Evaluation of molecular pathogenesis of colon cancer in Kerala using high-throughput expression, signaling pathways, and network analyses.

e16065 Background: The molecular pathogenesis of colon adenocarcinoma (COAD) is attributed to large molecular changes such as Chromosomal Instability and high somatic copy number variation or defective DNA mismatch repair and consequent microsatellite instability (MSI). The prevalence of this type of cancer is increasing in the state of Kerala, India. A detailed study of the signaling pathways could lead to a better understanding of the central molecular pathological changes and potential biomarkers particular to this population. Methods: High throughput somatic expression analysis using Nanostring PanCancer pathway panel assay was performed. Differentially expressed (DE) genes were selected and KEGG pathway enrichment analysis was performed for assessment of canonical signaling pathways. Expression profiles were compared against the public database, Colon Adenocarcinoma cohort of the Cancer Genome Atlas (TCGA-COAD), using the Genome Expression Profiling Interactive Analysis (GEPIA). Protein-protein interaction network analysis was done using Cytoscape. DE genes were compared against immune cell infiltration in the TCGA-COAD from Tumor Immune Estimation Resource (TIMER) databases. Results: Nanostring assay was performed in 10 Tumor-Normal paired FFPE samples of stage II/III colon adenocarcinoma. Out of > 700 genes, significant difference in expression was found in 83 genes (FDR adjusted p -value < 0.01) with fold-change |fc(log2)| of at least one. Fold-change |fc(log2)| ≥ 2 was found in 19/83 genes. Network analysis clustered 13 out of 17 upregulated genes. Superimposition of the current data on TCGA study showed that among the three genes, four (MET, MCM2, ETV4 and MMP7), were common. DE Genes which were not significant in TCGA COAD study such as INHBA, COL1A1, COL11A1, COMP, SFRP4, SPP1, IL11, LIF, WT1 and DDIT4, were found to be significant in the current study. A few of the unique genes identified in the current study were found to have significant correlation with antigen presenting cells infiltration in the TCGA-COAD studies. Conclusions: Many DE genes from the study population were found to be different from previous large cohort studies in other population. This may suggest a different pathogenesis of COAD in this population, warranting a detailed study on the pathogenesis.

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Intermediate microRNA expression profile in Graves’ disease falls between that of normal thyroid tissue and papillary thyroid carcinoma

Journal of Clinical Pathology ◽

10.1136/jclinpath-2016-203739 ◽

2016 ◽

Vol 70 (1) ◽

pp. 33-39 ◽

Cited By ~ 7

Author(s):

Matthias Pohl ◽

Florian Grabellus ◽

Karl Worm ◽

Georg Arnold ◽

Martin Walz ◽

...

Keyword(s):

Mirna Expression ◽

Expression Profiles ◽

Thyroid Tissue ◽

Fold Change ◽

Graves Disease ◽

Papillary Thyroid ◽

Normal Thyroid Tissue ◽

Normal Thyroid ◽

Significant Difference ◽

Benign Thyroid

AimsMany studies have previously reported a higher prevalence of papillary thyroid carcinomas (PTC) in patients with Graves' disease (GD). MicroRNAs (miRNAs) are small, non-coding RNAs that are upregulated in PTC compared with benign thyroid tissue. The objective of the study was to examine the miRNA expression of selected miRNAs that are known to be upregulated in PTC in patients with GD.MethodsParaffin embedded thyroid tissue from 159 patients with GD was screened for expression of the miRNAs 146b, 181b, 21, 221 and 222 by RT-PCR. The expression profiles of four normal thyroids, 50 PTCs without concomitant GD and 11 patients with untreated GD served as the controls.ResultsThe expression pattern of these miRNAs in patients with GD is intermediate between that of benign thyroid tissue (p<0.001) and PTC (in three out of five miRNAs, p<0.001). This corresponds to a 15-fold change for GD versus PTC, and a 31-fold change for GD versus normal thyroid tissue. The miRNA expression in 11 papillary microcarcinomas found in our study (a prevalence of 0.07) was not different from that in PTC samples from patients without GD for four of five miRNA types. Furthermore, we found a significant difference in the expression of miRNA 221/222 between treated and untreated GD tissue.ConclusionsIn conclusion, we found an intermediate expression of specific miRNAs in thyroid tissue from patients with GD that fell between the expression levels found in normal thyroid glands and PTC, which suggests a possible influence of certain miRNAs on developing PTC in patients with GD.

