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A Downmodulated MicroRNA Profiling in Patients with Gastric Cancer. Gastroenterol Res Pract 2017; 2017:1526981. [PMID: 28546810 PMCID: PMC5436063 DOI: 10.1155/2017/1526981] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/24/2017] [Accepted: 03/09/2017] [Indexed: 01/02/2023] Open
Abstract
Objective. Here, we aim to investigate the microRNA (miR) profiling in human gastric cancer (GC). Methods. Tumoral and matched peritumoral gastric specimens were collected from 12 GC patients who underwent routine surgery. A high-throughput miR sequencing method was applied to detect the aberrantly expressed miRs in a subset of 6 paired samples. The stem-loop quantitative real-time polymerase chain reaction (qRT-PCR) assay was subsequently performed to confirm the sequencing results in the remaining 6 paired samples. The profiling results were also validated in vitro in three human GC cell lines (BGC-823, MGC-803, and GTL-16) and a normal gastric epithelial cell line (GES-1). Results. The miR sequencing approach detected 5 differentially expressed miRs, hsa-miR-132-3p, hsa-miR-155-5p, hsa-miR-19b-3p, hsa-miR-204-5p, and hsa-miR-30a-3p, which were significantly downmodulated between the tumoral and peritumoral GC tissues. Most of the results were further confirmed by qRT-PCR, while no change was observed for hsa-miR-30a-3p. The in vitro finding also agreed with the results of both miR sequencing and qRT-PCR for hsa-miR-204-5p, hsa-miR-155-5p, and hsa-miR-132-3p. Conclusion. Together, our findings may serve to identify new molecular alterations as well as to enrich the miR profiling in human GC.
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102
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Kao HW, Pan CY, Lai CH, Wu CW, Fang WL, Huang KH, Lin WC. Urine miR-21-5p as a potential non-invasive biomarker for gastric cancer. Oncotarget 2017; 8:56389-56397. [PMID: 28915598 PMCID: PMC5593569 DOI: 10.18632/oncotarget.16916] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Many reports have implicated that microRNAs involve in cancer development and progression, such as miR-155 in breast cancers and miR-196 in gastric cancers. Furthermore, microRNAs are more stable than typical protein-coding gene mRNAs in varieties of clinical samples including body fluids. This suggests that they are potentially valuable biomarkers for cancer monitoring. In this study, we have used urine samples of gastric cancer patients to demonstrate the feasibility of urine microRNAs for gastric cancer detection. Urine samples of gastric cancer patients were extracted for total RNA, which were examined for the expression of miR-21-5p using quantitative stem-loop PCR. Our results demonstrated that miR-21-5p could be detected in small amounts of urine samples with good stability, and the expression levels of miR-21-5p were reduced following surgical removal of gastric cancer tissues. These results implicate that urine miR-21-5p could be utilized as a novel non-invasive biomarker of gastric cancer detection and monitoring.
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Affiliation(s)
- Hsiao-Wei Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chao-Yu Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Hung Lai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chew-Wun Wu
- Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan
| | - Wen-Liang Fang
- Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan
| | - Kuo-Hung Huang
- Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
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103
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Circulating microRNAs and extracellular vesicles as potential cancer biomarkers: a systematic review. Int J Clin Oncol 2017; 22:413-420. [PMID: 28243946 DOI: 10.1007/s10147-017-1104-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/14/2022]
Abstract
Circulating non-coding RNAs, including microRNAs and long non-coding RNAs, and the protein components of extracellular vesicles are promising biomarkers for the non-invasive detection of cancer at an early stage. This systematic review discusses the increasing number of well-designed cancer biomarker-related studies that have been published worldwide. In many of these studies, high diagnostic accuracy, which is represented as the area under the receiver operating characteristic curve being >0.8, could be achieved using combinations of circulating microRNAs. In addition, similar diagnostic accuracies were reported using long non-coding RNAs or proteins present in extracellular vesicles, although these evidences were based on a limited number of studies.
