Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation

It is reported that microRNAs (miRNA) have paramount functions in many cellular biological processes, development, metabolism, differentiation, survival, proliferation, and apoptosis included, some of which are involved in metastasis of tumors, such as melanoma. Here, three metastasis-associated miRNAs, miR-18a-5p (upregulated), miR-155-5p (downregulated), and miR-93-5p (upregulated), were identified from a total of 63 different expression miRNAs (DEMs) in metastatic melanoma compared with primary melanoma. We predicted 262 target genes of miR-18a-5p, 904 miR-155-5p target genes, and 1220 miR-93-5p target genes. They participated in pathways concerning melanoma, such as TNF signaling pathway, pathways in cancer, FoxO signaling pathway, cell cycle, Hippo signaling pathway, and TGF-beta signaling pathway. We identified the top 10 hub nodes whose degrees were higher for each survival-associated miRNA as hub genes through constructing the PPI network. Using the selected miRNA and the hub genes, we constructed the miRNA-hub gene network, and PTEN and CCND1 were found to be regulated by all three miRNAs. Of note, miR-155-5p was obviously downregulated in metastatic melanoma tissues, and miR-18a-5p and miR-93-5p were obviously regulated positively in metastatic melanoma tissues. In validating experiments, miR-155-5p's overexpression inhibited miR-18a-5p's and miR-93-5p's expression, which could all significantly reduce SK-MEL-28 cells' invasive ability. Finally, miR-93-5p and its potential target gene UBC were selected for further validation. We found that miR-93-5p's inhibition could reduce SK-MEL-28 cell's invasive ability through upregulated the expression of UBC, and the anti-invasive effect was reserved by downregulation of UBC. The results show that the selected three metastasis-associated miRNAs participate in the process of melanoma metastasis via regulating their target genes, providing a potential molecular mechanism for this disease.

Download Full-text

Identification of core genes and pathways in melanoma metastasis via bioinformatics analysis

10.21203/rs.3.rs-39969/v1 ◽

2020 ◽

Author(s):

Yumei Li ◽

Bifei Li ◽

Fan Chen ◽

Weiyu Shen ◽

Vladimir L. Katanaev ◽

...

Keyword(s):

Gene Expression ◽

Metastatic Melanoma ◽

Molecular Mechanisms ◽

Therapeutic Targets ◽

Primary Melanoma ◽

Melanoma Cells ◽

Receptor Interaction ◽

Melanoma Metastasis ◽

Hub Genes ◽

Core Genes

Abstract Background Metastasis is the leading cause of melanoma mortality. Current therapies are rarely curative for metastatic melanoma, revealing the urgent need to identify more effective preventive and therapeutic targets. This study aimed to screen for the key core genes and molecular mechanisms related to the metastasis of melanoma. Methods Gene expression profile, GSE8401 including 31 primary melanoma and 52 metastatic melanoma clinical samples, was downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between metastatic melanoma and primary melanoma were screened using GEO2R. Assays of gene ontology (GO), Kyoto Encyclopedia of Gene and Genome (KEGG) pathway and protein-protein interaction (PPI) were performed to visualize these DEGs through Database for Annotation, Visualization and Integrated Discovery (DAVID) software and Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape with Molecular Complex Detection (MCODE) plug-in tools. Top 10 genes with high degree were defined as hub genes. Furthermore, paired post-metastatic melanoma cells and pre-metastatic melanoma cells were established by experimental mouse model of melanoma metastasis to verify the expression of these hub genes. Results 424 DEGs between the metastatic melanoma and primary melanoma were screened, including 60 upregulated genes enriched in ECM-receptor interaction and progesterone-mediated oocyte maturation and 364 downregulated genes enriched in amoebiasis, melanogenesis, and ECM-receptor interaction. CDH1, EGFR, KRT5, COL17A1, KRT14, IVL, DSP, DSG1, FLG and CDK1 were defined as the hub genes. . In addition, paired post-metastatic melanoma cells (A375M) and pre-metastatic melanoma cells (A375) were established and qRT-PCR analysis confirmed the expression of the hub genes during melanoma metastasis. Conclusion This bioinformatic study has provided a deeper understanding of the molecular mechanisms of melanoma metastasis. KRT5, IVL and COL17A1 have emerged as possible biomarkers and therapeutic targets in metastasis of melanoma.

