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Wang L, Wang YX, Zhang DZ, Fang XJ, Sun PS, Xue HC. Let-7a mimic attenuates CCL18 induced breast cancer cell metastasis through Lin 28 pathway. Biomed Pharmacother 2016; 78:301-307. [PMID: 26898455 DOI: 10.1016/j.biopha.2016.01.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 01/17/2016] [Accepted: 01/20/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND MicroRNAs are believed to influence breast cancer cell tumorgenicity by interacting with the production of tumor associated macrophages. At this stage, this hypothesis lacks sufficient empirical evidence. Our study is an investigation of the effects of let-7a on the function of human breast cancer cell lines that had undergone chemokine ligand 18 (CCL18) stimulation. METHODS Two breast cancer cell lines MDA-MB-231 and MCF-7 were transfected with let-7a mimics with or without CCL18 simulation. The expression level of let-7a was evaluated with qRT-PCR. Our study examined cell proliferation, migration and cell cycles following let-7a treatment. The predicted target of let-7a was identified and confirmed in vitro by a dual luciferase reporter system. The associations between let-7a, CCL18 and target gene expression were evaluated using RT-PCR and the Western blotting method. RESULTS The downregulated expression level of let-7a was observed in both breast cancer cell lines. When compared to the control and CCL18 stimulation groups, cell proliferation and migration in MDA-MB-231 and MCF-7 cells were significantly inhibited by let-7a. Furthermore, the cell cycle was dramatically blocked at the G2/M phase. The luciferase reporter identified Lin28 as the direct binding target of let-7a in both breast cancer cell lines. CONCLUSION Upregulation of let-7a carries the potential to reverse CCL18 induced cell proliferation and migration alteration in breast cancer cells by regulating Lin28 expression. Our results provided evidence which suggests the use of let-7a as a therapeutic agent in the treatment of breast cancer.
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Affiliation(s)
- Lei Wang
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, Xinxiang, PR China
| | - Yu-Xia Wang
- Department of Pathophysiology, Xinxiang Medical University, 453003, Xinxiang, PR China
| | - De-Zhong Zhang
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, Xinxiang, PR China
| | - Xiang-Jie Fang
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, Xinxiang, PR China
| | - Pei-Sheng Sun
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, Xinxiang, PR China
| | - Hui-Chao Xue
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, Xinxiang, PR China.
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Wang Y, Han R, Chen Z, Fu M, Kang J, Li K, Li L, Chen H, He Y. A transcriptional miRNA-gene network associated with lung adenocarcinoma metastasis based on the TCGA database. Oncol Rep 2016; 35:2257-69. [PMID: 26781266 DOI: 10.3892/or.2016.4560] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/20/2015] [Indexed: 11/05/2022] Open
Abstract
Lung adenocarcinoma is the most common subtype of non-small cell lung cancer (NSCLC), leading to the largest number of cancer-related deaths worldwide. The high mortality rate may be attributed to the delay of detection. Therefore, it is of great importance to explore the mechanism of lung adenocarcinoma metastasis and the strategy to block metastasis of the disease. We searched and downloaded mRNA and miRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA and miRNA expression of primary tumor tissues from lung adenocarcinoma that did and did not metastasize. In addition, combined with bioinformatic prediction, we constructed an miRNA-target gene regulatory network. Finally, we employed RT-qPCR to validate the bioinformatic approach by determining the expression of 10 significantly differentially expressed genes which were also putative targets of several dysregulated miRNAs. RT-qPCR results indicated that the bioinformatic approach in our study was acceptable. Our data suggested that some of the genes including PKM2, STRAP and FLT3, may participate in the pathology of lung adenocarcinoma metastasis and could be applied as potential markers or therapeutic targets for lung adenocarcinoma.
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Affiliation(s)
- Yubo Wang
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Rui Han
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Zhaojun Chen
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Ming Fu
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Jun Kang
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Kunlin Li
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Li Li
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Hengyi Chen
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Yong He
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
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Ke J, Zhao Z, Hong SH, Bai S, He Z, Malik F, Xu J, Zhou L, Chen W, Martin-Trevino R, Wu X, Lan P, Yi Y, Ginestier C, Ibarra I, Shang L, McDermott S, Luther T, Clouthier SG, Wicha MS, Liu S. Role of microRNA221 in regulating normal mammary epithelial hierarchy and breast cancer stem-like cells. Oncotarget 2016; 6:3709-21. [PMID: 25686829 PMCID: PMC4414148 DOI: 10.18632/oncotarget.2888] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/09/2014] [Indexed: 12/25/2022] Open
Abstract
Increasing evidence suggests that lineage specific subpopulations and stem-like cells exist in normal and malignant breast tissues. Epigenetic mechanisms maintaining this hierarchical homeostasis remain to be investigated. In this study, we found the level of microRNA221 (miR-221) was higher in stem-like and myoepithelial cells than in luminal cells isolated from normal and malignant breast tissue. In normal breast cells, over-expression of miR-221 generated more myoepithelial cells whereas knock-down of miR-221 increased luminal cells. Over-expression of miR-221 stimulated stem-like cells in luminal type of cancer and the miR-221 level was correlated with clinical outcome in breast cancer patients. Epithelial-mesenchymal transition (EMT) was induced by overexpression of miR-221 in normal and breast cancer cells. The EMT related gene ATXN1 was found to be a miR-221 target gene regulating breast cell hierarchy. In conclusion, we propose that miR-221 contributes to lineage homeostasis of normal and malignant breast epithelium.
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Affiliation(s)
- Jia Ke
- Department of Colorectal Surgery, Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zhiju Zhao
- Innovation Center for Cell Biology and The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui, China
| | - Su-Hyung Hong
- Department of Oral Microbiology, School of Dentistry Kyungpook National University, Jung-gu, Daegu, South Korea
| | - Shoumin Bai
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun-Yat-Sen University, Guangzhou, China
| | - Zhen He
- Department of Colorectal Surgery, Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Fayaz Malik
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jiahui Xu
- Innovation Center for Cell Biology and The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui, China
| | - Lei Zhou
- Innovation Center for Cell Biology and The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui, China
| | - Weilong Chen
- Innovation Center for Cell Biology and The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui, China
| | - Rachel Martin-Trevino
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Xiaojian Wu
- Department of Colorectal Surgery, Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ping Lan
- Department of Colorectal Surgery, Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yongju Yi
- Network Information Center, Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Christophe Ginestier
- Centre de Recherche en Cancérologie de Marseille, Laboratoire d'Oncologie Moléculaire, UMR891 Inserm/Institut Paoli-Calmettes, Université de la Méditerranée, Marseille, France
| | - Ingrid Ibarra
- Cold Spring Harbor Laboratory, Program in Genetics and Bioinformatics, Cold Spring Harbor, NY, USA
| | - Li Shang
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sean McDermott
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Tahra Luther
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Shawn G Clouthier
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Comprehensive Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Suling Liu
- Innovation Center for Cell Biology and The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, Anhui, China
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Abstract
Breast cancer affects approximately 12 % women worldwide and results in 14 % of all cancer-related fatalities. Breast cancer is commonly categorized into one of four main subtypes (luminal A, luminal B, human epidermal growth factor receptor 2 (HER2) positive and basal), indicating molecular characteristics and informing treatment regimes. The most severe form of breast cancer is metastasis, when the tumour spreads from the breast tissue to other parts of the body. Significantly, the primary tumour subtype affects rates and sites of metastasis. Currently, up to 5 % of patients present with incurable metastasis, with an additional 10–15 % of patients going on to develop metastasis within 3 years of diagnosis. MicroRNAs (miRNAs) are short 21–25 long nucleotides that have been shown to significantly affect gene expression. Currently, >2000 miRNAs have been identified and significantly, specific miRNAs have been found associated with diseases states. Importantly, miRNAs are found circulating in the blood, presenting an opportunity to use these circulating disease-related miRNAs as biomarkers. Clearly, the identification of circulating miRNA specific to metastatic breast cancer presents a unique opportunity for early disease identification and for monitoring disease burden. Currently however, few groups have identified miRNA associated with metastatic breast cancer. Here, we review the literature surrounding the identification of metastatic miRNA in breast cancer patients, highlighting key areas where miRNA biomarker discovery could be beneficial, identifying key concepts, recognizing critical areas requiring further research and discussing potential problems.
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105
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The Six1 oncoprotein downregulates p53 via concomitant regulation of RPL26 and microRNA-27a-3p. Nat Commun 2015; 6:10077. [PMID: 26687066 PMCID: PMC4703841 DOI: 10.1038/ncomms10077] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 11/02/2015] [Indexed: 12/18/2022] Open
Abstract
TP53 is mutated in 50% of all cancers, and its function is often compromised in cancers where it is not mutated. Here we demonstrate that the pro-tumorigenic/metastatic Six1 homeoprotein decreases p53 levels through a mechanism that does not involve the negative regulator of p53, MDM2. Instead, Six1 regulates p53 via a dual mechanism involving upregulation of microRNA-27a and downregulation of ribosomal protein L26 (RPL26). Mutation analysis confirms that RPL26 inhibits miR-27a binding and prevents microRNA-mediated downregulation of p53. The clinical relevance of this interaction is underscored by the finding that Six1 expression strongly correlates with decreased RPL26 across numerous tumour types. Importantly, we find that Six1 expression leads to marked resistance to therapies targeting the p53–MDM2 interaction. Thus, we identify a competitive mechanism of p53 regulation, which may have consequences for drugs aimed at reinstating p53 function in tumours. p53 is a tumour suppressor that is mutated in a large number of cancers and its expression is controlled largely by the ubiquitin ligase MDM2. Here, the authors show that the homeoprotein, Six1, can regulate p53 in an MDM2- independent manner via regulation of miR-27a and the RNA binding protein, RPL26.
