Construction of miRNA-mRNA-TF Regulatory Network for Diagnosis of Gastric Cancer

Gastric cancer (GC), as an epidemic cancer worldwide, has more than 1 million new cases and an estimated 769,000 deaths worldwide in 2020, ranking fifth and fourth in global morbidity and mortality. In mammals, both miRNAs and transcription factors (TFs) play a partial role in gene expression regulation. The mRNA expression profile and miRNA expression profile of GEO database were screened by GEO2R for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Then, DAVID annotated the functions of DEGs to understand the functions played in biological processes. The prediction of potential target genes of miRNA and key TFs of mRNA was performed by mipathDB V2.0 and CHEA3, respectively, and the gene list comparison was performed to look for overlapping genes coregulated by key TFs and DEMs. Finally, the obtained miRNAs, TF, and overlapping genes were used to construct the miRNA-mRNA-TF regulatory network, which was verified by RT-qPCR. 76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively. Through database prediction and gene list comparison, it was found that among the 199 downregulated DEGs, 61, 71, and 69 genes were the potential targets of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p, respectively. 199 downregulated DEGs were used as the gene list for the prediction of key TFs, and the results showed that RFX6 ranked the highest. The potential target overlap genes of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p were 4 genes (SH3GL2, ATP4B, CTSE, and SORBS2), 7 genes (SLC7A8, RNASE4, ESRRG, PGC, MUC6, Fam3B, and FMO5), and 6 genes (CHGA, PDK4, TMPRSS2, CLIC6, GPX3, and PSCA), respectively. Finally, we constructed a miRNA-mRNA-TF regulatory network based on the above 17 mRNAs, 3 miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression of RFX6 was downregulated in GC tissues. These identified miRNAs, mRNAs, and TF have a certain reference value for further exploration of the regulatory mechanism of GC.

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Screening Driving Transcription Factors in the Processing of Gastric Cancer

Gastroenterology Research and Practice ◽

10.1155/2016/8431480 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Guangzhong Xu ◽

Kai Li ◽

Nengwei Zhang ◽

Bin Zhu ◽

Guosheng Feng

Keyword(s):

Gastric Cancer ◽

Transcription Factors ◽

Regulatory Network ◽

Target Genes ◽

Transcriptional Regulatory Network ◽

Expression Profiles ◽

Functional Enrichment ◽

Regulatory Mechanisms ◽

Integrated Analysis ◽

Transcriptional Regulatory

Background. Construction of the transcriptional regulatory network can provide additional clues on the regulatory mechanisms and therapeutic applications in gastric cancer.Methods. Gene expression profiles of gastric cancer were downloaded from GEO database for integrated analysis. All of DEGs were analyzed by GO enrichment and KEGG pathway enrichment. Transcription factors were further identified and then a global transcriptional regulatory network was constructed.Results. By integrated analysis of the six eligible datasets (340 cases and 43 controls), a bunch of 2327 DEGs were identified, including 2100 upregulated and 227 downregulated DEGs. Functional enrichment analysis of DEGs showed that digestion was a significantly enriched GO term for biological process. Moreover, there were two important enriched KEGG pathways: cell cycle and homologous recombination. Furthermore, a total of 70 differentially expressed TFs were identified and the transcriptional regulatory network was constructed, which consisted of 566 TF-target interactions. The top ten TFs regulating most downstream target genes were BRCA1, ARID3A, EHF, SOX10, ZNF263, FOXL1, FEV, GATA3, FOXC1, and FOXD1. Most of them were involved in the carcinogenesis of gastric cancer.Conclusion. The transcriptional regulatory network can help researchers to further clarify the underlying regulatory mechanisms of gastric cancer tumorigenesis.

