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Lawarde A, Sharif Rahmani E, Nath A, Lavogina D, Jaal J, Salumets A, Modhukur V. ExplORRNet: An interactive web tool to explore stage-wise miRNA expression profiles and their interactions with mRNA and lncRNA in human breast and gynecological cancers. Noncoding RNA Res 2024; 9:125-140. [PMID: 38035042 PMCID: PMC10686811 DOI: 10.1016/j.ncrna.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 12/02/2023] Open
Abstract
Background MicroRNAs (miRNAs) are key regulators of gene expression that have been implicated in gynecological and breast cancers. Understanding the cancer stage-wise expression patterns of miRNAs and their interactions with other RNA molecules in cancer is crucial to improve cancer diagnosis and treatment planning. Comprehensive web tools that integrate data on the transcriptome, circulating miRNAs, and their validated targets to derive beneficial conclusions in cancer research are lacking. Methods Using the Shiny R package, we developed a web tool called ExplORRNet that integrates transcriptomic profiles from The Cancer Genome Atlas and miRNA expression data derived from various sources, including tissues, cell lines, exosomes, serum, and plasma, available in the Gene Expression Omnibus database. Differential expression analyses between normal and tumor tissue samples as well as different stages of cancer, accompanied by gene enrichment and survival analyses, can be performed using specialized R packages. Additionally, a miRNA-messenger RNA (mRNA)-long non-coding RNA (lncRNA) networks are constructed to identify regulatory modules. Results Our tool identifies cancer stage-wise differentially regulated miRNAs, mRNAs, and lncRNAs in gynecological and breast cancers. Survival analysis identifies miRNAs associated with patient survival, and functional enrichment analysis provides insights into dysregulated miRNA-related biological processes and pathways. The miRNA-mRNA-lncRNA networks highlight interconnected regulatory molecular modules driving cancer progression. Case studies demonstrate the utility of the ExplORRNet for studying gynecological and breast cancers. Conclusion ExplORRNet is an intuitive and user-friendly web tool that provides a deeper understanding of dysregulated miRNAs and their functional implications in gynecological and breast cancers. We hope our ExplORRNet tool has potential utility among the clinical and basic researchers and will be beneficial to the entire cancer genomics community to encourage and facilitate mining the rapidly growing public databases to progress the field of precision oncology. The ExplORRNet is available at https://mirna.cs.ut.ee.
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Affiliation(s)
- Ankita Lawarde
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | - Adhiraj Nath
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India
| | - Darja Lavogina
- Competence Centre on Health Technologies, Tartu, Estonia
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Estonia
- Institute of Chemistry, University of Tartu, Estonia
| | - Jana Jaal
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Estonia
- Haematology and Oncology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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Liu X, Chen B, Chen J, Su Z, Sun S. Deubiquitinase ubiquitin-specific peptidase 10 maintains cysteine rich angiogenic inducer 61 expression via Yes1 associated transcriptional regulator to augment immune escape and metastasis of pancreatic adenocarcinoma. Cancer Sci 2022; 113:1868-1879. [PMID: 35271750 PMCID: PMC9128165 DOI: 10.1111/cas.15326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/24/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD) remains an extremely fatal malignancy with a high mortality rate worldwide. This study focuses on the roles of ubiquitin-specific peptidase 10 (USP10) and cysteine rich angiogenic inducer 61 (Cyr61) in macrophage polarization, immune escape, and metastasis of PAAD. USP10 showed a positive correlation with Yes1 associated transcriptional regulator (YAP1), which, according to the TCGA-PAAD database, is highly expressed in PAAD and indicates poor patient prognosis. USP10 knockdown increased ubiquitination and degradation of YAP1, which further decreased the programmed cell death ligand 1 (PD-L1) and Galectin-9 expression, suppressed immune escape, and reduced the proliferation and metastasis of PAAD cells in vitro and in vivo. Cyr61, a downstream factor of YAP1, was overexpressed in PAAD cells after USP10 silencing for rescue experiments. Overexpression of Cyr61 restored the PD-L1 and Galectin-9 expression in cells and triggered M2 polarization of macrophages, which enhanced the immune escape and maintained the proliferation and metastasis ability of PAAD cells. In conclusion, this work demonstrates that USP10 inhibits YAP1 ubiquitination and degradation to promote Cyr61 expression, which induces immune escape and promotes growth and metastasis of PAAD.
