1
|
Pal R, Choudhury T, Ghosh M, Vernakar M, Nath P, Nasare VD. A signature of circulating miRNAs predicts the prognosis and therapeutic outcome of taxane/platinum regimen in advanced ovarian carcinoma patients. Clin Transl Oncol 2024; 26:1716-1724. [PMID: 38472557 DOI: 10.1007/s12094-024-03394-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/19/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE Ovarian carcinoma (OC) is ranked as the eighth most lethal gynecological cancer due to late diagnosis and high recurrence. Existing biomarkers are lacking to predict the recurrence and stratify patients who are likely to benefit from chemotherapy. MicroRNAs (miRNAs/miRs) are persistently present in humans and are capable of predicting treatment outcomes. Thus, the purpose of the study was to assess the potential of circulatory miRNAs to predict the efficacy of OC. METHODS Newly diagnosed n = 208 OC patients were administrated neoadjuvant/adjuvant chemotherapy (taxane + platinum) after surgery. Their demographic, gynecologic, clinical parameters, response, and survival were recorded. MiR-27a, miR-182, miR-199a, miR-214, and miR-591 were taken and the expression were analyzed using real-time PCR at different treatment intervals. Further, its prognostic value (Kaplan-Meier, and Cox regression analysis) and diagnostic importance (receiver operating characteristic curve) were validated. RESULT The mean age of patients with poorly differentiated (45.2%) serous OC was 48.69 ± 10.38. The majority experienced menarche at ≥ 12 (62.2%) with poor menstrual hygiene (81.8%) and were post-menopausal (69.4%), some were associated with high risk of survival (HR = > 1). MiRNA signature showed three over-expression and two under-expression (miR-27a, miR-182, and miR-214; miR-199a and miR-591) in advanced OC compared to the control (P= < 0.05). Also, a significant difference was detected at each time interval of treatment with the response (P = ≤ 0.001) associated with resistance and overall survival (P = ≤ 0.001) with risk (HR = > 1). ROC analysis showed enhanced the diagnostics accuracy (< 0.001). CONCLUSION Our findings indicate that circulating miRNAs might be a potential minimally invasive diagnostic marker for treatment outcome and recurrence in ovarian carcinoma.
Collapse
Affiliation(s)
- Ranita Pal
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, India
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Rd, Kolkata, 700019, India
| | - Trisha Choudhury
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, India
| | - Madhurima Ghosh
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, India
| | - Manisha Vernakar
- Department of Gynaecological Oncology, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, India
| | - Partha Nath
- Department of Medical Oncology, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, India
| | - Vilas Deorao Nasare
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, India.
| |
Collapse
|
2
|
Bhadra M, Sachan M, Nara S. Current strategies for early epithelial ovarian cancer detection using miRNA as a potential tool. Front Mol Biosci 2024; 11:1361601. [PMID: 38690293 PMCID: PMC11058280 DOI: 10.3389/fmolb.2024.1361601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Ovarian cancer is one of the most aggressive and significant malignant tumor forms in the female reproductive system. It is the leading cause of death among gynecological cancers owing to its metastasis. Since its preliminary disease symptoms are lacking, it is imperative to develop early diagnostic biomarkers to aid in treatment optimization and personalization. In this vein, microRNAs, which are short sequence non-coding molecules, displayed great potential as highly specific and sensitive biomarker. miRNAs have been extensively advocated and proven to serve an instrumental part in the clinical management of cancer, especially ovarian cancer, by promoting the cancer cell progression, invasion, delayed apoptosis, epithelial-mesenchymal transition, metastasis of cancer cells, chemosensitivity and resistance and disease therapy. Here, we cover our present comprehension of the most up-to-date microRNA-based approaches to detect ovarian cancer, as well as current diagnostic and treatment strategies, the role of microRNAs as oncogenes or tumor suppressor genes, and their significance in ovarian cancer progression, prognosis, and therapy.
Collapse
|
3
|
Yu Y, Liu Y. LncRNA LINC01339 Hinders the Development of Wilms' Tumor via MiR-135b-3p/ADH1C Axis. Horm Metab Res 2024; 56:244-254. [PMID: 37890508 DOI: 10.1055/a-2184-8945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Wilms' tumor is a malignant renal cancer that arises within the pediatric urinary system. This study intended to investigate how a novel long non-coding RNA LINC01339 functions in the pathogenesis of Wilms' tumor. An elevated miR-135b-3p expression as well as reduced levels of LINC01339 and ADH1C were observed in Wilms' tumor. LINC01339 mediated ADH1C expression by directly binding to miR-135b-3p. The enforced LINC01339 or ADH1C markedly hindered cell growth and migration in Wilms' tumor. The LINC01339 overexpression also repressed the growth of Wilms' tumors in vivo, whereas miR-135b-3p overexpression exerted the opposite effects on Wilms' tumor cells in vitro. Additionally, upregulating miR-135b-3p reversed LINC01339's effects on the cellular processes of Wilms' tumor cells, whereas ADH1C overexpression offset the cancer-promoting influence of miR-135b-3p upregulation on Wilms' tumor progression. Therefore, LINC01339 prevents Wilms' tumor progression by modulating the miR-135b-3p/ADH1C axis. Our findings substantiate that the LINC01339/miR-135 b-3p/ADH1C regulatory axis has potential to be a target for the treatment of Wilms' tumor.
Collapse
Affiliation(s)
- Yang Yu
- Department of Nephrology, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Yanfei Liu
- Department of Oncology, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| |
Collapse
|
4
|
Zheng Y, Sukocheva O, Tse E, Neganova M, Aleksandrova Y, Zhao R, Chubarev V, Fan R, Liu J. MicroRNA-183 cluster: a promising biomarker and therapeutic target in gastrointestinal malignancies. Am J Cancer Res 2023; 13:6147-6175. [PMID: 38187051 PMCID: PMC10767355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Small non-coding RNAs (microRNA, miR), powerful epigenetic regulators, were found involved in the regulation of most biological functions via post-translational inhibition of protein expression. Increased expression of pro-oncogenic miRs (known as miR cancer biomarkers) and inhibition of pro-apoptotic miR expression have been demonstrated in different tumors. The recently identified miR-183 was found implicated in gastrointestinal tumor metabolism regulation. Elevated miR-183 expression and cancer-promoting effects were reported in esophageal and colorectal cancers, which was partially contradicted by controversial data observed in gastric cancers. Anti-cancer effect of miR-183 in gastric cancer cells was associated with the Bim-1 and Ezrin genes regulation. Many studies indicated that miR-183 can inhibit tumor suppressor genes in most cell lines, promoting tumor cell proliferation and migration. Increased miR-183 level results in the downregulation of FOXO1, PDCD4, and other tumor suppressor genes in gastrointestinal tumor cells. MiR-183 also influences the signaling of PI3K/AKT/mTOR, Wnt/β-catenin, and Bcl-2/p53 signaling pathways. Mir-183 inhibits apoptosis and autophagy, and promotes epithelial-to-mesenchymal transition, cancer cell proliferation, and migration. Accordingly, gastrointestinal cancer occurrence, development of chemoradiotherapy resistance, recurrence/metastasis, and prognosis were associated with miR-183 expression. The current study assessed reported miR-183 functions and signaling, providing new insights for the diagnosis and treatment of gastrointestinal malignancies.
Collapse
Affiliation(s)
- Yufei Zheng
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Olga Sukocheva
- Department of Hepatology, Royal Adelaide HospitalAdelaide, SA 5000, Australia
| | - Edmund Tse
- Department of Hepatology, Royal Adelaide HospitalAdelaide, SA 5000, Australia
| | - Margarita Neganova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of SciencesSevernij Pr. 1, Chernogolovka 142432, Russia
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of SciencesAkad. Arbuzov St. 8, Kazan 420088, Russia
| | - Yulia Aleksandrova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of SciencesSevernij Pr. 1, Chernogolovka 142432, Russia
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of SciencesAkad. Arbuzov St. 8, Kazan 420088, Russia
| | - Ruiwen Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Vladimir Chubarev
- Sechenov First Moscow State Medical University (Sechenov University)8-2 Trubetskaya St., Moscow 119991, Russia
| | - Ruitai Fan
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Junqi Liu
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| |
Collapse
|
5
|
Miśkiewicz J, Mielczarek-Palacz A, Gola JM. MicroRNAs as Potential Biomarkers in Gynecological Cancers. Biomedicines 2023; 11:1704. [PMID: 37371799 DOI: 10.3390/biomedicines11061704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/25/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
MicroRNAs are non-coding transcripts that, thanks to the ability to regulate the mRNA of target genes, can affect the expression of genes encoding tumor suppressors and oncogenes. They can control many important cellular processes, including apoptosis, differentiation, growth, division, and metabolism. Therefore, miRNAs play an important role in the development of many cancers, including gynecological cancers. Ovarian cancer, endometrial cancer, cervical cancer, and vulvar cancer are the most common cancers in women and are a frequent cause of death. The heterogeneity of the pathogenesis of these gynecological diseases makes the diagnostic process a significant obstacle for modern medicine. To date, many studies have been carried out, in which particular attention has been paid to the molecular pathomechanism of these diseases, with particular emphasis on miRNAs. To date, the changed profile of many miRNAs, which influenced the promotion of proliferation, migration, invasion processes and the simultaneous inhibition of programmed cell death, has been proven many times. Detailed understanding of the molecular effects of miRNAs in the above-mentioned gynecological cancers will enable the development of potential predictive and prognostic biomarkers, as well as the optimization of the diagnostic process.
Collapse
Affiliation(s)
- Joanna Miśkiewicz
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Aleksandra Mielczarek-Palacz
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Joanna Magdalena Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| |
Collapse
|
6
|
Salmerón-Bárcenas EG, Mendoza-Catalan MA, Ramírez-Bautista ÁU, Lozano-Santos RA, Torres-Rojas FI, Ávila-López PA, Zacapala-Gómez AE. Identification of Mir-182-3p/FLI-1 Axis as a Key Signaling in Immune Response in Cervical Cancer: A Comprehensive Bioinformatic Analysis. Int J Mol Sci 2023; 24:ijms24076032. [PMID: 37047006 PMCID: PMC10094573 DOI: 10.3390/ijms24076032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
miRNAs modulate gene expression and play critical functions as oncomiRs or tumor suppressors. The miR-182-3p is important in chemoresistance and cancer progression in breast, lung, osteosarcoma, and ovarian cancer. However, the role of miR-182-3p in cervical cancer (CC) has not been elucidated. AIM To analyze the role of miR-182-3p in CC through a comprehensive bioinformatic analysis. METHODS Gene Expression Omnibus (GEO) databases were used for the expression analysis. The mRNA targets of miR-182-3p were identified using miRDB, TargetScanHuman, and miRPathDB. The prediction of island CpG was performed using the MethPrimer program. The transcription factor binding sites in the FLI-1 promoter were identified using ConSite+, Alibaba2, and ALGGEN-PROMO. The protein-protein interaction (PPI) analysis was performed in STRING 11.5. RESULTS miR-182-3p was significantly overexpressed in CC patients and has potential as a diagnostic. We identified 330 targets of miR-182-3p including FLI-1, which downregulates its expression in CC. Additionally, the aberrant methylation of the FLI-1 promoter and Ap2a transcription factor could be involved in downregulating FLI1 expression. Finally, we found that FLI-1 is a possible key gene in the immune response in CC. CONCLUSIONS The miR-182-3p/FLI-1 axis plays a critical role in immune response in CC.
Collapse
Affiliation(s)
- Eric Genaro Salmerón-Bárcenas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, CINVESTAV, Ciudad de México 07360, Mexico
| | - Miguel Angel Mendoza-Catalan
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Ángela Uray Ramírez-Bautista
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Rafael Acxel Lozano-Santos
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Francisco Israel Torres-Rojas
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| | - Pedro Antonio Ávila-López
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ana Elvira Zacapala-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Mexico
| |
Collapse
|
7
|
Li H, Xia M, Zheng S, Lin Y, Yu T, Xie Y, Shen Y, Liu X, Qian X, Yin Z. Cerebrospinal fluid exosomal microRNAs as biomarkers for diagnosing or monitoring the progression of non-small cell lung cancer with leptomeningeal metastases. Biotechnol Genet Eng Rev 2023:1-22. [PMID: 36852928 DOI: 10.1080/02648725.2023.2183613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
Non-small-cell lung cancer (NSCLC) has a terrible consequence called leptomeningeal metastases (LM). It is crucial to look for novel biomarkers because none of the known biomarkers could effectively reflect the oncogenesis, progression and therapeutic responses of LM. Exosomal miRNAs from plasma have a critical function in lung cancer, according to growing data. However, unique biomarkers of cerebrospinal fluid (CSF) are more representative for patients with LM, which have not been reported. Here, we explore the possibility of using CSF-derived exosomal microRNAs as potential biomarkers for NSCLC-LM. Nine NSCLC-LM patients who received regular intrathecal chemotherapy with permetexed were divided into a partial response (PR) group and a progressive disease (PD) group. CSF samples were taken from all patients before and after intrathecal treatment and five non-cancerous controls. Using the size exclusion chromatography (SEC) method, the exosome microRNAs were isolated and profiled. Between LM patients and controls, 56 differentially expressed genes (DEGs) were found, of which three highly elevated diagnostic biomarkers (hsa-miR-183-5p, hsa-miR-96-5p and hsa-miR-182-5p) were ruled out. The two most significant DEGs between the untreated PR group and the PD group were determined to be upregulated hsa-miR-509-3p and downregulated hsa-miR-449a, and they may serve as potential indicators of intrathecal anti-pemetrexed treatment. Hsa-miR-1-3p increased gradually with the intrathecal chemotherapy in the PR group, which might offer a new approach to screen optimal patients and estimate the efficacy. This study revealed specific CSF exosomal miRNAs profile and dynamic changes of patients with NSCLC-LM for the first time and identified several potential exosomal miRNA biomarkers in diagnosis, drug resistance and prognosis.