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Identification of Potential ceRNA Network and Patterns of Immune Cell Infiltration in Systemic Sclerosis-Associated Interstitial Lung Disease

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.622021 ◽

2021 ◽

Vol 9 ◽

Author(s):

Qiuhong Wu ◽

Yang Liu ◽

Yan Xie ◽

Shixiong Wei ◽

Yi Liu

Keyword(s):

Systemic Sclerosis ◽

Interstitial Lung Disease ◽

Lung Disease ◽

Immune Cells ◽

Regulatory Network ◽

Target Genes ◽

Immune Cell ◽

Differentially Expressed ◽

Immune Cell Infiltration ◽

Overlapping Genes

PurposeSystemic sclerosis-associated interstitial lung disease (SSc-ILD) is one of the most severe complications of systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. However, the precise pathogenesis of pulmonary fibrosis in SSc-ILD remains unknown. This study aimed to evaluate the competing endogenous RNA (ceRNA) regulatory network and immune cell infiltration patterns in SSc-ILD.MethodsOne microRNA (miRNA) and three messenger RNA (mRNA) microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. Then, the differentially expressed miRNAs (DEmiRs) and mRNAs (DEMs) between SSc-ILD patients and normal controls were identified, respectively, followed by the prediction of the target genes and target lncRNAs of DEmiRs. The overlapping genes between DEmiRs target genes and DEMs were identified as core mRNAs to construct the ceRNA network. In addition, the “Cell Type Identification by Estimating Relative Subsets of Known RNA Transcripts (CIBERSORT)” algorithm was used to analyze the composition of infiltrating immune cells in lung tissues of SSc-ILD patients and controls, and differentially expressed immune cells were recognized. The correlation between immune cells and core mRNAs was evaluated by Pearson correlation analysis.ResultsTotally, 42 SSc-ILD lung tissues and 18 normal lung tissues were included in this study. We identified 35 DEmiRs and 142 DEMs and predicted 1,265 target genes of DEmiRs. Then, 9 core mRNAs related to SSc-ILD were recognized, which were the overlapping genes between DEmiRs target genes and DEMs. Meanwhile, 9 DEmiRs related to core mRNAs were identified reversely, and their target lncRNAs were predicted. In total, 9 DEmiRs, 9 core mRNAs, and 51 predicted lncRNAs were integrated to construct the ceRNA regulatory network of SSc-ILD. In addition, 9 types of immune cells were differentially expressed in lung tissues between SSc-ILD patients and controls. Some core mRNAs, such as COL1A1, FOS, and EDN1, were positively or negatively correlated with the number of infiltrating immune cells.ConclusionThis is the first comprehensive study to construct the potential ceRNA regulatory network and analyze the composition of infiltrating immune cells in lung tissues of SSc-ILD patients, which improves our understanding of the pathogenesis of SSc-ILD.

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Potential Regulatory Effects of miR-182-3p in Osteosarcoma via Targeting EBF2

BioMed Research International ◽

10.1155/2019/4897905 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Gaoyang Chen ◽

Wenqing Yu ◽

Zhaoyan Li ◽

Qingyu Wang ◽

Qiwei Yang ◽

...

Keyword(s):

Target Genes ◽

Expression Profiles ◽

Differential Expression Analysis ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Luciferase Reporter ◽

Luciferase Reporter Gene ◽

Potential Target ◽

Proliferation Activity ◽

Regulatory Effects

Osteosarcoma (OS) is one of the most common primary malignant bone tumors in adolescents with a high mortality rate. MicroRNA (miRNA) is a kind of noncoding RNAs and has been proved to participate in many physiological processes. Many miRNAs have been reported to act as function regulators in OS. In our study, the miRNA and gene expression profiles of OS were downloaded from GEO Datasets and the differential expression analysis was performed using GEO2R. 58 up- and 126 downregulated miRNAs were found. In the three OS gene profiles, 125 up- and 27 downregulated genes were found to be differentially expressed in at least two profiles. The miRNA-mRNA networks were constructed to predict the potential target genes of 10 most up- and downregulated miRNA. Venn analysis was used to detect the coexpressed differentially expressed genes (DEGs). EBF2, one of the upregulated DEGs, was also a potential target gene of miR-182-3p. Knockdown and overexpression of miR-182-3p resulted in overexpression and downexpression of EBF2 separately. Luciferase reporter gene experiment further verified the binding site of miR-182-3p and EBF2. CCK8 assay showed that miR-182-3p knockdown can further enhance the proliferation activity of OS cells, while overexpressing miR-182-3p can inhibit the proliferation activity of OS cells. Our research indicated that downexpression of miR-182-3p in OS cells results in overexpression of EBF2 and promotes the progression of OS.