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104
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Kong P, Zhu X, Geng Q, Xia L, Sun X, Chen Y, Li W, Zhou Z, Zhan Y, Xu D. The microRNA-423-3p-Bim Axis Promotes Cancer Progression and Activates Oncogenic Autophagy in Gastric Cancer. Mol Ther 2017; 25:1027-1037. [PMID: 28254439 DOI: 10.1016/j.ymthe.2017.01.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/04/2017] [Accepted: 01/14/2017] [Indexed: 12/19/2022] Open
Abstract
Human serum microRNAs (miRNAs) have been shown to serve as disease fingerprints for predicting survival of cancer patients. However, the roles of specific miRNAs involved in gastric cancer (GC) are largely unknown. In this study, miRNA profiling was performed on sera obtained from six patients in good- and poor-survival groups. Expression of miR-423-3p was validated by quantitative RT-PCR in another 67 GC serum samples and paired normal and cancerous gastric tissues. Luciferase reporter assays were used to identify the target gene Bcl-2-interacting mediator of cell death (Bim). As a result, between the good-survival and poor-survival groups, the expression of nine serum miRNAs was altered more than two-fold. Among these, miR-423-3p was significantly increased in the poor-survival group, and its overexpression in GC tissues predicted poor survival in 119 patients with GC. miR-423-3p was found to promote cell proliferation, migration, and invasion in cell lines and animal models. Mechanistically, knockdown of the autophagy-related gene (Atg) 7 rescued the GC-promoting effect of miR-423-3p. In conclusion, miR-423-3p activates oncogenic and Beclin-1-dependent autophagy and promotes GC progression by reducing the expression of Bim. The newly identified miR-423-3p-Bim axis might be a potential therapeutic target in GC.
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Affiliation(s)
- Pengfei Kong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China; Department of the VIP Region, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Xiaofeng Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China
| | - Qirong Geng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Hematology Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Liangping Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of the VIP Region, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Xiaowei Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Yingbo Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Wei Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Zhiwei Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Youqing Zhan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China
| | - Dazhi Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510006, China; Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou 510006, China.
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Abstract
Background Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regulating miRNAs is limited. This work introduces a computational method to group miRNAs of similar functions to identify co-regulating miRNAsfrom a similarity matrix of miRNAs. Results We define a novel information content of gene ontology (GO) to measure similarity between two sets of GO graphs corresponding to the two sets of target genes of two miRNAs. This between-graph similarity is then transferred as a functional similarity between the two miRNAs. Our definition of the information content is based on the size of a GO term’s descendants, but adjusted by a weight derived from its depth level and the GO relationships at its path to the root node or to the most informative common ancestor (MICA). Further, a self-tuning technique and the eigenvalues of the normalized Laplacian matrix are applied to determine the optimal parameters for the spectral clustering of the similarity matrix of the miRNAs. Conclusions Experimental results demonstrate that our method has better clustering performance than the existing edge-based, node-based or hybrid methods. Our method has also demonstrated a novel usefulness for the function annotation of new miRNAs, as reported in the detailed case studies.
