarkers using Kaplan-Meier survival analysis. Differential expression and association with the prognosis of 4 miRNAs were verified in independent data sets. A total of 1220 differentially expressed genes were identified between HCC and normal samples. Differentially expressed mRNAs were significantly enriched in functions and pathways related to “plasma membrane structure,” “sensory perception,” “metabolism,” and “cell proliferation.” Two disease-associated gene modules were identified. Among genes in lncRNA-mRNA and miRNA-mRNA coexpression networks, 9 DEmRNAs and 7 DEmiRNAs were identified to be potential prognostic biomarkers. MIMAT0000102, MIMAT0003882, and MIMAT0004677 were successfully validated in independent data sets. Our results may advance our understanding of molecular mechanisms underlying HCC. The biomarkers may contribute to diagnosis in future clinical practice.

A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

Background

Lymphovascular invasion (LOI), a key pathological feature of head and neck squamous cell carcinoma (HNSCC), is predictive of poor survival; however, the associated clinical characteristics and underlying molecular mechanisms remain largely unknown.

Methods

We performed weighted gene co-expression network analysis to construct gene co-expression networks and investigate the relationship between key modules and the LOI clinical phenotype. Functional enrichment and KEGG pathway analyses were performed with differentially expressed genes. A protein–protein interaction network was constructed using Cytoscape, and module analysis was performed using MCODE. Prognostic value, expression analysis, and survival analysis were conducted using hub genes; GEPIA and the Human Protein Atlas database were used to determine the mRNA and protein expression levels of hub genes, respectively. Multivariable Cox regression analysis was used to establish a prognostic risk formula and the areas under the receiver operating characteristic curve (AUCs) were used to evaluate prediction efficiency. Finally, potential small molecular agents that could target LOI were identified with DrugBank.

Results

Ten co-expression modules in two key modules (turquoise and pink) associated with LOI were identified. Functional enrichment and KEGG pathway analysis revealed that turquoise and pink modules played significant roles in HNSCC progression. Seven hub genes (CNFN, KIF18B, KIF23, PRC1, CCNA2, DEPDC1, and TTK) in the two modules were identified and validated by survival and expression analyses, and the following prognostic risk formula was established: [risk score = EXP_DEPDC1 * 0.32636 + EXP_CNFN * (− 0.07544)]. The low-risk group showed better overall survival than the high-risk group (P < 0.0001), and the AUCs for 1-, 3-, and 5-year overall survival were 0.582, 0.634, and 0.636, respectively. Eight small molecular agents, namely XL844, AT7519, AT9283, alvocidib, nelarabine, benzamidine, L-glutamine, and zinc, were identified as novel candidates for controlling LOI in HNSCC (P < 0.05).

Conclusions

The two-mRNA signature (CNFN and DEPDC1) could serve as an independent biomarker to predict LOI risk and provide new insights into the mechanisms underlying LOI in HNSCC. In addition, the small molecular agents appear promising for LOI treatment.

Identification of Four Pathological Stage-Relevant Genes in Association with Progression and Prognosis in Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis

Clear cell renal cell carcinoma (ccRCC) is a major histological subtype of renal cell carcinoma and can be clinically divided into four stages according to the TNM criteria. Identifying clinical stage-related genes is beneficial for improving the early diagnosis and prognosis of ccRCC. By using bioinformatics analysis, we aim to identify clinical stage-relevant genes that are significantly associated with the development of ccRCC. First, we analyzed the gene expression microarray data sets: GSE53757 and GSE73731. We divided these data into five groups by staging information-normal tissue and ccRCC stages I, II, III, and IV-and eventually identified 500 differentially expressed genes (DEGs). To obtain precise stage-relevant genes, we subsequently applied weighted gene coexpression network analysis (WGCNA) to the GSE73731 dataset and KIRC data from The Cancer Genome Atlas (TCGA). Two modules from each dataset were identified to be related to the tumor TNM stage. Several genes with high inner connection inside the modules were considered hub genes. The intersection results between hub genes of key modules and 500 DEGs revealed UBE2C, BUB1B, RRM2, and TPX2 as highly associated with the stage of ccRCC. In addition, the candidate genes were validated at both the RNA expression level and the protein level. Survival analysis also showed that 4 genes were significantly correlated with overall survival. In conclusion, our study affords a deeper understanding of the molecular mechanisms associated with the development of ccRCC and provides potential biomarkers for early diagnosis and individualized treatment for patients at different stages of ccRCC.