Collapse
Affiliation(s)
- Huiying Li
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mao Xia
- Department of Laboratory Medicine, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shengnan Zheng
- Department of Pharmacy, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yongjuan Lin
- Department of Geriatric Oncology, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Tingting Yu
- Department of Geriatric Oncology, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yu Xie
- Department of Geriatric Oncology, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yanting Shen
- Department of Geriatric Oncology, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiangyu Liu
- Department of Neurosurgery, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaoping Qian
- The Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenyu Yin
- Department of Geriatric Oncology, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| |
Collapse
|
8
|
Beg A, Parveen R, Fouad H, Yahia ME, Hassanein AS. Identification of Driver Genes and miRNAs in Ovarian Cancer through an Integrated In-Silico Approach. BIOLOGY 2023; 12:biology12020192. [PMID: 36829472 PMCID: PMC9952540 DOI: 10.3390/biology12020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023]
Abstract
Ovarian cancer is the eighth-most common cancer in women and has the highest rate of death among all gynecological malignancies in the Western world. Increasing evidence shows that miRNAs are connected to the progression of ovarian cancer. In the current study, we focus on the identification of miRNA and its associated genes that are responsible for the early prognosis of patients with ovarian cancer. The microarray dataset GSE119055 used in this study was retrieved via the publicly available GEO database by NCBI for the analysis of DEGs. The miRNA GSE119055 dataset includes six ovarian carcinoma samples along with three healthy/primary samples. In our study, DEM analysis of ovarian carcinoma and healthy subjects was performed using R Software to transform and normalize all transcriptomic data along with packages from Bioconductor. Results: We identified miRNA and its associated hub genes from the samples of ovarian cancer. We discovered the top five upregulated miRNAs (hsa-miR-130b-3p, hsa-miR-18a-5p, hsa-miR-182-5p, hsa-miR-187-3p, and hsa-miR-378a-3p) and the top five downregulated miRNAs (hsa-miR-501-3p, hsa-miR-4324, hsa-miR-500a-3p, hsa-miR-1271-5p, and hsa-miR-660-5p) from the network and their associated genes, which include seven common genes (SCN2A, BCL2, MAF, ZNF532, CADM1, ELAVL2, and ESRRG) that were considered hub genes for the downregulated network. Similarly, for upregulated miRNAs we found two hub genes (PRKACB and TAOK1).
Collapse
Affiliation(s)
- Anam Beg
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
- Correspondence: or (A.B.); (R.P.); Tel.: +91-965-049-3477 (R.P.)
| | - Rafat Parveen
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
- Correspondence: or (A.B.); (R.P.); Tel.: +91-965-049-3477 (R.P.)
| | - Hassan Fouad
- Applied Medical Science Department, CC, King Saud University, Riyadh 11433, Saudi Arabia
| | - M. E. Yahia
- Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnička Cesta 15, Ilidža, 71210 Sarajevo, Bosnia and Herzegovina
| | - Azza S. Hassanein
- Biomedical Engineering Department, Faculty of Engineering, Helwan University, Cairo 11792, Egypt
| |
Collapse
|
9
|
Hua X, Li Y, Pentaparthi SR, McGrail DJ, Zou R, Guo L, Shrawat A, Cirillo KM, Li Q, Bhat A, Xu M, Qi D, Singh A, McGrath F, Andrews S, Aung KL, Das J, Zhou Y, Lodi A, Mills GB, Eckhardt SG, Mendillo ML, Tiziani S, Wu E, Huang JH, Sahni N, Yi SS. Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer. Cancer Res 2023; 83:59-73. [PMID: 36265133 PMCID: PMC9811166 DOI: 10.1158/0008-5472.can-20-0371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 12/15/2020] [Accepted: 10/14/2022] [Indexed: 02/05/2023]
Abstract
Somatic mutations are a major source of cancer development, and many driver mutations have been identified in protein coding regions. However, the function of mutations located in miRNA and their target binding sites throughout the human genome remains largely unknown. Here, we built detailed cancer-specific miRNA regulatory networks across 30 cancer types to systematically analyze the effect of mutations in miRNAs and their target sites in 3' untranslated region (3' UTR), coding sequence (CDS), and 5' UTR regions. A total of 3,518,261 mutations from 9,819 samples were mapped to miRNA-gene interactions (mGI). Mutations in miRNAs showed a mutually exclusive pattern with mutations in their target genes in almost all cancer types. A linear regression method identified 148 candidate driver mutations that can significantly perturb miRNA regulatory networks. Driver mutations in 3'UTRs played their roles by altering RNA binding energy and the expression of target genes. Finally, mutated driver gene targets in 3' UTRs were significantly downregulated in cancer and functioned as tumor suppressors during cancer progression, suggesting potential miRNA candidates with significant clinical implications. A user-friendly, open-access web portal (mGI-map) was developed to facilitate further use of this data resource. Together, these results will facilitate novel noncoding biomarker identification and therapeutic drug design targeting the miRNA regulatory networks. SIGNIFICANCE A detailed miRNA-gene interaction map reveals extensive miRNA-mediated gene regulatory networks with mutation-induced perturbations across multiple cancers, serving as a resource for noncoding biomarker discovery and drug development.
Collapse
Affiliation(s)
- Xu Hua
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Sairahul R. Pentaparthi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Daniel J. McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Raymond Zou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Guo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aditya Shrawat
- College of Natural Sciences, The University of Texas at Austin, Austin, Texas
| | - Kara M. Cirillo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Akshay Bhat
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Min Xu
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, Texas
| | - Dan Qi
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, Texas
| | - Ashok Singh
- Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Francis McGrath
- Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Steven Andrews
- Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Kyaw Lwin Aung
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Jishnu Das
- Center for Systems Immunology, Department of Immunology, and Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yunyun Zhou
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alessia Lodi
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas
- Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Gordon B. Mills
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Precision Oncology, Knight Cancer Institute, Portland, Oregon
| | - S. Gail Eckhardt
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, Texas
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Stefano Tiziani
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas
- Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, Texas
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, Texas
| | - Erxi Wu
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, Texas
- Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, Texas
- Department of Pharmaceutical Sciences, Texas A & M University Health Science Center, College of Pharmacy, College Station, Texas
| | - Jason H. Huang
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, Texas
- Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, Texas
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, Texas
| | - S. Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, Texas
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, Texas
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas
| |
Collapse
|
10
|
Davies M, Davey MG, Miller N. The Potential of MicroRNAs as Clinical Biomarkers to Aid Ovarian Cancer Diagnosis and Treatment. Genes (Basel) 2022; 13:2054. [PMID: 36360295 PMCID: PMC9690044 DOI: 10.3390/genes13112054] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/24/2022] [Accepted: 11/04/2022] [Indexed: 07/30/2023] Open
Abstract
Ovarian cancer is a commonly diagnosed malignancy in women. When diagnosed at an early stage, survival outcomes are favourable for the vast majority, with up to 90% of ovarian cancer patients being free of disease at 5 years follow-up. Unfortunately, ovarian cancer is typically diagnosed at an advanced stage due to the majority of patients remaining asymptomatic until the cancer has metastasised, resulting in poor outcomes for the majority. While the molecular era has facilitated the subclassification of the disease into distinct clinical subtypes, ovarian cancer remains managed and treated as a single disease entity. MicroRNAs (miRNAs) are small (19-25 nucleotides), endogenous molecules which are integral to regulating gene expression. Aberrant miRNA expression profiles have been described in several cancers, and have been implicated to be useful biomarkers which may aid cancer diagnostics and treatment. Several preliminary studies have identified candidate tumour suppressor and oncogenic miRNAs which may be involved in the development and progression of ovarian cancer, highlighting their candidacy as oncological biomarkers; understanding the mechanisms by which these miRNAs regulate the key processes involved in oncogenesis can improve our overall understanding of cancer development and identify novel biomarkers and therapeutic targets. This review highlights the potential role of miRNAs which may be utilised to aid diagnosis, estimate prognosis and enhance therapeutic strategies in the management of primary ovarian cancer.
Collapse
|
11
|
Wang X, Zhao Y, Strohmer DF, Yang W, Xia Z, Yu C. The prognostic value of MicroRNAs associated with fatty acid metabolism in head and neck squamous cell carcinoma. Front Genet 2022; 13:983672. [PMID: 36110217 PMCID: PMC9468645 DOI: 10.3389/fgene.2022.983672] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most frequent cancer in humans globally. In addition to smoking and drinking, genetic and epigenetic changes also play a big role in how HNSCC starts and grows. MicroRNAs are short, non-coding RNAs that control cell differentiation and apoptosis by interfering with gene expression. In addition, microRNAs in HNSCC have been shown to affect the clinical behaviors of HNSCC in amazing ways. Moreover, metabolic reprogramming is a key part of cancer and is needed for cancer to turn into a tumor and grow. But it is still not clear what effect microRNAs related to fatty acid metabolism have on the prognosis of HNSCC patients. We downloaded the data of HNSCC patients from the TCGA database and obtained the genes associated with fatty acid metabolism according to the GSEA database. Then, the microRNAs associated with fatty acid metabolism genes were matched. Finally, fatty acid metabolism gene-associated microRNAs for calculating risk scores and then building multifactorial Cox regression models in patients with HNSCC. Heatmap analysis showed that microRNAs involved in fatty acid metabolism were significantly different in HNSCC patients than in healthy controls. A total of 27 microRNAs associated with fatty acid metabolism were screened by univariate Cox analysis (p < 0.05). Using lasso regression, 18 microRNAs substantially linked with the prognosis of HNSCC patients were identified and included in risk scores. The ROC curves demonstrate that risk scores derived from microRNAs involved in fatty acid metabolism can accurately predict the prognosis of HNSCC patients at 1, 3, and 5 years. Moreover, we discovered that 11 microRNAs included in the risk score properly distinguished the prognosis of HNSCC patients. This paper indicated that microRNAs involved with fatty acid metabolism are strongly linked to the prognosis of HNSCC patients. It also indicated that reprogramming of fatty acid metabolism in tumor tissues may play an important role in HNSCC cancer.
Collapse
Affiliation(s)
- Xiaojing Wang
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yue Zhao
- Department of Breast Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Dorothee Franziska Strohmer
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Wenjin Yang
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
- *Correspondence: Zhijia Xia, ; Cong Yu,
| | - Cong Yu
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
- *Correspondence: Zhijia Xia, ; Cong Yu,
| |
Collapse
|
12
|
Noncoding RNA actions through IGFs and IGF binding proteins in cancer. Oncogene 2022; 41:3385-3393. [PMID: 35597813 PMCID: PMC9203274 DOI: 10.1038/s41388-022-02353-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/17/2022]
Abstract
The insulin-like growth factors (IGFs) and their regulatory proteins—IGF receptors and binding proteins—are strongly implicated in cancer progression and modulate cell survival and proliferation, migration, angiogenesis and metastasis. By regulating the bioavailability of the type-1 IGF receptor (IGF1R) ligands, IGF-1 and IGF-2, the IGF binding proteins (IGFBP-1 to -6) play essential roles in cancer progression. IGFBPs also influence cell communications through pathways that are independent of IGF1R activation. Noncoding RNAs (ncRNAs), which encompass a variety of RNA types including microRNAs (miRNAs) and long-noncoding RNAs (lncRNAs), have roles in multiple oncogenic pathways, but their many points of intersection with IGF axis functions remain to be fully explored. This review examines the functional interactions of miRNAs and lncRNAs with IGFs and their binding proteins in cancer, and reveals how the IGF axis may mediate ncRNA actions that promote or suppress cancer. A better understanding of the links between ncRNA and IGF pathways may suggest new avenues for prognosis and therapeutic intervention in cancer. Further, by exploring examples of intersecting ncRNA-IGF pathways in non-cancer conditions, it is proposed that new opportunities for future discovery in cancer control may be generated.
Collapse
|
13
|
Ge L, Sun Y, Shi Y, Liu G, Teng F, Geng Z, Chen X, Xu H, Xu J, Jia X. Plasma circRNA microarray profiling identifies novel circRNA biomarkers for the diagnosis of ovarian cancer. J Ovarian Res 2022; 15:58. [PMID: 35550610 PMCID: PMC9097182 DOI: 10.1186/s13048-022-00988-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/23/2022] [Indexed: 12/14/2022] Open
Abstract
Background Circular RNA (circRNA), a class of RNA with a covalent closed circular structure that widely existed in serum and plasma, has been considered an ideal liquid biopsy marker in many diseases. In this study, we employed microarray and qRT-PCR to evaluate the potential circulating circRNAs with diagnostic efficacy in ovarian cancer. Methods We used microarray to explore the circRNA expression profile in ovarian cancer patients’ plasma and quantitative real-time (qRT)-PCR approach to assessing the candidate circRNA’s expression. Then the receiver operating characteristic (ROC) curve was employed to analyze the diagnostic values of candidate circRNAs. The diagnostic model circCOMBO was a combination of hsa_circ_0003972 and hsa_circ_0007288 built by binary logistic regression. Then bioinformatic tools were used to predict their potential mechanisms. Results Hsa_circ_0003972 and hsa_circ_0007288 were downregulated in ovarian cancer patients’ plasma, tissues, and cell lines, comparing with the controls. Hsa_circ_0003972 and hsa_circ_0007288 exhibited diagnostic values with the Area Under Curve (AUC) of 0.724 and 0.790, respectively. circCOMBO showed a better diagnostic utility (AUC: 0.781), while the combination of circCOMBO and carbohydrate antigen 125 (CA125) showed the highest diagnostic value (AUC: 0.923). Furthermore, the higher expression level of hsa_circ_0007288 in both plasma and ovarian cancer tissues was associated with lower lymph node metastasis potential in ovarian cancer. Conclusions Our results revealed that hsa_circ_0003972 and hsa_circ_0007288 may serve as novel circulating biomarkers for ovarian cancer diagnosis. Supplementary information The online version contains supplementary material available at 10.1186/s13048-022-00988-0.