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106
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Ben-Hamo R, Efroni S. MicroRNA regulation of molecular pathways as a generic mechanism and as a core disease phenotype. Oncotarget 2015; 6:1594-604. [PMID: 25593195 PMCID: PMC4359317 DOI: 10.18632/oncotarget.2734] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/12/2014] [Indexed: 12/21/2022] Open
Abstract
The role of microRNAs as key regulators of a wide variety of fundamental cellular processes, such as apoptosis, differentiation, proliferation and cell cycle is increasingly recognized in most aspects of biology and biomedicine. Accretion of results from multiple microRNA studies over multiple pathway networks, led us to hypothesize that microRNAs target molecular pathways. As we show here, this is a network-wide phenomenon. The work presented, uses statistical tools that show how single microRNAs target molecular pathways. We demonstrate that this targeting could not be the result of random associations and cannot be the result of the sheer numeracy of microRNA targets. Furthermore, the strongest evidence for the association microRNA-pathway, is in a demonstration of the way by which these associations are disease-relevant. In our analyses we study ten different types of cancer involving thousands of samples, and show that the identified microRNA–pathway associations demonstrate a clinical affiliation and an ability to stratify patients. The work presented here shows the first evidence for a mechanism of microRNAs-pathway generic regulation. This regulation is tightly associated with clinical phenotype. The presented approach may catalyze targeted treatment through exposure of hidden regulatory mechanisms and a systems-medicine view of clinical observation.
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Affiliation(s)
- Rotem Ben-Hamo
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
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107
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Schummer M, Thorpe J, Giraldez M, Bergan L, Tewari M, Urban N. Evaluating Serum Markers for Hormone Receptor-Negative Breast Cancer. PLoS One 2015; 10:e0142911. [PMID: 26565788 PMCID: PMC4643893 DOI: 10.1371/journal.pone.0142911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/27/2015] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death in females worldwide. Death rates have been declining, largely as a result of early detection through mammography and improved treatment, but mammographic screening is controversial because of over-diagnosis of breast disease that might not require treatment, and under-diagnosis of cancer in women with dense breasts. Breast cancer screening could be improved by pairing mammography with a tumor circulating marker, of which there are currently none. Given genomic similarities between the basal breast cancer subtype and serous ovarian cancer, and given our success in identifying circulating markers for ovarian cancer, we investigated the performance in hormone receptor-negative breast cancer detection of both previously identified ovarian serum markers and circulating markers associated with transcripts that were differentially expressed in breast cancer tissue compared to healthy breast tissue from reduction mammaplasties. METHODS We evaluated a total of 15 analytes (13 proteins, 1 miRNA, 1 autoantibody) in sera drawn at or before breast cancer surgery from 43 breast cancer cases (28 triple-negative-TN-and 15 hormone receptor-negative-HRN-/ HER2-positive) and 87 matched controls. RESULTS In the analysis of our whole cohort of breast cancer cases, autoantibodies to TP53 performed significantly better than the other selected 14 analytes showing 25.6% and 34.9% sensitivity at 95% and 90% specificity respectively with AUC: 0.7 (p<0.001). The subset of 28 TN cancers showed very similar results. We observed no correlation between anti-TP53 and the 14 other markers; however, anti-TP53 expression correlated with Body-Mass-Index. It did not correlate with tumor size, positive lymph nodes, tumor stage, the presence of metastases or recurrence. CONCLUSION None of the 13 serum proteins nor miRNA 135b identified women with HRN or TN breast cancer. TP53 autoantibodies identified women with HRN breast cancer and may have potential for early detection, confirming earlier reports. TP53 autoantibodies are long lasting in serum but may be affected by storage duration. Autoantibodies to TP53 might correlate with Body-Mass-Index.
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Affiliation(s)
- Michèl Schummer
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, United States of America
| | - Jason Thorpe
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, United States of America
| | - Maria Giraldez
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lindsay Bergan
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, United States of America
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, United States of America
- Divisions of Hematology/Oncology and Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicole Urban
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, United States of America
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He T, Qi F, Jia L, Wang S, Wang C, Song N, Fu Y, Li L, Luo Y. Tumor cell-secreted angiogenin induces angiogenic activity of endothelial cells by suppressing miR-542-3p. Cancer Lett 2015; 368:115-125. [DOI: 10.1016/j.canlet.2015.07.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 11/25/2022]
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Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
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110
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Wang N, Xu ZW, Wang KH. Systematical analysis of cutaneous squamous cell carcinoma network of microRNAs, transcription factors, and target and host genes. Asian Pac J Cancer Prev 2015; 15:10355-61. [PMID: 25556475 DOI: 10.7314/apjcp.2014.15.23.10355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNA molecules found in multicellular eukaryotes which are implicated in development of cancer, including cutaneous squamous cell carcinoma (cSCC). Expression is controlled by transcription factors (TFs) that bind to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA. Interactions result in biological signal control networks. MATERIALS AND METHODS Molecular components involved in cSCC were here assembled at abnormally expressed, related and global levels. Networks at these three levels were constructed with corresponding biological factors in term of interactions between miRNAs and target genes, TFs and miRNAs, and host genes and miRNAs. Up/down regulation or mutation of the factors were considered in the context of the regulation and significant patterns were extracted. RESULTS Participants of the networks were evaluated based on their expression and regulation of other factors. Sub-networks with two core TFs, TP53 and EIF2C2, as the centers are identified. These share self-adapt feedback regulation in which a mutual restraint exists. Up or down regulation of certain genes and miRNAs are discussed. Some, for example the expression of MMP13, were in line with expectation while others, including FGFR3, need further investigation of their unexpected behavior. CONCLUSIONS The present research suggests that dozens of components, miRNAs, TFs, target genes and host genes included, unite as networks through their regulation to function systematically in human cSCC. Networks built under the currently available sources provide critical signal controlling pathways and frequent patterns. Inappropriate controlling signal flow from abnormal expression of key TFs may push the system into an incontrollable situation and therefore contributes to cSCC development.
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Affiliation(s)
- Ning Wang
- Department of Computer Science and Technology, Jilin University, Changchun, China E-mail :
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111
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Haakensen VD, Steinfeld I, Saldova R, Shehni AA, Kifer I, Naume B, Rudd PM, Børresen-Dale AL, Yakhini Z. Serum N-glycan analysis in breast cancer patients--Relation to tumour biology and clinical outcome. Mol Oncol 2015; 10:59-72. [PMID: 26321095 DOI: 10.1016/j.molonc.2015.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/02/2015] [Accepted: 08/03/2015] [Indexed: 12/13/2022] Open
Abstract
Glycosylation and related processes play important roles in cancer development and progression, including metastasis. Several studies have shown that N-glycans have potential diagnostic value as cancer serum biomarkers. We have explored the significance of the abundance of particular serum N-glycan structures as important features of breast tumour biology by studying the serum glycome and tumour transcriptome (mRNA and miRNA) of 104 breast cancer patients. Integration of these types of molecular data allows us to study the relationship between serum glycans and transcripts representing functional pathways, such as metabolic pathways or DNA damage response. We identified tri antennary trigalactosylated trisialylated glycans in serum as being associated with lower levels of tumour transcripts involved in focal adhesion and integrin-mediated cell adhesion. These glycan structures were also linked to poor prognosis in patients with ER negative tumours. High abundance of simple monoantennary glycan structures were associated with increased survival, particularly in the basal-like subgroup. The presence of circulating tumour cells was found to be significantly associated with several serum glycome structures like bi and triantennary, di- and trigalactosylated, di- and trisialylated. The link between tumour miRNA expression levels and N-glycan production is also examined.
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Affiliation(s)
- Vilde D Haakensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Israel Steinfeld
- Department of Computer Science, Technion, Haifa, Israel; Agilent Laboratories, Agilent Technologies, Tel-Aviv, Israel
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Akram Asadi Shehni
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Ilona Kifer
- Agilent Laboratories, Agilent Technologies, Tel-Aviv, Israel
| | - Bjørn Naume
- Department of Oncology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Pauline M Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Zohar Yakhini
- Department of Computer Science, Technion, Haifa, Israel; Agilent Laboratories, Agilent Technologies, Tel-Aviv, Israel.
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112
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MicroRNAs and Growth Factors: An Alliance Propelling Tumor Progression. J Clin Med 2015; 4:1578-99. [PMID: 26287249 PMCID: PMC4555078 DOI: 10.3390/jcm4081578] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 02/06/2023] Open
Abstract
Tumor progression requires cancer cell proliferation, migration, invasion, and attraction of blood and lymph vessels. These processes are tightly regulated by growth factors and their intracellular signaling pathways, which culminate in transcriptional programs. Hence, oncogenic mutations often capture growth factor signaling, and drugs able to intercept the underlying biochemical routes might retard cancer spread. Along with messenger RNAs, microRNAs play regulatory roles in growth factor signaling and in tumor progression. Because growth factors regulate abundance of certain microRNAs and the latter modulate the abundance of proteins necessary for growth factor signaling, the two classes of molecules form a dense web of interactions, which are dominated by a few recurring modules. We review specific examples of the alliance formed by growth factors and microRNAs and refer primarily to the epidermal growth factor (EGF) pathway. Clinical applications of the crosstalk between microRNAs and growth factors are described, including relevance to cancer therapy and to emergence of resistance to specific drugs.