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106
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Kränkel N, Blankenberg S, Zeller T. Early detection of myocardial infarction-microRNAs right at the time? ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:502. [PMID: 28149864 DOI: 10.21037/atm.2016.12.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nicolle Kränkel
- Department of Cardiology, Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany; ; German Center for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Stefan Blankenberg
- Univeristy Heart Center Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany; ; German Center for Cardiovascular Research, partner site Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Tanja Zeller
- Univeristy Heart Center Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany; ; German Center for Cardiovascular Research, partner site Hamburg/Lübeck/Kiel, Hamburg, Germany
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107
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Huang Z, Zhu D, Wu L, He M, Zhou X, Zhang L, Zhang H, Wang W, Zhu J, Cheng W, Chen Y, Fan Y, Qi L, Yin Y, Zhu W, Shu Y, Liu P. Six Serum-Based miRNAs as Potential Diagnostic Biomarkers for Gastric Cancer. Cancer Epidemiol Biomarkers Prev 2016; 26:188-196. [PMID: 27756776 DOI: 10.1158/1055-9965.epi-16-0607] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Circulating miRNAs in serum may serve as promising diagnostic biomarkers for patients with gastric cancer. METHODS Using qRT-PCR-based Exiqon panel, we identified 58 differentially expressed miRNAs from three gastric cancer pool samples and one normal control (NC) pool in the initial screening phase. Identified miRNAs were further validated in the training (49 gastric cancer vs. 47 NCs) and validation phases (154 gastric cancer vs. 120 NCs) using qRT-PCR. The expression levels of the miRNAs were also determined in tissues, arterial serum, and exosomes. RESULTS Consequently, six serum miRNAs (miR10b-5p, miR132-3p, miR185-5p, miR195-5p, miR-20a3p, and miR296-5p) were significantly overexpressed in gastric cancer compared with NCs. The areas under the receiver operating characteristic curve of the six-miRNA panel were 0.764 and 0.702 for the training and validation phases, respectively. miR10b-5p and miR296-5p were significantly upregulated in gastric cancer tissues (n = 188). In addition, patients who did not receive adjuvant chemotherapy with high expression of miR10b-5p or miR296-5p in tissues tended to suffer worse overall survival. Furthermore, the expression levels of miR10b-5p, miR195-5p, miR20a-3p, and miR296-5p were significantly elevated in exosomes from gastric cancer serum samples (n = 30). CONCLUSIONS We identified a six-miRNA panel in serum for the detection of gastric cancer. IMPACT Our findings provide a novel serum miRNA signature for gastric cancer diagnosis, and will serve as the basis of the application of circulating miRNAs in clinical for the detection of gastric cancer in the future. Cancer Epidemiol Biomarkers Prev; 26(2); 188-96. ©2016 AACR.
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Affiliation(s)
- Zebo Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Danxia Zhu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Lirong Wu
- Department of Radiation Oncology, Jiangsu Cancer Hospital, Nanjing, China
| | - Mingfeng He
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Zhou
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lan Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huo Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Weiwei Wang
- Department of Emergency, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Zhu
- Department of Radiation Oncology, Jiangsu Cancer Hospital, Nanjing, China
| | - Wenfang Cheng
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Chen
- Department of Emergency, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Fan
- State Key Laboratory of Natural Medicines and Department of Pharmacognosy, China Pharmaceutical University, Nanjing, China
| | - Lianwen Qi
- State Key Laboratory of Natural Medicines and Department of Pharmacognosy, China Pharmaceutical University, Nanjing, China
| | - Yin Yin
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China. .,Cancer Center of Nanjing Medical University, Nanjing, China
| | - Ping Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China. .,Cancer Center of Nanjing Medical University, Nanjing, China
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108
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miR-203 Expression in Exfoliated Cells of Tongue Coating Represents a Sensitive and Specific Biomarker of Gastroesophageal Reflux Disease. Gastroenterol Res Pract 2016; 2016:2349453. [PMID: 27667995 PMCID: PMC5030450 DOI: 10.1155/2016/2349453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/26/2016] [Indexed: 01/29/2023] Open
Abstract
Background and Aim. MicroRNAs (miRNAs) have been implicated in the pathophysiology of numerous human diseases including gastroesophageal reflux disease (GERD). The objective of this study was to investigate the miRNA expression of exfoliated cells of the tongue in patients with GERD versus healthy controls (Ctrls). Methods. Using quantitative reverse-transcription PCR (qRT-PCR), expression levels of six candidate miRNAs (miR-143, miR-145, miR-192, miR-194, miR-203, and miR-205) were examined across a discovery cohort of patients with GERD (n = 24) versus Ctrls (n = 24). These findings were confirmed across a validation cohort (GERD, n = 142; Ctrls, n = 48). Differences in miRNA expression levels were evaluated using the Mann-Whitney U test while the specificity and sensitivity were obtained using receiver-operator characteristic (ROC) curves. Results. miR-203 was significantly downregulated in GERD patients as compared to Ctrls (P < 0.0001) with ROC curve of 0.94 (95% CI: 0.90-0.97). The sensitivity and the specificity of miR-203 were 91.7% and 87.3%, respectively, in the GERD and Ctrls. These results suggest that miR-203 may be a useful diagnostic marker for discriminating GERD from Ctrls. Conclusions. miR-203 testing may assist in the diagnosis of patients with symptoms suggestive of GERD.