Collapse
Affiliation(s)
- Lili Ge
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Yu Sun
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Yaqian Shi
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Guangquan Liu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Fang Teng
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Zhe Geng
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Xiyi Chen
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China
| | - Hanzi Xu
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, China.
| | - Juan Xu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China.
| | - Xuemei Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), 123 Mochou Rd, 210004, Nanjing, China.
| |
Collapse
|
14
|
Zhou M, Wu T, Yuan Y, Dong SJ, Zhang ZM, Wang Y, Wang J. A risk score system based on a six-microRNA signature predicts the overall survival of patients with ovarian cancer. J Ovarian Res 2022; 15:54. [PMID: 35513874 PMCID: PMC9074233 DOI: 10.1186/s13048-022-00980-8] [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: 04/07/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ovarian cancer (OVC) is a devastating disease worldwide; therefore the identification of prognostic biomarkers is urgently needed. We aimed to determine a robust microRNA signature-based risk score system that could predict the overall survival (OS) of patients with OVC. METHODS We extracted the microRNA expression profiles and corresponding clinical data of 467 OVC patients from The Cancer Genome Atlas (TCGA) database and further divided this data into training, validation and complete cohorts. The key prognostic microRNAs for OVC were identified and evaluated by robust likelihood-based survival analysis (RLSA) and multivariable Cox regression. Time-dependent receiver operating characteristic (ROC) curves were then constructed to evaluate the prognostic performance of these microRNAs. A total of 172 ovarian cancer samples and 162 normal ovarian tissues were used to verify the credibility and accuracy of the selected markers of the TCGA cohort by quantitative real-time polymerase chain reaction (PCR). RESULTS We successfully established a risk score system based on a six-microRNA signature (hsa-miR-3074-5p, hsa-miR-758-3p, hsa-miR-877-5p, hsa-miR-760, hsa-miR-342-5p, and hsa-miR-6509-5p). This microRNA based system is able to characterize patients as either high or low risk. The OS of OVC patients, with either high or low risk, was significantly different when compared in the training cohort (p < 0.001), the validation cohort (p < 0.001) and the complete cohort (p < 0.001). Analysis of clinical samples further demonstrated that these microRNAs were aberrantly expressed in OVC tissues. The six-miRNA-based signature was correlated with the prognosis of OVC patients (p < 0.001). CONCLUSIONS The study established a novel risk score system that is predictive of patient prognosis and is a potentially useful guide for the personalized treatment of OVC patients.
Collapse
Affiliation(s)
- Min Zhou
- Department of Gynecologic Cancer, Shaanxi Provincial Cancer Hospital, No. 309 Yanta West Road, Shaanxi, 710061, Xi'an, People's Republic of China
| | - Tao Wu
- Department of Gynecologic Cancer, Shaanxi Provincial Cancer Hospital, No. 309 Yanta West Road, Shaanxi, 710061, Xi'an, People's Republic of China
| | - Yuan Yuan
- Department of Gynecologic Cancer, Shaanxi Provincial Cancer Hospital, No. 309 Yanta West Road, Shaanxi, 710061, Xi'an, People's Republic of China
| | - Shu-Juan Dong
- Department of Obstetrics and Gynecology, Shaanxi Provincial Rehabilitation Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Zhi-Ming Zhang
- Department of Clinical Laboratory, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Yan Wang
- Department of Gynecology, Xi'an Central Hospital, No.161 five West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Jing Wang
- Department of Gynecologic Cancer, Shaanxi Provincial Cancer Hospital, No. 309 Yanta West Road, Shaanxi, 710061, Xi'an, People's Republic of China.
| |
Collapse
|
15
|
Kandettu A, Adiga D, Devi V, Suresh PS, Chakrabarty S, Radhakrishnan R, Kabekkodu SP. Deregulated miRNA clusters in ovarian cancer: Imperative implications in personalized medicine. Genes Dis 2022; 9:1443-1465. [PMID: 36157483 PMCID: PMC9485269 DOI: 10.1016/j.gendis.2021.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/04/2021] [Accepted: 12/31/2021] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer (OC) is one of the most common and fatal types of gynecological cancer. OC is usually detected at the advanced stages of the disease, making it highly lethal. miRNAs are single-stranded, small non-coding RNAs with an approximate size ranging around 22 nt. Interestingly, a considerable proportion of miRNAs are organized in clusters with miRNA genes placed adjacent to one another, getting transcribed together to result in miRNA clusters (MCs). MCs comprise two or more miRNAs that follow the same orientation during transcription. Abnormal expression of the miRNA cluster has been identified as one of the key drivers in OC. MC exists both as tumor-suppressive and oncogenic clusters and has a significant role in OC pathogenesis by facilitating cancer cells to acquire various hallmarks. The present review summarizes the regulation and biological function of MCs in OC. The review also highlights the utility of abnormally expressed MCs in the clinical management of OC.
Collapse
|
16
|
Zhao L, Liang X, Wang L, Zhang X. The Role of miRNA in Ovarian Cancer: an Overview. Reprod Sci 2022; 29:2760-2767. [PMID: 34973152 PMCID: PMC9537199 DOI: 10.1007/s43032-021-00717-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/14/2021] [Indexed: 12/30/2022]
Abstract
Ovarian cancer (OC) is a highly malignant disease that seriously threatens women’s health and poses challenges for clinicians. MicroRNAs (miRNAs) have recently been intensively studied in the field of oncology due to their regulatory roles in gene expressions through RNA degradation and/or translation inhibition. This review summarizes the current studies on miRNAs in OC and introduces the latest updates of miRNAs in the early screening, treatment, and prognostic prediction of OC, thereby demonstrating the clinical significance of miRNAs in OC. Further exploration on potential targets of miRNAs in OC may provide new insights on optimizing the diagnosis and treatment of OC. MiRNAs are important driving factors for the progression of OC and the dysregulation of miRNAs can serve as biomarkers in the diagnosis, treatment and prognosis of OC. Therefore, miRNAs are potential biological targets for early screening, targeted therapy, drug resistance monitoring, and prognosis improvement in malignancies such as OC.
Collapse
Affiliation(s)
- Lihui Zhao
- Key Laboratory for Reproductive Medicine and Embryo of Gansu, First Affiliated Hospital, Lanzhou University, No.1, Donggangxi Rd, Chengguan District, Lanzhou City, Gansu, 730000, People's Republic of China
| | - Xiaolei Liang
- Key Laboratory for Reproductive Medicine and Embryo of Gansu, First Affiliated Hospital, Lanzhou University, No.1, Donggangxi Rd, Chengguan District, Lanzhou City, Gansu, 730000, People's Republic of China
| | - Liyan Wang
- Key Laboratory for Reproductive Medicine and Embryo of Gansu, First Affiliated Hospital, Lanzhou University, No.1, Donggangxi Rd, Chengguan District, Lanzhou City, Gansu, 730000, People's Republic of China
| | - Xuehong Zhang
- Key Laboratory for Reproductive Medicine and Embryo of Gansu, First Affiliated Hospital, Lanzhou University, No.1, Donggangxi Rd, Chengguan District, Lanzhou City, Gansu, 730000, People's Republic of China.
| |
Collapse
|
17
|
Yao C, Li Y, Luo L, Xiong Q, Zhong X, Xie F, Feng P. Identification of miRNAs and genes for predicting Barrett's esophagus progressing to esophageal adenocarcinoma using miRNA-mRNA integrated analysis. PLoS One 2021; 16:e0260353. [PMID: 34818353 PMCID: PMC8612537 DOI: 10.1371/journal.pone.0260353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022] Open
Abstract
Barrett's esophagus (BE) is defined as any metaplastic columnar epithelium in the distal esophagus, which predisposes to esophageal adenocarcinoma (EAC). Yet, the mechanism through which BE develops to EAC still remain unclear. Moreover, the miRNA-mRNA regulatory network in distinguishing BE from EAC still remains poorly understood. To identify differentially expressed miRNAs (DEMs) and genes (DEGs) between EAC and BE from tissue samples, gene expression microarray datasets GSE13898, GSE26886, GSE1420 and miRNA microarray datasets GSE16456, GSE20099 were downloaded from Gene Expression Omnibus (GEO) database. GEO2R was used to screen the DEMs and DEGs. Pathway and functional enrichment analysis were performed by DAVID database. The protein-protein interaction (PPI) network was constructed by STRING and been visualized by Cytoscape software. Finnal, survival analysis was performed basing TCGA database. A total of 21 DEMs were identified. The enriched functions and pathways analysis inclued Epstein-Barr virus infection, herpesvirus infection and TRP channels. GART, TNFSF11, GTSE1, NEK2, ICAM1, PSMD12, CTNNB1, CDH1, PSEN1, IL1B, CTNND1, JAG1, CDH17, ITCH, CALM1 and ITGA6 were considered as the hub-genes. Hsa-miR-143 and hsa-miR-133b were the highest connectivity target gene. JAG1 was predicted as the largest number of target miRNAs. The expression of hsa-miR-181d, hsa-miR-185, hsa-miR-15b, hsa-miR-214 and hsa-miR-496 was significantly different between normal tissue and EAC. CDH1, GART, GTSE1, NEK2 and hsa-miR-496, hsa-miR-214, hsa-miR-15b were found to be correlated with survival.
Collapse
Affiliation(s)
- Chengjiao Yao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Geriatrics of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yilin Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lihong Luo
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qin Xiong
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiaowu Zhong
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- * E-mail: (PF); (XZ)
| | - Fengjiao Xie
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Peimin Feng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- * E-mail: (PF); (XZ)
| |
Collapse
|
18
|
Zhu R, Li X, Cai Z, Liang S, Yuan Y, Xu Y, Lai D, Zhao H, Yang W, Bian J, Liu L, Xu G. Risk Scores Based on Six Survival-Related RNAs in a Competing Endogenous Network Composed of Differentially Expressed RNAs Between Clear Cell Renal Cell Carcinoma Patients Carrying Wild-Type or Mutant Von Hippel-Lindau Serve Well to Predict Malignancy and Prognosis. Front Oncol 2021; 11:726671. [PMID: 34760693 PMCID: PMC8573174 DOI: 10.3389/fonc.2021.726671] [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: 06/17/2021] [Accepted: 10/01/2021] [Indexed: 12/24/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) carrying wild-type Von Hippel–Lindau (VHL) tumor suppressor are more invasive and of high morbidity. Concurrently, competing endogenous RNA (ceRNA) network has been suggested to play an important role in ccRCC malignancy. In order to understand why the patients carrying wild-type VHL gene have high degrees of invasion and morbidity, we applied bioinformatics approaches to identify 861 differentially expressed RNAs (DE-RNAs) between patients carrying wild-type and patients carrying mutant VHL from The Cancer Genome Atlas (TCGA) database, established a ceRNA network including 122 RNAs, and elected six survival-related DE-RNAs including Linc00942, Linc00858, RP13_392I16.1, hsa-miR-182-5p, hsa-miR-183-5p, and PAX3. Examining clinical samples from our hospital revealed that patients carrying wild-type VHL had significantly higher levels of all six RNAs than those carrying mutant VHL. Patients carrying wild-type VHL had significantly higher risk scores, which were calculated based on expression levels of all six RNAs, than those carrying mutant VHL. Patients with higher risk scores had significantly shorter survival times than those with lower risk scores. Therefore, the risk scores serve well to predict malignancy and prognosis.
Collapse
Affiliation(s)
- Rui Zhu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiezhao Li
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiduan Cai
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Siyang Liang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yaoji Yuan
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuyu Xu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dehui Lai
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haibo Zhao
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiqing Yang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Bian
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Leyuan Liu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guibin Xu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
19
|
Corrêa S, Lopes FP, Panis C, Basili T, Binato R, Abdelhay E. miRNome Profiling Reveals Shared Features in Breast Cancer Subtypes and Highlights miRNAs That Potentially Regulate MYB and EZH2 Expression. Front Oncol 2021; 11:710919. [PMID: 34646766 PMCID: PMC8502886 DOI: 10.3389/fonc.2021.710919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
Breast cancer (BC) has been extensively studied, as it is one of the more commonly diagnosed cancer types worldwide. The study of miRNAs has increased what is known about the complexity of pathways and signaling and has identified potential biomarkers and therapeutic targets. Thus, miRNome profiling could provide important information regarding the molecular mechanisms involved in BC. On average, more than 430 miRNAs were identified as differentially expressed between BC cell lines and normal breast HMEC cells. From these, 110 miRNAs were common to BC subtypes. The miRNome enrichment analysis and interaction maps highlighted epigenetic-related pathways shared by all BC cell lines and revealed potential miRNA targets. Quantitative evaluation of BC patient samples and GETx/TCGA-BRCA datasets confirmed MYB and EZH2 as potential targets from BC miRNome. Moreover, overall survival was impacted by EZH2 expression. The expression of 15 miRNAs, selected according to aggressiveness of BC subtypes, was confirmed in TCGA-BRCA dataset. Of these miRNAs, miRNA-mRNA interaction prediction revealed 7 novel or underexplored miRNAs in BC: miR-1271-5p, miR-130a-5p, and miR-134 as MYB regulators and miR-138-5p, miR-455-3p, miR-487a, and miR-487b as EZH2 regulators. Herein, we report a novel molecular miRNA signature for BC and identify potential miRNA/mRNAs involved in disease subtypes.
Collapse
Affiliation(s)
- Stephany Corrêa
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Francisco P Lopes
- Grupo de Biologia do Desenvolvimento e Sistemas Dinâmicos, Universidade Federal do Rio de Janeiro (UFRJ), Duque de Caxias, Brazil
| | - Carolina Panis
- Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná (UNIOESTE), Francisco Beltrão, Brazil
| | - Thais Basili
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Renata Binato
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Eliana Abdelhay
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| |
Collapse
|
20
|
Záveský L, Jandáková E, Weinberger V, Hanzíková V, Slanař O, Kohoutová M. Ascites in ovarian cancer: MicroRNA deregulations and their potential roles in ovarian carcinogenesis. Cancer Biomark 2021; 33:1-16. [PMID: 34511487 DOI: 10.3233/cbm-210219] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ovarian cancer comprises the most lethal gynecologic malignancy and is accompanied by the high potential for the incidence of metastasis, recurrence and chemotherapy resistance, often associated with a formation of ascitic fluid. The differentially expressed ascites-derived microRNAs may be linked to ovarian carcinogenesis. The article focuses on a number of miRNAs that share a common expression pattern as determined by independent studies using ascites samples and with regard to their functions and outcomes in experimental and clinical investigations.Let-7b and miR-143 have featured as tumor suppressors in ovarian cancer, which is in line with data on other types of cancer. Although two miRNAs, i.e. miR-26a-5p and miR-145-5p, act principally as tumor suppressor miRNAs, they occasionally exhibit oncogenic roles. The performance of miR-95-3p, upregulated in ascites, is open to debate given the current lack of supportive data on ovarian cancer; however, data on other cancers indicates its probable oncogenic role. Different findings have been reported for miR-182-5p and miR-200c-3p; in addition to their presumed oncogenic roles, contrasting findings have indicated their ambivalent functions. Further research is required for the identification and evaluation of the potential of specific miRNAs in the diagnosis, prediction, treatment and outcomes of ovarian cancer patients.