Download Full-text

Exploration and Validation of Metastasis-associated Genes for Skin Cutaneous Melanoma

10.21203/rs.3.rs-940144/v2 ◽

2021 ◽

Author(s):

Hong Luan ◽

Linge Jian ◽

Ye He ◽

Tuo Zhang ◽

Yanna Su ◽

...

Keyword(s):

Metastatic Melanoma ◽

Cutaneous Melanoma ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Primary Melanoma ◽

Gene Interaction ◽

Skin Tumor ◽

Melanoma Metastasis ◽

Hub Genes ◽

Hub Gene

Abstract Background: Skin cutaneous melanoma is a malignant and highly metastatic skin tumor, and its morbidity and mortality are still rising worldwide. However, the molecular mechanisms that promote melanoma metastasis are unclear. Methods: Two datasets (GSE15605 and GSE46517) were retrieved to identify the differentially expressed genes (DEGs), including 23 normal skin tissues (N), 77 primary melanoma tissues (T) and 85 metastatic melanoma tissues (M). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed to explore the functions of the DEGs. The protein–protein interaction (PPI) network was constructed using the STRING tool and Cytoscape software. We used the cytoHubba plugin of Cytoscape to identify the most significant hub genes by five topological analyses (Degree, Bottleneck, MCC, MNC, and EPC). Hub gene expression was validated using the UALCAN website. Clinical relevance was investigated using The Cancer Genome Atlas (TCGA) resources. Finally, we explored the association between metastasis-associated genes and immune infiltrates through the Tumor Immune Estimation Resource (TIMER) database and performed drug-gene interaction analysis using the Drug-Gene Interaction database.Results: A total of 294 specific genes were related to melanoma metastasis and were mainly involved in the positive regulation of locomotion, mitotic cell cycle process, and epithelial cell differentiation. Four hub genes (CDK1, FOXM1, KIF11, and RFC4) were identified from the cytoHubba plugin of Cytoscape. CDK1 was significantly upregulated in metastatic melanoma compared with primary melanoma, and high expression of CDK1 was positively correlated with poor prognosis. We found that CDK1 expression correlated positively with the infiltration levels of macrophage cells (Rho = -0.164, P = 2.02e-03) and neutrophil cells (Rho = 0.269, P = 2.72e-07) in SKCM metastasis. In addition, we identified that CDK1 had a close interaction with 10 antitumor drugs. Conclusions: CDK1 was identified as a hub gene involved in the progression of melanoma metastasis and may be regarded as a therapeutic target for melanoma patients to improve prognosis and prevent metastasis in the future.

Download Full-text

Exploration and Validation of Metastasis-associated Genes for Skin Cutaneous Melanoma

10.21203/rs.3.rs-940144/v1 ◽

2021 ◽

Author(s):

Hong Luan ◽

Linge Jian ◽

Ye He ◽

Tuo Zhang ◽

Yanna Su ◽

...

Keyword(s):

Metastatic Melanoma ◽

Cutaneous Melanoma ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Primary Melanoma ◽

Gene Interaction ◽

Skin Tumor ◽

Melanoma Metastasis ◽

Hub Genes ◽

Hub Gene

Download Full-text

YAP Activation and Implications in Patients and a Mouse Model of Biliary Atresia

Frontiers in Pediatrics ◽

10.3389/fped.2020.618226 ◽

2021 ◽

Vol 8 ◽

Author(s):

Chao Zheng ◽

Jiaqian Luo ◽

Yifan Yang ◽

Rui Dong ◽

Fa-Xing Yu ◽

...