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113
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Győrffy B, Bottai G, Fleischer T, Munkácsy G, Budczies J, Paladini L, Børresen-Dale AL, Kristensen VN, Santarpia L. Aberrant DNA methylation impacts gene expression and prognosis in breast cancer subtypes. Int J Cancer 2015; 138:87-97. [PMID: 26174627 DOI: 10.1002/ijc.29684] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/19/2015] [Accepted: 07/02/2015] [Indexed: 02/02/2023]
Abstract
DNA methylation has a substantial impact on gene expression, affecting the prognosis of breast cancer (BC) patients dependent on molecular subtypes. In this study, we investigated the prognostic relevance of the expression of genes reported as aberrantly methylated, and the link between gene expression and DNA methylation in BC subtypes. The prognostic value of the expression of 144 aberrantly methylated genes was evaluated in ER+/HER2-, HER2+, and ER-/HER2- molecular BC subtypes, in a meta-analysis of two large transcriptomic cohorts of BC patients (n = 1,938 and n = 1,640). The correlation between gene expression and DNA methylation in distinct gene regions was also investigated in an independent dataset of 104 BCs. Survival and Pearson correlation analyses were computed for each gene separately. The expression of 48 genes was significantly associated with BC prognosis (p < 0.05), and 32 of these prognostic genes exhibited a direct expression-methylation correlation. The expression of several immune-related genes, including CD3D and HLA-A, was associated with both relapse-free survival (HR = 0.42, p = 3.5E-06; HR = 0.35, p = 1.7E-08) and overall survival (HR = 0.50, p = 5.5E-04; HR = 0.68, p = 4.5E-02) in ER-/HER2- BCs. On the overall, the distribution of both positive and negative expression-methylation correlation in distinct gene regions have different effects on gene expression and prognosis in BC subtypes. This large-scale meta-analysis allowed the identification of several genes consistently associated with prognosis, whose DNA methylation could represent a promising biomarker for prognostication and clinical stratification of patients with distinct BC subtypes.
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Affiliation(s)
- Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,2nd Dept. of Pediatrics, Semmelweis University, Budapest, Hungary.,MTA-SE Pediatrics and Nephrology Research Group, Budapest, Hungary
| | - Giulia Bottai
- Oncology Experimental Therapeutics Unit, IRCCS Clinical and Research Institute Humanitas, Rozzano - Milan, Italy
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Gyöngyi Munkácsy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary
| | - Jan Budczies
- Institute of Pathology, Campus Charité Mitte, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Laura Paladini
- Oncology Experimental Therapeutics Unit, IRCCS Clinical and Research Institute Humanitas, Rozzano - Milan, Italy
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Division of Medicine, Lørenskog, Norway
| | - Libero Santarpia
- Oncology Experimental Therapeutics Unit, IRCCS Clinical and Research Institute Humanitas, Rozzano - Milan, Italy
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114
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Shah SH, Miller P, Garcia-Contreras M, Ao Z, Machlin L, Issa E, El-Ashry D. Hierarchical paracrine interaction of breast cancer associated fibroblasts with cancer cells via hMAPK-microRNAs to drive ER-negative breast cancer phenotype. Cancer Biol Ther 2015; 16:1671-81. [PMID: 26186233 DOI: 10.1080/15384047.2015.1071742] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Multiple juxtacrine and paracrine interactions occur between cancer cells and non-cancer cells of the tumor microenvironment (TME) that direct tumor progression. Cancer Associated Fibroblasts (CAFs) are an integral component of the TME, and the majority of breast tumor stroma is comprised of CAFs. Heterotypic interactions between cancer cells and non-cancer cells of the TME occur via soluble agents, including cytokines, hormones, growth factors, and secreted microRNAs. We previously identified a microRNA signature indicative of hyperactive MAPK signaling (hMAPK-miRNA signature) that significantly associated with reduced recurrence-free and overall survival. Here we report that the hMAPK-miRNA signature associates with a high metric of stromal cell infiltrate, and we investigate the role of microRNAs, particularly hMAPK-microRNAs, secreted by CAFs on estrogen receptor (ER) expression in breast cancer cells. ER-positive MCF-7/ltE2- cells were treated with conditioned media (CM) from CAFs derived from breast cancers of different PAM50 subtypes (CAFBAS, CAFHER2, and CAFLA). CAF CM isolated specifically from ER-negative primary breast tumors led to ER repression in vitro. Nanoparticle tracking analysis and transmission electron microscopy confirmed the presence of CAF-secreted exosomes in CM and the uptake of these exosomes by the ER+ MCF-7/ltE2- cells. Differentially expressed microRNAs in CAF CM as well as in MCF-7/ltE2- cells treated with this CM were identified. Knockdown of miR-221/222 in CAFBAS resulted in knockdown of miR221/222 levels in the conditioned media and the CM from CAFBAS; miR221/222 knockdown rescued ER repression in ER-positive cell lines treated with CAFBAS-CM. Collectively, our results demonstrate that CAF-secreted microRNAs are directly involved in ER-repression, and may contribute to the MAPK-induced ER repression in breast cancer cells.
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Affiliation(s)
- Sanket H Shah
- a Cancer Biology; University of Miami ; Miami , FL USA
| | - Philip Miller
- c Sylvester Comprehensive Cancer Center; University of Miami Miller School of Medicine ; Miami , FL USA
| | - Marta Garcia-Contreras
- d Diabetes Research Institute; University of Miami Miller School of Medicine ; Miami , FL USA
| | - Zheng Ao
- a Cancer Biology; University of Miami ; Miami , FL USA
| | - Leah Machlin
- c Sylvester Comprehensive Cancer Center; University of Miami Miller School of Medicine ; Miami , FL USA
| | - Emilio Issa
- e Department of Biology ; University of Miami ; Miami , FL USA
| | - Dorraya El-Ashry
- b Department of Internal Medicine ; University of Miami Miller School of Medicine ; Miami , FL USA.,c Sylvester Comprehensive Cancer Center; University of Miami Miller School of Medicine ; Miami , FL USA
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115
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Yan M, Shield-Artin K, Byrne D, Deb S, Waddell N, Haviv I, Fox SB. Comparative microRNA profiling of sporadic and BRCA1 associated basal-like breast cancers. BMC Cancer 2015; 15:506. [PMID: 26152113 PMCID: PMC4494690 DOI: 10.1186/s12885-015-1522-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/26/2015] [Indexed: 01/29/2023] Open
Abstract
Background While a number of studies have examined miRNA profiles across the molecular subtypes of breast cancer, it is unclear whether BRCA1 basal-like cancers have a specific miRNA profile. This study aims to compare grade independent miRNA expression in luminal cancers, sporadic and BRCA1 basal-type breast cancers. It also aims to ascertain an immunohistochemical profile regulated by BRCA1 specific miRNAs for potential diagnostic use. Methods miRNA expression was assessed in 11 BRCA1 basal, 16 sporadic basal, 17 luminal grade 3 cancers via microarrays. The expression of Cyclin D1, FOXP1, FIH-1, pan-ERβ, NRP1 and CD99, predicted to be regulated by BRCA1 specific miRNAs by computer prediction algorithms, was assessed via immunohistochemistry in a cohort of 35 BRCA1 and 52 sporadic basal-like cancers. Assessment of cyclin D1, FOXP1, NRP1 and CD99 expression was repeated on a validation cohort of 82 BRCA1 and 65 sporadic basal-like breast cancers. Results Unsupervised clustering of basal cancers resulted in a “sporadic” cluster of 11 cancers, and a “BRCA1” cluster of 16 cancers, including a subgroup composed entirely of 10 BRCA1 cancers. Compared with sporadic basal cancers, BRCA1 cancers showed reduced positivity for proteins predicted to be regulated by miRNAs: FOXP1 (6/20[30 %] vs. 37/49[76 %], p < 0.001), cyclin D1 (8/22[36 %] vs. 30/46[65 %], p = 0.025), NRP1 (2/20[10 %] vs. 23/46[50 %], p = 0.002). This was confirmed in the validation cohort (all p < 0.001). Negative staining for 2 or more out of FOXP1, cyclin D1 and NRP1 predicts germline BRCA1 mutation with a sensitivity of 92 %, specificity of 44 %, positive predictive value of 38 % and a negative predictive value of 94 %. Conclusion Sporadic and BRCA1 basal-like cancers have grade independent miRNA expression profiles. Furthermore miRNA driven differences in the expression of proteins in BRCA1 basal cancers may be detected via immunohistochemistry. These findings may have important diagnostic implications, as immunohistochemical assessment of basal cancers, in addition to the patient’s family and clinical history, may potentially identify patients who may benefit from BRCA1 gene testing. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1522-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Max Yan
- Department of Anatomical Pathology, Prince of Wales Hospital, School of Medical Sciences, University of New South Wales, Randwick, 2031, Australia.
| | | | - David Byrne
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, 3002, Australia.
| | - Siddhartha Deb
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, 3002, Australia.
| | - Nic Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia.
| | | | - Izhak Haviv
- Baker IDI Heart and Diabetes Institute, Prahran, 3004, Australia.
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, 3002, Australia.