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Affiliation(s)
- Xun Liu
- Department of General SurgeryShengjing Hospital of China Medical UniversityShenyangChina
| | - Bobo Chen
- Department of General SurgeryShengjing Hospital of China Medical UniversityShenyangChina
| | - Jiahui Chen
- Department of General SurgeryShengjing Hospital of China Medical UniversityShenyangChina
| | - Zuoyuan Su
- Department of General SurgeryShengjing Hospital of China Medical UniversityShenyangChina
| | - Shaolong Sun
- Department of General SurgeryShengjing Hospital of China Medical UniversityShenyangChina
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Nachtigall PG, Bovolenta LA. Computational Detection of MicroRNA Targets. Methods Mol Biol 2022; 2257:187-209. [PMID: 34432280 DOI: 10.1007/978-1-0716-1170-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that are recognized as posttranscriptional regulators of gene expression. These molecules have been shown to play important roles in several cellular processes. MiRNAs act on their target by guiding the RISC complex and binding to the mRNA molecule. Thus, it is recognized that the function of a miRNA is determined by the function of its target (s). By using high-throughput methodologies, novel miRNAs are being identified, but their functions remain uncharted. Target validation is crucial to properly understand the specific role of a miRNA in a cellular pathway. However, molecular techniques for experimental validation of miRNA-target interaction are expensive, time-consuming, laborious, and can be not accurate in inferring true interactions. Thus, accurate miRNA target predictions are helpful to understand the functions of miRNAs. There are several algorithms proposed for target prediction and databases containing miRNA-target information. However, these available computational tools for prediction still generate a large number of false positives and fail to detect a considerable number of true targets, which indicates the necessity of highly confident approaches to identify bona fide miRNA-target interactions. This chapter focuses on tools and strategies used for miRNA target prediction, by providing practical insights and outlooks.
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Affiliation(s)
- Pedro Gabriel Nachtigall
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil.
| | - Luiz Augusto Bovolenta
- Department of Morphology, Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu, Brazil
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Rana NK, Srivastava N, Koch B. Identification of the key miRNA; hsa-miR-1269a targeting TP53, Caspase-9 and FOXO3a in breast cancer cells under hypoxia by integrated bioinformatics analysis. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Rogers CJ, Kyubwa EM, Lukaszewicz AI, Starbird MA, Nguyen M, Copeland BT, Yamada-Hanff J, Menon N. Observation of Unique Circulating miRNA Signatures in Non-Human Primates Exposed to Total-Body vs. Whole Thorax Lung Irradiation. Radiat Res 2021; 196:547-559. [PMID: 34525208 DOI: 10.1667/rade-21-00043.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/26/2021] [Indexed: 11/03/2022]
Abstract
A radiological/nuclear (RAD-NUC) incident, especially in an urban setting, results in diverse radiation-induced injuries due to heterogeneities in dose, the extent of partial-body shielding, human biodiversity and pre-existing health conditions. For example, acute radiation syndrome (ARS) can result in death within days to weeks of exposure to 0.7-10 Gy doses and is associated with destruction of the bone marrow, known as hematopoietic ARS (H-ARS). However, partial-body shielding that spares a portion of the bone marrow from exposure can significantly reduce the occurrence of H-ARS, but delayed effects of acute radiation exposure (DEARE) can still occur within months or years after exposure depending on the individual. In a mass casualty event, ideal triage must be able to pre-symptomatically identify individuals likely to develop radiation-induced injuries and provide an appropriate treatment plan. Today, while there are FDA approved treatments for hematopoietic ARS, there are no approved diagnosis for radiation injury and no approved treatments for the broad spectra of injuries associated with radiation. This has resulted in a major capability gap in the nations preparedness to a potentially catastrophic RAD-NUC event. Circulating microRNA (miRNA) are a promising class of biomarkers for this application because the molecules are accessible via a routine blood draw and are excreted by various tissues throughout the body. To test if miRNA can be used to predict distinct tissue-specific radiation-induced injuries, we compared the changes to the circulating miRNA profiles after total-body irradiation (TBI) and whole thorax lung irradiation (WTLI) in non-human primates at doses designed to induce ARS (day 2 postirradiation; 2-6.5 Gy) and DEARE (day 15 postirradiation; 9.8 or 10.7 Gy), respectively. In both models, miRNA sequences were identified that correlated with the onset of severe neutropenia (counts <500 µL-1; TBI) or survival (WTLI). This method identified panels of eleven miRNA for both model and assigned functional roles for the panel members using gene ontology enrichment analysis. A common signature of radiation-induced injury was observed in both models: apoptosis, DNA damage repair, p53 signaling, pro-inflammatory response, and growth factor/cytokine signaling pathways were predicted to be disrupted. In addition, injury-specific pathways were identified. In TBI, pathways associated with ubiquitination, specifically of histone H2A, were enriched, suggesting more impact to DNA damage repair mechanisms and apoptosis. In WTLI, pro-fibrotic pathways including transforming growth factor (TGF-β) and bone morphogenetic protein (BMP) signaling pathways were enriched, consistent with the onset of late lung injury. These results suggest that miRNA may indeed be able to predict the onset of distinct types of radiation-induced injuries.