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Construction of potential periodontitis-related miRNA-mRNA regulatory network

10.21203/rs.3.rs-109574/v1 ◽

2020 ◽

Author(s):

Zheng Zhang ◽

Youli Zheng ◽

Xiaowei Bian ◽

Mingguang Jin

Keyword(s):

Candidate Genes ◽

Regulatory Network ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Multivariate Logistic Regression Analysis ◽

Gene Expression Profiles ◽

Mirna Expression Profile ◽

Differentially Expressed ◽

B Cell Differentiation

Abstract Background MicroRNAs (miRNAs) are found to be involved in the pathogenesis of periodontitis, a major cause of tooth loss in adults. However, a comprehensive miRNA-mRNA regulatory network has still not been established. Methods One miRNA expression profile and 2 gene expression profiles were downloaded from the GEO database and analyzed using GEO2R. Candidate genes commonly appeared in differentially expressed mRNAs (DE-mRNAs) and target genes of differentially expressed miRNAs (DE-miRNAs) were selected for functional and pathway enrichment analyses using Enrichr database. Multivariate Logistic regression analysis was used to screen independent variables among candidate genes. The diagnostic values of screened genes were determined by the area under the receiver operating characteristic (ROC) curve (AUC). Results A total of 5 DE-miRNAs (4 upregulated and 1 downregulated) and 11 candidate genes (3 upregulated and 8 downregulated) were screened. After the construction of miRNA-mRNA regulatory network, 12 miRNA-mRNA pairs were identified. In the network, the upregulated genes were significantly enriched in cellular triglyceride homeostasis and positive regulation of B cell differentiation, whereas the downregulated genes were enriched in vesicle organization, negative regulation of lymphocyte and leukocyte migration. EPCAM and RAB30 were screened as risk factors of periodontitis. The combined AUC of these 2 genes was 0.896 (GSE10334) and 0.916 (GSE16134). Conclusion In this study, we established a potential periodontitis-related miRNA-mRNA regulatory network, which brings new insights into the molecular mechanisms and provides key clues in seeking novel therapeutic targets for periodontitis. In the future, more experiments need to be carried out to validate our current findings.

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High-Throughput Sequencing Reveals the Differential MicroRNA Expression Profiles of Human Gastric Cancer SGC7901 Cell Xenograft Nude Mouse Models Treated with Traditional Chinese Medicine Si Jun Zi Tang Decoction

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/6119212 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Junfu Guo ◽

Xiangnan Li ◽

Lanying Miao ◽

Hongwei Sun ◽

Xia Gao ◽

...

Keyword(s):

Gastric Cancer ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Human Gastric Cancer ◽