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116
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Cizeron-Clairac G, Lallemand F, Vacher S, Lidereau R, Bieche I, Callens C. MiR-190b, the highest up-regulated miRNA in ERα-positive compared to ERα-negative breast tumors, a new biomarker in breast cancers? BMC Cancer 2015; 15:499. [PMID: 26141719 PMCID: PMC4491222 DOI: 10.1186/s12885-015-1505-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 06/19/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) show differential expression across breast cancer subtypes and have both oncogenic and tumor-suppressive roles. Numerous microarray studies reported different expression patterns of miRNAs in breast cancers and found clinical interest for several miRNAs but often with contradictory results. Aim of this study is to identify miRNAs that are differentially expressed in estrogen receptor positive (ER(+)) and negative (ER(-)) breast primary tumors to better understand the molecular basis for the phenotypic differences between these two sub-types of carcinomas and to find potential clinically relevant miRNAs. METHODS We used the robust and reproductive tool of quantitative RT-PCR in a large cohort of well-annotated 153 breast cancers with long-term follow-up to identify miRNAs specifically differentially expressed between ER(+) and ER(-) breast cancers. Cytotoxicity tests and transfection experiments were then used to examine the role and the regulation mechanisms of selected miRNAs. RESULTS We identified a robust collection of 20 miRNAs significantly deregulated in ER(+) compared to ER(-) breast cancers : 12 up-regulated and eight down-regulated miRNAs. MiR-190b retained our attention as it was the miRNA the most strongly over-expressed in ER(+) compared to ER(-) with a fold change upper to 23. It was also significantly up-regulated in ER(+)/Normal breast tissue and down-regulated in ER(-)/Normal breast tissue. Functional experiments showed that miR-190b expression is not directly regulated by estradiol and that miR-190b does not affect breast cancer cell lines proliferation. Expression level of miR-190b impacts metastasis-free and event-free survival independently of ER status. CONCLUSIONS This study reveals miR-190b as the highest up-regulated miRNA in hormone-dependent breast cancers. Due to its specificity and high expression level, miR-190b could therefore represent a new biomarker in hormone-dependent breast cancers but its exact role carcinogenesis remains to elucidate.
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Affiliation(s)
- Geraldine Cizeron-Clairac
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, 26 rue d'ulm, 75005, Paris, France.
| | - François Lallemand
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, 26 rue d'ulm, 75005, Paris, France.
| | - Sophie Vacher
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, 26 rue d'ulm, 75005, Paris, France.
| | - Rosette Lidereau
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, 26 rue d'ulm, 75005, Paris, France.
| | - Ivan Bieche
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, 26 rue d'ulm, 75005, Paris, France.
| | - Celine Callens
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, 26 rue d'ulm, 75005, Paris, France.
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117
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He C, Gao H, Fan X, Wang M, Liu W, Huang W, Yang Y. Identification of a novel miRNA-target gene regulatory network in osteosarcoma by integrating transcriptome analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:8348-8357. [PMID: 26339404 PMCID: PMC4555732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/23/2015] [Indexed: 06/05/2023]
Abstract
Osteosarcoma remains a leading cause of cancer death in children and young adolescents. Although the introduction of multiagent chemotherapy, survival rates have not improved in two decades. Therefore, it is urgently needed to know the details regarding molecular etiology to driving therapeutic inroads for this disease. In this study we performed an integrated analysis of miRNA and mRNA expression data to explore the dysregulation of miRNA and miRNA-target gene regulatory network underlying OS. 59 differentially expressed miRNAs were identified, with 28 up-regulated and 31 down-regulated miRNAs by integrating OS miRNA expression data sets available. Using miRWalk databases prediction, we performed an anticorrelated analysis of miRNA and genes expression identified by a integrated analysis of gene expression data to identify 109 differently expressed miRNA target genes. A novel miRNA-target gene regulatory network was constructed with the miRNA-target gene pairs. miR-19b-3p, miR-20a-5p, miR-124-3p and their common target CCND2, the nodal points of regulatory network, may play important roles in OS. Bioinformatics analysis of biological functions and pathways demonstrated that target genes of miRNAs are highly correlated with carcinogenesis. Our findings may help to understand the molecular mechanisms of OS and identify targets of effective targeted therapies for OS.
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Affiliation(s)
- Chunlei He
- Department of Orthopedics, First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
| | - Hui Gao
- Department of Orthopedics, First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
| | - Xiaona Fan
- Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
| | - Maoyuan Wang
- Department of Orthopedics, First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
| | - Wuyang Liu
- Department of Orthopedics, First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
| | - Weiming Huang
- Department of Orthopedics, First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
| | - Yadong Yang
- Department of Orthopedics, First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000, Jiangxi Province, China
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118
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Pal B, Chen Y, Bert A, Hu Y, Sheridan JM, Beck T, Shi W, Satterley K, Jamieson P, Goodall GJ, Lindeman GJ, Smyth GK, Visvader JE. Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits. Breast Cancer Res 2015; 17:85. [PMID: 26080807 PMCID: PMC4497411 DOI: 10.1186/s13058-015-0585-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/13/2015] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION MicroRNAs (miRNAs) have been implicated in governing lineage specification and differentiation in multiple organs; however, little is known about their specific roles in mammopoiesis. We have determined the global miRNA expression profiles of functionally distinct epithelial subpopulations in mouse and human mammary tissue, and compared these to their cognate transcriptomes and epigenomes. Finally, the human miRNA signatures were used to interrogate the different subtypes of breast cancer, with a view to determining miRNA networks deregulated during oncogenesis. METHODS RNA from sorted mouse and human mammary cell subpopulations was subjected to miRNA expression analysis using the TaqMan MicroRNA Array. Differentially expressed (DE) miRNAs were correlated with gene expression and histone methylation profiles. Analysis of miRNA signatures of the intrinsic subtypes of breast cancer in The Cancer Genome Atlas (TCGA) database versus those of normal human epithelial subpopulations was performed. RESULTS Unique miRNA signatures characterized each subset (mammary stem cell (MaSC)/basal, luminal progenitor, mature luminal, stromal), with a high degree of conservation across species. Comparison of miRNA and transcriptome profiles for the epithelial subtypes revealed an inverse relationship and pinpointed key developmental genes. Interestingly, expression of the primate-specific miRNA cluster (19q13.4) was found to be restricted to the MaSC/basal subset. Comparative analysis of miRNA signatures with H3 lysine modification maps of the different epithelial subsets revealed a tight correlation between active or repressive marks for the top DE miRNAs, including derepression of miRNAs in Ezh2-deficient cellular subsets. Interrogation of TCGA-identified miRNA profiles with the miRNA signatures of different human subsets revealed specific relationships. CONCLUSIONS The derivation of global miRNA expression profiles for the different mammary subpopulations provides a comprehensive resource for understanding the interplay between miRNA networks and target gene expression. These data have highlighted lineage-specific miRNAs and potential miRNA-mRNA networks, some of which are disrupted in neoplasia. Furthermore, our findings suggest that key developmental miRNAs are regulated by global changes in histone modification, thus linking the mammary epigenome with genome-wide changes in the expression of genes and miRNAs. Comparative miRNA signature analyses between normal breast epithelial cells and breast tumors confirmed an important linkage between luminal progenitor cells and basal-like tumors.
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Affiliation(s)
- Bhupinder Pal
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Yunshun Chen
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
| | - Andrew Bert
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.
| | - Yifang Hu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
| | - Julie M Sheridan
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Tamara Beck
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Keith Satterley
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
| | - Paul Jamieson
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia. .,School of Medicine and School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Geoffrey J Lindeman
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Medical Oncology, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia.
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Jane E Visvader
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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119
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miR-30e* is an independent subtype-specific prognostic marker in breast cancer. Br J Cancer 2015; 113:290-8. [PMID: 26057454 PMCID: PMC4506390 DOI: 10.1038/bjc.2015.206] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Background: Breast cancer clinical outcome is affected by tumor molecular features, and the identification of subtype-specific prognostic biomarkers is relevant for breast cancer translational research. Gene expression signatures proved to be able to complement prognostic information provided by classical clinico-pathological features. Recently, microRNAs (miRNAs) have been causally linked to tumorigenesis and cancer progression and have been associated with patient outcome, also in breast cancer. Methods: MicroRNAs associated with the development of distant metastasis were identified in a cohort of 92 ESR1+/ERBB2− lymph node-negative breast cancers from patients not receiving adjuvant treatment. Results were confirmed and further investigated in a total of 1246 miRNA and gene expression profiles of the Molecular Taxonomy of Breast Cancer International Consortium data set. Moderated t-test, univariable and multivariable Cox regression models were used for statistical analyses. Results: miR-30e* was identified as independent protective prognostic factor in lymph node-negative untreated patients with ESR1+/ERBB2− tumours and retained a significant association with a good prognosis in treated patients with the same tumor subtype as well as in the ERBB2+ subtype, but not in ESR1−/ERBB2− tumours. Conclusions: We highlighted a relevant and subtype-specific role in breast cancer for miR-30e* and demonstrated that adding miRNA markers to gene signatures and clinico-pathological features can help for a better prognostication.