Genetic networks in Parkinson's and Alzheimer's disease

Parkinson’s disease (PD) and Alzheimer’s disease (AD) are the most common neurodegenerative diseases and there is increasing evidence that they share common physiological and pathological links. Here we have conducted the largest network analysis of PD and AD based on their gene expressions in blood to date. We identified modules that were not preserved between disease and healthy control (HC) networks, and important hub genes and transcription factors (TFs) in these modules. We highlighted that the PD module not preserved in HCs was associated with insulin resistance, and HDAC6 was identified as a hub gene in this module which may have the role of influencing tau phosphorylation and autophagic flux in neurodegenerative disease. The AD module associated with regulation of lipolysis in adipocytes and neuroactive ligand-receptor interaction was not preserved in healthy and mild cognitive impairment networks and the key hubs TRPC5 and BRAP identified as potential targets for therapeutic treatments of AD. Our study demonstrated that PD and AD share common disrupted genetics and identified novel pathways, hub genes and TFs that may be new areas for mechanistic study and important targets in both diseases.

Weighted gene co-expression network analysis identified six hub genes associated with rupture of intracranial aneurysms

Intracranial aneurysms (IAs) are characterized by localized dilation or ballooning of a cerebral artery. When IAs rupture, blood leaks into the space around the brain to create a subarachnoid hemorrhage. The latter is associated with a higher risk of disability and mortality. The aims of this study were to gain greater insight into the pathogenesis of ruptured IAs, and to clarify whether identified hub genes represent potential biological markers for assessing the likelihood of IA progression and rupture. Briefly, the GSE36791 and GSE73378 datasets from the National Center of Biotechnology Information Gene Expression Omnibus database were reanalyzed and subjected to a weighted gene co-expression network analysis to test the association between gene sets and clinical features. The clinical significance of these genes as potential biomarkers was also examined, with their expression validated by quantitative real-time PCR. A total of 14 co-expression modules and 238 hub genes were identified. In particular, three modules (labeled turquoise, blue, and brown) were found to highly correlate with IA rupture events. Additionally, six potential biomarkers were identified (BASP1, CEBPB, ECHDC2, GZMK, KLHL3, and SLC2A3), which are strongly associated with the progression and rupture of IAs. Taken together, these findings provide novel insights into potential molecular mechanisms responsible for IAs and they highlight the potential for these particular genes to serve as biomarkers for monitoring IA rupture.

Mining conditions specific hub genes from RNA-Seq gene-expression data via biclustering and their application to drug discovery

Gene‐expression data is being widely used for various clinical research. It represents expression levels of thousands of genes across the various experimental conditions simultaneously. Mining conditions specific hub genes from gene‐expression data is a challenging task. Conditions specific hub genes signify the functional behaviour of bicluster across the subset of conditions and can act as prognostic or diagnostic markers of the diseases. In this study, the authors have introduced a new approach for identifying conditions specific hub genes from the RNA‐Seq data using a biclustering algorithm. In the proposed approach, efficient ‘runibic’ biclustering algorithm, the concept of gene co‐expression network and concept of protein–protein interaction network have been used for getting better performance. The result shows that the proposed approach extracts biologically significant conditions specific hub genes which play an important role in various biological processes and pathways. These conditions specific hub genes can be used as prognostic or diagnostic biomarkers. Conditions specific hub genes will be helpful to reduce the analysis time and increase the accuracy of further research. Also, they summarised application of the proposed approach to the drug discovery process.