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The ATO/miRNA-885-5p/MTPN axis induces reversal of drug-resistance in cholangiocarcinoma. Cell Oncol (Dordr) 2021; 44:907-916. [PMID: 34170484 DOI: 10.1007/s13402-021-00610-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 10/21/2022] Open
Abstract
PURPOSE Cholangiocarcinoma (CCA) is the second most malignant tumor of the hepatobiliary system. Due to its cumbersome early diagnosis and rapid progression, chemotherapy has become the main treatment option. Primary drug resistance is a major cause of the poor efficacy of chemotherapeutic drugs. Therefore, it is considered urgent to explore new drugs to overcome primary drug resistance of CCA. METHODS Western blot and qRT-PCR assays were used to assess the expression of myotrophin (MTPN) and microRNA-885-5p (miR-885-5p) in CCA tissues and cells. The viability of CCA cells treated with arsenic trioxide (ATO), 5-fluorouracil (5-Fu) and cisplatin (CDDP) was analyzed using a CCK-8 assay. A luciferase reporter assay was used to assess the interaction between miR-885-5p and MTPN. Kaplan-Meier analyses were used for survival assessments. RESULT We found that ATO can reduce the resistance of CCA cells to 5-Fu and CDDP and promote the killing effect of 5-Fu and CDDP. Low-dose ATO showed an anti-drug-resistance effect through up-regulation of the expression of miR-885-5p. Combined with sequencing results and database predictions, we found that MTPN may serve as a direct target of miR-885-5p. After MTPN knockdown, the sensitivity of CCA cells to 5-FU and CDDP was increased. Finally, we found that ATO can reverse chemotherapy resistance induced by overexpression of MTPN. CONCLUSION Our data indicate that the ATO/miR-885-5p/MTPN axis may serve as a target for improving the sensitivity of CCA cells to chemotherapy.
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Olgun G, Nabi A, Tastan O. NoRCE: non-coding RNA sets cis enrichment tool. BMC Bioinformatics 2021; 22:294. [PMID: 34078267 PMCID: PMC8170991 DOI: 10.1186/s12859-021-04112-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. RESULTS We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. CONCLUSIONS NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users' preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE .