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Modular network inference between miRNA–mRNA expression profiles using weighted co-expression network analysis

Journal of Integrative Bioinformatics ◽

10.1515/jib-2021-0029 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Nisar Wani ◽

Debmalya Barh ◽

Khalid Raza

Keyword(s):

Network Analysis ◽

Mrna Expression ◽

Mirna Expression ◽

Regulatory Networks ◽

Network Inference ◽

Expression Profiles ◽

Interaction Network ◽

Pathway Enrichment Analysis ◽

Expression Data ◽

Cancer Data

Abstract Connecting transcriptional and post-transcriptional regulatory networks solves an important puzzle in the elucidation of gene regulatory mechanisms. To decipher the complexity of these connections, we build co-expression network modules for mRNA as well as miRNA expression profiles of breast cancer data. We construct gene and miRNA co-expression modules using the weighted gene co-expression network analysis (WGCNA) method and establish the significance of these modules (Genes/miRNAs) for cancer phenotype. This work also infers an interaction network between the genes of the turquoise module from mRNA expression data and hubs of the turquoise module from miRNA expression data. A pathway enrichment analysis using a miRsystem web tool for miRNA hubs and some of their targets, reveal their enrichment in several important pathways associated with the progression of cancer.

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Potential Biomarkers of Colon Adenocarcinoma Based on Weighted Gene Co-Expression Network Analysis

10.21203/rs.3.rs-871616/v1 ◽

2021 ◽

Author(s):

Zhongze Cui ◽

Shuang He ◽

Feifei Wen ◽

Xiaoyang Xu ◽

Yangyang Li ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Colon Cancer ◽

Network Analysis ◽

Expression Profiles ◽

Differential Expression Analysis ◽

Colon Adenocarcinoma ◽

The Cancer Genome Atlas ◽

Future Research ◽

Related Gene

Abstract Background: Colon adenocarcinoma (COAD) is one of the most common malignancies worldwide. Although a large number of studies have elucidated the aetiology of colorectal cancer, the exact mechanism of colorectal cancer development remains to be determined.To identify key modules and prognostic genes that may be involved in the occurrence and development of COAD, weighted gene coexpression network analysis (WGCNA) and differential expression analysis were performed on datasets GSE41657 and GSE74602 from the Gene Expression Omnibus (GEO) database to screen for prognostic differentially expressed genes. Gene expression profiles and clinical information were collected from The Cancer Genome Atlas (TCGA) database for verification.Results: Through WGCNA and DEGs analysis, 439 genes in key functional modules were obtained, and 26 prognostic related genes were finally obtained through prognostic analysis: (1) We screened 5 genes（RPP40, DUSP18, PPRC1, MFSD11 and PDCD11） that have not been studied in COAD.（2）We obtained the most critical module in the occurrence and development of colon cancer and obtained one prognosis-related gene, NUP85, from the most critical module.The relationship between it and tumor immune microenvironment was verified.（3） A prognostic model comprising four coexpressed differential genes was constructed; TIMP1, PMM2, E2F3 and MORC2 were selected as the key prognosis-related genes.Conclusions: （1）As new biomarkers，prognostic genes RPP40, DUSP18, PPRC1, MFSD11 and PDCD11 may be potential therapeutic targets for COAD, and provide new ideas for future research on the mechanism of COAD. （2）NUP85 may be an immune-related gene which was negatively correlated with CD4+ T cell and M2 macrophagesthat plays an important role in inhibiting the occurrence and development of colorectal adenocarcinoma. （3）A Cox proportional risk model based on gene expression can be used to predict the prognosis and survival time of patients with colon cancer.

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Transcriptomic Evaluation of CD34+ Marrow Cells from Myelodysplastic Syndrome (MDS) Patients

Blood ◽

10.1182/blood.v124.21.1894.1894 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1894-1894

Author(s):

Hogune Im ◽

Varsha Rao ◽

Kunju Joshi Sridhar ◽

Rui Chen ◽

George Mias ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Differential Expression ◽