Model Group ◽

Sgc7901 Cell ◽

Qrt Pcr ◽

Differentially Expressed Mirnas

Objective. The present study aimed to investigate the potential mechanism underlying the antitumor effect of Si Jun Zi Tang (SJZT) decoction on gastric cancer. Methods. Twelve human gastric cancer SGC7901 cell xenograft nude mouse models were established. The mice were randomly divided into the Model group and SJZT group. SJZT exerted significant antitumor effects after 21 days of decoction administration. High-throughput sequencing was used to analyze the microRNA (miRNA) expression profiles of tumor tissues. Bioinformatics analysis was performed to provide further information regarding the differentially expressed miRNAs. Five representative differentially expressed miRNAs and four predicted target genes were further validated using quantitative real-time reverse transcription PCR (qRT-PCR). Results. We identified 33 miRNAs that were differentially expressed in the SJZT group compared with the Model group. Among them, 32 miRNAs were upregulated and 1 miRNA was downregulated. Bioinformatic analysis showed that most of miRNAs acted as tumor suppressors and their target genes participated in multiple signaling pathways, including the PI3K/Akt signaling pathway, microRNAs in cancer, and Wnt signaling pathway. The qRT-PCR result confirmed that miR-223-3p, miR-205-5p, miR-147b-3p, and miR-223-5p were overexpressed and their respective paired target genes FUT9, POU2F1, MUC4, and RAB14 mRNA were obviously downregulated in the SJZT group compared with those in the Model group. Network analysis revealed that miR-223-3p and miR-205-5p shared two targets POU2F1 (encoding POU class 2 homeobox 1) and FUT9 (encoding fucosyltransferase 9), suggesting they have a common role in certain pathways. Conclusion. This study provided novel insights into the anticancer mechanism of SJZT against gastric cancer, which might be partly related to the modulation of miRNA expression and their target pathways in tumors.

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Joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in gastric cancer

Cancer Cell International ◽

10.1186/s12935-020-01554-8 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Zhi Lv ◽

Liping Sun ◽

Qian Xu ◽

Chengzhong Xing ◽

Yuan Yuan

Keyword(s):

Gastric Cancer ◽

Mrna Expression ◽

Expression Analysis ◽

Target Genes ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Joint Analysis ◽

Gene Enrichment Analysis ◽

Gene Enrichment

Abstract Background N6-methyladenosine (m6A) modification might be closely associated with the genesis and development of gastric cancer (GC). Currently, the evidence established by high-throughput assay for GC-related m6A patterns based on long non-coding RNAs (lncRNAs) remains limited. Here, a joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in GC was performed to explore the regulatory roles of m6A modification in lncRNAs. Methods Three subjects with primary GC were enrolled in our study and paired sample was randomly selected from GC tissue and adjacent normal tissue for each case. Methylated RNA Immunoprecipitation NextGeneration Sequencing (MeRIP-Seq) and Microarray Gene Expression Profiling was subsequently performed. Then co-expression analysis and gene enrichment analysis were successively conducted. Results After data analysis, we identified 191 differentially m6A-methylated lncRNAs, 240 differentially expressed lncRNAs and 229 differentially expressed mRNAs in GC. Furthermore, four differentially m6A-methylated and expressed lncRNAs (dme-lncRNAs) were discovered including RASAL2-AS1, LINC00910, SNHG7 and LINC01105. Their potential target genes were explored by co-expression analysis. And gene enrichment analysis suggested that they might influence the cellular processes and biological behaviors involved in mitosis and cell cycle. The potential impacts of these targets on GC cells were further validated by CCLE database and literature review. Conclusions Four novel dme-lncRNAs were identified in GC, which might exert regulatory roles on GC cell proliferation. The present study would provide clues for the lncRNA m6A methylation-based research on GC epigenetic etiology and pathogenesis.

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Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Life ◽

10.3390/life10110300 ◽

2020 ◽

Vol 10 (11) ◽

pp. 300

Author(s):

Leyland Fraser ◽

Łukasz Paukszto ◽

Anna Mańkowska ◽

Paweł Brym ◽

Przemysław Gilun ◽

...

Keyword(s):

Target Genes ◽

De Novo ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Differentially Expressed ◽

Biological Processes ◽

Protein Coding ◽

Protein Coding Genes ◽

Potential Target ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

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Expression profiles of potential target genes in disseminated gastric cancer

Russian Journal of Biotherapy ◽

10.17650/1726-9784-2017-16-4-25-28 ◽

2017 ◽

Vol 16 (4) ◽

pp. 25-28

Author(s):

F. M. Kipkeeva ◽

T. A. Muzaffarova ◽

M. N. Narimanov ◽

O. A. Malekhova ◽

T. A. Bogush ◽

...

