Bioinformatics analysis of microRNAs related to blood stasis syndrome in diabetes mellitus patients

In traditional Chinese medicine (TCM), blood stasis syndrome (BSS) is mainly manifested by the increase of blood viscosity, platelet adhesion rate and aggregation, and the change of microcirculation, resulting in vascular endothelial injury. It is an important factor in the development of diabetes mellitus (DM). The aim of the present study was to screen out the potential candidate microRNAs (miRNAs) in DM patients with BSS by high-throughput sequencing (HTS) and bioinformatics analysis. Human umbilical vein endothelial cells (HUVECs) were incubated with 10% human serum to establish models of DM with BSS, DM without BSS (NBS), and normal control (NC). Total RNA of each sample was extracted and sequenced by the Hiseq2000 platform. Differentially expressed miRNAs (DE-miRNAs) were screened between samples and compared with known changes in mRNA abundance. Target genes of miRNAs were predicted by softwares. Gene Ontology (GO) and pathway enrichment analysis of the target genes were conducted. According to the significantly enriched GO annotations and pathways (P-value ≤ 0.001), we selected the key miRNAs of DM with BSS. It showed that the number of DE-miRNAs in BSS was 32 compared with non-blood stasis syndrome (NBS) and NC. The potential candidate miRNAs were chosen from GO annotations in which target genes were significantly enriched (−log10 (P-value) > 5), which included miR-140-5p, miR-210, miR-362-5p, miR-590-3p, and miR-671-3p. The present study screened out the potential candidate miRNAs in DM patients with BSS by HTS and bioinformatics analysis. The miRNAs will be helpful to provide valuable suggestions on clinical studies of DM with BSS at the gene level.

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Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

Current Bioinformatics ◽

10.2174/1574893615999200508091615 ◽

2020 ◽

Vol 15 ◽

Author(s):

Na Wang ◽

Yukun Li ◽

Sijing Liu ◽

Liu Gao ◽

Chang Liu ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Functional Study ◽

Regulation Network ◽

Glucagon Like Peptide 1 ◽

G Protein Coupled ◽

Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

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A bioinformatics approach to investigate serum and hematopoietic cell-specific therapeutic microRNAs targeting the 3' UTRs of all four Dengue virus serotypes

Pathogens and Disease ◽

10.1093/femspd/ftab050 ◽

2021 ◽

Author(s):

Mirza Sarwar Baig ◽

Anuja Krishnan

Keyword(s):

Dengue Virus ◽

Antigen Processing ◽

Target Genes ◽

Public Health Problem ◽

Hematopoietic Cell ◽

Viral Gene ◽

P Value ◽

Pathway Enrichment Analysis ◽

Global Public Health ◽

Denv Serotypes

Abstract Hyperendemic circulation of all four Dengue virus (DENV) serotypes is a severe global public health problem, so any vaccine or therapeutics should be able to target all four of them. Cells of hemopoietic origin are believed to be primary sites of DENV replication. This study aimed to identify potential host miRNAs that target 3' UTR of all 4 DENV serotypes, thereby directly regulating viral gene expression or indirectly modulating the host system at different virus infection steps. We used four prediction algorithms viz. miRanda, RNA22, RNAhybrid, and StarMir for predicting miRNA, targeting 3'UTR of all four DENV serotypes. Statistically, the most significant miRNA targets were screened based on their Log10 P-value (> 0.0001) of GO term and KEGG pathway enrichment analysis. The intersection test of at least three prediction tools identified a total of 30 miRNAs, which could bind to 3'UTR of all four DENV serotypes. Of the 30, eight miRNAs were of hematopoietic cell origin. GO term enrichment and KEGG analysis showed four hemopoietic origin miRNAs target genes of the biological processes mainly involved in the innate immune response, mRNA 3'-end processing, antigen processing, and presentation and nuclear-transcribed mRNA catabolic process.

