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Bahramy A, Zafari N, Rajabi F, Aghakhani A, Jayedi A, Khaboushan AS, Zolbin MM, Yekaninejad MS. Prognostic and diagnostic values of non-coding RNAs as biomarkers for breast cancer: An umbrella review and pan-cancer analysis. Front Mol Biosci 2023; 10:1096524. [PMID: 36726376 PMCID: PMC9885171 DOI: 10.3389/fmolb.2023.1096524] [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: 11/12/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Background: Breast cancer (BC) is the most common cancer in women. The incidence and morbidity of BC are expected to rise rapidly. The stage at which BC is diagnosed has a significant impact on clinical outcomes. When detected early, an overall 5-year survival rate of up to 90% is possible. Although numerous studies have been conducted to assess the prognostic and diagnostic values of non-coding RNAs (ncRNAs) in breast cancer, their overall potential remains unclear. In this field of study, there are various systematic reviews and meta-analysis studies that report volumes of data. In this study, we tried to collect all these systematic reviews and meta-analysis studies in order to re-analyze their data without any restriction to breast cancer or non-coding RNA type, to make it as comprehensive as possible. Methods: Three databases, namely, PubMed, Scopus, and Web of Science (WoS), were searched to find any relevant meta-analysis studies. After thoroughly searching, the screening of titles, abstracts, and full-text and the quality of all included studies were assessed using the AMSTAR tool. All the required data including hazard ratios (HRs), sensitivity (SENS), and specificity (SPEC) were extracted for further analysis, and all analyses were carried out using Stata. Results: In the prognostic part, our initial search of three databases produced 10,548 articles, of which 58 studies were included in the current study. We assessed the correlation of non-coding RNA (ncRNA) expression with different survival outcomes in breast cancer patients: overall survival (OS) (HR = 1.521), disease-free survival (DFS) (HR = 1.33), recurrence-free survival (RFS) (HR = 1.66), progression-free survival (PFS) (HR = 1.71), metastasis-free survival (MFS) (HR = 0.90), and disease-specific survival (DSS) (HR = 0.37). After eliminating low-quality studies, the results did not change significantly. In the diagnostic part, 22 articles and 30 datasets were retrieved from 8,453 articles. The quality of all studies was determined. The bivariate and random-effects models were used to assess the diagnostic value of ncRNAs. The overall area under the curve (AUC) of ncRNAs in differentiated patients is 0.88 (SENS: 80% and SPEC: 82%). There was no difference in the potential of single and combined ncRNAs in differentiated BC patients. However, the overall potential of microRNAs (miRNAs) is higher than that of long non-coding RNAs (lncRNAs). No evidence of publication bias was found in the current study. Nine miRNAs, four lncRNAs, and five gene targets showed significant OS and RFS between normal and cancer patients based on pan-cancer data analysis, demonstrating their potential prognostic value. Conclusion: The present umbrella review showed that ncRNAs, including lncRNAs and miRNAs, can be used as prognostic and diagnostic biomarkers for breast cancer patients, regardless of the sample sources, ethnicity of patients, and subtype of breast cancer.