Keyword(s):

Bile Duct ◽

Liver Fibrosis ◽

Mouse Model ◽

Biliary Atresia ◽

Signaling Pathway ◽

Target Genes ◽

Hippo Signaling ◽

Mice Model ◽

Hippo Signaling Pathway ◽

Ductal Cells

Background and Aim: Biliary atresia (BA), an inflammatory destruction of the bile ducts, leads to liver fibrosis in infants and accounts for half of cases undergoing pediatric liver transplantation. Yes-associated protein (YAP), an effector of the Hippo signaling pathway, is critical in maintaining identities of bile ductal cells. Here, we evaluated the expression of YAP and YAP target genes in BA livers and a rhesus rotavirus (RRV)-induced BA mice model.Methods: Liver specimens collected from 200 BA patients were compared with those of 30 non-BA patients. Model mice liver tissues were also collected. The expression of YAP and YAP target genes were measured by transfection, RNA-seq, immunohistochemistry, immunoblot, and quantitative PCR. Masson's trichrome staining and the Biliary Atresia Research Consortium (BARC) system were utilized to score liver fibrosis status.Results: The expression of YAP is elevated and positively correlated with fibrosis in BA livers. Moreover, ANKRD1, which is identified as the target gene of YAP, is also highly expressed in BA livers. Consistent with clinical data, YAP and ANKRD1 are significantly upregulated in RRV-induced BA mouse model.Conclusions: YAP expression is closely correlated with the bile duct hyperplasia and liver fibrosis, and may serve as an indicator for liver fibrosis and BA progression. This study indicates an involvement of the Hippo signaling pathway in the development of BA, and the YAP induced ANKRD1 expression may also be related to bile duct hyperplasia in BA. This provides a new direction for more in-depth exploration of the etiology and pathogenesis of biliary atresia.

Download Full-text

miR-130b Acts as an Oncogene and Prognostic Biomarker of Breast Cancer: A Bioinformatic Analysis

10.21203/rs.3.rs-132700/v1 ◽

2020 ◽

Author(s):

Xinyue Chen ◽

Lijun Hao

Keyword(s):

Breast Cancer ◽

Thyroid Hormone ◽

Signaling Pathway ◽

Target Genes ◽

Kegg Pathway ◽

Prognostic Biomarker ◽

Pathway Enrichment Analysis ◽

Hormone Signaling ◽

Ppi Network ◽

Hub Genes

Abstract Background: Breast cancer (BC) is the most prevalent cancer among females globally. microRNAs (miRNAs) could regulate the expression levels of cancer-related genes through binding with target mRNAs. In various cancers, the abnormal expression of miR-130b has been detected. We aims to investigate the molecular mechanism and biological function of miR130b in breast cancer.Methods: We obtained two microRNA expression profiles from the Gene Expression Omnibus (GEO) database, including GSE45666 and GSE26659. We identified differentially expressed miRNAs (DE-miRNAs) between BC tissue and normal breast tissue based on the GEO2R web tool. DE-miRNAs were filtered by significant prognostic value resulting from Kaplan–Meier plotter. We used the JASPAR database to explore upstream regulators of miR-130b. The potential molecular mechanisms of miR-130b correlation genes were revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis in WebGestalt. Protein–protein interaction (PPI) network of miR-130b target genes was constructed by STRING. Cytoscape software was used to visualize the PPI network and hub genes.Results: miR-130b was highly expressed in breast cancer tissues, which positively correlates with poor prognostic. JASPAR revealed THAP11 might be the upstream regulator of miR-130b. In addition, GO, and KEGG pathway revealed that miR-130b positively regulated PFKP, STAT1, SRC, and NOTCH2, participating in the Thyroid hormone signaling pathway. The PPI network further identified that AR, KIT, and ESR1 as hub genes in BC development.Conclusion: miR-130b, which is regulated by THAP11, acts as an oncogene and prognostic biomarker in BC by mediating the Thyroid hormone signaling pathway and potential target genes. miR-130b might be a novel therapeutic target for BC treatment.