Collapse
Affiliation(s)
- Luděk Záveský
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague and General University Hospital, Prague, Czech Republic.,Institute of Pharmacology, First Faculty of Medicine, Charles University, Prague and General University Hospital, Prague, Czech Republic
| | - Eva Jandáková
- Department of Pathology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Vít Weinberger
- Department of Obstetrics and Gynecology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Veronika Hanzíková
- Faculty Transfusion Center, General University Hospital, Prague, Czech Republic
| | - Ondřej Slanař
- Institute of Pharmacology, First Faculty of Medicine, Charles University, Prague and General University Hospital, Prague, Czech Republic
| | - Milada Kohoutová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague and General University Hospital, Prague, Czech Republic
| |
Collapse
|
21
|
Su R, Jin C, Zhou L, Cao Y, Kuang M, Li L, Xiang J. Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA. BMC Cancer 2021; 21:970. [PMID: 34461858 PMCID: PMC8404317 DOI: 10.1186/s12885-021-08711-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 08/19/2021] [Indexed: 12/22/2022] Open
Abstract
Background Ovarian cancer is the leading cause of death among gynecological malignancies. Immunotherapy has demonstrated potential effects in ovarian cancer. However, few studies on immune-related prognostic signatures in ovarian cancer have been reported. This study aimed to identify hub genes associated with immune infiltrates to provide insight into the immune regulatory mechanisms in ovarian cancer. Methods Raw data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and University of California, Santa Cruz (UCSC) Xena websites. Single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network analysis (WGCNA) were used to identify hub genes. Kaplan-Meier analysis and differential expression analysis were applied to explore the real hub genes. Results Through ssGSEA and WGCNA, 7 hub genes (LY9, CD5, CXCL9, IL2RG, SLAMF1, SLAMF6, and SLAMF7) were identified. Finally, LY9 and SLAMF1 were recognized as the real hub genes in immune infiltrates of ovarian cancer. LY9 and SLAMF1 are classified as SLAM family receptors involved in the activation of hematopoietic cells and the pathogenesis of multiple malignancies. Furthermore, 12 lncRNAs and 43 miRNAs significantly related to the 2 hub genes were applied to construct a lncRNA-miRNA-mRNA ceRNA network. The lncRNA-miRNA-mRNA ceRNA network shows upstream regulatory sites of the 2 hub genes. Conclusions These findings improve our understanding of the regulatory mechanism of and reveal potential immune checkpoints for immunotherapy for ovarian cancer.
Collapse
Affiliation(s)
- Rongjia Su
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China
| | - Chengjuan Jin
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China
| | - Lina Zhou
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China
| | - Yannan Cao
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China
| | - Menghua Kuang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China
| | - Linxia Li
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China
| | - Jiangdong Xiang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 650 Xin Songjiang Road, Shanghai, 201620, China.
| |
Collapse
|
22
|
Kandimalla R, Wang W, Yu F, Zhou N, Gao F, Spillman M, Moukova L, Slaby O, Salhia B, Zhou S, Wang X, Goel A. OCaMIR-A Noninvasive, Diagnostic Signature for Early-Stage Ovarian Cancer: A Multi-cohort Retrospective and Prospective Study. Clin Cancer Res 2021; 27:4277-4286. [PMID: 34035068 DOI: 10.1158/1078-0432.ccr-21-0267] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/08/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Due to the lack of effective screening approaches and early detection biomarkers, ovarian cancer has the highest mortality rates among gynecologic cancers. Herein, we undertook a systematic biomarker discovery and validation approach to identify microRNA (miRNA) biomarkers for the early detection of ovarian cancer. EXPERIMENTAL DESIGN During the discovery phase, we performed small RNA sequencing in stage I high-grade serous ovarian cancer (n = 31), which was subsequently validated in multiple, independent data sets (TCGA, n = 543; GSE65819, n = 87). Subsequently, we performed multivariate logistic regression-based training in a serum data set (GSE106817, n = 640), followed by its independent validation in three retrospective data sets (GSE31568, n = 85; GSE113486, n = 140; Czech Republic cohort, n = 192) and one prospective serum cohort (n = 95). In addition, we evaluated the specificity of OCaMIR, by comparing its performance in several other cancers (GSE31568 cohort, n = 369). RESULTS The OCaMIR demonstrated a robust diagnostic accuracy in the stage I high-grade serous ovarian cancer patients in the discovery cohort (AUC = 0.99), which was consistently reproducible in both stage I (AUC = 0.96) and all stage patients (AUC = 0.89) in the TCGA cohort. Logistic regression-based training and validation of OCaMIR achieved AUC values of 0.89 (GSE106817), 0.85 (GSE31568), 0.86 (GSE113486), and 0.82 (Czech Republic cohort) in the retrospective serum validation cohorts, as well as prospective validation cohort (AUC = 0.92). More importantly, OCaMIR demonstrated a significantly superior diagnostic performance compared with CA125 levels, even in stage I patients, and was more cost-effective, highlighting its potential role for screening and early detection of ovarian cancer. CONCLUSIONS Small RNA sequencing identified a robust noninvasive miRNA signature for early-stage serous ovarian cancer detection.
Collapse
Affiliation(s)
- Raju Kandimalla
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Wei Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, P.R. China.,Department of Gynecology, Huzhou Maternity & Child Health Care Hospital, Huzhou, P.R. China
| | - Fan Yu
- Department of Laboratory Medicine, West China Second Hospital, Sichuan University, Chengdu, P.R. China
| | - Nianxin Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE & State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P.R. China
| | - Feng Gao
- The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P.R. China
| | - Monique Spillman
- Department of Obstetrics and Gynecology, Baylor University Medical Center, Dallas, Texas
| | - Lucie Moukova
- Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Bodour Salhia
- Department of Translational Genomics, University of Southern California, Los Angeles, California
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE & State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P.R. China.
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, P.R. China. .,Shenzhen Research Institute, City University of Hong Kong, Shenzhen, P.R. China
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas. .,Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, California
| |
Collapse
|
23
|
Ning R, Meng S, Wang L, Jia Y, Tang F, Sun H, Zhang Z, Zhang C, Fan X, Xiao B, Yang C, Li S. 6 Circulating miRNAs can be used as Non-invasive Biomarkers for the Detection of Cervical Lesions. J Cancer 2021; 12:5106-5113. [PMID: 34335927 PMCID: PMC8317520 DOI: 10.7150/jca.51141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Cervical cancer is the most common malignant tumor in the female reproductive system, while the efficacy of routine screening strategy is unsatisfied. New molecular tests need to be developed. miRNAs participate in many pathologic processes, and circulating miRNAs are promising non-invasive biomarkers in tumors. Objectives: This study aimed to identify the circulating miRNAs associated with both cervical cancer and cervical intraepithelial neoplasia (CIN), and establish a non-invasive classifier for cervical lesions using circulating miRNAs. Methods: This study consisted of 5 steps: miRNAs screening, miRNAs validation, classifier establishment, independent validation and in silico analyses. Three cohorts were included in our study: In screening stage, 24 samples including 14 cases and 10 controls were retrieved; In validation stage, 380 samples including 200 cases and 180 controls were recruited; In independent validation stage, 47 samples comprising 26 cases and 21 controls were included. miRNAs were quantified by RT-qPCR. A classifier was built with random forest algorithm using validation samples and selected miRNAs, which were then validated in an independent cohort. To explore the function of selected miRNAs, in silico analyses were performed. Target genes of selected miRNAs were predicted by the overlap of three online tools. Enrichment analyses were executed with predicted target genes. Differential analysis of target genes was carried out with open access expression assay datasets of cervical tissues. Results: 6 miRNAs (hsa-miR-26b-5p, hsa-miR-146b-5p, hsa-miR-191-5p, hsa-miR-484, hsa-miR-574-3p, hsa-miR-625-3p) were screened out from 754 miRNAs. They were associated with cervical lesions and were selected to establish a classifier. The accuracy of the classifier were 0.7218 (0.7117, 0.7319) in validation samples, which was 0.7021 in the independent cohort. 958 target genes were predicted and enriched in 23 pathways (MAPK, human papillomavirus infection and Wnt signaling pathway, etc.). 55 genes were identified as the most likely target genes by differential analysis. Conclusion: The 6 circulating miRNAs were related to cervical lesions and could serve as non-invasive biomarkers.
Collapse
Affiliation(s)
- Ruoqi Ning
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Silu Meng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Lin Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China.,Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Yao Jia
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Fangxu Tang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Haiying Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Zhi Zhang
- National Engineering Research Center for Beijing Biochip Technology, Changping District, Beijing, 102206, P.R. China.,CapitalBio Corporation, Changping District, Beijing, 102206, P.R. China
| | - Chong Zhang
- National Engineering Research Center for Beijing Biochip Technology, Changping District, Beijing, 102206, P.R. China.,CapitalBio Corporation, Changping District, Beijing, 102206, P.R. China
| | - Xinran Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Bing Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Chunhua Yang
- National Engineering Research Center for Beijing Biochip Technology, Changping District, Beijing, 102206, P.R. China.,CapitalBio Corporation, Changping District, Beijing, 102206, P.R. China
| | - Shuang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| |
Collapse
|
24
|
Cifuentes-Bernal AM, Pham VV, Li X, Liu L, Li J, Le TD. A pseudotemporal causality approach to identifying miRNA-mRNA interactions during biological processes. Bioinformatics 2021; 37:807-814. [PMID: 33070184 DOI: 10.1093/bioinformatics/btaa899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/02/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION microRNAs (miRNAs) are important gene regulators and they are involved in many biological processes, including cancer progression. Therefore, correctly identifying miRNA-mRNA interactions is a crucial task. To this end, a huge number of computational methods has been developed, but they mainly use the data at one snapshot and ignore the dynamics of a biological process. The recent development of single cell data and the booming of the exploration of cell trajectories using 'pseudotime' concept have inspired us to develop a pseudotime-based method to infer the miRNA-mRNA relationships characterizing a biological process by taking into account the temporal aspect of the process. RESULTS We have developed a novel approach, called pseudotime causality, to find the causal relationships between miRNAs and mRNAs during a biological process. We have applied the proposed method to both single cell and bulk sequencing datasets for Epithelia to Mesenchymal Transition, a key process in cancer metastasis. The evaluation results show that our method significantly outperforms existing methods in finding miRNA-mRNA interactions in both single cell and bulk data. The results suggest that utilizing the pseudotemporal information from the data helps reveal the gene regulation in a biological process much better than using the static information. AVAILABILITY AND IMPLEMENTATION R scripts and datasets can be found at https://github.com/AndresMCB/PTC. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - Vu Vh Pham
- UniSA STEM, University of South Australia, Adelaide, South Australia, 5095 Mawson Lakes, Australia
| | - Xiaomei Li
- UniSA STEM, University of South Australia, Adelaide, South Australia, 5095 Mawson Lakes, Australia
| | - Lin Liu
- UniSA STEM, University of South Australia, Adelaide, South Australia, 5095 Mawson Lakes, Australia
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Adelaide, South Australia, 5095 Mawson Lakes, Australia
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Adelaide, South Australia, 5095 Mawson Lakes, Australia
| |
Collapse
|
25
|
Dwivedi SKD, Rao G, Dey A, Mukherjee P, Wren JD, Bhattacharya R. Small Non-Coding-RNA in Gynecological Malignancies. Cancers (Basel) 2021; 13:1085. [PMID: 33802524 PMCID: PMC7961667 DOI: 10.3390/cancers13051085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.
Collapse
Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Biochemistry and Molecular Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
26
|
Kumar V, Gupta S, Varma K, Sachan M. MicroRNA as Biomarker in Ovarian Cancer Management: Advantages and Challenges. DNA Cell Biol 2020; 39:2103-2124. [PMID: 33156705 DOI: 10.1089/dna.2020.6024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ovarian cancer is the most prevalent gynecological malignancy affecting women throughout the globe. Ovarian cancer has several subtypes, including epithelial ovarian cancer (EOC) with a whopping incidence rate of 239,000 per year, making it the sixth most common gynecological malignancy worldwide. Despite advancement of detection and therapeutics, death rate accounts for 152,000 per annum. Several protein-based biomarkers such as CA125 and HE4 are currently being used for diagnosis, but their sensitivity and specificity for early detection of ovarian cancer are under question. MicroRNA (a small noncoding RNA molecule that participates in post-transcription regulation of gene expression) and its functional deregulation in most cancers have been discovered in the previous two decades. Studies support that miRNA deregulation has an epigenetic component as well. Aberrant miRNA expression is often correlated with the form of EOC tumor, histological grade, prognosis, and FIGO stage. In this review, we addressed epigenetic regulation of miRNAs, the latest research on miRs as a biomarker in the detection of EOC, and tailored assays to use miRNAs as a biomarker in ovarian cancer diagnosis.