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Affiliation(s)
- Afshin Bahramy
- Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Narges Zafari
- Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amirhossein Aghakhani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Jayedi
- Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Alireza Soltani Khaboushan
- Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran,Students’ Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Majidi Zolbin
- Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran,*Correspondence: Mir Saeed Yekaninejad, , ; Masoumeh Majidi Zolbin, ,
| | - Mir Saeed Yekaninejad
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran,*Correspondence: Mir Saeed Yekaninejad, , ; Masoumeh Majidi Zolbin, ,
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Agrawal D, Kumari R, Ratre P, Rehman A, Srivastava RK, Reszka E, Goryacheva IY, Mishra PK. Cell-free circulating miRNAs-lncRNAs-mRNAs as predictive markers for breast cancer risk assessment in women exposed to indoor air pollution. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100267. [DOI: 10.1016/j.cscee.2022.100267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
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Kahng DH, Kim GH, Park SJ, Kim S, Lee MW, Lee BE, I H. MicroRNA Expression in Plasma of Esophageal Squamous Cell Carcinoma Patients. J Korean Med Sci 2022; 37:e197. [PMID: 35726148 PMCID: PMC9247724 DOI: 10.3346/jkms.2022.37.e197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Patients with esophageal squamous cell carcinoma (ESCC) have a poor prognosis and there are no effective clinical biomarkers. Recently, stable microRNAs detected in the blood have been suggested as potential biomarkers in various cancers. Therefore, we investigated whether plasma microRNAs could be feasible biomarkers for ESCC. METHODS Peripheral blood samples were obtained from 16 healthy volunteers and 66 ESCC patients before treatment between May 2016 and April 2021. Plasma miR-18b, miR-21, miR-31, and miR-375 expression levels were measured using reverse transcription-quantitative polymerase chain reaction. RESULTS Compared with those in healthy controls, the expression levels of plasma miR-21 were significantly higher (P = 0.022) and those of plasma miR-31 and miR-375 were significantly lower in ESCC patients (both P < 0.001). Plasma miR-18b expression levels increased in ESCC patients, but the difference was not significant (P = 0.164). The sensitivities and specificities of miR-21, miR-31, and miR-375 for differentiating ESCC patients from healthy controls were 87.5% and 61.9%, 87.5% and 98.4%, and 87.5% and 100%, respectively. There was no difference in expression levels of plasma miR-21, miR-31, and miR-375 according to clinicopathological characteristics of sex, age, tumor size and location, histologic grade, and tumor-node-metastasis stage. CONCLUSION Our study demonstrated that plasma miR-21, miR-31, and miR-375 could be potential biomarkers for the diagnosis of ESCC. Particularly, plasma miR-31 and miR-375 showed high sensitivity and specificity for differentiating ESCC patients from healthy controls.
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Affiliation(s)
- Dong Hwahn Kahng
- Department of Internal Medicine, Pusan National University College of Medicine, Busan, Korea
| | - Gwang Ha Kim
- Department of Internal Medicine, Pusan National University College of Medicine, Busan, Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.
| | - Su Jin Park
- Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Sora Kim
- Department of Convergence Medical Sciences, Pusan National University Graduate School of Medicine, Yangsan, Korea
| | - Moon Won Lee
- Department of Internal Medicine, Pusan National University College of Medicine, Busan, Korea
| | - Bong Eun Lee
- Department of Internal Medicine, Pusan National University College of Medicine, Busan, Korea
| | - Hoseok I
- Department of Thoracic Surgery, Pusan National University College of Medicine, Busan, Korea
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Ortega MA, Fraile-Martínez O, Guijarro LG, Casanova C, Coca S, Álvarez-Mon M, Buján J, García-Honduvilla N, Asúnsolo Á. The Regulatory Role of Mitochondrial MicroRNAs (MitomiRs) in Breast Cancer: Translational Implications Present and Future. Cancers (Basel) 2020; 12:cancers12092443. [PMID: 32872155 PMCID: PMC7564393 DOI: 10.3390/cancers12092443] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Mitochondrial microRNAs (mitomiRs) are an emerging field of study in a wide range of tumours including breast cancer. By targeting mitochondrial, or non-mitochondrial products, mitomiRs are able to regulate the functions of this organelle, thus controlling multiple carcinogenic processes. The knowledge of this system may provide a novel approach for targeted therapies, as potential biomarkers or helping in the diagnosis of such a complex malignancy. Abstract Breast cancer is the most prevalent and incident female neoplasm worldwide. Although survival rates have considerably improved, it is still the leading cause of cancer-related mortality in women. MicroRNAs are small non-coding RNA molecules that regulate the posttranscriptional expression of a wide variety of genes. Although it is usually located in the cytoplasm, several studies have detected a regulatory role of microRNAs in other cell compartments such as the nucleus or mitochondrion, known as “mitomiRs”. MitomiRs are essential modulators of mitochondrion tasks and their abnormal expression has been linked to the aetiology of several human diseases related to mitochondrial dysfunction, including breast cancer. This review aims to examine basic knowledge of the role of mitomiRs in breast cancer and discusses their prospects as biomarkers or therapeutic targets.