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120
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Niu J, Xue A, Chi Y, Xue J, Wang W, Zhao Z, Fan M, Yang CH, Shao ZM, Pfeffer LM, Wu J, Wu ZH. Induction of miRNA-181a by genotoxic treatments promotes chemotherapeutic resistance and metastasis in breast cancer. Oncogene 2015; 35:1302-1313. [PMID: 26028030 PMCID: PMC4666837 DOI: 10.1038/onc.2015.189] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 04/24/2015] [Accepted: 04/24/2015] [Indexed: 01/13/2023]
Abstract
Acquired therapeutic resistance is the major drawback to effective systemic therapies for cancers. Aggressive triple-negative breast cancers (TNBC) develop resistance to chemotherapies rapidly, whereas the underlying mechanisms are not completely understood. Here we show that genotoxic treatments significantly increased the expression of miR-181a in TNBC cells, which enhanced TNBC cell survival and metastasis upon Doxorubicin treatment. Consistently, high miR-181a level associated with poor disease free survival and overall survival after treatments in breast cancer patients. The upregulation of miR-181a was orchestrated by transcription factor STAT3 whose activation depended on NF-κB-mediated IL-6 induction in TNBC cells upon genotoxic treatment. Intriguingly, activated STAT3 not only directly bound to MIR181A1 promoter to drive transcription but also facilitated the recruitment of MSK1 to the same region where MSK1 promoted a local active chromatin state by phosphorylating histone H3. We further identified BAX as a direct functional target of miR-181a, whose suppression decreased apoptosis and increased invasion of TNBC cells upon Dox treatment. These results were further confirmed by evidence that suppression of miR-181a significantly enhanced therapeutic response and reduced lung metastasis in a TNBC orthotopic model. Collectively, our data suggested that miR-181a induction had a critical role in promoting therapeutic resistance and aggressive behavior of TNBC cells upon genotoxic treatment. Antagonizing miR-181a may serve as a promising strategy to sensitize TNBC cells to chemotherapy and mitigate metastasis.
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Affiliation(s)
- Jixiao Niu
- Department of Pathology and Laboratory Medicine, Shanghai Medical College, Fudan University, Shanghai.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai
| | - Aimin Xue
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai
| | - Yayun Chi
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai.,Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai
| | - Jingyan Xue
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai.,Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Shanghai Medical College, Fudan University, Shanghai.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai
| | - Ziqin Zhao
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai
| | - Meiyun Fan
- Department of Pathology and Laboratory Medicine, Shanghai Medical College, Fudan University, Shanghai.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai
| | - Chuan He Yang
- Department of Pathology and Laboratory Medicine, Shanghai Medical College, Fudan University, Shanghai.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai
| | - Zhi-Ming Shao
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai.,Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai
| | - Lawrence M Pfeffer
- Department of Pathology and Laboratory Medicine, Shanghai Medical College, Fudan University, Shanghai.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai
| | - Jiong Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai.,Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai
| | - Zhao-Hui Wu
- Department of Pathology and Laboratory Medicine, Shanghai Medical College, Fudan University, Shanghai.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, Shanghai Medical College, Fudan University, Shanghai
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Shukla A, Sehgal M, Singh TR. Hydroxymethylation and its potential implication in DNA repair system: A review and future perspectives. Gene 2015; 564:109-18. [DOI: 10.1016/j.gene.2015.03.075] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/21/2015] [Accepted: 03/05/2015] [Indexed: 12/22/2022]
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Martignetti L, Tesson B, Almeida A, Zinovyev A, Tucker GC, Dubois T, Barillot E. Detection of miRNA regulatory effect on triple negative breast cancer transcriptome. BMC Genomics 2015; 16:S4. [PMID: 26046581 PMCID: PMC4460783 DOI: 10.1186/1471-2164-16-s6-s4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Identifying key microRNAs (miRNAs) contributing to the genesis and development of a particular disease is a focus of many recent studies. We introduce here a rank-based algorithm to detect miRNA regulatory activity in cancer-derived tissue samples which combines measurements of gene and miRNA expression levels and sequence-based target predictions. The method is designed to detect modest but coordinated changes in the expression of sequence-based predicted target genes. We applied our algorithm to a cohort of 129 tumour and healthy breast tissues and showed its effectiveness in identifying functional miRNAs possibly involved in the disease. These observations have been validated using an independent publicly available breast cancer dataset from The Cancer Genome Atlas. We focused on the triple negative breast cancer subtype to highlight potentially relevant miRNAs in this tumour subtype. For those miRNAs identified as potential regulators, we characterize the function of affected target genes by enrichment analysis. In the two independent datasets, the affected targets are not necessarily the same, but display similar enriched categories, including breast cancer related processes like cell substrate adherens junction, regulation of cell migration, nuclear pore complex and integrin pathway. The R script implementing our method together with the datasets used in the study can be downloaded here (http://bioinfo-out.curie.fr/projects/targetrunningsum).
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123
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Oztemur Y, Bekmez T, Aydos A, Yulug IG, Bozkurt B, Dedeoglu BG. A ranking-based meta-analysis reveals let-7 family as a meta-signature for grade classification in breast cancer. PLoS One 2015; 10:e0126837. [PMID: 25978727 PMCID: PMC4433233 DOI: 10.1371/journal.pone.0126837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/08/2015] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is one of the most important causes of cancer-related deaths worldwide in women. In addition to gene expression studies, the progressing work in the miRNA area including miRNA microarray studies, brings new aspects to the research on the cancer development and progression. Microarray technology has been widely used to find new biomarkers in research and many transcriptomic microarray studies are available in public databases. In this study, the breast cancer miRNA and mRNA microarray studies were collected according to the availability of their data and clinical information, and combined by a newly developed ranking-based meta-analysis approach to find out candidate miRNA biomarkers (meta-miRNAs) that classify breast cancers according to their grades and explain the relation between miRNAs and mRNAs. This approach provided meta-miRNAs specific to breast cancer grades, pointing out let-7 family members as grade classifiers. The qRT-PCR studies performed with independent breast tumors confirmed the potential biomarker role of let-7 family members (meta-miRNAs). The concordance between the meta-mRNAs and miRNA target genes specific to tumor grade (common genes) supported the idea of mRNAs as miRNA targets. The pathway analysis results showed that most of the let-7 family miRNA targets, and also common genes, were significantly taking part in cancer-related pathways. The qRT-PCR studies, together with bioinformatic analyses, confirmed the results of meta-analysis approach, which is dynamic and allows combining datasets from different platforms.
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Affiliation(s)
| | - Tufan Bekmez
- Gazi University, Faculty of Dentistry, Ankara, Turkey
| | - Alp Aydos
- Ankara University, Biotechnology Institute, Ankara, Turkey
| | - Isik G. Yulug
- Bilkent University, Molecular Biology and Genetics Department, Ankara, Turkey
| | - Betul Bozkurt
- Ankara Numune Training and Research Hospital, Department of General Surgery, Ankara, Turkey
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Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling. BIOMED RESEARCH INTERNATIONAL 2015; 2015:746970. [PMID: 25961039 PMCID: PMC4413257 DOI: 10.1155/2015/746970] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 12/11/2022]
Abstract
Breast cancer is a heterogeneous disease with well-defined molecular subtypes. Currently, comparative genomic hybridization arrays (aCGH) techniques have been developed rapidly, and recent evidences in studies of breast cancer suggest that tumors within gene expression subtypes share similar DNA copy number aberrations (CNA) which can be used to further subdivide subtypes. Moreover, subtype-specific miRNA expression profiles are also proposed as novel signatures for breast cancer classification. The identification of mRNA or miRNA expression-based breast cancer subtypes is considered an instructive means of prognosis. Here, we conducted an integrated analysis based on copy number aberrations data and miRNA-mRNA dual expression profiling data to identify breast cancer subtype-specific biomarkers. Interestingly, we found a group of genes residing in subtype-specific CNA regions that also display the corresponding changes in mRNAs levels and their target miRNAs' expression. Among them, the predicted direct correlation of BRCA1-miR-143-miR-145 pairs was selected for experimental validation. The study results indicated that BRCA1 positively regulates miR-143-miR-145 expression and miR-143-miR-145 can serve as promising novel biomarkers for breast cancer subtyping. In our integrated genomics analysis and experimental validation, a new frame to predict candidate biomarkers of breast cancer subtype is provided and offers assistance in order to understand the potential disease etiology of the breast cancer subtypes.