Download Full-text

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

10.21203/rs.3.rs-22009/v1 ◽

2020 ◽

Author(s):

Yu Gong ◽

Xiaoyang Qi ◽

Jinjin Fu ◽

Jun Qian ◽

Yuwen Jiao ◽

...

Keyword(s):

Gastric Cancer ◽

Signaling Pathway ◽

Cancer Progression ◽

Regulatory Network ◽

Target Genes ◽

Human Cancer ◽

Microarray Dataset ◽

Circular Rnas ◽

Cancer Tissue ◽

Hub Genes

Abstract Background: Increasing evidence implicates circular RNAs (circRNAs) have been involved in human cancer progression. However, the mechanism remains unclear. In this study, we identified novel circRNAs related to gastric cancer and constructed a circRNA-miRNA-mRNA network.Methods: Microarray dataset GSE83521 and GSE93541 were obtained from Gene Expression Omnibus (GEO). Then, we used computational biology to select differentially co-expressed circRNAs in GC tissue and plasma and detected the expression of selected circRNAs in gastric cell lines by quantitative real‑time polymerase chain reaction (qRT‑PCR). We also chose the candidate miRNAs and their target genes for circRNAs through online tools. Combining the predictions of miRNAs and target mRNAs, a competing endogenous RNA regulatory network was established. Functional and pathway enrichment analyses were performed, and interactions between proteins were predicted by using String and Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the possible functions of these differentially expressed circRNAs.Results: The regulatory network constructed using the microarray datasets (GSE83521 and GSE93541) contained three differentially co-expressed circRNAs (DECs). A circRNA-miRNA-mRNA network was constructed based on 3 circRNAs, 43 miRNAs and 119 mRNAs. GO and KEGG analysis showed that regulation of apoptotic signaling pathway and PI3K−Akt signaling pathway were highest degrees of enrichment respectively. We established a protein-protein interaction (PPI) network consisting of 165 nodes and 170 edges and identified hub genes by MCODE plugin in Cytoscape. Furthermore, a core circRNA-miRNA-mRNA network was constructed base on hub genes. Hsa_circ_0001013 was finally determined to play an important role in the pathogenesis of GC according to the core circRNA-miRNA-mRNA network.Conclusions: We propose a new circRNA-miRNA-mRNA network associated with the pathogenesis of GC. The network may become a new molecular biomarker and be used to develop potential therapeutic strategies for gastric cancer.

Download Full-text

Identification of exosomal miRNAs associated with the anthracycline-induced liver injury in postoperative breast cancer patients by small RNA sequencing

PeerJ ◽

10.7717/peerj.9021 ◽

2020 ◽

Vol 8 ◽

pp. e9021 ◽

Cited By ~ 1

Author(s):

Yue Zhang ◽

Di Wang ◽

Di Shen ◽

Yang Luo ◽

Yi-Qun Che

Keyword(s):