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109
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Circulating MicroRNAs: A Next-Generation Clinical Biomarker for Digestive System Cancers. Int J Mol Sci 2016; 17:ijms17091459. [PMID: 27598137 PMCID: PMC5037738 DOI: 10.3390/ijms17091459] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that post-transcriptionally regulate gene expression and play important roles in various physiological and developmental processes such as oncogenic or tumor suppressive regulators. Specific miRNA expression signatures have been identified in a number of human cancers. Cell-free miRNAs have recently been stably detected in plasma and serum (circulating miRNAs), and their presence in blood has attracted the attention of researchers due to their potential as non-invasive biomarkers. Circulating miRNAs have emerged as tumor-associated biomarkers that reflect not only the existence of early-stage tumors, but also the dynamics and status of advanced stage tumors, tumor recurrence, and drug sensitivities. This methodology for liquid biopsy may provide non-invasive and reproductive biomarkers and individualized therapeutic strategies for cancer patients. We herein review the current phase of biological and clinical research on the circulating miRNAs of solid cancers, particularly digestive tract cancers, and discuss future perspectives. The present review may be beneficial for future research on miRNAs used to detect various cancers.
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110
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Wang H, Xiong M, Hu Y, Sun Y, Ma Q. MicroRNA-19b inhibits proliferation of gastric cancer cells by targeting B-cell CLL/lymphoma 3. Oncol Rep 2016; 36:2079-86. [PMID: 27572553 DOI: 10.3892/or.2016.5029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/16/2016] [Indexed: 11/05/2022] Open
Abstract
Previous studies reported that the aberrant expression of miR-19b in gastric cancer tissues and circulating miR-19b is a potential biomarker to indicate progression of gastric cancer. However, the prognostic significance of miR-19b, and its role and underlying mechanisms in gastric cancer remain poorly investigated. In the present study, we demonstrated that the expression of miR-19b was aberrantly downregulated in both gastric cancer tissues and cell lines. Clinical association analyses disclosed that the reduced expression of miR-19b was significantly associated with adverse clinicopathological characteristics including poor differentiation, large tumor size and advanced tumor-node-metastasis (TNM) stage. Gastric cancer patients with low expression of miR-19b had prominent shorter overall survival and disease-free survival. Gain-of-function studies indicated that miR-19b overexpression inhibited cell proliferation and cell cycle progression in MGC-803 cells. While miR-19b silencing promoted cell proliferation and cell cycle progression in SGC-7901 cells. Furthermore, in vivo experiments showed that miR-19b overexpression suppressed the tumor growth of MGC-803 cells. Notably, miR-19b inversely regulated B-cell CLL/lymphoma 3 (BCL3) abundance in gastric cancer cells. BCL3 was identified as a direct target of miR-19b using luciferase reporter assays. Moreover, BCL3 knockdown abolished the effects of miR-19b knockdown on gastric cancer cells. In conclusion, our data suggest that miR-19b may potentially serve as a novel prognostic biomarker and therapeutic target for gastric cancer.