Integrated Analysis Revealed Prognostic Factors for Prostate Cancer Patients

BACKGROUND Prostate cancer (PCa) is one of the major causes of cancer-induced death among males. Here, we applied integrated bioinformatics analysis to identify key prognostic factors for PCa patients. MATERIAL AND METHODS The gene expression data were obtained from the UCSC Xena website. We calculated the differentially expressed genes between PCa tissues and normal controls. Pathway enrichment analyses found cell cycle-related pathways might play crucial roles during PCa tumorigenesis. The genes were assigned into 22 modules established via weighted gene co-expression network analysis (WGCNA). RESULTS The results indicated that the purple and red modules were obviously linked to the Gleason score, pathological N, pathological T, recurrence, and recurrence-free survival (RFS). In addition, Kaplan-Meier curve analysis found 8 modules were markedly correlated with RFS, serving as prognostic markers for PCa patients. Then, the hub genes in the most 2 critical modules (purple and red) were visualized by Cytoscape software. Pathway enrichment analyses confirmed the above findings that cell cycle-related pathways might play vital roles during PCa initiation and progression. Lastly, we randomly chose the PILRß (also termed PILRB) in the red module for clinical validation. The immunohistochemistry (IHC) results showed that PILRß was significantly increased in the high-risk PCa population compared with low-/middle-risk patients. CONCLUSIONS We used integrated bioinformatics approaches to identify hub genes that can serve as prognosis markers and potential treatment targets for PCa patients.

Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us understand the molecular mechanisms underlying the carcinogenesis and progression of ccRCC, and provide potential diagnostic, therapeutic and prognostic biomarkers.

Development and validation of a metastasis-associated prognostic signature based on single-cell RNA-seq in clear cell renal cell carcinoma

Single-cell RNA sequencing (scRNA-seq) was recently adopted for deciphering intratumoral heterogeneity across cell sub-populations, including clear cell renal cell carcinoma (ccRCC). Here, we characterized the single-cell expression profiling of 121 cell samples and found 44 metastasis-associated marker genes. Accordingly, we trained and validated 17 pivotal metastasis-associated genes (MAGs) in 626 patients incorporating internal and external cohorts to evaluate the model for predicting overall survival (OS) and progression-free survival (PFS). Correlation analysis revealed that the MAGs correlated significantly with several risk clinical characteristics. Moreover, we conducted Cox regression analysis integrating these independent clinical variables into a MAGs nomogram with superior accuracy in predicting progression events. We further revealed the differential landscape of somatic tumor mutation burden (TMB) between two nomogram-score groups and observed that TMB was also a prognostic biomarker; patients with high MAGs-nomogram scores suffered from a higher TMB, potentially leading to worse prognosis. Last, higher MAGs-nomogram scores correlated with the upregulation of oxidative phosphorylation, the Wnt signaling pathway, and MAPK signaling crosstalk in ccRCC. Overall, we constructed the robust MAGs through scRNA-seq and validated the model in a large patient population, which was valuable for prognostic stratification and providing potential targets against metastatic ccRCC.

Prognostic significance of KIF2A and KIF20A expression in human cancer: A systematic review and meta-analysis

BACKGROUND

The kinesin family (KIF) is reported to be aberrantly expressed and significantly correlated with survival outcomes in patients with various cancers. This meta-analysis was carried out to quantitatively evaluate the prognostic values of partial KIF members in cancer patients.

METHODS

Two well-known KIF members, KIF2A and KIF20A, were investigated to evaluate their potential values as novel prognostic biomarkers in human cancer. A comprehensive literature search was carried out of the PubMed, EMBASE, Cochrane Library, and Web of Science databases up to April 2019. Pooled hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association of KIF2A and KIF20A expression with overall survival (OS) and clinicopathological parameters.

RESULTS

Twenty-five studies involving 7262 patients were finally incorporated, including nine about KIF2A and sixteen about KIF20A. Our results indicated that patients with high expression of KIF2 and KIF20A tended to have shorter OS than those with low expression (HR = 2.23, 95% CI = 1.87-2.65, P < .001; HR = 1.77, 95% CI = 1.57-1.99, P < .001, respectively). Moreover, high expression of these 2 KIF members was significantly associated with advanced clinical stage (OR = 1.98, 95% CI: 1.57-2.50, P < .001; OR = 2.63, 95% CI: 2.03-3.41, P < .001, respectively), positive lymph node metastasis (OR = 2.32, 95% CI: 1.65-3.27, P < .001; OR = 2.13, 95% CI: 1.59-2.83, P < .001, respectively), and distant metastasis (OR = 2.20, 95% CI: 1.21-3.99, P = .010; OR = 5.25, 95% CI: 2.82-9.77, P < .001, respectively); only high KIF20A expression was related to poor differentiation grade (OR = 1.82, 95% CI: 1.09-3.07, P = .023).