Liver Injury ◽

Signaling Pathway ◽

Target Genes ◽

Small Rna Sequencing ◽

Breast Cancer Patients ◽

Hub Genes ◽

Related Target ◽

Injury Group ◽

Exosomal Mirnas ◽

Exosomal Mirna

Background Anthracycline-induced liver injury (AILI) is one of the serious complications of anthracycline-based adjuvant chemotherapy for postoperative breast cancer patients. Exosomal miRNAs, as signaling molecules in intercellular communication, play the essential roles in drug-induced liver injury (DILI). However, the expression profiles of them in patients with AILI remains unknown. Methods Seven post-chemotherapy patients were recruited in this study. After isolated plasma-derived exosomes, small RNA sequencing revealed exosomal miRNA profiles and differentially expressed miRNAs (DE-miRNAs) were identified between the liver injury group and non-liver injury group. miRTarBase and miRDB were used to predict the potential target genes of DE-miRNAs. DILI-related genes were downloaded from the CTD Database. The intersection of predicted genes and DILI-related genes were identified as the AILI-related target genes of the DE-miRNAs. GO annotation and KEGG pathway enrichment analysis were performed by the DAVID database. Furthermore, the protein-protein interaction (PPI) network was established by the STRING database and essential exosomal miRNAs were identified via Cytoscape software. Results A total of 30 DE-miRNAs and 79 AILI-related target genes were identified. AILI-related target genes of the DE-miRNAs are significantly enriched in NOD-like receptor signaling pathway, the HIF-1 signaling pathway, and the FoxO signaling pathway. Then, the hub genes were screened and we discovered that IL-6 and SOD2 are the most critical genes that may be involved in the development of AILI through the activation of immune response and the occurrence of oxidative stress, respectively. In addition, we found that miR-1-3p could potentially regulate most of the hub genes in the miRNA-hub gene network. Conclusion We explored the potential functions of DE-miRNAs and suggested exosomal miR-1-3p might be the essential exosomal miRNA in the pathogenesis of AILI. Moreover, our study provided an experimental basis for experimental verification to reveal the actual function and mechanism of miRNAs in AILI.

Download Full-text

Activated Hippo/Yes-Associated Protein Pathway Promotes Cell Proliferation and Anti-apoptosis in Endometrial Stromal Cells of Endometriosis

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2016-1120 ◽

2016 ◽

Vol 101 (4) ◽

pp. 1552-1561 ◽

Cited By ~ 30

Author(s):

Yong Song ◽

Jing Fu ◽

Min Zhou ◽

Li Xiao ◽

Xue Feng ◽

...

Keyword(s):

Cell Proliferation ◽

Signaling Pathway ◽

Nude Mice ◽

Stromal Cells ◽

Target Genes ◽

Critical Role ◽

B Cell Lymphoma ◽

Endometrial Stromal Cells ◽

Proliferation And Apoptosis

Abstract Context: The imbalance in cell proliferation and apoptosis is considered an important role in the pathogenesis of endometriosis, but the exact mechanisms remains unclear. A newly established signaling pathway–Hippo/Yes-associated protein (YAP) pathway plays a critical role in the proliferation and apoptosis processes. However, studies focusing on Hippo/YAP pathway and endometriosis are lacking. Objective: The objective was to explore the function of the Hippo/YAP pathway in endometriosis. Setting and Design: The expression of YAP was first investigated in endometrium of women with or without endometriosis. The role of YAP in cell proliferation and apoptosis is identified by transfection of endometrial stromal cells (ESCs) in vitro, subsequent Verteporfin treatments in eutopic ESCs in vitro, and endometriosis animal model of nude mice in vivo. Results: Our results revealed that increased expression of YAP and decreased expression of p-YAP in ectopic and eutopic endometrium compared with normal endometrium. YAP knockdown in eutopic ESCs decreased cell proliferation and enhanced cell apoptosis companied with decreased expression of TEAD1, CTGF, and B-cell lymphoma/leukemia (BCL)-2; whereas overexpression of YAP resulted in increased proliferation and decreased apoptosis of normal ESCs with increased expression of TEAD1, CTGF, and BCL-2. By chromatin immunoprecipitation qPCR CTGF and BCL-2 were identified as directly downstream target genes of YAP-TEAD1 active complex. Eutopic ESCs treated with Verteporfin revealed decreased proliferation and enhanced apoptosis whereas in endometriosis animal models of nude mice treated with Verteporfin, the size of endometriotic lesions was significantly reduced. Conclusions: Our study suggests that the Hippo/YAP-signaling pathway plays a critical role in the pathogenesis of endometriosis and should present a novel therapeutic method against endometriosis.