High Throughput ◽

Expression Profiles ◽

Gene Set Enrichment Analysis ◽

Reference Sequence ◽

Rna Seq ◽

Cd34 Cells ◽

Marrow Cells

Abstract Background: Prior studies using microarray platforms have shown alterations of gene expression profiles (GEPs) in MDS CD34+ marrow cells related to clinical outcomes (Sridhar et al, Blood 2009, Pellagatti et al, JCO 2013). Given the increased sensitivity and accuracy of high-throughput RNA sequencing (RNA-Seq) (Mortazavi et al, Nat Meth 2008, Soon et al, Mol Syst Bio 2012) for detecting and quantifying mRNA transcripts, we applied this methodology for evaluating differential gene expression between MDS and normal CD34+ marrow cells. Methods:RNA was isolated from magnetic bead affinity-enriched CD34+ (>90%) marrow aspirate cells (Miltenyi Biotec, Auburn, CA) and amplified using the Smarter Kit (Clontech, Mt View, CA). The amplified product (ds DNA) was fragmented to a size distribution of ~200-300bp using the E220 Focused Ultrasonicator (Covaris Inc, Woburn, MA). End repair, adapter ligation and PCR amplification were performed using the NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, Ipswich, MA). The indexed cDNA libraries were sequenced (paired end, 100bp) on an Illumina HiSeq2000 platform with median read counts of 69 million. The sequences were aligned to Human Reference sequence hg19 using DNAnexus mapper with gene detection focused on known annotated genes. The differential expression was analyzed using edgeR. DAVID and Ingenuity IPA programs were used for pathway analyses. Gene Set Enrichment Analysis (GSEA) was used to identify biologic processes in our dataset present across phenotypes. Results: Correlations of RNA-Seq data from unamplified to amplified transcripts demonstrated high fidelity of transcripts obtained (Pearson and Spearman R2 = 0.80). After filtering samples for adequate read counts, 12,323 genes were evaluated. Differential expression analysis yielded 719 differentially expressed genes (DEGs) in MDS (n=30) vs normal (n=21) with FDR <.05. Among the DEGs, 548 and 171 were over- and under-expressed ≥2 fold in MDS vs Normal, respectively: 20% of the overexpressed genes were present in >50% of the patients. Hierarchical cluster analysis using these DEGs confirmed clear separation of MDS patients from normals, with 2 differential expression clusters—one region overexpressed and one underexpressed. A distinctive trend toward clustering of the patients was seen which related to their IPSS categories and marrow blast %. In functional pathway analysis of the 2 distinctive gene clusters which distinguished MDS from normal, the underexpressed MDS DEGs demonstrated enrichment of inflammatory cytokines, oxidative stress and interleukin signaling pathways, plus mitochondrial calcium transport; whereas the MDS overexpressed DEG cluster showed enrichment of adherens junction/cytokeletal remodeling, cell cycle control of chromosome replication and DNA damage response pathways. Using GSEA analysis, significantly increased numbers of genes in MDS vs normal, common to those in gene sets present within curated public databases, were involved with TP53 targets and mTOR signaling pathways. Conclusions: Our study demonstrated that RNA-Seq methodology, a high-throughput and more comprehensive technique than most gene expression microarrays, was capable of showing significant and distinctive differences in gene expression between MDS and normal marrow CD34+ cells. Specific clustering of the DEGs was demonstrated to distinguish patient subsets associated with their major clinical features. Further, the stringently identified DEGs shown to be engaged in functional pathways and biologic processes highly relevant for MDS were extant within the patients’ CD34+ cells. These transcriptomic data provide information complementary to exomic mutational findings contributing to improved understanding of biologic mechanisms underlying MDS. Disclosures No relevant conflicts of interest to declare.

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Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein’s Anomaly

Cells ◽

10.3390/cells10051066 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1066

Author(s):

Masood Abu-Halima ◽

Viktoria Wagner ◽

Lea Simone Becker ◽

Basim M. Ayesh ◽

Mohammed Abd El-Rahman ◽

...

Keyword(s):

Expression Profiles ◽

Fold Change ◽

Mrna Abundance ◽

Ebstein’S Anomaly ◽

Cellular Interaction ◽

Integrated Analysis ◽

Pathway Enrichment Analysis ◽

Ebstein's Anomaly ◽

Mrna Targets ◽

Lower Abundance

Little is known about abundance level changes of circulating microRNAs (miRNAs) and messenger RNAs (mRNA) in patients with Ebstein’s anomaly (EA). Here, we performed an integrated analysis to identify the differentially abundant miRNAs and mRNA targets and to identify the potential therapeutic targets that might be involved in the mechanisms underlying EA. A large panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 EA patients and 16 age and gender-matched healthy control volunteers (HVs). Differential abundance level of single miRNA and mRNA was validated by Real-Time quantitative PCR (RT-qPCR). Enrichment analyses of altered miRNA and mRNA abundance levels were identified using bioinformatics tools. Altered miRNA and mRNA abundance levels were observed between EA patients and HVs. Among the deregulated miRNAs and mRNAs, 76 miRNAs (49 lower abundance and 27 higher abundance, fold-change of ≥2) and 29 mRNAs (25 higher abundance and 4 lower abundance, fold-change of ≥1.5) were identified in EA patients compared to HVs. Bioinformatics analysis identified 37 pairs of putative miRNA-mRNA interactions. The majority of the correlations were detected between the lower abundance level of miRNA and higher abundance level of mRNA, except for let-7b-5p, which showed a higher abundance level and their target gene, SCRN3, showed a lower abundance level. Pathway enrichment analysis of the deregulated mRNAs identified 35 significant pathways that are mostly involved in signal transduction and cellular interaction pathways. Our findings provide new insights into a potential molecular biomarker(s) for the EA that may guide the development of novel targeting therapies.