Collapse
Affiliation(s)
- Vivek Kumar
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Kachnar Varma
- Department of Pathology, Motilal Nehru Medical College, Allahabad, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| |
Collapse
|
27
|
Slow-Freezing Cryopreservation Ensures High Ovarian Tissue Quality Followed by In Vivo and In Vitro Methods and Is Safe for Fertility Preservation. ACTA ACUST UNITED AC 2020; 56:medicina56100547. [PMID: 33086522 PMCID: PMC7603126 DOI: 10.3390/medicina56100547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023]
Abstract
Background and objectives: Cancer incidence is growing with younger patients diagnosed with this disease every year. Improved cancer diagnostics and treatment lead to better survival of cancer patients. However, after aggressive chemo- or radiotherapy, cancer survivors suffer from various degrees of subfertility or infertility. Several fertility preservation technologies have been developed for young cancer patients: cryopreservation of germ cells, embryos, or reproductive tissues. The best results have been shown by cryopreservation of sperm and embryos. Yet the success of using cryopreserved oocytes or reproductive tissues (ovarian and testicular) is still insufficient. Therefore, this study was designed to assess the vitality, viability, general quality, and safety of frozen-thawed human ovarian tissue for retransplantation using modern molecular tests. Materials and Methods: The new miRNA array test was used to evaluate miRNA expression in thawed ovarian tissue in combination with standard xenotransplantation and pathological examination of microslides. Results: Our results demonstrated that slow freezing is an efficient way (80%) to cryopreserve ovarian tissue with no structural damage afterwards. We have shown that xenotransplantation into immunodeficient mice, histology, and immunohistochemistry could be potentially replaced by more recent molecular methods. Conclusions: The latter method has shown that altered expression of miRNAs might be used as identifiers of normal/damaged tissue after further analysis. Newer, safer, and more specific approaches need to be developed in order to eliminate the risk of disease reoccurrence.
Collapse
|
28
|
Wang Y, Wang X, Han L, Hu D. LncRNA MALAT1 Regulates the Progression and Cisplatin Resistance of Ovarian Cancer Cells via Modulating miR-1271-5p/E2F5 Axis. Cancer Manag Res 2020; 12:9999-10010. [PMID: 33116856 PMCID: PMC7567574 DOI: 10.2147/cmar.s261979] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were reported to be related to the development of ovarian cancer (OC). In this study, the functional mechanisms of lncRNA metastasis associated with lung adenocarcinoma transcript 1 (MALAT1) and microRNA-1271-5p (miR-1271-5p) were explored in OC. Methods The level of MALAT1, miR-1271-5p, or E2F transcription factor 5 (E2F5) was detected by qRT-PCR. MTT assay, flow cytometry analysis and transwell migration and invasion assays were performed to determine cell proliferation, apoptosis, migration and invasion, respectively. E2F5 protein expression was detected by Western blot. The interaction between miR-1271-5p and MALAT1 or E2F transcription factor 5 (E2F5) was confirmed by the dual-luciferase reporter assay. Results MALAT1 and E2F5 level were increased, while miR-1271-5p level was decreased in cisplatin (DDP)-resistant OC tissues and cells. MALAT1 knockdown or miR-1271-5p upregulation decreased IC50 of cisplatin, and inhibited cell proliferation, migration, invasion, and facilitated cell apoptosis in DDP-resistant OC cells. Moreover, MALAT1 sponged miR-1271-5p to upregulate E2F5 expression. Besides, MALAT1 knockdown decreased DDP resistance, inhibited cell proliferation, migration, invasion, and promoted cell apoptosis by sponging miR-1271-5p to downregulate E2F5 expression in DDP-resistant OC cell. Conclusion We demonstrated that MALAT1 mediated DDP-resistant OC development through miR-1271-5p/E2F5 axis, providing the theoretical basis for OC therapy.
Collapse
Affiliation(s)
- Yuqin Wang
- Department of Gynecology, The First People's Hospital of Lianyungang, Lianyungang 222000, Peoples' Republic of China
| | - Xiuying Wang
- Department of Gynecology, The First People's Hospital of Lianyungang, Lianyungang 222000, Peoples' Republic of China
| | - Liwei Han
- Department of Gynecology, The First People's Hospital of Lianyungang, Lianyungang 222000, Peoples' Republic of China
| | - Dongdong Hu
- Department of Gynecology, The First People's Hospital of Lianyungang, Lianyungang 222000, Peoples' Republic of China
| |
Collapse
|
29
|
Han FJ, Li J, Shen Y, Guo Y, Liu YC, Yu Y, Xu JY, Liu SX, Wang YH. microRNA-1271-5p/TIAM1 suppresses the progression of ovarian cancer through inactivating Notch signaling pathway. J Ovarian Res 2020; 13:110. [PMID: 32948241 PMCID: PMC7501628 DOI: 10.1186/s13048-020-00720-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022] Open
Abstract
Objective Ovarian cancer (OC) has been regarded as the most malignant gynecological neoplasm and often confers grave outcomes owing to the frequent metastasis and high recurrence. A previous study has demonstrated that miR-1271-5p is implicated in OC progression, however, the possible mechanism of it remains unknown. The purpose of this investigation was to explore how miR-1271-5p regulates the progression of OC. Methods Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were employed to analyze the differentially expressed miRNAs or genes as well as their corresponding prognostic values. miR-1271-5p expression in OC cells was examined by qRT-PCR. Cell counting kit 8 (CCK-8), colony formation, and transwell tests were conducted to evaluate the proliferation, migration and invasion potentials. Bioinformatics prediction and luciferase activity analysis were utilized to predict and verify the target gene of miR-1271-5p. Western blot assay was carried out to measure protein expression. Results miR-1271-5p was significantly decreased in OC and its down-regulation was associated with the grave outcome of OC patients. Upregulation of miR-1271-5p inhibited cell viability, but miR-1271-5p knockdown promoted the proliferation of OC cells. TIAM1 was a direct target gene of miR-1271-5p and expressed in OC tissues at higher level. High expression of TIAM1 induced the poorer prognosis of patients with OC. Further functional analyses showed that the suppressive role of miR-1271-5p on OC cell malignant behaviors was overturned by the upregulation of TIAM1. The protein levels of Cyclin D1, HES1, NOTCH and NUMB were remarkably changed due to the abnormal expression of miR-1271-5p and TIAM1. Conclusion To sum up, miR-1271-5p inhibits proliferation, invasion and migration of OC cells by directly repressing TIAM1 to inactivate the Notch signaling pathway, which provides an alternative therapeutic candidate for the advancement of OC treatment.
Collapse
Affiliation(s)
- Feng-Juan Han
- Department of Gynecology, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150040, Heilongjiang, China
| | - Jia Li
- Heilongjiang University of Traditional Chinese Medicine, First Clinical Medical College, Harbin, 150040, Heilongjiang, China
| | - Ying Shen
- Heilongjiang University of Traditional Chinese Medicine, First Clinical Medical College, Harbin, 150040, Heilongjiang, China
| | - Ying Guo
- Department of Gynecology, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150040, Heilongjiang, China
| | - Yi-Chao Liu
- Department of Chinese medicine, Harbin Institute of Technology Hospital, Harbin, 150006, Heilongjiang, China
| | - Yang Yu
- Heilongjiang University of Traditional Chinese Medicine, First Clinical Medical College, Harbin, 150040, Heilongjiang, China
| | - Jia-Yue Xu
- Heilongjiang University of Traditional Chinese Medicine, First Clinical Medical College, Harbin, 150040, Heilongjiang, China
| | - Shao-Xuan Liu
- Heilongjiang University of Traditional Chinese Medicine, First Clinical Medical College, Harbin, 150040, Heilongjiang, China
| | - Yan-Hong Wang
- Heilongjiang University of Traditional Chinese Medicine, College of Pharmacy, No. 24, Heping Road, Xiangfang District, Harbin, 150040, Heilongjiang Province, China.
| |
Collapse
|
30
|
Cimadomo D, Rienzi L, Giancani A, Alviggi E, Dusi L, Canipari R, Noli L, Ilic D, Khalaf Y, Ubaldi FM, Capalbo A. Definition and validation of a custom protocol to detect miRNAs in the spent media after blastocyst culture: searching for biomarkers of implantation. Hum Reprod 2020; 34:1746-1761. [PMID: 31419301 DOI: 10.1093/humrep/dez119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
STUDY QUESTION Can miRNAs be reliably detected in the spent blastocyst media (SBM) after IVF as putative biomarkers of the implantation potential of euploid embryos? SUMMARY ANSWER Adjustment of the data for blastocyst quality and the day of full-expansion hinders the predictive power of a fast, inexpensive, reproducible and user-friendly protocol based on the detection of 10 selected miRNAs from SBM. WHAT IS KNOWN ALREADY Euploidy represents so far the strongest predictor of blastocyst competence. Nevertheless, ~50% of the euploid blastocysts fail to implant. Several studies across the years have suggested that a dialogue exists between the embryo and the endometrium aimed at the establishment of a pregnancy. MicroRNAs have been proposed as mediators of such a dialogue and investigated in this respect. Several expensive, time-consuming and complex protocols have been adopted and promising results have been produced, but conclusive evidence from large clinical studies is missing. STUDY DESIGN, SIZE, DURATION This study was conducted in two phases from September 2015 to December 2017. In Phase 1, the human blastocyst miRNome profile was defined from the inner cell mass (ICM) and the corresponding whole-trophectoderm (TE) of six donated blastocysts. Two different protocols were adopted to this end. In parallel, 6 pools of 10 SBM each were run (3 from only implanted euploid blastocysts, IEBs; and 3 from only not-implanted euploid blastocysts, not-IEBs). A fast, inexpensive and user-friendly custom protocol for miRNA SBM profiling was designed. In Phase 2, 239 SBM from IEB and not-IEB were collected at three IVF centres. After 18 SBM from poor-quality blastocysts were excluded from the analysis, data from 107 SBM from not-IEB and 114 from IEB were produced through the previously developed custom protocol and compared. The data were corrected through logistic regressions. PARTICIPANT/MATERIALS, SETTINGS, METHODS Donated blastocysts underwent ICM and whole-TE isolation. SBM were collected during IVF cycles characterized by ICSI, blastocyst culture in a continuous media, TE biopsy without zona pellucida opening in Day 3, quantitative PCR (qPCR)-based aneuploidy testing and vitrified-warmed single euploid embryo transfer. Not-IEB and IEB were clustered following a negative pregnancy test and a live birth, respectively. The Taqman Low Density Array (TLDA) cards and the Exiqon microRNA human panel I+II qPCR analysis protocols were adopted to analyse the ICM and whole-TE. The latter was used also for SBM pools. A custom protocol and plate was then designed based on the Exiqon workflow, validated and finally adopted for SBM analysis in study Phase 2. This custom protocol allows the analysis of 10 miRNAs from 10 SBM in 3 hours from sample collection to data inspection. MAIN RESULTS AND ROLE OF THE CHANCE The TLDA cards protocol involved a higher rate of false positive results (5.6% versus 2.8% with Exiqon). There were 44 miRNAs detected in the ICM and TE from both the protocols. One and 24 miRNAs were instead detected solely in the ICM and the TE, respectively. Overall, 29 miRNAs were detected in the pooled SBM: 8 only from not-IEB, 8 only from IEB and 13 from both. Most of them (N = 24/29, 82.7%) were also detected previously in both the ICM and TE with the Exiqon protocol; two miRNAs (N = 2/29, 6.9%) were previously detected only in the TE, and three (N = 3/29, 10.3%) were never detected previously. In study Phase 2, significant differences were shown between not-IEB and IEB in terms of both miRNA detection and relative quantitation. However, when the data were corrected for embryo morphology and day of full development (i.e. SBM collection), no significant association was confirmed. LIMITATIONS, REASONS FOR CAUTION This study did not evaluate specifically exosomal miRNAs, thereby reducing the chance of identifying the functional miRNAs. Ex-vivo experiments are required to confirm the role of miRNAs in mediating the dialogue with endometrial cells, and higher throughput technologies need to be further evaluated for miRNA profiling from clinical SBM samples. WIDER IMPLICATIONS OF THE FINDINGS Although no clinical predictive power was reported in this study, the absence of invasiveness related with SBM analysis and the evidence that embryonic genetic material can be reliably detected and analysed from SBM make this waste product of IVF an important source for further investigations aimed at improving embryo selection. STUDY FUNDING/COMPETING INTEREST(S) This project has been financially supported by Merck KgaA (Darmstadt, Germany) with a Grant for Fertility Innovation (GFI) 2015. The authors have no conflict of interest to declare related with this study. TRIAL REGISTRATION NUMBER None.
Collapse
Affiliation(s)
- Danilo Cimadomo
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Laura Rienzi
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Adriano Giancani
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy
| | - Erminia Alviggi
- Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy
| | - Ludovica Dusi
- G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Rita Canipari
- DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy
| | - Laila Noli
- Fakeeh College of Medical Sciences, Jeddah, Saudi Arabia.,Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Dusko Ilic
- Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Yacoub Khalaf
- Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Filippo Maria Ubaldi
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Antonio Capalbo
- DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy.,Igenomix, Marostica, Italy
| |
Collapse
|
31
|
Guo R, Qin Y. LEMD1-AS1 Suppresses Ovarian Cancer Progression Through Regulating miR-183-5p/TP53 Axis. Onco Targets Ther 2020; 13:7387-7398. [PMID: 32801762 PMCID: PMC7395824 DOI: 10.2147/ott.s250850] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022] Open
Abstract
Background/Aims Long noncoding RNAs (lncRNAs) play a critical role in tumorigenesis and progression of ovarian cancer (OC). This study focused on the function and potential mechanism toward LEMD1-AS1 (LEMD1 antisense RNA 1) in the progression of ovarian cancer. Materials and Methods The expression of LEMD1-AS1 in OC tissues was evaluated in TCGA and Gene Expression Omnibus datasets (GSE119056) and confirmed in OC cell lines via qRT-PCR (quantitative real-time polymerase chain reaction). Then, the location of LEMD1-AS1 in the cytoplasmic and nuclear RNAs extracted from OV cells was detected by qRT-PCR. Cell Counting Kit-8 (CCK-8), colony formation, wound-healing and transwell assays were applied to examine cell viability, proliferation, migration and invasion, respectively. Further, the effect of LEMD1-AS1 on OC tumor growth was determined via subcutaneous xenotransplanted tumor model. The potential target for LEMD1-AS1 was validated via dual-luciferase activity assay, RNA pull-down and RNA immunoprecipitation. Results The expression of LEMD1-AS1 was decreased in OC tissues and cell lines. Forced overexpression of LEMD1-AS1 inhibited the proliferation, migration and invasion of ovarian cancer cells and transplanted tumor growth in nude mice. We found that LEMD1-AS1 was mainly located in the cytoplasm of OC cells and contained complementary sites of miR-183-5p. Mechanistically, our results showed that LEMD1-AS1 could directly interact with miR-183-5p and tumor protein p53 (TP53). The anti-tumor role of LEMD1-AS1 on OC progression depended on miR-183-5p-mediated TP53 expression. Conclusion LEMD1-AS1 suppresses OC progression through sponging miR-183-5p and regulation of TP53, suggesting a novel biomarker and target for OC.