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A Network Pharmacology Approach to Predict the Proangiogenesis Mechanism of Huangqi-Honghua Herb Pair after Cerebral Ischemia

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/9834856 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Jinyi Cao ◽

Lu Lei ◽

Kai Wang ◽

Jing Sun ◽

Yi Qiao ◽

...

Keyword(s):

Cerebral Ischemia ◽

Signaling Pathway ◽

Target Genes ◽

Blood Stasis ◽

Blood Stasis Syndrome ◽

Network Pharmacology ◽

Western Blot Assay ◽

Medicinal Value ◽

Pharmacological Method

Objective. Huangqi-Honghua herb pair is known for its medicinal value to treat Qi deficiency and blood stasis syndrome with a long history in clinical practice. To understand its possible mechanism in a systematic study, a network pharmacological method was addressed. Methods. Detailed information on the HH compounds was obtained from two public databases, and oral bioavailability (OB) and drug-like (DL) of the compounds were evaluated. A correlation between HH compounds, its potential targets, and known targets was extrapolated, and the herb-compound-target-disease (H-C-T-D) network was established. Next, the pathway enrichment and essential genes were analyzed. Then, three key genes (VEGFA, VEGFR2, and eNOS), highly associated with angiogenesis, were screened and verified through western blot assay. Results. Out of 276 compounds, 21 HH compounds and 78 target genes regulating the major pathways associated with CI in the network are analyzed. The bioactive compounds in HH were active in various signal transduction pathways such as the toll-like receptor signaling pathway, VEGF signaling pathway, TNF signaling pathway, and HIF-1 signaling pathway are important pathways that may regulate anti-inflammatory, antiapoptotic, immune correlation, and antioxidative effects. The core genes are PTGS2, TNF, NOS2, IL6, BCL2, IL1B, SOD2, NOS3, SOD1, MMP9, and VEGFA. The in vitro results suggested that HH treatment could significantly elevate the expression of proangiogenic genes such as VEGFA, VEGFR2, and eNOS compared with OGD groups. Conclusions. Our results predict that HH may regulate the expression of VEGFA, VEGFR2, and eNOS via the VEGF and HIF-1 signaling pathway to promote angiogenesis and alleviate cerebral ischemia injury.

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Screening and Functional Analysis of Hub MicroRNAs Related to Tumor Development in Colon Cancer

BioMed Research International ◽

10.1155/2020/3981931 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8

Author(s):

Dong-Hu Yu ◽

Wei Li ◽

Jing-Yu Huang ◽

Xiao-Ping Liu ◽

Chi Zhang ◽

...

Keyword(s):

Colon Cancer ◽

Functional Analysis ◽

Gene Networks ◽

Target Genes ◽

Bioinformatics Analysis ◽

Tumor Development ◽

Therapeutic Targets ◽

Cancer Development ◽

Candidate Mirnas ◽

The Future

Various microRNAs (miRNAs) are of importance in the development of colon cancer, but most of the mechanisms of the miRNAs are still unclear. In order to clarify the hub miRNAs and their roles in colon cancer development, GSE98406 was used to screen hub miRNAs by bioinformatics analysis. 46 DE-miRNAs (14 were upregulated and 32 were downregulated) and 1738 target genes of DE-miRNAs were ascertained. miRNAs-gene-networks and miRNAs-GO-networks were built to get more knowledge about the function of candidate miRNAs. After validation, three miRNAs (miR-17-5p, miR-182-5p and miR-200a-3p) were recognized to be hub miRNAs associated with the progression of colon cancer. More importantly, the hub miRNAs and the putative targets genes might be new diagnostic and therapeutic targets for colon cancer in the future.