CONCLUSIONS

High expression of KIF2 and KIF20A in human cancer was significantly correlated with worse prognosis and unfavorable clinicopathological features, suggesting that these 2 KIF members can be used as prognostic biomarkers for different types of tumors.

PROSPERO REGISTRATION NUMBER

CRD42019134928.

Three novel hub genes and their clinical significance in clear cell renal cell carcinoma

Purpose. To investigate the association of biomarkers correlated with clinical stages and survival of clear cell renal cell carcinoma (ccRCC).

Methods. The GSE36895 dataset was downloaded and differentially expressed or methylated genes were analyzed. Hub genes were identified with weighted gene co-expression network analysis (WGCNA) and protein-protein interaction network (PPI), and validated with TCGA database and our own tissues. The biological processes of hub genes were further explored by functional enrichment analysis. Survival analyses were also performed. The underlying mechanisms for ccRCC development were detected with Gene set enrichment analyses.

Results. A total of 1624 differentially expressed genes were analyzed by WGCNA and 6 co-expressed gene modules were identified. Three hub genes (EHHADH, ACADM and AGXT2) were met the criterion of both WGCNA and PPI networks analysis, which showed highest negative association with pathological T stage (r = - 0.45, p = 0.01) and tumor grade (r = - 0.45, p = 0.01). The downregulation of these hub genes was validated with using both TCGA database and samples harvested at our institute The biological processes that hub genes involved, such as metabolic process (p = 9.63E - 09), oxidation-reduction process (p = 1.05E - 08) and oxidoreductase activity (p = 1.72E - 04), were revealed. Survival analysis showed a higher expression or lower methylation of these hub genes, a longer survival of ccRCC patients. ccRCC samples with higher expression of hub genes were enriched in gene sets correlated with signaling like biosynthesis of unsaturated fatty acids, butanoate metabolism, and PPAR signaling pathway.

Conclusions. We identified three novel tumor suppressors associated with pathological T stage and overall survival of ccRCC. They might be potential as individualized therapeutic targets and diagnostic biomarkers for ccRCC.

Identifying hub genes of clear cell renal cell carcinoma associated with the proportion of regulatory T cells by weighted gene co-expression network analysis

BACKGROUND

Numerous patients with clear cell renal cell carcinoma (ccRCC) experience drug resistance after immunotherapy. Regulatory T (Treg) cells may work as a suppressor for anti-tumor immune response.

PURPOSE

We performed bioinformatics analysis to better understand the role of Treg cells in ccRCC.

RESULTS

Module 10 revealed the most relevance with Treg cells. Functional annotation showed that biological processes and pathways were mainly related to activation of the immune system and the processes of immunoreaction. Four hub genes were selected: LCK, MAP4K1, SLAMF6, and RHOH. Further validation showed that the four hub genes well-distinguished tumor and normal tissues and were good prognostic biomarkers for ccRCC.

CONCLUSION

The identified hub genes facilitate our knowledge of the underlying molecular mechanism of how Treg cells affect ccRCC in anti-tumor immune therapy.

METHODS

The CIBERSORT algorithm was performed to evaluate tumor-infiltrating immune cells based on the Cancer Genome Atlas cohort. Weighted gene co-expression network analysis was conducted to explore the modules related to Treg cells. Gene Ontology analysis and pathway enrichment analysis were performed for functional annotation and a protein-protein interaction network was built. Samples from the International Cancer Genomics Consortium database was used as a validation set.

Identifying novel biomarkers of the pediatric influenza infection by weighted co-expression network analysis

Background

Despite the high yearly prevalence of Influenza, the pathogenesis mechanism and involved genes have not been fully known. Finding the patterns and mapping the complex interactions between different genes help us to find the possible biomarkers and treatment targets.