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Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Madrid, Spain
- Correspondence: ; Tel.: +34-91-885-4540; Fax: +34-91-885-4885
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
| | - Luis G. Guijarro
- Department of System Biology, Unit of Biochemistry and Molecular Biology (CIBEREHD), University of Alcalá, 28801 Alcalá de Henares, Spain;
| | - Carlos Casanova
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
| | - Santiago Coca
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine, University Hospital Príncipe de Asturias, (CIBEREHD), 28806 Alcalá de Henares, Madrid, Spain
| | - Julia Buján
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Ángel Asúnsolo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Madrid, Spain
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Gao Y, Liu M, Shi S, Sun Y, Li M, Zhang M, Sheng Z, Zhang J, Tian J. Diagnostic value of seven biomarkers for breast cancer: an overview with evidence mapping and indirect comparisons of diagnostic test accuracy. Clin Exp Med 2020; 20:97-108. [PMID: 31894424 DOI: 10.1007/s10238-019-00598-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023]
Abstract
Several meta-analyses have evaluated the value of biomarkers in diagnosing breast cancer, but which biomarker has the optimal diagnostic value remains unclear. This overview aimed to compare the accuracy of different biomarkers in diagnosing breast cancer. PubMed, Embase.com, the Cochrane Library of Systematic Reviews, and Web of Science were searched. The assessment of multiple systematic reviews-2 (AMSTAR-2) was used to assess the methodological quality and preferred reporting items for a systematic review and meta-analysis of diagnostic test accuracy (PRISMA-DTA) for reporting quality. Pairwise meta-analyses were performed to estimate the pooled results for each biomarker, and indirect comparisons were conducted to compare diagnostic accuracy between biomarkers. Eleven systematic reviews (SRs) involving 218 original studies were included. All SRs were of critically low methodological quality, 3 SRs had minimal reporting flaws and 8 SRs had minor flaws. The pooled sensitivity and specificity were 0.77 and 0.87 for miRNA, 0.70 and 0.87 for circulating cell-free DNA, 0.29 and 0.96 for APC gene promoter methylation, 0.69 and 0.99 for 14-3-3σ promoter methylation, 0.63 and 0.82 for CA153, 0.58 and 0.87 for CEA, and 0.73 and 0.56 for PSA. Compared with CA153 and PSA, miRNA had a higher sensitivity and specificity. The sensitivity of miRNA was higher than circulating cell-free DNA and CEA, although they had the same specificities. APC gene promoter methylation and 14-3-3σ promoter methylation were more specific than miRNA, but they had unacceptably low sensitivity. In conclusion, miRNA had better diagnostic accuracy than the other six biomarkers. But due to the low quality of included SRs, the results need to be interpreted with caution. Further study should investigate the diagnostic accuracy of different biomarkers in direct comparisons and focus on the value of combined biomarkers.
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Affiliation(s)
- Ya Gao
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Ming Liu
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Shuzhen Shi
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Yue Sun
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China
| | - Muyang Li
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Mei Zhang
- Department of Radiology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Zhijuan Sheng
- Department of Galactophore, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Junhua Zhang
- Evidence-Based Medicine Center, Tianjin University of Traditional Chinese Medicine, No. 312 Anshanxi Street, Nankai District, Tianjin, 300193, China.
| | - Jinhui Tian
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.
- Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Lanzhou City, 730000, Gansu Province, China.