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Identification of The Key miRNAs And Target Genes In Basal Cell Carcinoma By Bioinformatics Analysis

10.21203/rs.3.rs-455253/v1 ◽

2021 ◽

Author(s):

Hao Liu ◽

Ling Chen

Keyword(s):

Basal Cell Carcinoma ◽

Cell Carcinoma ◽

Basal Cell ◽

Target Genes ◽

Bioinformatics Analysis ◽

Interaction Network ◽

Pathway Enrichment Analysis ◽

Therapeutic Effects ◽

Hub Genes ◽

Skin Potential

Abstract Background The highly tissue-destructive and localized accumulation of basal cell carcinoma(BCC) makes it one of the most important cancers affecting people's lives. Existing therapeutic approaches, including surgical treatment, chemotherapy, and Hedgehog pathway inhibitors, have failed to achieve broad therapeutic effects for various reasons. This study aims to explore additional potential therapeutic targets and possible diagnostic and prognostic biomarkers using bioinformatics analysis.Material/Methods The Gene Expression Omnibus (GEO) database identified the microarray dataset GSE34535. The GEO2R tool was used to screen out differentially expressed genes (DEGs) between BCC and non-lesional skin. Potential target genes of DE-miRNA were screened using the miRWalk, mirDIP and miRTarBase databases. Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis for target genes were established using the DAVID database. Protein–protein interaction network and miRNA-hub gene network were analyzed based on the STRING database and visualized by Cytoscape software. Results 51 up-regulated DE-miRNAs and 38 down-regulated DE-miRNAs were identified from the BCC samples. miR-455-5p was mainly up-regulated and miR-139-5p was mainly down-regulated. Two key bub genes MAPK1 and EGFR were identified in the PPI network. Four out of the ten hub genes were regulated by up-regulated miR-18a and four by down-regulated miR-133b. Viral infections were also identified in the study.Conclusions Bioinformatics identified four miRNAs and two important hub genes that may be associated with BCC, and it was suggested that viruses may play a role in BCC.

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Novel MicroRNA Biomarkers for Colorectal Cancer Early Diagnosis and 5-Fluorouracil Chemotherapy Resistance but Not Prognosis: A Study from Databases to AI-Assisted Verifications

Cancers ◽

10.3390/cancers12020341 ◽

2020 ◽

Vol 12 (2) ◽

pp. 341 ◽

Cited By ~ 1

Author(s):

Zhang ◽

Shen ◽

Sun

Keyword(s):

Colorectal Cancer ◽

Early Diagnosis ◽

Messenger Rna ◽

Target Genes ◽

Function Analysis ◽

Therapy Resistance ◽

Individual Therapy ◽

Potential Candidate ◽

Mirna Candidate ◽

Candidate Mirnas

Colorectal cancer (CRC) is one of the major causes of cancer death worldwide. In general, early diagnosis for CRC and individual therapy have led to better survival for the cancer patients. Accumulating studies concerning biomarkers have provided positive evidence to improve cancer early diagnosis and better therapy. It is, however, still necessary to further investigate the precise biomarkers for cancer early diagnosis and precision therapy and predicting prognosis. In this study, AI-assisted systems with bioinformatics algorithm integrated with microarray and RNA sequencing (RNA-seq) gene expression (GE) data has been approached to predict microRNA (miRNA) biomarkers for early diagnosis of CRC based on the miRNA-messenger RNA (mRNA) interaction network. The relationships between the predicted miRNA biomarkers and other biological components were further analyzed on biological networks. Bayesian meta-analysis of diagnostic test was utilized to verify the diagnostic value of the miRNA candidate biomarkers and the combined multiple biomarkers. Biological function analysis was performed to detect the relationship of candidate miRNA biomarkers and identified biomarkers in pathways. Text mining was used to analyze the relationships of predicted miRNAs and their target genes with 5-fluorouracil (5-FU). Survival analyses were conducted to evaluate the prognostic values of these miRNAs in CRC. According to the number of miRNAs single regulated mRNAs (NSR) and the number of their regulated transcription factor gene percentage (TFP) on the miRNA-mRNA network, there were 12 promising miRNA biomarkers were selected. There were five potential candidate miRNAs (miRNA-186-5p, miRNA-10b-5, miRNA-30e-5p, miRNA-21 and miRNA-30e) were confirmed as CRC diagnostic biomarkers, and two of them (miRNA-21 and miRNA-30e) were previously reported. Furthermore, the combinations of the five candidate miRNAs biomarkers showed better prediction accuracy for CRC early diagnosis than the single miRNA biomarkers. miRNA-10b-5p and miRNA-30e-5p were associated with the 5-FU therapy resistance by targeting the related genes. These miRNAs biomarkers were not statistically associated with CRC prognosis.