Methods

Herein, weighted gene co-expression network analysis (WGCNA) was employed to construct a co-expression network among genes identified by microarray analysis of the pediatric influenza-infected samples.

Results

Three of the 38 modules were found as the most related modules to influenza infection. At a functional level, we found that the genes in these modules regulate the immune responses, protein targeting, and defense to virus. Moreover, the analysis of differentially expressed genes disclosed 719 DEGs between the normal and infected subjects. The comprehensive investigation of genes in the module involved in immune system and viral defense (yellow module) revealed that SP110, HERC5, SAMD9L, RTP4, C19orf66, HELZ2, EPSTI1, and PHF11 which were also identified as DEGs (except C19orf66) have the potential to be as the biomarkers and also drug targeting for the treatment of pediatric influenza.

Conclusions

The WGCN analysis revealed co-expressed genes which were involved in the innate immune system and defense to virus. The differentially expressed genes in the identified modules can be considered for designing drug targets. Moreover, modules can help to find pathogenesis routes in the future.

PPWD1 is associated with the occurrence of postmenopausal osteoporosis as determined by weighted gene co‑expression network analysis

Postmenopausal osteoporosis (PMO) is the most common type of primary osteoporosis (OP), a systemic skeletal disease. Although many factors have been revealed to contribute to the occurrence of PMO, specific biomarkers for the early diagnosis and therapy of PMO are not available. In the present study, a weighted gene co-expression network analysis (WGCNA) was performed to screen gene modules associated with menopausal status. The turquoise module was verified as the clinically significant module, and 12 genes (NUP133, PSMD12, PPWD1, RBM8A, CRNKL1, PPP2R5C, RBM22, PIK3CB, SKIV2L2, PAPOLA, SRSF1 and COPS2) were identified as ‘real’ hub genes in both the protein-protein interaction (PPI) network and co-expression network. Furthermore, gene expression analysis by microarray in blood monocytes from pre- and post-menopausal women revealed an increase in the expression of these hub genes in postmenopausal women. However, only the expression of peptidylprolyl isomerase domain and WD repeat containing 1 (PPWD1) was correlated with bone mineral density (BMD) in postmenopausal women. In the validation set, a similar expression pattern of PPWD1 was revealed. Functional enrichment analysis revealed that the fatty acid metabolism pathway was significantly abundant in the samples that exhibited a higher expression of PPWD1. Collectively, PPWD1 is indicated as a potential diagnostic biomarker for the occurrence of PMO.

Identification of Prognostic Candidate Genes in Breast Cancer by Integrated Bioinformatic Analysis

Breast cancer is one of the most common malignancies. However, the molecular mechanisms underlying its pathogenesis remain to be elucidated. The present study aimed to identify the potential prognostic marker genes associated with the progression of breast cancer. Weighted gene coexpression network analysis was used to construct free-scale gene coexpression networks, evaluate the associations between the gene sets and clinical features, and identify candidate biomarkers. The gene expression profiles of GSE48213 were selected from the Gene Expression Omnibus database. RNA-seq data and clinical information on breast cancer from The Cancer Genome Atlas were used for validation. Four modules were identified from the gene coexpression network, one of which was found to be significantly associated with patient survival time. The expression status of 28 genes formed the black module (basal); 18 genes, dark red module (claudin-low); nine genes, brown module (luminal), and seven genes, midnight blue module (nonmalignant). These modules were clustered into two groups according to significant difference in survival time between the groups. Therefore, based on betweenness centrality, we identified TXN and ANXA2 in the nonmalignant module, TPM4 and LOXL2 in the luminal module, TPRN and ADCY6 in the claudin-low module, and TUBA1C and CMIP in the basal module as the genes with the highest betweenness, suggesting that they play a central role in information transfer in the network. In the present study, eight candidate biomarkers were identified for further basic and advanced understanding of the molecular pathogenesis of breast cancer by using co-expression network analysis.