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Affiliation(s)
- Huan Wang
- Department of Medical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Mei Xiong
- Department of Medical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Yongwu Hu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Yusheng Sun
- Department of Traumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Qing Ma
- Department of Medical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
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111
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Singh R, Ramasubramanian B, Kanji S, Chakraborty AR, Haque SJ, Chakravarti A. Circulating microRNAs in cancer: Hope or hype? Cancer Lett 2016; 381:113-21. [PMID: 27471105 DOI: 10.1016/j.canlet.2016.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/29/2016] [Accepted: 07/02/2016] [Indexed: 12/20/2022]
Abstract
Circulating miRNAs are a novel class of stable, minimally invasive disease biomarkers that are considered to be valuable in diagnosis, prognosis and treatment response monitoring. Unlike intracellular miRNAs, circulating miRNAs are released from their producer cells and, based on their targeted functions, they may shuttle in and out of circulation. Their discovery has opened up new avenues for clinical realms and led to a quest for targeted biomarkers. Subsequently, as more cell-free miRNAs are being discovered, their expression is expected to provide precise information regarding disease progression and treatment outcomes, thereby fostering personalized therapeutic strategies. The significance of circulating miRNAs capitalizes on the fact that they are highly stable in body fluids and their expression levels can be detected by common techniques such as qPCR and microarray. However, discrepancies have started to emerge in terms of their reliability and their response under physiological and pathological conditions. Functional studies are still pending, which may determine whether circulating miRNAs play a role as a central component or just as an auxiliary tuner. Also, the distinct clinical signatures that they display have never been subjected to an extensive critical review and experimental validation. As a consequence, the applicability of circulating miRNAs remains a matter of deliberation, despite many intriguing perspectives about their competency. In this review, we highlight some ambiguous issues with the application of circulating miRNAs, which may warrant an immediate consideration. We propose that the circulating miRNA domain needs to be reevaluated to authenticate their specific role and to probe whether they actually carry any clinical weightage.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Brinda Ramasubramanian
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Suman Kanji
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Arup R Chakraborty
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Saikh Jaharul Haque
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
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Kori M, Gov E, Arga KY. Molecular signatures of ovarian diseases: Insights from network medicine perspective. Syst Biol Reprod Med 2016; 62:266-82. [PMID: 27341345 DOI: 10.1080/19396368.2016.1197982] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Dysfunctions and disorders in the ovary lead to a host of diseases including ovarian cancer, ovarian endometriosis, and polycystic ovarian syndrome (PCOS). Understanding the molecular mechanisms behind ovarian diseases is a great challenge. In the present study, we performed a meta-analysis of transcriptome data for ovarian cancer, ovarian endometriosis, and PCOS, and integrated the information gained from statistical analysis with genome-scale biological networks (protein-protein interaction, transcriptional regulatory, and metabolic). Comparative and integrative analyses yielded reporter biomolecules (genes, proteins, metabolites, transcription factors, and micro-RNAs), and unique or common signatures at protein, metabolism, and transcription regulation levels, which might be beneficial to uncovering the underlying biological mechanisms behind the diseases. These signatures were mostly associated with formation or initiation of cancer development, and pointed out the potential tendency of PCOS and endometriosis to tumorigenesis. Molecules and pathways related to MAPK signaling, cell cycle, and apoptosis were the mutual determinants in the pathogenesis of all three diseases. To our knowledge, this is the first report that screens these diseases from a network medicine perspective. This study provides signatures which could be considered as potential therapeutic targets and/or as medical prognostic biomarkers in further experimental and clinical studies. Abbreviations DAVID: Database for Annotation, Visualization and Integrated Discovery; DEGs: differentially expressed genes; GEO: Gene Expression Omnibus; KEGG: Kyoto Encyclopedia of Genes and Genomes; LIMMA: Linear Models for Microarray Data; MBRole: Metabolite Biological Role; miRNA: micro-RNA; PCOS: polycystic ovarian syndrome; PPI: protein-protein interaction; RMA: Robust Multi-Array Average; TF: transcription factor.