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125
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Perdigão-Henriques R, Petrocca F, Altschuler G, Thomas MP, Le MTN, Tan SM, Hide W, Lieberman J. miR-200 promotes the mesenchymal to epithelial transition by suppressing multiple members of the Zeb2 and Snail1 transcriptional repressor complexes. Oncogene 2015; 35:158-72. [PMID: 25798844 DOI: 10.1038/onc.2015.69] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 02/07/2023]
Abstract
The miR-200 family promotes the epithelial state by suppressing the Zeb1/Zeb2 epithelial gene transcriptional repressors. To identify other miR-200-regulated genes, we isolated mRNAs bound to transfected biotinylated miR-200c in mouse breast cancer cells. In all, 520 mRNAs were significantly enriched in miR-200c binding at least twofold. Putative miR-200-regulated genes included Zeb2, enriched 3.5-fold in the pull down. However, Zeb2 knockdown does not fully recapitulate miR-200c overexpression, suggesting that regulating other miR-200 targets contributes to miR-200's enhancement of epithelial gene expression. Candidate genes were highly enriched for miR-200c seed pairing in their 3'UTR and coding sequence and for genes that were downregulated by miR-200c overexpression. Epidermal growth factor receptor and downstream MAPK signaling pathways were the most enriched pathways. Genes whose products mediate transforming growth factor (TGF)-β signaling were also significantly overrepresented, and miR-200 counteracted the suppressive effects of TGF-β and bone morphogenic protein 2 (BMP-2) on epithelial gene expression. miR-200c regulated the 3'UTRs of 12 of 14 putative miR-200c-binding mRNAs tested. The extent of mRNA binding to miR-200c strongly correlated with gene suppression. Twelve targets of miR-200c (Crtap, Fhod1, Smad2, Map3k1, Tob1, Ywhag/14-3-3γ, Ywhab/14-3-3β, Smad5, Zfp36, Xbp1, Mapk12, Snail1) were experimentally validated by identifying their 3'UTR miR-200 recognition elements. Smad2 and Smad5 form a complex with Zeb2 and Ywhab/14-3-3β and Ywhag/14-3-3γ form a complex with Snail1. These complexes that repress transcription assemble on epithelial gene promoters. miR-200 overexpression induced RNA polymerase II localization and reduced Zeb2 and Snail1 binding to epithelial gene promoters. Expression of miR-200-resistant Smad5 modestly, but significantly, reduced epithelial gene induction by miR-200. miR-200 expression and Zeb2 knockdown are known to inhibit cell invasion in in vitro assays. Knockdown of each of three novel miR-200 target genes identified here, Smad5, Ywhag and Crtap, also profoundly suppressed cell invasion. Thus, miR-200 suppresses TGF-β/BMP signaling, promotes epithelial gene expression and suppresses cell invasion by regulating a network of genes.
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Affiliation(s)
- R Perdigão-Henriques
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, USA.,Animal Cell Technology Unit, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal.,Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
| | - F Petrocca
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, USA
| | - G Altschuler
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - M P Thomas
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, USA
| | - M T N Le
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, USA
| | - S M Tan
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, USA
| | - W Hide
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.,Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - J Lieberman
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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126
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Aakula A, Leivonen SK, Hintsanen P, Aittokallio T, Ceder Y, Børresen-Dale AL, Perälä M, Östling P, Kallioniemi O. MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth. Mol Oncol 2015; 9:1287-300. [PMID: 25907805 DOI: 10.1016/j.molonc.2015.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) regulate a wide range of cellular signaling pathways and biological processes in both physiological and pathological states such as cancer. We have previously identified miR-135b as a direct regulator of androgen receptor (AR) protein level in prostate cancer (PCa). We wanted to further explore the relationship of miR-135b to hormonal receptors, particularly estrogen receptor α (ERα). Here we show that miR-135b expression is lower in ERα-positive breast tumors as compared to ERα-negative samples in two independent breast cancer (BCa) patient cohorts (101 and 1302 samples). Additionally, the miR-135b expression is higher in AR-low PCa patient samples (47 samples). We identify ERα as a novel miR-135b target by demonstrating miR-135b binding to the 3'UTR of the ERα and decreased ERα protein and mRNA level upon miR-135b overexpression in BCa cells. MiR-135b reduces proliferation of ERα-positive BCa cells MCF-7 and BT-474 as well as AR-positive PCa cells LNCaP and 22Rv1 when grown in 2D. To identify other genes regulated by miR-135b we performed gene expression studies and found a link to the hypoxia inducible factor 1α (HIF1α) pathway. We show that miR-135b influences the protein level of the inhibitor for hypoxia inducible factor 1α (HIF1AN) and is able to bind to HIF1AN 3'UTR. Our study demonstrates that miR-135b regulates ERα, AR and HIF1AN protein levels through interaction with their 3'UTR regions, and proliferation in ERα-positive BCa and AR-positive PCa cells.
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Affiliation(s)
- Anna Aakula
- Institute for Molecular Medicine Finland, FIMM, Helsinki, Finland; VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland; Turku Centre for Biotechnology, University of Turku, Turku, Finland.
| | - Suvi-Katri Leivonen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, Helsinki, Finland
| | - Yvonne Ceder
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Merja Perälä
- VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland
| | - Päivi Östling
- Institute for Molecular Medicine Finland, FIMM, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland, FIMM, Helsinki, Finland
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127
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Kedmi M, Ben-Chetrit N, Körner C, Mancini M, Ben-Moshe NB, Lauriola M, Lavi S, Biagioni F, Carvalho S, Cohen-Dvashi H, Schmitt F, Wiemann S, Blandino G, Yarden Y. EGF induces microRNAs that target suppressors of cell migration: miR-15b targets MTSS1 in breast cancer. Sci Signal 2015; 8:ra29. [PMID: 25783158 DOI: 10.1126/scisignal.2005866] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Growth factors promote tumor growth and metastasis. We found that epidermal growth factor (EGF) induced a set of 22 microRNAs (miRNAs) before promoting the migration of mammary cells. These miRNAs were more abundant in human breast tumors relative to the surrounding tissue, and their abundance varied among breast cancer subtypes. One of these miRNAs, miR-15b, targeted the 3' untranslated region of MTSS1 (metastasis suppressor protein 1). Although xenografts in which MTSS1 was knocked down grew more slowly in mice initially, longer-term growth was unaffected. Knocking down MTSS1 increased migration and Matrigel invasion of nontransformed mammary epithelial cells. Overexpressing MTSS1 in an invasive cell line decreased cell migration and invasiveness, decreased the formation of invadopodia and actin stress fibers, and increased the formation of cellular junctions. In tissues from breast cancer patients with the aggressive basal subtype, an inverse correlation occurred with the high expression of miRNA-15b and the low expression of MTSS1. Furthermore, low abundance of MTSS1 correlated with poor patient prognosis. Thus, growth factor-inducible miRNAs mediate mechanisms underlying the progression of cancer.
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Affiliation(s)
- Merav Kedmi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nir Ben-Chetrit
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Cindy Körner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Maicol Mancini
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noa Bossel Ben-Moshe
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mattia Lauriola
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sara Lavi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Francesca Biagioni
- Translational Oncogenomics Unit, Italian National Cancer Institute "Regina Elena," Rome 00144, Italy
| | - Silvia Carvalho
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Cohen-Dvashi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Fernando Schmitt
- Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto and Department of Pathology, University Health Network, Toronto, Ontario M5C 2C4, Canada. IPATIMUP, University of Porto, Porto 4200-465, Portugal
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Giovanni Blandino
- Translational Oncogenomics Unit, Italian National Cancer Institute "Regina Elena," Rome 00144, Italy
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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128
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Zhu J, Xiong G, Fu H, Evers BM, Zhou BP, Xu R. Chaperone Hsp47 Drives Malignant Growth and Invasion by Modulating an ECM Gene Network. Cancer Res 2015; 75:1580-91. [PMID: 25744716 DOI: 10.1158/0008-5472.can-14-1027] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 01/21/2015] [Indexed: 01/08/2023]
Abstract
The extracellular matrix (ECM) is a determining factor in the tumor microenvironment that restrains or promotes malignant growth. In this report, we show how the molecular chaperone protein Hsp47 functions as a nodal hub in regulating an ECM gene transcription network. A transcription network analysis showed that Hsp47 expression was activated during breast cancer development and progression. Hsp47 silencing reprogrammed human breast cancer cells to form growth-arrested and/or noninvasive structures in 3D cultures, and to limit tumor growth in xenograft assays by reducing deposition of collagen and fibronectin. Coexpression network analysis also showed that levels of microRNA(miR)-29b and -29c were inversely correlated with expression of Hsp47 and ECM network genes in human breast cancer tissues. We found that miR-29 repressed expression of Hsp47 along with multiple ECM network genes. Ectopic expression of miR-29b suppressed malignant phenotypes of breast cancer cells in 3D culture. Clinically, increased expression of Hsp47 and reduced levels of miR-29b and -29c were associated with poor survival outcomes in breast cancer patients. Our results show that Hsp47 is regulated by miR-29 during breast cancer development and progression, and that increased Hsp47 expression promotes cancer progression in part by enhancing deposition of ECM proteins.
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Affiliation(s)
- Jieqing Zhu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky
| | - Gaofeng Xiong
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky
| | - Hanjiang Fu
- Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Surgery, University of Kentucky, Lexington, Kentucky
| | - Binhua P Zhou
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Ren Xu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky.