nm23, TOP2A and VEGF expression: Potential prognostic biologic factors in peripheral T-cell lymphoma, not otherwise specified

Peripheral T-cell lymphoma not otherwise specified (PTCL-NOS) is an aggressive lymphoma associated with a poor outcome. To date, the factor consistently associated with prognosis is the International Prognostic Index (IPI) score; however, it is considered that the IPI score cannot be beneficial for guiding potential targeted therapies. New scoring systems have recently been developed. The aim of the present study was to observe the expression of NME/NM23 nucleoside diphosphate kinase 1 (nm23), nuclear DNA topoisomerase 2-α (TOP2A), multiple myeloma oncogene-1 (MUM-1) and vascular endothelial growth factor (VEGF), and evaluate their prognostic value in PTCL-NOS. A retrospective analysis of 124 cases of PTCL-NOS showed that 70/122 (57.4%) cases were positive for nm23, 71/122 (58.2%) for TOP2A, 30/119 (25.2%) for MUM-1 and 64/122 (52.5%) for VEGF. Of note, 50/122 cases concurrently expressed nm23, TOP2A and VEGF. The univariate analysis results revealed that the nm23 (P=0.012), TOP2A (P=0.002) and VEGF (P=0.008) expression had a negative prognostic effect in patients with PTCL-NOS, while the MUM-1 expression did not have a significant prognostic value (P=0.918). In addition, the concurrent expression of nm23, TOP2A and VEGF was significantly associated with a worse prognosis (P=0.002). However, in multivariate Cox regression analysis, the concurrent expression of nm23, TOP2A and VEGF tended to predict a worse prognosis, however the P-value was borderline (hazard ratio, 1.495; 95% confidence interval, 0.993-2.250; P=0.054). It is speculated that there may be an association among the expression of nm23, TOP2A and VEGF, and that their expression may serve as a promising prognostic factor for PTCL-NOS.

Computational identification and analysis of early diagnostic biomarkers for kidney cancer

Renal cell carcinoma is one of the most common urinary system tumors in adults, it is usually asymptomatic in its early stage and the patients are often diagnosed late. MicroRNA has a higher diagnostic accuracy than traditional markers and may become a new type of early diagnostic biomarker for kidney cancer. Three computational methods and several bioinformatic methods including PPI network, overall survival analysis and enrichment analysis were used to identify the significant differentially expressed miRNAs. Thirteen miRNAs that were significantly differentially expressed in RCC patients were identified, 10 of them have been proved to be associated with kidney cancer in other studies, miR-576, miR-616 and miR-133a-2 are three newly discovered biomarkers of RCC in this study. We found that the target genes of miR-576 (CUL3 and RAC1) are involved in the regulation of multiple cancer-related biological pathways, and the target gene of miR-616 (ASB13 and FBXW2) has been reported to be associated with the development of other cancers. Our findings may have guiding significance for the early diagnosis of renal cell carcinoma.

Genome‑wide investigation of the clinical significance and prospective molecular mechanisms of kinesin family member genes in patients with lung adenocarcinoma

The current study aimed to identify the potential clinical significance and molecular mechanisms of kinesin (KIF) family member genes in lung adenocarcinoma (LUAD) using genome-wide RNA sequencing (RNA-seq) datasets derived from The Cancer Genome Atlas (TCGA) database. Clinical parameters and RNA-seq data of patients with LUAD from the TCGA database enabled the assessment of the clinical significance of KIF genes, while the potential mechanisms of their interactions in LUAD were investigated by gene set enrichment analysis (GSEA). A gene signature with potential prognostic value was constructed via a stepwise multivariable Cox analysis. In total, 23 KIF genes were identified to be differentially expressed genes (DEGs) between the LUAD tumor and adjacent non-cancerous tissues. Of these, 8 differentially expressed KIF genes were strongly found to be strongly associated with the overall survival of patients with LUAD. Three of these genes were found to be able to be grouped as a potential prognostic gene signature. Patients with higher risk scores calculated using this gene signature were found to have a markedly higher risk of mortality (adjusted P=0.003; adjusted HR, 1.576; 95% CI, 1.166–2.129). Time-dependent receiver operating characteristic analysis indicated that this prognostic signature was able to accurately predict patient prognosis with an area under curve of 0.636, 0.643,0.665, 0.670 and 0.593 for the 1-, 2-, 3-, 4- and 5-year survival, respectively. This prognostic gene signature was identified as an independent risk factor for LUAD and was able to more accurately predict prognosis in comparison to other known clinical parameters, as shown via comprehensive survival analysis. GSEA enrichment revealed that that KIF14, KIF18B and KIF20A mediated basic cell physiology through the regulation of the cell cycle, DNA replication, and DNA repair biological processes and pathways. On the whole, the findings of this study identified 23 KIF genes that were DEGs between LUAD tumor and adjacent non-cancerous tissues. In total, 8 of these genes had the potential to function as prognostic and diagnostic biomarkers in patients with LUAD.