Collapse
Affiliation(s)
- Ruowen Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - Yide Qin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| |
Collapse
|
32
|
Sehovic E, Hadrovic A, Dogan S. Detection and analysis of stable and flexible genes towards a genome signature framework in cancer. Bioinformation 2019; 15:772-779. [PMID: 31831960 PMCID: PMC6900328 DOI: 10.6026/97320630015772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/05/2019] [Accepted: 11/09/2019] [Indexed: 01/11/2023] Open
Abstract
Comparison and detection of stable cancer genes across cancer types is of interest. The gene expression data of 6 different cancer types (colon, breast, lung, ovarian, brain
and renal) and a control group from The Cancer Genome Atlas (TCGA) database were used in this study. The comparison of gene expression data together with the calculation standard
deviations of such data was completed using a statistical model for the detection of stable genes. Genes having similar expression (referred as flexible genes) pattern to the
control group in four out of six cancer types are PATE, NEUROD4 and TRAFD1. Moreover, 13 genes showed low difference compared to the control group with low standard deviation
across cancer types (referred as stable genes). Among them, genes GDF2, KCNT1 and RNF151 showed consistent low expression while ODF4, OR5I1, MYOG and OR2B11 showed consistent high
expression. Thus, the detection and analysis of stable and flexible cancer genes help towards the design and development of a framework (outline) for specific genome signature
(biomarker) in cancer.
Collapse
Affiliation(s)
- Emir Sehovic
- International Burch University Sarajevo, Francuske Revolucije BB, 71210 Sarajevo
| | - Adem Hadrovic
- Sarajevo School of Science and Technology, Hrasnicka Cesta 3a, 71210 Sarajevo
| | - Senol Dogan
- The University of Leipzig, Faculty of Physics and Earth Science, Peter Debye Institute for Soft Matter Physics, LinnestraBe 5, 04103 Leipzig, Germany
| |
Collapse
|
33
|
Xu G, Zhang H, Li X, Hu J, Yang G, Sun S. Genome-Wide Differential Expression Profiling of Ovarian circRNAs Associated With Litter Size in Pigs. Front Genet 2019; 10:1010. [PMID: 31803223 PMCID: PMC6873881 DOI: 10.3389/fgene.2019.01010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs) have been emerging as an important regulator in mammalian reproduction via acting as miRNA sponges. However, the circRNAs in porcine ovaries related with litter size remains largely unknown. In this study, porcine ovaries with smaller or larger litter size (LLS) were subjected to high-throughput RNA sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig (|log2 (fold change) | > 1, FDR < 0.05). Bioinformatics predicted that most of circRNAs harbored miRNA binding sites, and the expression patterns of circRNAs and their putative binding miRNAs were validated by qPCR. Moreover, the expression of circ-TCP11/miR-183 was significantly reversely correlated and their direct interaction was confirmed by dual-luciferase assay. Our study indicates that circRNAs may play potential effects on modulating porcine litter size.
Collapse
Affiliation(s)
- Gaoxiao Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Sciences and Technologies, Northwest A&F University, Yangling, China.,Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Huifang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Sciences and Technologies, Northwest A&F University, Yangling, China
| | - Xiao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Sciences and Technologies, Northwest A&F University, Yangling, China
| | - Jianhong Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Sciences and Technologies, Northwest A&F University, Yangling, China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Sciences and Technologies, Northwest A&F University, Yangling, China
| | - Shiduo Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Sciences and Technologies, Northwest A&F University, Yangling, China
| |
Collapse
|
34
|
Li Y, Li L. Prognostic values and prospective pathway signaling of MicroRNA-182 in ovarian cancer: a study based on gene expression omnibus (GEO) and bioinformatics analysis. J Ovarian Res 2019; 12:106. [PMID: 31703725 PMCID: PMC6839211 DOI: 10.1186/s13048-019-0580-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Ovarian carcinoma (OC) is a common cause of death among women with gynecological cancer. MicroRNAs (miRNAs) are believed to have vital roles in tumorigenesis of OC. Although miRNAs are broadly recognized in OC, the role of has-miR-182-5p (miR-182) in OC is still not fully elucidated. METHODS We evaluated the significance of miR-182 expression in OC by using analysis of a public dataset from the Gene Expression Omnibus (GEO) database and a literature review. Furthermore, we downloaded three mRNA datasets of OC and normal ovarian tissues (NOTs), GSE14407, GSE18520 and GSE36668, from GEO to identify differentially expressed genes (DEGs). Then the targeted genes of hsa-miR-182-5p (TG_miRNA-182-5p) were predicted using miRWALK3.0. Subsequently, we analyzed the gene overlaps integrated between DEGs in OC and predicted target genes of miR-182 by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. STRING and Cytoscape were used to construct a protein-protein interaction (PPI) network and the prognostic effects of the hub genes were analyzed. RESULTS A common pattern of up-regulation for miR-182 in OC was found in our review of the literature. A total of 268 DEGs, both OC-related and miR-182-related, were identified, of which 133 genes were discovered from the PPI network. A number of DEGs were enriched in extracellular matrix organization, pathways in cancer, focal adhesion, and ECM-receptor interaction. Two hub genes, MCM3 and GINS2, were significantly associated with worse overall survival of patients with OC. Furthermore, we identified covert miR-182-related genes that might participate in OC by network analysis, such as DCN, AKT3, and TIMP2. The expressions of these genes were all down-regulated and negatively correlated with miR-182 in OC. CONCLUSIONS Our study suggests that miR-182 is essential for the biological progression of OC.
Collapse
Affiliation(s)
- Yaowei Li
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, China.,Department of Gynecology and obstetrics, Shangyu People's Hospital, Shangyu, Zhejiang, China
| | - Li Li
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, China.
| |
Collapse
|
35
|
Qi X, Yu C, Wang Y, Lin Y, Shen B. Network vulnerability-based and knowledge-guided identification of microRNA biomarkers indicating platinum resistance in high-grade serous ovarian cancer. Clin Transl Med 2019; 8:28. [PMID: 31664600 PMCID: PMC6820656 DOI: 10.1186/s40169-019-0245-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/19/2019] [Indexed: 02/07/2023] Open
Abstract
Background High-grade serous ovarian cancer (HGSC), the most common ovarian carcinoma type, is associated with the highest mortality rate among all gynecological malignancies. As chemoresistance has been demonstrated as the major challenge in improving the prognosis of HGSC patients, we here aimed to identify microRNA (miRNA) biomarkers for predicting platinum resistance and further explore their functions in HGSC. Results We developed and applied our network vulnerability-based and knowledge-guided bioinformatics model first time for the study of drug-resistance in cancer. Four miRNA biomarkers (miR-454-3p, miR-98-5p, miR-183-5p and miR-22-3p) were identified with potential in stratifying platinum-sensitive and platinum-resistant HGSC patients and predicting prognostic outcome. Among them, miR-454-3p and miR-183-5p were newly discovered to be closely implicated in platinum resistance in HGSC. Functional analyses highlighted crucial roles of the four miRNA biomarkers in platinum resistance through mediating transcriptional regulation, cell proliferation and apoptosis. Moreover, expression patterns of the miRNA biomarkers were validated in both platinum-sensitive and platinum-resistant ovarian cancer cells. Conclusions With bioinformatics modeling and analysis, we identified and confirmed four novel putative miRNA biomarkers, miR-454-3p, miR-98-5p, miR-183-5p and miR-22-3p that could serve as indicators of resistance to platinum-based chemotherapy, thereby contributing to the improvement of chemotherapeutic efficiency and optimization of personalized treatments in HGSC.
Collapse
Affiliation(s)
- Xin Qi
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Chunjiang Yu
- Center for Systems Biology, Soochow University, Suzhou, 215006, China.,School of Nanotechnology, Suzhou Industrial Park Institute of Services Outsourcing, Suzhou, 215006, China
| | - Yi Wang
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
36
|
Yang L, Dou Y, Sui Z, Cheng H, Liu X, Wang Q, Gao P, Qu Y, Xu M. Upregulated miRNA-182-5p expression in tumor tissue and peripheral blood samples from patients with non-small cell lung cancer is associated with downregulated Caspase 2 expression. Exp Ther Med 2019; 19:603-610. [PMID: 31897103 PMCID: PMC6923754 DOI: 10.3892/etm.2019.8074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/10/2019] [Indexed: 12/24/2022] Open
Abstract
Lung cancer has the highest morbidity and mortality rates among all malignant tumors worldwide. Previous studies demonstrated that microRNA (miR)-182-5p may serve different roles in different types of cancer, including renal cell carcinoma and liver cancer. However, the functional role of miR-182-5p in non-small cell lung cancer (NSCLC) remains unknown. In the current study, the expression level of miR-182-5p in tumor tissue and peripheral blood samples obtained from patients with NSCLC was examined. The biological function of miR-182-5p on NSCLC cell proliferation was also investigated. Tissue and adjacent normal tissue samples were collected from 33 patients with NSCLC. In addition, peripheral blood samples were obtained from patients with NSCLC and 26 healthy control patients. The NSCLC cell line H1299 was used for all functional assays. Reverse transcription-quantitative polymerase chain reaction was used to determine the miR-182-5p or Caspase 2 (CASP2) mRNA expression levels in NSCLC tissue and peripheral blood samples, as well as in the NSCLC cell line. Western blotting was used to examine the protein expression level of CASP2 in tissue samples and cells, and ELISA was performed to measure the protein level of CASP2 in peripheral blood samples. MTT assay was performed to examine NSCLC cell proliferation. Flow cytometry was used to detect apoptosis. Dual-luciferase reporter assay was used to examine whether miRN182-5p directly interacts with CASP2. The current study demonstrated that miR-182-5p expression was upregulated in NSCLC tissue and peripheral blood samples from patients with NSCLC, which suggests that miR-182-5p, may serve a functional role in NSCLC. In addition, inhibition of miR-182-5p expression suppressed cell proliferation and enhanced cell apoptosis in NSCLC cells. CASP2 expression was downregulated in NSCLC tissue and peripheral blood samples from patients with NSCLC. The current study demonstrated that miR-182-5p may regulate NSCLC cell proliferation and apoptosis by regulating CASP2 expression as miR-182-5p directly binds with the 3′-untranslated region of CASP2, thereby regulating CASP2 expression.
Collapse
Affiliation(s)
- Lu Yang
- Department of Pathology and Pathophysiology, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Ye Dou
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Zhuxin Sui
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Hui Cheng
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Xia Liu
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Qinglu Wang
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Peifu Gao
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| | - Yin'e Qu
- Department of Histology and Embryology, School of Basic Medicine, North China University of Science and Technology, Tangshan, Hebei 063210, P.R. China
| | - Ming Xu
- Department of Human Anatomy, Histology and Embryology, Teaching Department of Basic Medicine, Qilu Medical University, Zibo, Shandong 255213, P.R. China
| |
Collapse
|
37
|
Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
Collapse
Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| |
Collapse
|
38
|
Sheikhvatan M, Chaichian S, Moazzami B. A Systematic Review and Bioinformatics Study on Genes and micro-RNAs Involving the Transformation of Endometriosis into Ovarian Cancer. Microrna 2019; 9:101-111. [PMID: 31530272 PMCID: PMC7366012 DOI: 10.2174/2211536608666190917152104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/01/2019] [Accepted: 08/05/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Along with the description of tumorigenesis processes in endometriosisrelated ovarian cancer, identifying dysregulated miRNAs, the target genes of these miRNAs, and the processes abnormally affected by dysregulated miRNAs is essential, which was our goal. METHODS Two reviewers individually evaluated the articles which collected relevant information including genes and miRNAs involved in the transformation of endometriosis into ovarian cancer. To assess the mature sequence of miRNAs and also their chromosomal positions, miRPathDB software was employed. To determine the main target gene predicted for each considered miRNAs, the TargetScanS Web server was applied. The interaction of each gene with other genes associated with endometrial- related ovarian cancer was determined by GeneMANIA software. Finally, to design integrated model of miRNAs-targeted genes interaction network, the Cytoscape software was used. RESULTS The final number of studies available for analysis was 6 manuscripts including 22 miRNAs described as involved in the transformation of endometriosis into different subtypes of ovarian cancers (14 miRNAs up-regulated and 8 miRNAs down-regulated). Three miRNAs of miR-141 (upregulated), miR-205 (down-regulated), and miR-125b (down-regulated) were revealed as the originator for genetic interactions leading to carcinogenesis. We could show some common loops and pathways including uncontrolled cell proliferation and abnormal apoptosis (mediated by PTEN gene induced by miR-21 and miR-214), and disaggregation and epithelialization (mediated by ZEB1 and ZEB2 genes induced by miR-200). CONCLUSION According to our analysis, up-regulation of miR-141 and down-regulation of miR-205 and miR-125b have a central role in transforming endometriosis to ovarian cancer.