Download Full-text

Differentially expressed circulating miRNAs in postmenopausal osteoporosis: a meta-analysis

Bioscience Reports ◽

10.1042/bsr20190667 ◽

2019 ◽

Vol 39 (5) ◽

Cited By ~ 5

Author(s):

Elif Pala ◽

Tuba Denkçeken

Keyword(s):

Postmenopausal Osteoporosis ◽

Signaling Pathway ◽

Target Genes ◽

Meta Analysis ◽

Adherens Junction ◽

Enrichment Analysis ◽

Rank Aggregation ◽

Cochrane Library ◽

Pathway Enrichment Analysis ◽

Hub Genes

AbstractMicroRNAs (miRNAs) have been proven to play a crucial role in postmenopausal osteoporosis (PMO), and studies on their diagnostic value have been increasing. In our study, we aim to identify the key miRNAs in the PMO that might be potential biomarkers. A comprehensive systematic literature search was conducted by searching PubMed, Web of Science, Embase and Cochrane Library databases. In the total of 16 independent miRNA expression studies which contained 327 PMO patients and 328 postmenopausal (PM) healthy control samples, miRNAs were evaluated by using robust rank aggregation (RRA) method. A statistically significant meta-signature of up-regulated hsa-miR-133a-3p (P = 1.38e−03) was determined. Then bioinformatics analysis to recruit putative target genes prediction of hsa-miR-133a-3p and pathway enrichment analysis to reveal what biological processes this miRNA may affect were conducted. It was indicated that pathways were commonly associated with adrenergic signaling in cardiomyocytes, adherens junction, PI3K-Akt signaling pathway and AMPK signaling pathway. Furthermore, STRING and Cytoscape tools were used to visualize the interactions between target genes of hsa-miR-133a-3p. Six genes were detected as hub genes among 576 targets which were CDC42, RHOA, EGFR, VAMP2, PIK3R2 and FN1. After Kyoto Encyclopedia of Genes and Genomes pathway analysis, it was detected that these hub genes were mostly enriched in signaling pathways and cancer. In this meta-analysis, it is stated that circulating hsa-miR-133a-3p may serve as a potential non-invasive biomarker and therapeutic target in PMO.

Download Full-text

Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

BMC Genomics ◽

10.1186/s12864-021-07916-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Leila Gharehdaghi ◽

Mohammad Reza Bakhtiarizadeh ◽

Kang He ◽

Taher Harkinezhad ◽

Gholamhosein Tahmasbi ◽

...

Keyword(s):

Signaling Pathway ◽

Honey Bee ◽

Honey Bees ◽

Target Genes ◽

Hippo Signaling ◽

Plant Mirnas ◽

Small Noncoding Rnas ◽

Regulation Function ◽

Regulation Functions ◽

Insect Interactions

Abstract Background MicroRNA (miRNA) is a class of small noncoding RNAs, which targets on thousands of mRNA and thus plays important roles in many biological processes. It has been reported that miRNA has cross-species regulation functions between parasitoid-host, or plant-animal, etc. For example, several plant miRNAs enter into the honey bees and regulate gene expression. However, whether cross-species regulation function of miRNAs is a universal mechanism remains a debate question. Results We have evaluated transmission of miRNAs from sunflower and sedr plants into the midgut of honey bee using RNA-Seq analyses complemented with confirmation by RT-qPCR. The results showed that at least 11 plant miRNAs were found in the midgut of honey bee feeding by sunflower and sedr pollen. Among which, nine miRNAs, including miR-30d, miR-143, miR-148a, miR-21, let-7 g, miR-26a, miR-126, miR-27a, and miR-203, were shared between the sunflower- and sedr-fed honey bees, suggesting they might have essential roles in plant-insect interactions. Moreover, existence of these co-shared miRNAs presents a strong evidence to support the successful transmission of miRNAs into the midgut of the insect. In total, 121 honeybee mRNAs were predicted to be the target of these 11 plant-derived miRNAs. Interestingly, a sedr-derived miRNA, miR-206, targets on 53 honeybee genes. Kyoto Encyclopedia of Genes and Genome (KEGG) analyses showed that these target genes are significantly involved in hippo signaling pathway-fly, Wnt signaling pathway, and N-Glycan biosynthesis. Conclusions In summary, these results provide evidence of cross-species regulation function of miRNA between honeybee and flowering host plants, extending our understanding of the molecular interactions between plants and animals.

Download Full-text