Considering smoking status, coexpression network analysis of non-small cell lung cancer at different cancer stages, exhibits important genes and pathways

Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer among smokers, nonsmokers, women, and young individuals. Tobacco smoking and different stages of the NSCLC have important roles in cancer evolution and require different treatments. Existence of poorly effective therapeutic options for the NSCLC brings special attention to targeted therapies by considering genetic alterations. In this study, we used RNA-Seq data to compare expression levels of RefSeq genes and to find some genes with similar expression levels. We utilized the "Weighted Gene Co-expression Network Analysis" method for three different datasets to create coexpressed genetic modules having relations with the smoking status and different stages of the NSCLC. Our results indicate seven important genetic modules having important associations with the smoking status and cancer stages. Based on investigated genetic modules and their biological explanation, we then identified 13 newly candidate genes and 7 novel transcription factors in association with the NSCLC, the smoking status, and cancer stages. We then examined those results using other datasets and explained our results biologically to illustrate some important genes in relation with the smoking status and metastatic stage of the NSCLC that can bring some crucial information about cancer evolution. Our genetic findings also can be used as some therapeutic targets for different clinical conditions of the NSCLC.

Prognostic significance of VHL, HIF1A, HIF2A, VEGFA and p53 expression in patients with clear‑cell renal cell carcinoma treated with sunitinib as first‑line treatment

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell cancer, characterized by the highest mortality rate among other RCC subtypes due to the occurrence of metastasis and drug resistance following surgery. The Von Hippel-Lindau tumor suppressor (VHL)-hypoxia-inducible factor 1 subunit α (HIF1A)/hypoxia-inducible factor 2α (HIF2A)-vascular endothelial growth factor A (VEGFA) protein axis is involved in the development and progression of ccRCC, whereas sunitinib, a tyrosine kinase inhibitor, blocks the binding of VEGFA to its receptor. The aim of the present study was to examine the possible association of the gene expression of VHL, HIF1A, HIF2A, VEGFA and tumor protein P53 (P53) in cancer tissue with the outcome of ccRCC patients who were treated with sunitinib as first-line therapy following nephrec-tomy. A total of 36 ccRCC patients were enrolled, 11 of whom were administered sunitinib post-operatively. Tumor and control samples were collected, and mRNA and protein levels were assessed by reverse transcription-quantitative polymerase chain reaction and western blot analysis, respectively. High mRNA and protein expression levels of HIF2A and VEGFA were found to be associated with shorter overall survival (OS) and progression-free survival (PFS) rates, as well as with unfavorable risk factors of cancer recurrence and mortality. Resistance to sunitinib was also observed; the OS and PFS rates were shorter (median OS and PFS: 12 and 6 months, respectively, vs. undetermined). Sunitinib resistance was associated with high HIF2A and VEGFA protein levels (b=0.57 and b=0.69 for OS and PFS, respectively; P<0.001). Taken together, the findings of this study suggest that the protein levels of HIF2A and VEGFA in tumor tissue may serve as independent prognostic factors in ccRCC. ccRCC patients with increased intratumoral HIF2A and VEGFA protein levels, and unaltered VHL protein levels, are not likely to benefit from sunitinib treatment following nephrectomy; however, this hypothesis requires verification by large-scale replication studies.