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129
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Duhachek-Muggy S, Zolkiewska A. ADAM12-L is a direct target of the miR-29 and miR-200 families in breast cancer. BMC Cancer 2015; 15:93. [PMID: 25886595 PMCID: PMC4352249 DOI: 10.1186/s12885-015-1108-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/20/2015] [Indexed: 12/18/2022] Open
Abstract
Background ADAM12-L and ADAM12-S represent two major splice variants of human metalloproteinase-disintegrin 12 mRNA, which differ in their 3′-untranslated regions (3′UTRs). ADAM12-L, but not ADAM12-S, has prognostic and chemopredictive values in breast cancer. Expression levels of the two ADAM12 splice variants in clinical samples are highly discordant, suggesting post-transcriptional regulation of the ADAM12 gene. The miR-29, miR-30, and miR-200 families have potential target sites in the ADAM12-L 3′UTR and they may negatively regulate ADAM12-L expression. Methods miR-29b/c, miR-30b/d, miR-200b/c, or control miRNA mimics were transfected into SUM159PT, BT549, SUM1315MO2, or Hs578T breast cancer cells. ADAM12-L and ADAM12-S mRNA levels were measured by qRT-PCR, and ADAM12-L protein was detected by Western blotting. Direct targeting of the ADAM12-L 3′UTR by miRNAs was tested using an ADAM12-L 3′UTR luciferase reporter. The rate of ADAM12-L translation was evaluated by metabolic labeling of cells with 35S cysteine/methionine. The roles of endogenous miR-29b and miR-200c were tested by transfecting cells with miRNA hairpin inhibitors. Results Transfection of miR-29b/c mimics strongly decreased ADAM12-L mRNA levels in SUM159PT and BT549 cells, whereas ADAM12-S levels were not changed. ADAM12-L, but not ADAM12-S, levels were also significantly diminished by miR-200b/c in SUM1315MO2 cells. In Hs578T cells, miR-200b/c mimics impeded translation of ADAM12-L mRNA. Importantly, both miR-29b/c and miR-200b/c strongly decreased steady state levels of ADAM12-L protein in all breast cancer cell lines tested. miR-29b/c and miR-200b/c also significantly decreased the activity of an ADAM12-L 3′UTR reporter, and this effect was abolished when miR-29b/c and miR-200b/c target sequences were mutated. In contrast, miR-30b/d did not elicit consistent and significant effects on ADAM12-L expression. Analysis of a publicly available gene expression dataset for 100 breast tumors revealed a statistically significant negative correlation between ADAM12-L and both miR-29b and miR-200c. Inhibition of endogenous miR-29b and miR-200c in SUM149PT and SUM102PT cells led to increased ADAM12-L expression. Conclusions The ADAM12-L 3′UTR is a direct target of miR-29 and miR-200 family members. Since the miR-29 and miR-200 families play important roles in breast cancer progression, these results may help explain the different prognostic and chemopredictive values of ADAM12-L and ADAM12-S in breast cancer.
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Affiliation(s)
- Sara Duhachek-Muggy
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
| | - Anna Zolkiewska
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
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130
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Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HKM, Vaske C, Siegel JU, Troyanskaya O, Chin SF, Caldas C, Balmain A, Børresen-Dale AL, Kristensen V. Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53. Mol Cancer Res 2015; 13:493-501. [PMID: 25351767 PMCID: PMC4465579 DOI: 10.1158/1541-7786.mcr-14-0387] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
UNLABELLED Lymphocytic infiltration is associated with better prognosis in several epithelial malignancies including breast cancer. The tumor suppressor TP53 is mutated in approximately 30% of breast adenocarcinomas, with varying frequency across molecular subtypes. In this study of 1,420 breast tumors, we tested for interaction between TP53 mutation status and tumor subtype determined by PAM50 and integrative cluster analysis. In integrative cluster 10 (IC10)/basal-like breast cancer, we identify an association between lymphocytic infiltration, determined by an expression score, and retention of wild-type TP53. The expression-derived score agreed with the degree of lymphocytic infiltration assessed by pathologic review, and application of the Nanodissect algorithm was suggestive of this infiltration being primarily of cytotoxic T lymphocytes (CTL). Elevated expression of this CTL signature was associated with longer survival in IC10/Basal-like tumors. These findings identify a new link between the TP53 pathway and the adaptive immune response in estrogen receptor (ER)-negative breast tumors, suggesting a connection between TP53 inactivation and failure of tumor immunosurveillance. IMPLICATIONS The association of lymphocytic invasion of ER-negative breast tumors with the retention of wild-type TP53 implies a novel protective connection between TP53 function and tumor immunosurveillance.
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Affiliation(s)
- David Quigley
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Laxmi Silwal-Pandit
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ruth Dannenfelser
- Department of Computer Science, Princeton University, Princeton New Jersey. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hans Kristian Moen Vollan
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | | | - Olga Troyanskaya
- Department of Computer Science, Princeton University, Princeton New Jersey. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute and Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute and Department of Oncology, University of Cambridge, Cambridge, United Kingdom. Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation, Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom. Cambridge Experimental Cancer Medicine Centre, Cambridge, United Kingdom
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway.
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131
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Tordonato C, Di Fiore PP, Nicassio F. The role of non-coding RNAs in the regulation of stem cells and progenitors in the normal mammary gland and in breast tumors. Front Genet 2015; 6:72. [PMID: 25774169 PMCID: PMC4343025 DOI: 10.3389/fgene.2015.00072] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022] Open
Abstract
The outlook on stem cell (SC) biology is shifting from a rigid hierarchical to a more flexible model in which the identity and the behavior of adult SCs, far from being fixed, are determined by the dynamic integration of cell autonomous and non-autonomous mechanisms. Within this framework, the recent discovery of thousands of non-coding RNAs (ncRNAs) with regulatory function is redefining the landscape of transcriptome regulation, highlighting the interplay of epigenetic, transcriptional, and post-transcriptional mechanisms in the specification of cell fate and in the regulation of developmental processes. Furthermore, the expression of ncRNAs is often tissue- or even cell type-specific, emphasizing their involvement in defining space, time and developmental stages in gene regulation. Such a role of ncRNAs has been investigated in embryonic and induced pluripotent SCs, and in numerous types of adult SCs and progenitors, including those of the breast, which will be the topic of this review. We will focus on ncRNAs with an important role in breast cancer, in particular in mammary cancer SCs and progenitors, and highlight the ncRNA-based circuitries whose subversion alters a number of the epigenetic, transcriptional, and post-transcriptional events that control “stemness” in the physiological setting.
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Affiliation(s)
- Chiara Tordonato
- Department of Experimental Oncology, European Institute of Oncology, Milan Italy
| | - Pier Paolo Di Fiore
- Department of Experimental Oncology, European Institute of Oncology, Milan Italy ; Fondazione Istituto FIRC di Oncologia Molecolare, Milan Italy ; Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan Italy
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132
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Drasin DJ, Guarnieri AL, Neelakantan D, Kim J, Cabrera JH, Wang CA, Zaberezhnyy V, Gasparini P, Cascione L, Huebner K, Tan AC, Ford HL. TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation. Cancer Res 2015; 75:1908-21. [PMID: 25716682 DOI: 10.1158/0008-5472.can-14-2394] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/19/2014] [Indexed: 12/19/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a dynamic process that relies on cellular plasticity. Recently, the process of an oncogenic EMT, followed by a reverse mesenchymal-to-epithelial transition (MET), has been implicated as critical in the metastatic colonization of carcinomas. Unlike governance of epithelial programming, regulation of mesenchymal programming is not well understood in EMT. Here, we describe and characterize the first microRNA that enhances exclusively mesenchymal programming. We demonstrate that miR-424 is upregulated early during a TWIST1 or SNAI1-induced EMT, and that it causes cells to express mesenchymal genes without affecting epithelial genes, resulting in a mixed/intermediate EMT. Furthermore, miR-424 increases motility, decreases adhesion, and induces a growth arrest, changes associated with a complete EMT that can be reversed when miR-424 expression is lowered, concomitant with an MET-like process. Breast cancer patient miR-424 levels positively associate with TWIST1/2 and EMT-like gene signatures, and miR-424 is increased in primary tumors versus matched normal breast. However, miR-424 is downregulated in patient metastases versus matched primary tumors. Correspondingly, miR-424 decreases tumor initiation and is posttranscriptionally downregulated in macrometastases in mice, suggesting the need for biphasic expression of miR-424 to transit the EMT-MET axis. Next-generation RNA sequencing revealed miR-424 regulates numerous EMT and cancer stemness-associated genes, including TGFBR3, whose downregulation promotes mesenchymal phenotypes, but not tumor-initiating phenotypes. Instead, we demonstrate that increased MAPK-ERK signaling is critical for miR-424-mediated decreases in tumor-initiating phenotypes. These findings suggest miR-424 plays distinct roles in tumor progression, potentially facilitating earlier, but repressing later, stages of metastasis by regulating an EMT-MET axis.
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Affiliation(s)
- David J Drasin
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Anna L Guarnieri
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Deepika Neelakantan
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jihye Kim
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Joshua H Cabrera
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Chu-An Wang
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Vadym Zaberezhnyy
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Pierluigi Gasparini
- Department of Molecular Virology, Immunology and Molecular Genetics, Ohio State University, Columbus, Ohio
| | - Luciano Cascione
- Department of Molecular Virology, Immunology and Molecular Genetics, Ohio State University, Columbus, Ohio
| | - Kay Huebner
- Department of Molecular Virology, Immunology and Molecular Genetics, Ohio State University, Columbus, Ohio
| | - Aik-Choon Tan
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Heide L Ford
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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133
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Yang Y, Xing Y, Liang C, Hu L, Xu F, Chen Y. Crucial microRNAs and genes of human primary breast cancer explored by microRNA-mRNA integrated analysis. Tumour Biol 2015; 36:5571-9. [PMID: 25680412 DOI: 10.1007/s13277-015-3227-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/04/2015] [Indexed: 12/27/2022] Open
Abstract
This study aimed to screen potential microRNAs (miRNAs) and genes related to human primary breast cancer. The gene and miRNA expression profile data of GSE19783 was obtained from Gene Expression Omnibus. The matched messenger RNA (mRNA) and miRNA expression profiles of 100 human primary breast cancer samples were chosen for further analysis. The miRNA-gene regulatory modules were screened via iterative multiplicative updating algorithm. The potential functions of genes in modules were predicted by functional and pathway enrichment analysis; meanwhile, the potential functions of miRNAs were predicted by functional enrichment analysis. Furthermore, miRNA-miRNA functional synergistic network and miRNA-miRNA co-regulatory network were constructed. Totally, 16 miRNA-gene modules were screened, containing 222 miRNA-gene interactions. The genes in these modules were mainly related to breast cancer. Genes in module 6 (e.g., SFRP1) were enriched in cell junction assembly; genes in module 8 and 12 (e.g., ESR1 and ERBB4) were significantly implicated in mammary gland alveolus and lobule development. Meanwhile, genes in module 12 (e.g., ERBB4) were enriched in the pathway of endocytosis. Besides, several miRNAs (e.g., miR-375) were enriched in inflammatory cell apoptotic process; some other miRNAs (e.g., miR-139-5p and miR-9) were enriched in response to vitamin D. Additionally, miR-139-5p with several other miRNAs (e.g., miR-9) co-regulated SFRP1; miR-375, miR-592, and miR-135a co-regulated ESR1 and ERBB4. Some miRNAs (e.g., miR-139-5p and miR-9) and their target gene SFRP1, as well as several other miRNAs (e.g., miR-375, miR-592, and miR-135a) and their target genes (e.g., ESR1 and ERBB4), might be crucial in the pathogenesis of primary breast cancer.