Collapse
Affiliation(s)
- Mehrdad Sheikhvatan
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany.,Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Shahla Chaichian
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Bahram Moazzami
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
39
|
Chen Y, Wang L, Zhou J. Effects of microRNA‐1271 on ovarian cancer via inhibition of epithelial‐mesenchymal transition and cisplatin resistance. J Obstet Gynaecol Res 2019; 45:2243-2254. [PMID: 31411791 DOI: 10.1111/jog.14079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/15/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Yanyan Chen
- Department of Outpatient PharmacyNingbo Women & Children's Hospital Ningbo China
| | - Li Wang
- Department of Outpatient PharmacyNingbo Women & Children's Hospital Ningbo China
| | - Jiefang Zhou
- Department of Clinical PharmacologyShaoxing Traditional Chinese Medicine Hospital Shaoxing China
| |
Collapse
|
40
|
Gunaratne PH, Pan Y, Rao AK, Lin C, Hernandez‐Herrera A, Liang K, Rait AS, Venkatanarayan A, Benham AL, Rubab F, Kim SS, Rajapakshe K, Chan CK, Mangala LS, Lopez‐Berestein G, Sood AK, Rowat AC, Coarfa C, Pirollo KF, Flores ER, Chang EH. Activating p53 family member TAp63: A novel therapeutic strategy for targeting p53-altered tumors. Cancer 2019; 125:2409-2422. [PMID: 31012964 PMCID: PMC6617807 DOI: 10.1002/cncr.32053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/25/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND Over 96% of high-grade ovarian carcinomas and 50% of all cancers are characterized by alterations in the p53 gene. Therapeutic strategies to restore and/or reactivate the p53 pathway have been challenging. By contrast, p63, which shares many of the downstream targets and functions of p53, is rarely mutated in cancer. METHODS A novel strategy is presented for circumventing alterations in p53 by inducing the tumor-suppressor isoform TAp63 (transactivation domain of tumor protein p63) through its direct downstream target, microRNA-130b (miR-130b), which is epigenetically silenced and/or downregulated in chemoresistant ovarian cancer. RESULTS Treatment with miR-130b resulted in: 1) decreased migration/invasion in HEYA8 cells (p53 wild-type) and disruption of multicellular spheroids in OVCAR8 cells (p53-mutant) in vitro, 2) sensitization of HEYA8 and OVCAR8 cells to cisplatin (CDDP) in vitro and in vivo, and 3) transcriptional activation of TAp63 and the B-cell lymphoma (Bcl)-inhibitor B-cell lymphoma 2-like protein 11 (BIM). Overexpression of TAp63 was sufficient to decrease cell viability, suggesting that it is a critical downstream effector of miR-130b. In vivo, combined miR-130b plus CDDP exhibited greater therapeutic efficacy than miR-130b or CDDP alone. Mice that carried OVCAR8 xenograft tumors and were injected with miR-130b in 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) liposomes had a significant decrease in tumor burden at rates similar to those observed in CDDP-treated mice, and 20% of DOPC-miR-130b plus CDDP-treated mice were living tumor free. Systemic injections of scL-miR-130b plus CDDP in a clinically tested, tumor-targeted nanocomplex (scL) improved survival in 60% and complete remissions in 40% of mice that carried HEYA8 xenografts. CONCLUSIONS The miR-130b/TAp63 axis is proposed as a new druggable pathway that has the potential to uncover broad-spectrum therapeutic options for the majority of p53-altered cancers.
Collapse
Affiliation(s)
- Preethi H. Gunaratne
- Department of Biochemistry and BiologyUniversity of HoustonHoustonTexas
- Department of Molecular and Cell BiologyBaylor College of MedicineHoustonTexas
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTexas
| | - Yinghong Pan
- Department of Biochemistry and BiologyUniversity of HoustonHoustonTexas
- UPMC Genome CenterPittsburghPennsylvania
| | - Abhi K. Rao
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDistrict of Columbia
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, Division of Basic ScienceThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | | | - Ke Liang
- Department of Molecular and Cellular Oncology, Division of Basic ScienceThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Antonina S. Rait
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDistrict of Columbia
| | - Avinashnarayan Venkatanarayan
- Department of Molecular and Cellular Oncology, Division of Basic ScienceThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Genentech, Inc.South San FranciscoCalifornia
| | - Ashley L. Benham
- Department of Biochemistry and BiologyUniversity of HoustonHoustonTexas
- 10X Genomics Inc.PleasantonCalifornia
| | | | - Sang Soo Kim
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDistrict of Columbia
- SynerGene Therapeutics, Inc.PotomacMaryland
| | - Kimal Rajapakshe
- Department of Molecular and Cell BiologyBaylor College of MedicineHoustonTexas
| | - Clara K. Chan
- Department of Integrative Biology and PhysiologyUniversity of CaliforniaLos AngelesCalifornia
| | - Lingegowda S. Mangala
- Gynecologic Oncology and Reproductive MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Center for RNAi and Non-Coding RNAsThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Gabriel Lopez‐Berestein
- Center for RNAi and Non-Coding RNAsThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Department of Experimental TherapeuticsThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Anil K. Sood
- Gynecologic Oncology and Reproductive MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Center for RNAi and Non-Coding RNAsThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Amy C. Rowat
- Department of Integrative Biology and PhysiologyUniversity of CaliforniaLos AngelesCalifornia
| | - Cristian Coarfa
- Department of Molecular and Cell BiologyBaylor College of MedicineHoustonTexas
| | - Kathleen F. Pirollo
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDistrict of Columbia
| | - Elsa R. Flores
- Department of Molecular and Cellular Oncology, Division of Basic ScienceThe University of Texas MD Anderson Cancer CenterHoustonTexas
- Department of Molecular OncologyCancer Biology and Evolution Program, Moffitt Cancer CenterTampaFlorida
| | - Esther H. Chang
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDistrict of Columbia
- SynerGene Therapeutics, Inc.PotomacMaryland
| |
Collapse
|
41
|
Alqurashi N, Hashimi SM, Alowaidi F, Ivanovski S, Farag A, Wei MQ. miR-496, miR-1185, miR-654, miR-3183 and miR-495 are downregulated in colorectal cancer cells and have putative roles in the mTOR pathway. Oncol Lett 2019; 18:1657-1668. [PMID: 31423233 PMCID: PMC6614670 DOI: 10.3892/ol.2019.10508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/02/2019] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by suppressing the target mRNA and inhibiting translation in order to regulate multiple biological processes. miRNAs play important roles as oncogenes or tumor suppressors in the development of various types of human cancer. The regulation of mammalian target of rapamycin (mTOR) by miRNAs has been studied in several types of cancer, including colorectal cancer (CRC). However, to the best of our knowledge, only limited information regarding the function of miRNAs in human CRC is available. In the present study, the expression of 22 miRNAs in CRC cell lines were investigated in regard to key genes in the mTOR pathway. Initially, it was revealed that mTOR, regulatory-associated protein of mTOR complex I and rapamycin-intensive companion of mTOR were overexpressed in CRC cell lines when compared with a normal colorectal cell line. Subsequently, putative miRNA-mRNA associations were identified via multiple miRNA target prediction programs. The expression levels for the candidate miRNAs were validated using quantitative real-time polymerase chain reaction. Expression analysis revealed that, among 20 miRNAs, five miRNAs (miR-496, miR-1185, miR-654, miR-3183 and miR-495) exhibited significant downregulation in association with the mTOR signaling pathway. Taken together, the results from the present study suggest that several miRNAs that are associated with CRC, with possible roles in mTOR signaling, may have potential therapeutic or diagnostic benefits in CRC treatment.
Collapse
Affiliation(s)
- Naif Alqurashi
- Department of Basic Science, Deanship of Preparatory Year and Supporting Studies, and Department of Stem Cells, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Saeed M Hashimi
- Department of Basic Science, Deanship of Preparatory Year and Supporting Studies, and Department of Stem Cells, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Faisal Alowaidi
- Department of Pathology and Laboratory Medicine, College of Medicine and University Hospitals, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saso Ivanovski
- School of Dentistry, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Amro Farag
- School of Dentistry, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Ming Q Wei
- Division of Molecular and Gene Therapies, School of Medical Science, Griffith University, Gold Coast, QLD 4222, Australia
| |
Collapse
|
42
|
Tang H, Liu Y, Cheng W, He Z, Zhou N. microRNA-96-5p induces the epithelial-mesenchymal transition to promote the metastasis of hepatocellular carcinoma by post-transcriptionally downregulating Talin 1. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1897-1908. [PMID: 31934013 PMCID: PMC6947103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/27/2019] [Indexed: 06/10/2023]
Abstract
Numerous microRNAs (miRNAs) have been shown to play an important regulatory role in the progression of hepatocellular carcinoma (HCC). miR-96-5p, a cancer-related microRNA, was previously reported to inhibit cell apoptosis in HCC, but the function and underlying mechanism of miR-96-5p's involvement in HCC metastasis and progression still remain unknown. In this study, we showed that a significant up-regulation of miR-96-5p in HCC tissues and cell lines, and its increased expression, are associated with microvascular invasion and with the TNM stages of HCC patients. Gain-of-function assays revealed that miR-96-5p induced the epithelial-mesenchymal transition (EMT) to promote the migration and invasion of HCC in vitro. The expression of TLN1 (Talin 1) is significantly decreased in HCC tissues and is inversely correlated to miR-96-5p levels. Notably, through a luciferase reporter assay and a Western blot analysis, TLN1 was confirmed to be a direct target gene of miR-96-5p. Furthermore, results of cell functional assays revealed that the over-expression of TLN1 partially reverses the promotive effects of miR-96-5p overexpression on the migration, invasion, and EMT of HCC. Overall, data from the present study demonstrate that miR-96-5p induces EMT to promote the migration and invasion of HCC by post-transcriptionally downregulating TLN1, indicating that the miR-96-5p/TLN1 axis might provide a potential therapeutic target for the treatment of HCC.
Collapse
Affiliation(s)
- Hongying Tang
- Laboratory of Hepatobiliary Molecular Oncology, Department of Hepatopancreatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University Changsha, P. R. China
| | - Yi Liu
- Laboratory of Hepatobiliary Molecular Oncology, Department of Hepatopancreatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University Changsha, P. R. China
| | - Wei Cheng
- Laboratory of Hepatobiliary Molecular Oncology, Department of Hepatopancreatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University Changsha, P. R. China
| | - Zili He
- Laboratory of Hepatobiliary Molecular Oncology, Department of Hepatopancreatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University Changsha, P. R. China
| | - Ning Zhou
- Laboratory of Hepatobiliary Molecular Oncology, Department of Hepatopancreatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University Changsha, P. R. China
| |
Collapse
|
43
|
Perez‐Añorve IX, Gonzalez‐De la Rosa CH, Soto‐Reyes E, Beltran‐Anaya FO, Del Moral‐Hernandez O, Salgado‐Albarran M, Angeles‐Zaragoza O, Gonzalez‐Barrios JA, Landero‐Huerta DA, Chavez‐Saldaña M, Garcia‐Carranca A, Villegas‐Sepulveda N, Arechaga‐Ocampo E. New insights into radioresistance in breast cancer identify a dual function of miR-122 as a tumor suppressor and oncomiR. Mol Oncol 2019; 13:1249-1267. [PMID: 30938061 PMCID: PMC6487688 DOI: 10.1002/1878-0261.12483] [Citation(s) in RCA: 30] [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: 10/31/2018] [Revised: 02/10/2019] [Accepted: 03/13/2019] [Indexed: 12/25/2022] Open
Abstract
Radioresistance of tumor cells gives rise to local recurrence and disease progression in many patients. MicroRNAs (miRNAs) are master regulators of gene expression that control oncogenic pathways to modulate the radiotherapy response of cells. In the present study, differential expression profiling assays identified 16 deregulated miRNAs in acquired radioresistant breast cancer cells, of which miR-122 was observed to be up-regulated. Functional analysis revealed that miR-122 has a role as a tumor suppressor in parental cells by decreasing survival and promoting radiosensitivity. However, in radioresistant cells, miR-122 functions as an oncomiR by promoting survival. The transcriptomic landscape resulting from knockdown of miR-122 in radioresistant cells showed modulation of the ZNF611, ZNF304, RIPK1, HRAS, DUSP8 and TNFRSF21 genes. Moreover, miR-122 and the set of affected genes were prognostic factors in breast cancer patients treated with radiotherapy. Our data indicate that up-regulation of miR-122 promotes cell survival in acquired radioresistant breast cancer and also suggest that miR-122 differentially controls the response to radiotherapy by a dual function as a tumor suppressor an and oncomiR dependent on cell phenotype.