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Affiliation(s)
- Gulden Olgun
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.,Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Afshan Nabi
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Oznur Tastan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey. .,Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
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Raga-Cervera J, Bolarin JM, Millan JM, Garcia-Medina JJ, Pedrola L, Abellán-Abenza J, Valero-Vello M, Sanz-González SM, O’Connor JE, Galarreta-Mira D, Bendala-Tufanisco E, Mayordomo-Febrer A, Pinazo-Durán MD, Zanón-Moreno V. miRNAs and Genes Involved in the Interplay between Ocular Hypertension and Primary Open-Angle Glaucoma. Oxidative Stress, Inflammation, and Apoptosis Networks. J Clin Med 2021; 10:jcm10112227. [PMID: 34063878 PMCID: PMC8196557 DOI: 10.3390/jcm10112227] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
Glaucoma has no cure and is a sight-threatening neurodegenerative disease affecting more than 100 million people worldwide, with primary open angle glaucoma (POAG) being the most globally prevalent glaucoma clinical type. Regulation of gene expression and gene networks, and its multifactorial pathways involved in glaucoma disease are landmarks for ophthalmic research. MicroRNAs (miRNAs/miRs) are small endogenous non-coding, single-stranded RNA molecules (18–22 nucleotides) that regulate gene expression. An analytical, observational, case-control study was performed in 42 patients of both sexes, aged 50 to 80 years, which were classified according to: (1) suffering from ocular hypertension (OHT) but no glaucomatous neurodegeneration (ND) such as the OHT group, or (2) have been diagnosed of POAG such as the POAG group. Participants were interviewed for obtaining sociodemographic and personal/familial records, clinically examined, and their tear samples were collected and frozen at 80 °C until processing for molecular-genetic assays. Tear RNA extraction, libraries construction, and next generation sequencing were performed. Here, we demonstrated, for the first time, the differential expression profiling of eight miRNAs when comparing tears from the OHT versus the POAG groups: the miR-26b-5p, miR-152-3p, miR-30e-5p, miR-125b-2-5p, miR-224-5p, miR-151a-3p, miR-1307-3p, and the miR-27a-3p. Gene information was set up from the DIANA-TarBase v7, DIANA-microT-CDS, and TargetScan v7.1 databases. To build a network of metabolic pathways, only genes appearing in at least four of the following databases: DisGeNet, GeneDistiller, MalaCards, OMIM PCAN, UniProt, and GO were considered. We propose miRNAs and their target genes/signaling pathways as candidates for a better understanding of the molecular-genetic bases of glaucoma and, in this way, to gain knowledge to achieve optimal diagnosis strategies for properly identifying HTO at higher risk of glaucoma ND. Further research is needed to validate these miRNAs to discern the potential role as biomarkers involved in oxidative stress, immune response, and apoptosis for the diagnosis and/or prognosis of OHT and the prevention of glaucoma ND.
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Affiliation(s)
| | - Jose M. Bolarin
- Technological Centre of Information and Communication Technologies (CENTIC), 30100 Murcia, Spain; (J.M.B.); (J.A.-A.)
| | - Jose M. Millan
- Sequencing Service at the University and Polytechnic Hospital La Fe, 46026 Valencia, Spain; (J.M.M.); (L.P.)
| | - Jose J. Garcia-Medina
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (J.J.G.-M.); (M.V.-V.); (M.D.P.-D.); (V.Z.-M.)
- Department of Ophthalmology, General University Hospital “Morales Meseguer”, 30007 Murcia, Spain
- Department of Ophthalmology and Optometry, University of Murcia, 30120 Murcia, Spain
- Spanish Net of Ophthalmic Research OFTARED RD16/0008/0022, Institute of Health Carlos III, 28029 Madrid, Spain; (E.B.-T.); (A.M.-F.)
| | - Laia Pedrola
- Sequencing Service at the University and Polytechnic Hospital La Fe, 46026 Valencia, Spain; (J.M.M.); (L.P.)
| | - Javier Abellán-Abenza
- Technological Centre of Information and Communication Technologies (CENTIC), 30100 Murcia, Spain; (J.M.B.); (J.A.-A.)
| | - Mar Valero-Vello
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (J.J.G.-M.); (M.V.-V.); (M.D.P.-D.); (V.Z.-M.)
| | - Silvia M. Sanz-González
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (J.J.G.-M.); (M.V.-V.); (M.D.P.-D.); (V.Z.-M.)
- Spanish Net of Ophthalmic Research OFTARED RD16/0008/0022, Institute of Health Carlos III, 28029 Madrid, Spain; (E.B.-T.); (A.M.-F.)
- Cellular and Molecular Ophthalmobiology Group, Department of Surgery, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
- Correspondence:
| | - José E. O’Connor
- Laboratory of Cytomics, Joint Research Unit Principe Felipe Research Center and University of Valencia, 46010 Valencia, Spain;
| | | | - Elena Bendala-Tufanisco
- Spanish Net of Ophthalmic Research OFTARED RD16/0008/0022, Institute of Health Carlos III, 28029 Madrid, Spain; (E.B.-T.); (A.M.-F.)