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Vychytilova-Faltejskova P, Slaby O. MicroRNA-215: From biology to theranostic applications. Mol Aspects Med 2019; 70:72-89. [DOI: 10.1016/j.mam.2019.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/10/2019] [Accepted: 03/17/2019] [Indexed: 02/07/2023]
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Xue F, Liang Y, Li Z, Liu Y, Zhang H, Wen Y, Yan L, Tang Q, Xiao E, Zhang D. MicroRNA-9 enhances sensitivity to cetuximab in epithelial phenotype hepatocellular carcinoma cells through regulation of the eukaryotic translation initiation factor 5A-2. Oncol Lett 2017; 15:813-820. [PMID: 29399149 PMCID: PMC5772877 DOI: 10.3892/ol.2017.7399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 09/22/2017] [Indexed: 12/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most widespread malignant human tumors worldwide. Treatment options include radiotherapy, surgical intervention and chemotherapy; however, drug resistance is an ongoing treatment concern. In the present study, the effects of a microRNA (miR/miRNA), miR-9, on the sensitivity of HCC cell lines to the epidermal growth factor receptor inhibitor, cetuximab, were examined. miR-9 has been proposed to serve a role in tumorigenesis and tumor progression. In the present study, bioinformatics analyses identified the eukaryotic translation initiation factor 5A2 (eIF-5A-2) as a target of miR-9. The expression levels of miR-9 and eIF-5A-2 were examined by reverse transcription-quantitative polymerase chain reaction and HCC cell lines were transfected with miR-9 mimics and inhibitors to determine the effects of the miRNA on cell proliferation and viability. The miR-9 mimic was revealed to significantly increase the sensitivity of epithelial phenotype HCC cells (Hep3B and Huh7) to cetuximab, while the miR-9 inhibitor triggered the opposite effect. There were no significant differences in sensitivity to cetuximab observed in mesenchymal phenotype HCC cells (SNU387 and SNU449). Cells lines displaying high expression levels of eIF-5A-2 were more resistant to cetuximab. Transfection of cells with a miR-9 mimic resulted in downregulation of the expression of eIF-5A-2 mRNA, while an miR-9 inhibitor increased expression. When expression of eIF-5A-2 was knocked down with siRNA, the effects of miR-9 on cetuximab sensitivity were no longer observed. Taken together, these data support a role for miR-9 in enhancing the sensitivity of epithelial phenotype HCC cells to cetuximab through regulation of eIF-5A-2.
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Affiliation(s)
- Fei Xue
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Yuntian Liang
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Zhenrong Li
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Yanhui Liu
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Hongwei Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Yu Wen
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Lei Yan
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Qiang Tang
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Erhui Xiao
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
| | - Dongyi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 410003, P.R. China
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Telonis AG, Magee R, Loher P, Chervoneva I, Londin E, Rigoutsos I. Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res 2017; 45:2973-2985. [PMID: 28206648 PMCID: PMC5389567 DOI: 10.1093/nar/gkx082] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/07/2017] [Indexed: 12/21/2022] Open
Abstract
Isoforms of human miRNAs (isomiRs) are constitutively expressed with tissue- and disease-subtype-dependencies. We studied 10 271 tumor datasets from The Cancer Genome Atlas (TCGA) to evaluate whether isomiRs can distinguish amongst 32 TCGA cancers. Unlike previous approaches, we built a classifier that relied solely on ‘binarized’ isomiR profiles: each isomiR is simply labeled as ‘present’ or ‘absent’. The resulting classifier successfully labeled tumor datasets with an average sensitivity of 90% and a false discovery rate (FDR) of 3%, surpassing the performance of expression-based classification. The classifier maintained its power even after a 15× reduction in the number of isomiRs that were used for training. Notably, the classifier could correctly predict the cancer type in non-TCGA datasets from diverse platforms. Our analysis revealed that the most discriminatory isomiRs happen to also be differentially expressed between normal tissue and cancer. Even so, we find that these highly discriminating isomiRs have not been attracting the most research attention in the literature. Given their ability to successfully classify datasets from 32 cancers, isomiRs and our resulting ‘Pan-cancer Atlas’ of isomiR expression could serve as a suitable framework to explore novel cancer biomarkers.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Rogan Magee
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Inna Chervoneva
- Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