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miRNA Regulation Network Analysis in Qianliening Capsule Treatment of Benign Prostatic Hyperplasia

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2015/365484 ◽

2015 ◽

Vol 2015 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Liya Liu ◽

Yun Wan ◽

Aling Shen ◽

Jinyan Zhao ◽

Jiumao Lin ◽

...

Keyword(s):

Gene Expression ◽

Cell Proliferation ◽

Benign Prostatic Hyperplasia ◽

Network Analysis ◽

Signaling Pathways ◽

Expression Profiles ◽

Prostatic Hyperplasia ◽

Differentially Expressed ◽

Epithelial Cell Line ◽

Mirna Regulation

Objective. The objective of this study was to evaluate the molecular mechanism by which Qianliening capsule (QC) treats benign prostatic hyperplasia (BPH).Methods. Benign prostatic hyperplasia epithelial cell line BPH-1 was treated with 0, 1.25, 2.5, and 5 mg/mL QC for 48 h, respectively. Evaluation of cell viability and observation of morphologic changes of BPH-1 cell gene expression and miRNA expression profiles were analyzed. Real-time quantitative PCR was used to confirm changes in miRNA and gene expression. GO and KEGG pathway-based approaches were used to investigate biological functions and signaling pathways affected by differentially expressed mRNAs.Results. QC inhibited BPH-1 cell proliferation. Differential expression of 19 upregulated and 2 downregulated miRNAs was observed in QC-treated BPH-1 cells compared to untreated control cells. 107 upregulated and 71 downregulated genes were identified between the two groups. Significantly enriched signaling pathways based on deregulated mRNAs were mainly involved in regulation of cell proliferation, apoptosis, and so on. Additionally, miRNA-mRNA network analysis integrated these miRNAs and genes by outlining interactions of miRNA and related genes.Conclusion. The study was the first report of differentially expressed miRNA and mRNA in QC-treated BPH-1 cells.

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Identification of key genes and pathways in endometriosis by integrated expression profiles analysis

PeerJ ◽

10.7717/peerj.10171 ◽

2020 ◽

Vol 8 ◽

pp. e10171

Author(s):

Ding Cui ◽

Yang Liu ◽

Junyan Ma ◽

Kaiqing Lin ◽

Kaihong Xu ◽

...

Keyword(s):

Network Analysis ◽

Differentially Expressed Genes ◽

Western Blotting ◽

Expression Profiles ◽

Hippo Pathway ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Ppi Network ◽

Hub Genes ◽

Normal Endometrium

The purpose of this study was to integrate the existing expression profile data on endometriosis (EM)-related tissues in order to identify the differentially expressed genes. In this study, three series of raw expression data were downloaded from GEO database. Differentially expressed genes (DEGs) in three tissue types were screened. GO, KEGG pathway enrichment analysis, core differential genes (CDGs) protein–protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) were performed, finally, the dysregulation of Hippo pathway in ectopic endometrium (EC) was detected by Western blotting. A total of 1,811 DEGs between eutopic (EU) and normal endometrium (NE), 5,947 DEGs between EC and EU, and 3,192 DEGs between EC and NE datasets were identified. After screening, 394 CDGs were obtained, and 5 hub genes identified in the PPI network. CDGs enrichment and WGCNA network analysis revealed cell proliferation, differentiation, migration and other biological processes, Hippo and Wnt signaling pathways, and a variety of tumor-related pathways. Western blotting results showed that YAP/TAZ was upregulated, and MOB1, pMOB1, SAV1, LATS1 and LATS2 were downregulated in EC. Moreover, CDGs, especially the hub genes, are potential biomarkers and therapeutic targets. Finally, the Hippo pathway might play a key role in the development of endometriosis.

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Network-based identification of biomarkers for colon adenocarcinoma

10.21203/rs.2.23793/v2 ◽

2020 ◽

Author(s):

Fuyan Hu ◽

Qing Wang ◽

Zhiyuan Yang ◽

Zeng Zhang ◽

Xiaoping Liu

Keyword(s):

Colon Cancer ◽

Expression Profiles ◽

Rapid Development ◽

Gene Expression Profiles ◽

Colon Adenocarcinoma ◽

Enrichment Analysis ◽

Functional Networks ◽

Functional Genes ◽

Pathway Enrichment Analysis ◽

New Biomarkers

Abstract Background: As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges.Methods: We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively.Results: Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD.Conclusions: In conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD. And the subtypes could be used in realizing the personalized medicine of COAD.