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Affiliation(s)
- Medi Kori
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
| | - Esra Gov
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
| | - Kazim Yalcin Arga
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
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113
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Urinary miR-16 transactivated by C/EBPβ reduces kidney function after ischemia/reperfusion-induced injury. Sci Rep 2016; 6:27945. [PMID: 27297958 PMCID: PMC4906401 DOI: 10.1038/srep27945] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Ischemia-reperfusion (I/R) induced acute kidney injury (AKI) is regulated by transcriptional factors and microRNAs (miRs). However, modulation of miRs by transcriptional factors has not been characterized in AKI. Here, we found that urinary miR-16 was 100-fold higher in AKI patients. MiR-16 was detected earlier than creatinine in mouse after I/R. Using TargetScan, the 3′UTR of B-cell lymphoma 2 (BCL-2) was found complementary to miR-16 to decrease the fluorescent reporter activity. Overexpression of miR-16 in mice significantly attenuated renal function and increased TUNEL activity in epithelium tubule cells. The CCAAT enhancer binding protein beta (C/EBP-β) increased the expression of miR-16 after I/R injury. The ChIP and luciferase promoter assay indicated that about −1.0 kb to −0.5 kb upstream of miR-16 genome promoter region containing C/EBP-β binding motif transcriptionally regulated miR-16 expression. Meanwhile, the level of pri-miR-16 was higher in mice infected with lentivirus containing C/EBP-β compared with wild-type (WT) mice and overexpression of C/EBP-β in the kidney of WT mice reduced kidney function, increased kidney apoptosis, and elevated urinary miR-16 level. Our results indicated that miR-16 was transactivated by C/EBP-β resulting in aggravated I/R induced AKI and that urinary miR-16 may serve as a potential biomarker for AKI.
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114
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Larrea E, Sole C, Manterola L, Goicoechea I, Armesto M, Arestin M, Caffarel MM, Araujo AM, Araiz M, Fernandez-Mercado M, Lawrie CH. New Concepts in Cancer Biomarkers: Circulating miRNAs in Liquid Biopsies. Int J Mol Sci 2016; 17:ijms17050627. [PMID: 27128908 PMCID: PMC4881453 DOI: 10.3390/ijms17050627] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 12/19/2022] Open
Abstract
The effective and efficient management of cancer patients relies upon early diagnosis and/or the monitoring of treatment, something that is often difficult to achieve using standard tissue biopsy techniques. Biological fluids such as blood hold great possibilities as a source of non-invasive cancer biomarkers that can act as surrogate markers to biopsy-based sampling. The non-invasive nature of these “liquid biopsies” ultimately means that cancer detection may be earlier and that the ability to monitor disease progression and/or treatment response represents a paradigm shift in the treatment of cancer patients. Below, we review one of the most promising classes of circulating cancer biomarkers: microRNAs (miRNAs). In particular, we will consider their history, the controversy surrounding their origin and biology, and, most importantly, the hurdles that remain to be overcome if they are really to become part of future clinical practice.
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Affiliation(s)
- Erika Larrea
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - Carla Sole
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - Lorea Manterola
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - Ibai Goicoechea
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María Armesto
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María Arestin
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María M Caffarel
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Angela M Araujo
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
| | - María Araiz
- Hematology Department, Donostia Hospital, 20014 San Sebastián, Spain.
| | | | - Charles H Lawrie
- Molecular Oncology, Biodonostia Research Institute, 20014 San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, UK.