- Mixed Research Unit for Visual Health and Veterinary Ophthalmology CEU/FISABIO, 46020 Valencia, Spain
- Physiology Department, Faculty of Health Sciences, CEU University, Alfara del Patriarca, 46115 Valencia, Spain
| | - Aloma Mayordomo-Febrer
- Spanish Net of Ophthalmic Research OFTARED RD16/0008/0022, Institute of Health Carlos III, 28029 Madrid, Spain; (E.B.-T.); (A.M.-F.)
- Mixed Research Unit for Visual Health and Veterinary Ophthalmology CEU/FISABIO, 46020 Valencia, Spain
- Animal Medicine and Surgery Department, Veterinary Medicine Faculty, CEU University, Alfara del Patriarca, 46115 Valencia, Spain
| | - Maria D. Pinazo-Durán
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (J.J.G.-M.); (M.V.-V.); (M.D.P.-D.); (V.Z.-M.)
- Spanish Net of Ophthalmic Research OFTARED RD16/0008/0022, Institute of Health Carlos III, 28029 Madrid, Spain; (E.B.-T.); (A.M.-F.)
- Cellular and Molecular Ophthalmobiology Group, Department of Surgery, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
| | - Vicente Zanón-Moreno
- Ophthalmic Research Unit “Santiago Grisolía”/FISABIO, 46017 Valencia, Spain; (J.J.G.-M.); (M.V.-V.); (M.D.P.-D.); (V.Z.-M.)
- Spanish Net of Ophthalmic Research OFTARED RD16/0008/0022, Institute of Health Carlos III, 28029 Madrid, Spain; (E.B.-T.); (A.M.-F.)
- Faculty of Health Sciences, Valencian International University, 46002 Valencia, Spain
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Chen S, Gao C, Yu T, Qu Y, Xiao GG, Huang Z. Bioinformatics Analysis of a Prognostic miRNA Signature and Potential Key Genes in Pancreatic Cancer. Front Oncol 2021; 11:641289. [PMID: 34094925 PMCID: PMC8174116 DOI: 10.3389/fonc.2021.641289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/31/2021] [Indexed: 12/11/2022] Open
Abstract
Background In this study, miRNAs and their critical target genes related to the prognosis of pancreatic cancer were screened based on bioinformatics analysis to provide targets for the prognosis and treatment of pancreatic cancer. Methods R software was used to screen differentially expressed miRNAs (DEMs) and genes (DEGs) downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, respectively. A miRNA Cox proportional hazards regression model was constructed based on the miRNAs, and a miRNA prognostic model was generated. The target genes of the prognostic miRNAs were predicted using TargetScan and miRDB and then intersected with the DEGs to obtain common genes. The functions of the common genes were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses. A protein-protein interaction (PPI) network of the common genes was constructed with the STRING database and visualized with Cytoscape software. Key genes were also screened with the MCODE and cytoHubba plug-ins of Cytoscape. Finally, a prognostic model formed by the key gene was also established to help evaluate the reliability of this screening process. Results A prognostic model containing four downregulated miRNAs (hsa-mir-424, hsa-mir-3613, hsa-mir-4772 and hsa-mir-126) related to the prognosis of pancreatic cancer was constructed. A total of 118 common genes were enriched in two KEGG pathways and 33 GO functional annotations, including extracellular matrix (ECM)-receptor interaction and cell adhesion. Nine key genes related to pancreatic cancer were also obtained: MMP14, ITGA2, THBS2, COL1A1, COL3A1, COL11A1, COL6A3, COL12A1 and COL5A2. The prognostic model formed by nine key genes also possessed good prognostic ability. Conclusions The prognostic model consisting of four miRNAs can reliably predict the prognosis of patients with pancreatic cancer. In addition, the screened nine key genes, which can also form a reliable prognostic model, are significantly related to the occurrence and development of pancreatic cancer. Among them, one novel miRNA (hsa-mir-4772) and two novel genes (COL12A1 and COL5A2) associated with pancreatic cancer have great potential to be used as prognostic factors and therapeutic targets for this tumor.
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Affiliation(s)
- Shuoling Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Chang Gao
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Tianyang Yu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yueyang Qu
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Gary Guishan Xiao
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
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Zamil BM, Ali-Labib R, Youssef WY, Khairy E. Evaluation of miR-106a and ADARB1 in autistic children. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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