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Liu F, Tian T, Xia LL, Ding Y, Cormier RT, He Y. Circulating miRNAs as novel potential biomarkers for esophageal squamous cell carcinoma diagnosis: a meta-analysis update. Dis Esophagus 2017; 30:1-9. [PMID: 27003597 DOI: 10.1111/dote.12489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Early detection of esophageal squamous cell carcinoma (ESCC) is urgently needed to reduce the high morbidity and mortality of disease. Circulating microRNAs (miRNAs) are promising molecular biomarkers for ESCC prediction. We performed a comprehensive meta-analysis to systematically evaluate the diagnostic accuracy of circulating miRNAs in diagnosis of ESCC patients. Eligible studies were identified and assessed for quality employing multiple search strategies. Summary estimates for sensitivity, specificity, and other measures of accuracy of miRNAs in the diagnosis of ESCC were pooled using the bivariate random effects model. A total of 27 studies from 11 published articles were included in the meta-analysis. The overall sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio of circulating miRNAs for the diagnosis of ESCC were 79.9% (95% confidence intervals [CI]: 76.2%-83.1%), 81.3% (95% CI: 75.7-85.9), 4.27 (95%CI: 3.27-5.58), 0.25 (95% CI: 0.21-0.29), and 17.29 (95% CI: 12.01-24.86), respectively. The area under the summary receiver operating characteristic curve was 0.87 (95% CI: 0.84-0.90). The subgroup analyses based on research country (China vs. Japan), specimen type (plasma vs. serum), miRNAs profiling (single vs. multiple), and test method (screening vs. candidate; Taqman vs. SYBR) indicated no significant difference in the diagnostic accuracy of each subgroup. Collectively, our findings indicate that circulating miRNAs have significant potential to be used as noninvasive biomarkers for early detection of ESCC. Moreover, the subgroup analyses demonstrated the feasibility of using blood miRNAs as an ESCC diagnostic biomarker in Japanese and Chinese populations. Further, both plasma and serum are recommended as clinical specimens for miRNA detection. Further studies will be needed to validate these findings using larger numbers of patients.
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Affiliation(s)
- Fen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China.,Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Tian Tian
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Institute of Reproductive & Child Health, Peking University, Beijing, China
| | - Li-Li Xia
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China.,Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Yuanjie Ding
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China.,Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Robert T Cormier
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota, USA
| | - Yan He
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China.,Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
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Bertoli G, Cava C, Castiglioni I. MicroRNAs: New Biomarkers for Diagnosis, Prognosis, Therapy Prediction and Therapeutic Tools for Breast Cancer. Theranostics 2015; 5:1122-43. [PMID: 26199650 PMCID: PMC4508501 DOI: 10.7150/thno.11543] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 06/17/2015] [Indexed: 12/21/2022] Open
Abstract
Dysregulation of microRNAs (miRNAs) is involved in the initiation and progression of several human cancers, including breast cancer (BC), as strong evidence has been found that miRNAs can act as oncogenes or tumor suppressor genes. This review presents the state of the art on the role of miRNAs in the diagnosis, prognosis, and therapy of BC. Based on the results obtained in the last decade, some miRNAs are emerging as biomarkers of BC for diagnosis (i.e., miR-9, miR-10b, and miR-17-5p), prognosis (i.e., miR-148a and miR-335), and prediction of therapeutic outcomes (i.e., miR-30c, miR-187, and miR-339-5p) and have important roles in the control of BC hallmark functions such as invasion, metastasis, proliferation, resting death, apoptosis, and genomic instability. Other miRNAs are of interest as new, easily accessible, affordable, non-invasive tools for the personalized management of patients with BC because they are circulating in body fluids (e.g., miR-155 and miR-210). In particular, circulating multiple miRNA profiles are showing better diagnostic and prognostic performance as well as better sensitivity than individual miRNAs in BC. New miRNA-based drugs are also promising therapy for BC (e.g., miR-9, miR-21, miR34a, miR145, and miR150), and other miRNAs are showing a fundamental role in modulation of the response to other non-miRNA treatments, being able to increase their efficacy (e.g., miR-21, miR34a, miR195, miR200c, and miR203 in combination with chemotherapy).
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Affiliation(s)
| | | | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
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