Keyword(s):

Gene Expression ◽

Gastric Cancer ◽

Growth Factor ◽

Messenger Rna ◽

Target Genes ◽

Transforming Growth Factor ◽

Expression Profiles ◽

Inverse Correlation ◽

Metastatic Potential ◽

Potential Target

Objective is the investigation of messenger RNA quantitative expression profiles of potential target genes among disseminated gastric cancer cases. Materials and methods. Quantitative real-time polymerase chain reaction on paired tumor-normal samples. Results. The most frequently (25-41 % of cases) an increased level of messenger RNA in the tumor with respect to normal tissue was observed for the genes of TGF-ß (transforming growth factor ß), NRP-1 (neuropiline 1) and VEGF (vascular endothelial growth factor) family genes. For the first time a correlation between the expression levels of the three genes: NRP-1, TGF-ß and VEGFR-2, and the inverse correlation of the levels of VEGF and bFGF gene expression were found. Conclusion. The revealed correlation between the expression of TGF-ß, NRP-1 and VEGFR-2 genes is apparently due to the interaction of NRP-1 with the products of two other genes and may be associated with a high metastatic potential of the progressing tumor in disseminated gastric cancer. The observed inverse correlation of the VEGF-A and bFGF gene expression may indicate the stimulation of angiogenesis in the tumor with reduced activity of the VEGF pathway by activating the bFGF signaling pathway. The results obtained should be taken into account under targeted therapy.

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Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs

10.1101/546390 ◽

2019 ◽

Author(s):

Zhiguo Miao ◽

Jinzhou Zhang ◽

Shan Wang ◽

Paneng Wei

Keyword(s):

Expression Profile ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Circular Rna ◽

Differentially Expressed ◽

Real Time Quantitative Pcr ◽

Significant Difference ◽

Intermuscular Fat ◽

Fattening Period

AbstractCircular RNA (circRNA) plays an important regulatory role in development and differentiation. Intermuscular fat in pork affects the tenderness and juiciness of the meat. In this study, we investigated the performances of Landrace (lean) and Jinhua (obese) pigs at the fattening period and explored the expression profile of circRNAs in intermuscular fat from the two breeds by Illumina high-throughput sequencing. we identified 5 548 circRNAs, specifically 2 651 (47.78%) in the Jinhua pigs, and 2 897 (52.22%) in the Landrace pigs. A totale of 809 differentially expressed circRNAs were observed between the the Jinhua and Landrace pigs, but only 29 of these circRNAs showed significant difference (19 upregulated and 10 downregulated). All 1 306 unigenes and 27 differentially expressed unigenesinvolved in lipid transport and metabolism; replication, recombination and repair; and signaling pathway were annotated. A total of 550 target miRNAs were perfect seed matches and 20 522 target genes were foundBy RNAhybrid and miRanda software prediction. Results from real-time quantitative PCR also confirmed the differential expression of 13 mRNAs between the two pig breeds. This study provides comprehensive expression profiles of circRNAs in Sus scrofa adipose metabolism and development, which can be used to clarify their functions.Summary statementThe paper explored the expression profile of circRNAs in intermuscular fat from Landrace and Jinhua pigs at the fattening period, to provide insights into circRNAregulation in animal adipose metabolism.

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Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

Scientific Reports ◽

10.1038/s41598-021-85245-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Samina Shabbir ◽

Prerona Boruah ◽

Lingli Xie ◽

Muhammad Fakhar-e-Alam Kulyar ◽

Mohsin Nawaz ◽

...

Keyword(s):

Target Genes ◽

Expression Profiles ◽

Ovarian Follicle ◽

Follicular Development ◽

Differentially Expressed ◽

Ovary Development ◽

Estrogen Metabolism ◽

Genome Wide ◽

Micro Rnas ◽

Hu Sheep

AbstractOvary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

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