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115
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Zhang J, Li C, Zhi X, Ramón GA, Liu Y, Zhang C, Pan F, Cui D. Hairpin DNA-Templated Silver Nanoclusters as Novel Beacons in Strand Displacement Amplification for MicroRNA Detection. Anal Chem 2015; 88:1294-302. [PMID: 26675240 DOI: 10.1021/acs.analchem.5b03729] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MicroRNA (miRNA) biomarkers display great potential for cancer diagnosis and prognosis. The development of rapid and specific methods for miRNA detection has become a hotspot. Herein, hairpin DNA-templated silver nanoclusters (AgNCs/HpDNA) were prepared and integrated into strand-displacement amplification (SDA) as a novel beacon for miRNA detection. The light-up platform was established based on guanine (G)-rich fluorescence enhancement that essentially converted the excitation/emission pair of AgNCs/HpDNAs from a shorter wavelength to a longer wavelength, and then achieved fluorescent enhancement at longer wavelength. On the basis of the validation of the method, the single and duplex detection were conducted in two plasma biomarkers (miR-16-5p and miR-19b-3p) for the diagnosis of gastric cancer. The probe (AgNCs/RED 16(7s)C) utilized for miR-16-5p detection adopted a better conformation with high specificity to recognize single-base mismatches by producing dramatically opposite signals (increase or decrease at 580 nm ex/640 nm em) while the probe (AgNCs/GRE 19b(5s)C) for miR-19b-3p generated dual signals (increase at 490 nm ex/570 nm em and decrease at 430 nm ex/530 nm em) with bright fluorescence in one reaction during the amplification, but unexpectedly was partially digested. This is for the first time to allow the generation of enhanced fluorescent AgNCs and the target recognition integrated into a single process, which offers great opportunity for specific miRNA detection in an easy and rapid way.
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Affiliation(s)
- Jingpu Zhang
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Chao Li
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Xiao Zhi
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Gabriel Alfranca Ramón
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Yanlei Liu
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Chunlei Zhang
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Fei Pan
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
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116
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Xie Y, Zhi X, Su H, Wang K, Yan Z, He N, Zhang J, Chen D, Cui D. A Novel Electrochemical Microfluidic Chip Combined with Multiple Biomarkers for Early Diagnosis of Gastric Cancer. NANOSCALE RESEARCH LETTERS 2015; 10:477. [PMID: 26659608 PMCID: PMC4675772 DOI: 10.1186/s11671-015-1153-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/06/2015] [Indexed: 05/26/2023]
Abstract
Early diagnosis is very important to improve the survival rate of patients with gastric cancer and to understand the biology of cancer. In order to meet the clinical demands for early diagnosis of gastric cancer, we developed a disposable easy-to-use electrochemical microfluidic chip combined with multiple antibodies against six kinds of biomarkers (carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), Helicobacter pylori CagA protein (H.P.), P53oncoprotein (P53), pepsinogen I (PG I), and PG-II). The six kinds of biomarkers related to gastric cancer can be detected sensitively and synchronously in a short time. The specially designed three electrodes system enables cross-contamination to be avoided effectively. The linear ranges of detection of the electrochemical microfluidic chip were as follows: 0.37-90 ng mL(-1) for CEA, 10.75-172 U mL(-1) for CA19-9, 10-160 U L(-1) for H.P., 35-560 ng mL(-1) for P53, 37.5-600 ng mL(-1) for PG I, and 2.5-80 ng mL(-1)for PG II. This method owns better sensitivity compared with enzyme-linked immunosorbent assay (ELISA) results of 394 specimens of gastric cancer sera. Furthermore, we established a multi-index prediction model based on the six kinds of biomarkers for predicting risk of gastric cancer. In conclusion, the electrochemical microfluidic chip for detecting multiple biomarkers has great potential in applications such as early screening of gastric cancer patients, and therapeutic evaluation, and real-time dynamic monitoring the progress of gastric cancer in near future.
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Affiliation(s)
- Yao Xie
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China
| | - Xiao Zhi
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China
- Institute of Translation Medicine, Tumor Personalized Therapy and Molecular Diagnosis Base of Ministry of Health and Family Planning Commission, Collaborative Innovational Center for System Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China
| | - Haichuan Su
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, 569 Xinsi Road, Xi'an, 710032, Peoples' Republic of China
| | - Kan Wang
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China
| | - Zhen Yan
- Department of Pharmaceutics, Fourth Military Medical University, 18 Changle West Road, Xi'an, 710032, Peoples' Republic of China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Peoples' Republic of China
| | - Jingpu Zhang
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China
| | - Di Chen
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China.
| | - Daxiang Cui
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China.