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Effect of He Qi San on DNA Methylation in Type 2 Diabetes Mellitus Patients with Phlegm-blood Stasis Syndrome

Open Chemistry ◽

10.1515/chem-2019-0130 ◽

2019 ◽

Vol 17 (1) ◽

pp. 1213-1221

Author(s):

Chu Shufang ◽

Zhou Yinan ◽

Li Huilin ◽

Zhao Hengxia ◽

Liu Deliang ◽

...

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Dna Methylation ◽

Type 2 Diabetes Mellitus ◽

Lipid Metabolism ◽

Insulin Signaling ◽

Blood Stasis ◽

Blood Stasis Syndrome ◽

Glucose And Lipid Metabolism

AbstractThis study was performed to elucidate the potential influence of He Qi San (HQS) on glucose and lipid metabolism in type 2 diabetes mellitus (T2DM) patients with phlegm-blood stasis syndrome (PBSS), and to determine DNA methylation changes. Sixty T2DM patients with PBSS were randomly divided into control and HQS groups. The control group received conventional treatments, and the HQS group received conventional treatments plus HQS. Glucose metabolism (FPG, 2hPG, FINS, and HbA1c) and lipid metabolism indexes (TG, TC and LDL-C) were determined. Genes with differential DNA methylation were subjected to GO and KEGG analyses. Glucose and lipid metabolism indexes in both groups were reduced, but were much more pronounced in the HQS group. Differential promoter CpG methylation regions were identified in 682 genes, including 426 genes with high-CpG promoters, 150 genes with intermediate CpG promoters, and 106 genes with low CpG promoters. Genes with differential DNA methylation were mainly enriched in the AMPK and insulin signaling pathways, terpenoid backbone biosynthesis, and renin secretion. We concluded that HQS remarkably improved indexes of glucose and lipid metabolism in T2DM patients with PBSS through regulating the DNA methylation of genes in the AMPK and insulin signaling pathways and terpenoid backbone biosynthesis.

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Predicting Target Genes of San-Huang-Chai-Zhu Formula in Treating ANIT-Induced Acute Intrahepatic Cholestasis Rat Model via Bioinformatics Analysis Combined with Experimental Validation

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/5320445 ◽

2021 ◽

Vol 2021 ◽

pp. 1-17

Author(s):

Jiaming Yao ◽

Junbin Yan ◽

Jinting Wu ◽

Jianshun Yu ◽

Beihui He ◽

...

Keyword(s):

Intrahepatic Cholestasis ◽

Target Genes ◽

Bioinformatics Analysis ◽

Enrichment Analysis ◽

Normal Group ◽

Pathway Enrichment Analysis ◽

Qrt Pcr ◽

Group A ◽

Serum Biochemical ◽

Group Serum

Background. San-Huang-Chai-Zhu formula (SHCZF) has been used to improve cholestasis for many years. This study aims to predict the possible gene targets of SHCZF in treating acute intrahepatic cholestasis (AIC) in rats. Materials and Methods. Eighteen SD rats were randomly assigned to the normal group, ANIT group, and ANIT + SHCZF group. Alpha-naphthylisothiocyanate (ANIT) was used to induce AIC. Serum biochemical indexes were detected in each group. After treatment, the livers were collected and used to extract RNA. The library was constructed by TruSeq RNA, sequenced by Illumina, and analyzed by various bioinformatics methods. qRT-PCR was used to verify the target genes related to the efficacy of SHCZF. Results. Serum ALT, AST, ALP, and TBIL were significantly higher in the ANIT group than in the normal group. Serum ALT and AST levels in the ANIT + SHCZF group were substantially lower than those in the ANIT group. A total of 354 intersected genes were screened by expression level correlation and PCA analysis, GO and KEGG pathway enrichment analysis, and WGCNA and STEM analysis. Then, 4 overlapping genes were found by pathway/BP/gene network construction. SHCZF reversed the downregulation of expression of CYP4A1 and HACL1 and the upregulation of expression of DBI and F11R induced by ANIT. In addition, the qRT-PCR result showed that mRNA expression of CYP4A1, HACL1, and F11R genes in the liver was consistent with the prediction result of bioinformatics analysis. Conclusion. CYP4A1, HACL1, and F11R are genes related to the occurrence of ANIT-induced AIC in rats and may be considered as targets of SHCZF for the treatment of AIC.