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An insight to HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) pathogenesis; evidence from high-throughput data integration and meta-analysis

10.1101/754697 ◽

2019 ◽

Author(s):

Sayed-Hamidreza Mozhgani ◽

Mehran Piran ◽

Mohadeseh Zarei-Ghobadi ◽

Mohieddin Jafari ◽

Talat Mokhtari-Azad ◽

...

Keyword(s):

High Throughput ◽

Meta Analysis ◽

Spastic Paraparesis ◽

Tropical Spastic Paraparesis ◽

Hub Genes ◽

Down Regulation ◽

Major Genes ◽

Network Analyses ◽

Significant Difference ◽

Apoptosis Pathways

AbstractHuman T-lymphotropic virus 1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive disease of the central nervous system that affected significantly spinal cord, nevertheless, the pathogenesis pathway. This study aimed to employ high throughput meta-analysis to find major genes involved in the pathogenesis of HAM/TSP. High-throughput statistical analyses identified 385, 49, and 22 differentially expressed genes for normal vs. ACs, normal vs. HAM/TSP and ACs vs. HAM/TSP groups, respectively. STRING and further network analyses highlighted 32, 29, and 13 hub genes for normal vs. ACs, normal vs. HAM/TSP, and ACs vs. HAM/TSP groups, respectively. Biological network analyses indicated the involvement of hub genes in the HAM/TSP group in many vital pathways like apoptosis and immune pathways. Moreover, the meta-analysis results disclosed three major genes including STAT1, TAP1, and PSMB8 which have function role in HAM/TSP progression. Real-time PCR revealed the meaningful down-regulation of STAT1 in HAM/TSP samples than AC and normal samples (P=0.01 and P=0.02, respectively), up-regulation of PSMB8 in HAM/TSP samples than AC and normal samples (P=0.04 and P=0.01, respectively), and down-regulation of TAP1 in HAM/TSP samples than those in AC and normal samples (P=0.008 and P=0.02, respectively). No significant difference was found among three groups in terms of percentage of T helper and cytotoxic T lymphocytes (P= 0.55 and P=0.12). Our results confirm that STAT1, TAP1, and PSMB8 are three important genes which their expressions levels were changed in three different groups. These proteins in association with other proteins can involve in the immune and apoptosis pathways.

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Identification of key protein-coding genes and lncRNAs in spontaneous neutrophil apoptosis

Scientific Reports ◽

10.1038/s41598-019-51597-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Nan Jiang ◽

Xinzhuo Zhang ◽

Yancheng He ◽

Bo Luo ◽

Chengcheng He ◽

...

Keyword(s):

Network Analysis ◽

Expression Profiles ◽

Microarray Dataset ◽

Time Dependent ◽

Neutrophil Apoptosis ◽

Dependent Manner ◽

Stem Analysis ◽

Protein Coding ◽

Network Analyses ◽

Apoptosis Protein

Abstract Polymorphonuclear leukocytes (PMNs) are the most abundant cells of the innate immune system in humans, and spontaneous PMN apoptosis plays crucial roles in maintaining neutrophil homeostasis and resolving inflammation. However, the detailed mechanisms of spontaneous PMN apoptosis remain to be elucidated. By analysis of the public microarray dataset GSE37416, we identified a total of 3050 mRNAs and 220 long non-coding RNAs (lncRNAs) specifically expressed during PMN apoptosis in a time-dependent manner. By short time-series expression miner (STEM) analysis, Gene Ontology analysis, and lncRNA-mRNA co-expression network analyses, we identified some key molecules specifically related to PMN apoptosis. STEM analysis identified 12 gene profiles with statistically significance, including 2 associated with apoptosis. Protein-protein interaction (PPI) network analysis of the genes from 2 profiles and lncRNA-mRNA co-expression network analysis identified a 12-gene hub (including NFκB1 and BIRC3) associated with apoptosis, as well as 2 highly correlated lncRNAs (THAP9-AS1, and AL021707.6). We experimentally examined the expression profiles of two mRNA (NFκB1 and BIRC3) and two lncRNAs (THAP9-AS1 andAL021707.6) by quantitative real-time polymerase chain reaction to confirm their time-dependent expressions. These data altogether demonstrated that these genes are involved in the regulation of spontaneous neutrophil apoptosis and the corresponding gene products could also serve as potential key regulatory molecules for PMN apoptosis and/or therapeutic targets for over-reactive inflammatory response caused by the abnormality in PMN apoptosis.

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