- Institute of Translation Medicine, Tumor Personalized Therapy and Molecular Diagnosis Base of Ministry of Health and Family Planning Commission, Collaborative Innovational Center for System Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, Peoples' Republic of China.
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117
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Yang Q, Zhang RW, Sui PC, He HT, Ding L. Dysregulation of non-coding RNAs in gastric cancer. World J Gastroenterol 2015; 21:10956-10981. [PMID: 26494954 PMCID: PMC4607897 DOI: 10.3748/wjg.v21.i39.10956] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 08/28/2015] [Accepted: 09/15/2015] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is one of the most common cancers in the world and a significant threat to the health of patients, especially those from China and Japan. The prognosis for patients with late stage GC receiving the standard of care treatment, including surgery, chemotherapy and radiotherapy, remains poor. Developing novel treatment strategies, identifying new molecules for targeted therapy, and devising screening techniques to detect this cancer in its early stages are needed for GC patients. The discovery of non-coding RNAs (ncRNAs), primarily microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), helped to elucidate the mechanisms of tumorigenesis, diagnosis and treatment of GC. Recently, significant research has been conducted on non-coding RNAs and how the regulatory dysfunction of these RNAs impacts the tumorigenesis of GC. In this study, we review papers published in the last five years concerning the dysregulation of non-coding RNAs, especially miRNAs and lncRNAs, in GC. We summarize instances of aberrant expression of the ncRNAs in GC and their effect on survival-related events, including cell cycle regulation, AKT signaling, apoptosis and drug resistance. Additionally, we evaluate how ncRNA dysregulation affects the metastatic process, including the epithelial-mesenchymal transition, stem cells, transcription factor activity, and oncogene and tumor suppressor expression. Lastly, we determine how ncRNAs affect angiogenesis in the microenvironment of GC. We further discuss the use of ncRNAs as potential biomarkers for use in clinical screening, early diagnosis and prognosis of GC. At present, no ideal ncRNAs have been identified as targets for the treatment of GC.
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118
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Hudler P. Challenges of deciphering gastric cancer heterogeneity. World J Gastroenterol 2015; 21:10510-10527. [PMID: 26457012 PMCID: PMC4588074 DOI: 10.3748/wjg.v21.i37.10510] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 06/19/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer is in decline in most developed countries; however, it still accounts for a notable fraction of global mortality and morbidity related to cancer. High-throughput methods are rapidly changing our view and understanding of the molecular basis of gastric carcinogenesis. Today, it is widely accepted that the molecular complexity and heterogeneity, both inter- and intra-tumour, of gastric adenocarcinomas present significant obstacles in elucidating specific biomarkers for early detection of the disease. Although genome-wide sequencing and gene expression studies have revealed the intricate nature of the molecular changes that occur in tumour landscapes, the collected data and results are complex and sometimes contradictory. Several aberrant molecules have already been tested in clinical trials, although their diagnostic and prognostic utilities have not been confirmed thus far. The gold standard for the detection of sporadic gastric cancer is still the gastric endoscopy, which is considered invasive. In addition, genome-wide association studies have confirmed that genetic variations are important contributors to increased cancer risk and could participate in the initiation of malignant transformation. This hypothesis could in part explain the late onset of sporadic gastric cancers. The elaborate interplay of polymorphic low penetrance genes and lifestyle and environmental risk factors requires additional research to decipher their relative impacts on tumorigenesis. The purpose of this article is to present details of the molecular heterogeneity of sporadic gastric cancers at the DNA, RNA, and proteome levels and to discuss issues relevant to the translation of basic research data to clinically valuable tools. The focus of this work is the identification of relevant molecular changes that could be detected non-invasively.
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