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Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules

BMC Endocrine Disorders ◽

10.1186/s12902-021-00718-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

G. Prashanth ◽

Basavaraj Vastrad ◽

Anandkumar Tengli ◽

Chanabasayya Vastrad ◽

Iranna Kotturshetti

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Type 2 Diabetes Mellitus ◽

Target Genes ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Hub Genes ◽

Pathway Enrichment ◽

Drug Molecules

Abstract Background Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results A total of 820 DEGs were identified between healthy obese and metabolically unhealthy obese, among 409 up regulated and 411 down regulated genes. The GO enrichment analysis results showed that these DEGs were significantly enriched in ion transmembrane transport, intrinsic component of plasma membrane, transferase activity, transferring phosphorus-containing groups, cell adhesion, integral component of plasma membrane and signaling receptor binding, whereas, the REACTOME pathway enrichment analysis results showed that these DEGs were significantly enriched in integration of energy metabolism and extracellular matrix organization. The hub genes CEBPD, TP73, ESR2, TAB1, MAP 3K5, FN1, UBD, RUNX1, PIK3R2 and TNF, which might play an essential role in obesity associated type 2 diabetes mellitus was further screened. Conclusions The present study could deepen the understanding of the molecular mechanism of obesity associated type 2 diabetes mellitus, which could be useful in developing therapeutic targets for obesity associated type 2 diabetes mellitus.

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Combination of Systems Pharmacology and Experimental Evaluation to Explore the Mechanism of Synergistic Action of Frankincense-Myrrh in the Treatment of Cerebrovascular Diseases

Frontiers in Pharmacology ◽

10.3389/fphar.2021.796224 ◽

2022 ◽

Vol 12 ◽

Author(s):

Yucheng Liao ◽

Jingwen Wang ◽

Chao Guo ◽

Min Bai ◽

Bowei Ju ◽

...

Keyword(s):

Target Genes ◽

Inflammatory Responses ◽

Infarct Volume ◽

Blood Stasis ◽

Enrichment Analysis ◽

Cerebrovascular Diseases ◽

Pathway Enrichment Analysis ◽

Systems Pharmacology

Frankincense-Myrrh is a classic drug pair that promotes blood circulation, and eliminates blood stasis. The combination of the two drugs has a definite clinical effect on the treatment of cerebrovascular diseases (CBVDs), but its mechanism of action and compatibility have not been elucidated. In this study, the bioactive components, core targets, and possible synergistic mechanisms of Frankincense-Myrrh in the treatment of CBVDs are explored through systems pharmacology combined with in vivo and in vitro experiments. Comparing target genes of components in Frankincense and Myrrh with CBVD-related genes, common genes were identified; 15 core target genes of Frankincense-Myrrh for the treatment of CBVDs were then identified using protein-protein interaction (PPI) analysis. It was also predicted through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis that the molecular mechanism of Frankincense-Myrrh action on CBVDs was mainly related to the regulation of neurotrophic factors and inflammatory responses. Frankincense-Myrrh significantly improved neurological function, decreased infarct volume, alleviated histopathological damage, inhibited microglial expression, and promoted the expression of neurons in middle cerebral artery occlusion (MCAO)-induced rats. The results of this study not only provide important theoretical support and experimental basis for the synergistic effect of Frankincense-Myrrh, but also provide new ideas for the prevention and treatment of cerebral ischemic injuries.

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