Collapse
Affiliation(s)
- Isidro X. Perez‐Añorve
- Posgrado en Ciencias Naturales e IngenieriaDivision de Ciencias Naturales e IngenieriaUniversidad Autonoma MetropolitanaMexico CityMexico
- Departamento de Ciencias NaturalesUniversidad Autonoma Metropolitana, Unidad CuajimalpaMexico CityMexico
| | | | - Ernesto Soto‐Reyes
- Departamento de Ciencias NaturalesUniversidad Autonoma Metropolitana, Unidad CuajimalpaMexico CityMexico
| | - Fredy O. Beltran‐Anaya
- Laboratorio de Genomica del CancerInstituto Nacional de Medicina GenomicaMexico CityMexico
| | - Oscar Del Moral‐Hernandez
- Laboratorio de Virologia y Epigenetica del CancerFacultad de Ciencias Quimico BiologicasUniversidad Autonoma de GuerreroChilpancingoMexico
| | - Marisol Salgado‐Albarran
- Departamento de Ciencias NaturalesUniversidad Autonoma Metropolitana, Unidad CuajimalpaMexico CityMexico
| | | | | | - Daniel A. Landero‐Huerta
- Posgrado en Ciencias Naturales e IngenieriaDivision de Ciencias Naturales e IngenieriaUniversidad Autonoma MetropolitanaMexico CityMexico
- Departamento de Ciencias NaturalesUniversidad Autonoma Metropolitana, Unidad CuajimalpaMexico CityMexico
- Laboratorio de Biologia de la ReproduccionInstituto Nacional de PediatríaMexico CityMexico
| | | | - Alejandro Garcia‐Carranca
- Unidad de Investigacion Biomedica en Cancer‐Laboratorio de Virus y CancerInstituto Nacional de CancerologiaMexico CityMexico
| | - Nicolas Villegas‐Sepulveda
- Departamento de Biomedicina MolecularCentro de Investigacion y de Estudios Avanzados (CINVESTAV)Mexico CityMexico
| | - Elena Arechaga‐Ocampo
- Departamento de Ciencias NaturalesUniversidad Autonoma Metropolitana, Unidad CuajimalpaMexico CityMexico
| |
Collapse
|
44
|
Sun D, Zhong J, Wei W, Chen X, Liu J, Hu Z. Identification of microRNA expression in sentinel lymph nodes from patients with breast cancer via RNA sequencing for diagnostic accuracy. J Gene Med 2019; 21:e3075. [PMID: 30716792 DOI: 10.1002/jgm.3075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 01/12/2023] Open
Affiliation(s)
- Desheng Sun
- Department of UltrasonographyPeking University Shenzhen Hospital Shenzhen Guangdong China
| | - Jieyu Zhong
- Department of UltrasonographyPeking University Shenzhen Hospital Shenzhen Guangdong China
| | - Wei Wei
- Department of Breast SurgeryPeking University Shenzhen Hospital Shenzhen Guangdong China
| | - Xiangmei Chen
- Department of UltrasonographyPeking University Shenzhen Hospital Shenzhen Guangdong China
| | - Jun Liu
- Department of PathologyPeking University Shenzhen Hospital Shenzhen Guangdong China
| | - Zhengming Hu
- Department of UltrasonographyPeking University Shenzhen Hospital Shenzhen Guangdong China
| |
Collapse
|
45
|
Schiavon BN, Carvalho KC, Coutinho-Camillo CM, Baiocchi G, Valieris R, Drummond R, da Silva IT, De Brot L, Soares FA, da Cunha IW. miRNAs 144-3p, 34a-5p, and 206 are a useful signature for distinguishing uterine leiomyosarcoma from other smooth muscle tumors. SURGICAL AND EXPERIMENTAL PATHOLOGY 2019. [DOI: 10.1186/s42047-019-0032-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Background
Leiomyosarcoma (LMS) is a rare uterine neoplasm that has a high mortality rate and no specific treatment. The origin of LMS remains unknown; although, it is hypothesized that LMS arises from the malignant transformation of a degenerated uterine leiomyoma (LM). LMs are the most common benign tumors diagnosed and rare variants of LM (unconventional LM) morphologically resemble LMS, thereby making an early and precise diagnosis of LMS difficult. Various molecular features may influence the malignancy risk of LMS tumors, including microRNAs (miRNAs). However, the role of miRNAs in uterine mesenchymal tumors remains poorly understood. Here, our aim was to assess the miRNA expression profiles of LMS, LM, and LM variants (ULM) to identify a specific signature that may facilitate differentiation among these tumor types. Possible associations between these profiles and patients’ clinical and pathological features were also analyzed.
Methods
Total RNA was extracted from formalin-fixed paraffin-embedded tissue samples of uterine LMS (n = 37), LM (n = 3), ULM (n = 8), and myometrium (MM) (n = 2) to perform real-time PCR analyses and detect expression levels of a panel of 84 miRNA sequences related to cancer.
Results
Between the LMS and LM samples, 16 miRNAs were found to be differentially expressed, with miR-372 and miR-34a-5p exhibiting the highest and lowest levels of expression, respectively. When LMS and ULM were compared, 5 differentially expressed miRNAs were identified, with miR-34a-5p downregulated and miR-144-3p upregulated. Between ULM and LM, all of the differentially expressed miRNAs were upregulated, and miR122-5p exhibited 10-fold higher expression. In addition, significant correlations were found between various miRNAs and tumor relapse (miR-148a-3p), metastasis (miR-27b-3p), and patient death (miR-124-3p and miR-183-5p). Downregulation of miR135b-5p was associated with disease-free survival.
Conclusion
Expression profiling of miRNAs 144-3p, 34a-5p, and 206 may be useful in characterizing uterine LMS and distinguishing it from benign tumors. Furthermore, deregulation of miRNAs 148a-3p, 27b-3p, 124-3p, 183-5p, and 135b-5p appear to indicate a poor prognosis for LMS patients.
Collapse
|
46
|
Identifying a miRNA signature for predicting the stage of breast cancer. Sci Rep 2018; 8:16138. [PMID: 30382159 PMCID: PMC6208346 DOI: 10.1038/s41598-018-34604-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/12/2018] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a heterogeneous disease and one of the most common cancers among women. Recently, microRNAs (miRNAs) have been used as biomarkers due to their effective role in cancer diagnosis. This study proposes a support vector machine (SVM)-based classifier SVM-BRC to categorize patients with breast cancer into early and advanced stages. SVM-BRC uses an optimal feature selection method, inheritable bi-objective combinatorial genetic algorithm, to identify a miRNA signature which is a small set of informative miRNAs while maximizing prediction accuracy. MiRNA expression profiles of a 386-patient cohort of breast cancer were retrieved from The Cancer Genome Atlas. SVM-BRC identified 34 of 503 miRNAs as a signature and achieved a 10-fold cross-validation mean accuracy, sensitivity, specificity, and Matthews correlation coefficient of 80.38%, 0.79, 0.81, and 0.60, respectively. Functional enrichment of the 10 highest ranked miRNAs was analysed in terms of Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations. Kaplan-Meier survival analysis of the highest ranked miRNAs revealed that four miRNAs, hsa-miR-503, hsa-miR-1307, hsa-miR-212 and hsa-miR-592, were significantly associated with the prognosis of patients with breast cancer.
Collapse
|
47
|
Wang X, Han L, Zhou L, Wang L, Zhang LM. Prediction of candidate RNA signatures for recurrent ovarian cancer prognosis by the construction of an integrated competing endogenous RNA network. Oncol Rep 2018; 40:2659-2673. [PMID: 30226545 PMCID: PMC6151886 DOI: 10.3892/or.2018.6707] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/10/2018] [Indexed: 12/28/2022] Open
Abstract
Tumor recurrence hinders treatment of ovarian cancer. The present study aimed to identify potential biomarkers for ovarian cancer recurrence prognosis and explore relevant mechanisms. RNA-sequencing of data from the TCGA database and GSE17260 dataset was carried out. Samples of the data were grouped according to tumor recurrence information. Following data normalization, differentially expressed genes/micro RNAs (miRNAs)/long non-coding (lncRNAs) (DEGs/DEMs/DELs) were selected between recurrent and non-recurrent samples. Their correlations with clinical information were analyzed to identify prognostic RNAs. A support vector machine classifier was used to find the optimal gene set with feature genes that could conclusively distinguish different samples. A protein-protein interaction (PPI) network was established for DEGs using relevant protein databases. An integrated ‘lncRNA/miRNA/mRNA’ competing endogenous RNA (ceRNA) network was constructed to reveal potential regulatory relationships among different RNAs. We identified 36 feature genes (e.g. TP53 and RBPMS) for the classification of recurrent and non-recurrent ovarian cancer samples. Prediction with this gene set had a high accuracy (91.8%). Three DELs (WT1-AS, NBR2 and ZNF883) were highly associated with the prognosis of recurrent ovarian cancer. Predominant DEMs with their targets were hsa-miR-375 (target: RBPMS), hsa-miR-141 (target: RBPMS), and hsa-miR-27b (target: TP53). Highlighted interactions in the ceRNA network were ‘WT1-AS-hsa-miR-375-RBPMS’ and ‘WT1-AS-hsa-miR-27b-TP53’. TP53, RBPMS, hsa-miR-375, hsa-miR-141, hsa-miR-27b, and WT1-AS may be biomarkers for recurrent ovarian cancer. The interactions of ‘WT1-AS-hsa-miR-375-RBPMS’ and ‘WT1-AS-hsa-miR-27b-TP53’ may be potential regulatory mechanisms during cancer recurrence.
Collapse
Affiliation(s)
- Xin Wang
- Department of Gynecology and Obstetrics, The 306 Hospital of PLA, Beijing 100101, P.R. China
| | - Lei Han
- Department of Gynecology and Obstetrics, The 306 Hospital of PLA, Beijing 100101, P.R. China
| | - Ling Zhou
- Department of Gynecology and Obstetrics, The 306 Hospital of PLA, Beijing 100101, P.R. China
| | - Li Wang
- Department of Gynecology and Obstetrics, The 306 Hospital of PLA, Beijing 100101, P.R. China
| | - Lan-Mei Zhang
- Department of Gynecology and Obstetrics, The 306 Hospital of PLA, Beijing 100101, P.R. China
| |
Collapse
|
48
|
STAT3 regulated miR-216a promotes ovarian cancer proliferation and cisplatin resistance. Biosci Rep 2018; 38:BSR20180547. [PMID: 30061175 PMCID: PMC6131203 DOI: 10.1042/bsr20180547] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 12/14/2022] Open
Abstract
Cisplatin is the first-line treatment for ovarian cancer. However, the clinical outcome of cisplatin treatment in ovarian cancer is hindered by cancer resistance. Here we aim to explore the role and mechanism of miR-216a in the cisplatin resistance of ovarian cancer. The effects of miR-216a overexpression and inhibition on ovarian cell proliferation, colony formation, and cisplatin resistance were investigated by MTT assay and soft agar colony formation assay. Bioinformatics analyses using TargetScan and rVista, qPCR, and luciferase assay were also used to explore and verify downstream effectors and regulators of miR-216a. Proliferation, colony formation, and cisplatin resistance of ovarian cancer cells are promoted by miR-216a overexpression but inhibited by miR-216a inhibition. PTEN is a direct target of miR-216a and PTEN expression antagonizes the tumor-promoting function of miR-216a. STAT3 is a regulator of miR-216a, and PTEN is also regulated by STAT3. miR-216a up-regulation is associated with cisplatin resistance in ovarian cancer and this effect is mediated by PTEN. STAT3 is a regulator of miR-216a. Strategies that inhibit miR-216a is a potential strategy for overcoming the cisplatin resistance in ovarian cancer.
Collapse
|
49
|
Fort RS, Mathó C, Oliveira-Rizzo C, Garat B, Sotelo-Silveira JR, Duhagon MA. An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. Exp Hematol Oncol 2018; 7:10. [PMID: 29744254 PMCID: PMC5930504 DOI: 10.1186/s40164-018-0102-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/20/2018] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer is a major health problem worldwide due to its high incidence morbidity and mortality. There is currently a need of improved biomarkers, capable to distinguish mild versus aggressive forms of the disease, and thus guide therapeutic decisions. Although miRNAs deregulated in cancer represent exciting candidates as biomarkers, its scientific literature is frequently fragmented in dispersed studies. This problem is aggravated for miRNAs belonging to miRNA gene clusters with shared target genes. The miRNA cluster composed by hsa-mir-130b and hsa-mir-301b precursors was recently involved in prostate cancer pathogenesis, yet different studies assigned it opposite effects on the disease. We sought to elucidate the role of the human miR-130b/301b miRNA cluster in prostate cancer through a comprehensive data analysis of most published clinical cohorts. We interrogated methylomes, transcriptomes and patient clinical data, unifying previous reports and adding original analysis using the largest available cohort (TCGA-PRAD). We found that hsa-miR-130b-3p and hsa-miR-301b-3p are upregulated in neoplastic vs normal prostate tissue, as well as in metastatic vs primary sites. However, this increase in expression is not due to a decrease of the global DNA methylation of the genes in prostate tissues, as the promoter of the gene remains lowly methylated in normal and neoplastic tissue. A comparison of the levels of human miR-130b/301b and all the clinical variables reported for the major available cohorts, yielded positive correlations with malignance, specifically significant for T-stage, residual tumor status and primary therapy outcome. The assessment of the correlations between the hsa-miR-130b-3p and hsa-miR-301b-3p and candidate target genes in clinical samples, supports their repression of tumor suppressor genes in prostate cancer. Altogether, these results favor an oncogenic role of miR-130b/301b cluster in prostate cancer.
Collapse
Affiliation(s)
- Rafael Sebastián Fort
- 1Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,2Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Mathó
- 1Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,2Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Carolina Oliveira-Rizzo
- 1Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,2Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Garat
- 1Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- 3Depto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,4Depto. de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - María Ana Duhagon
- 1Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,2Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
50
|
Chen SF, Liu Z, Chaurasiya S, Dellinger TH, Lu J, Wu X, Qin H, Wang J, Fong Y, Yuan YC. Identification of core aberrantly expressed microRNAs in serous ovarian carcinoma. Oncotarget 2018; 9:20451-20466. [PMID: 29755664 PMCID: PMC5945511 DOI: 10.18632/oncotarget.24942] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/13/2018] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) have recently demonstrated great potential and enormous promise in the diagnosis, prognosis and therapy of various types of cancer. In this study, we performed a comprehensive miRNA expression analysis in the omental metastasis of serous ovarian carcinoma (SOC) using small RNA sequencing. Two hundred and fifty-one aberrantly expressed miRNAs were identified, which clearly separated malignant omentum from normal omentum. Furthermore, miRNA profiles in primary chemo-sensitive and chemo-resistant/refractory SOC were determined using publicly available data. Comparing miRNA expression profiles in omental metastases and primary chemo-sensitive and chemo-resistant/refractory tumors, a set of 70 miRNAs that were aberrantly expressed in both primary and metastatic SOC has been identified for the first time. These core aberrantly expressed miRNAs may play crucial roles in the tumorigenesis, growth, and metastasis of SOC. Therefore, they can serve as potential diagnostic biomarkers and as therapeutic targets for miRNA-mediated therapy. Kaplan-Meier overall survival analysis using The Cancer Genome Atlas data demonstrated that 10 miRNAs (hsa-miR-135, 150, -340, 625, 1908, 3187, -96, -196b, -449c, and -1275) were associated with survival of patients with SOC, which may serve as potential prognostic biomarkers.
Collapse
Affiliation(s)
- Steven F. Chen
- Bioinformatics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Zheng Liu
- Bioinformatics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Shyambabu Chaurasiya
- Department of Surgery, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Thanh H. Dellinger
- Department of Surgery, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Jianming Lu
- Department of Surgery, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Hanjun Qin
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Yuman Fong
- Department of Surgery, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Yate-Ching Yuan
- Bioinformatics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| |
Collapse
|