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Affiliation(s)
- Yang Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
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Gaj P, Zagozdzon R. In silico analysis of microRNA-510 as a potential oncomir in human breast cancer. Breast Cancer Res 2015; 16:403. [PMID: 25032262 PMCID: PMC4053154 DOI: 10.1186/bcr3624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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135
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Grawenda AM, Møller EK, Lam S, Repapi E, Teunisse AFAS, Alnæs GIG, Børresen-Dale AL, Kristensen VN, Goding CR, Jochemsen AG, Edvardsen H, Bond GL. Interaction between p53 mutation and a somatic HDMX biomarker better defines metastatic potential in breast cancer. Cancer Res 2015; 75:698-708. [PMID: 25649770 DOI: 10.1158/0008-5472.can-14-2637] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
TP53 gene mutation is associated with poor prognosis in breast cancer, but additional biomarkers that can further refine the impact of the p53 pathway are needed to achieve clinical utility. In this study, we evaluated a role for the HDMX-S/FL ratio as one such biomarker, based on its association with other suppressor mutations that confer worse prognosis in sarcomas, another type of cancer that is surveilled by p53. We found that HDMX-S/FL ratio interacted with p53 mutational status to significantly improve prognostic capability in patients with breast cancer. This biomarker pair offered prognostic utility that was comparable with a microarray-based prognostic assay. Unexpectedly, the utility tracked independently of DNA-damaging treatments and instead with different tumor metastasis potential. Finally, we obtained evidence that this biomarker pair might identify patients who could benefit from anti-HDM2 strategies to impede metastatic progression. Taken together, our work offers a p53 pathway marker, which both refines our understanding of the impact of p53 activity on prognosis and harbors potential utility as a clinical tool.
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Affiliation(s)
- Anna M Grawenda
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Elen K Møller
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. KG Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Suzanne Lam
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Emmanouela Repapi
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Amina F A S Teunisse
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Grethe I G Alnæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. KG Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. KG Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway
| | - Colin R Goding
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Aart G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hege Edvardsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gareth L Bond
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford, United Kingdom.
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136
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Sfakianakis S, Bei ES, Zervakis M, Vassou D, Kafetzopoulos D. On the identification of circulating tumor cells in breast cancer. IEEE J Biomed Health Inform 2015; 18:773-82. [PMID: 24808221 DOI: 10.1109/jbhi.2013.2295262] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Breast cancer is a highly heterogeneous disease and very common among western women. The main cause of death is not the primary tumor but its metastases at distant sites, such as lymph nodes and other organs (preferentially lung, liver, and bones). The study of circulating tumor cells (CTCs) in peripheral blood resulting from tumor cell invasion and intravascular filtration highlights their crucial role concerning tumor aggressiveness and metastasis. Genomic research regarding CTCs monitoring for breast cancer is limited due to the lack of indicative genes for their detection and isolation. Instead of direct CTC detection, in our study, we focus on the identification of factors in peripheral blood that can indirectly reveal the presence of such cells. Using selected publicly available breast cancer and peripheral blood microarray datasets, we follow a two-step elimination procedure for the identification of several discriminant factors. Our procedure facilitates the identification of major genes involved in breast cancer pathology, which are also indicative of CTCs presence.
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137
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Aure MR, Jernström S, Krohn M, Vollan HKM, Due EU, Rødland E, Kåresen R, Ram P, Lu Y, Mills GB, Sahlberg KK, Børresen-Dale AL, Lingjærde OC, Kristensen VN. Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer. Genome Med 2015; 7:21. [PMID: 25873999 PMCID: PMC4396592 DOI: 10.1186/s13073-015-0135-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/19/2015] [Indexed: 01/20/2023] Open
Abstract
Background The role played by microRNAs in the deregulation of protein expression in breast cancer is only partly understood. To gain insight, the combined effect of microRNA and mRNA expression on protein expression was investigated in three independent data sets. Methods Protein expression was modeled as a multilinear function of powers of mRNA and microRNA expression. The model was first applied to mRNA and protein expression for 105 selected cancer-associated genes and to genome-wide microRNA expression from 283 breast tumors. The model considered both the effect of one microRNA at a time and all microRNAs combined. In the latter case the Lasso penalized regression method was applied to detect the simultaneous effect of multiple microRNAs. Results An interactome map for breast cancer representing all direct and indirect associations between the expression of microRNAs and proteins was derived. A pattern of extensive coordination between microRNA and protein expression in breast cancer emerges, with multiple clusters of microRNAs being associated with multiple clusters of proteins. Results were subsequently validated in two independent breast cancer data sets. A number of the microRNA-protein associations were functionally validated in a breast cancer cell line. Conclusions A comprehensive map is derived for the co-expression in breast cancer of microRNAs and 105 proteins with known roles in cancer, after filtering out the in-cis effect of mRNA expression. The analysis suggests that group action by several microRNAs to deregulate the expression of proteins is a common modus operandi in breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0135-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miriam Ragle Aure
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway
| | - Sandra Jernström
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway
| | - Marit Krohn
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway
| | - Hans Kristian Moen Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway ; Department of Oncology, Division of Surgery, Cancer and Transplantation, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway
| | - Eldri U Due
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway
| | - Einar Rødland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; Centre for Cancer Biomedicine, University of Oslo, Oslo, 0316 Norway ; Department of Computer Science, University of Oslo, Oslo, 0316 Norway
| | - Rolf Kåresen
- Institute of Clinical Medicine, University of Oslo, Oslo, 0316 Norway
| | | | - Prahlad Ram
- Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030 USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030 USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030 USA
| | - Kristine Kleivi Sahlberg
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway ; Department of Research, Vestre Viken Hospital Trust, Drammen, 3004 Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway
| | - Ole Christian Lingjærde
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway ; Centre for Cancer Biomedicine, University of Oslo, Oslo, 0316 Norway ; Department of Computer Science, University of Oslo, Oslo, 0316 Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310 Norway ; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316 Norway ; Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, 1478 Norway
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138
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Goh JN, Loo SY, Datta A, Siveen KS, Yap WN, Cai W, Shin EM, Wang C, Kim JE, Chan M, Dharmarajan AM, Lee ASG, Lobie PE, Yap CT, Kumar AP. microRNAs in breast cancer: regulatory roles governing the hallmarks of cancer. Biol Rev Camb Philos Soc 2015; 91:409-28. [DOI: 10.1111/brv.12176] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Jen N. Goh
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
| | - Ser Y. Loo
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117597 Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR); Singapore 138672 Singapore
| | - Arpita Datta
- Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117597 Singapore
| | - Kodappully S. Siveen
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
| | - Wei N. Yap
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
| | - Wanpei Cai
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
| | - Eun M. Shin
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
| | - Chao Wang
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
| | - Ji E. Kim
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
| | - Maurice Chan
- Division of Medical Sciences; National Cancer Centre; Singapore 169610 Singapore
| | - Arun M. Dharmarajan
- Curtin Health Innovation Research Institute, Biosciences Research Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University; 6845 Perth Western Australia Australia
| | - Ann S.-G. Lee
- Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117597 Singapore
- Division of Medical Sciences; National Cancer Centre; Singapore 169610 Singapore
- Duke-NUS Graduate Medical School; Singapore 169857 Singapore
| | - Peter E. Lobie
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
- National University Cancer Institute; Singapore 1192288 Singapore
| | - Celestial T. Yap
- Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117597 Singapore
- National University Cancer Institute; Singapore 1192288 Singapore
| | - Alan P. Kumar
- Cancer Science Institute of Singapore, National University of Singapore; Singapore 117599 Singapore
- Department of Pharmacology; Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117599 Singapore
- Curtin Health Innovation Research Institute, Biosciences Research Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University; 6845 Perth Western Australia Australia
- National University Cancer Institute; Singapore 1192288 Singapore
- Department of Biological Sciences; University of North Texas; Denton TX 76203-5017 U.S.A
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Mäki-Jouppila JHE, Pruikkonen S, Tambe MB, Aure MR, Halonen T, Salmela AL, Laine L, Børresen-Dale AL, Kallio MJ. MicroRNA let-7b regulates genomic balance by targeting Aurora B kinase. Mol Oncol 2015; 9:1056-70. [PMID: 25682900 DOI: 10.1016/j.molonc.2015.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 01/07/2015] [Accepted: 01/19/2015] [Indexed: 11/29/2022] Open
Abstract
The let-7 microRNA (miRNA) family has been implicated in the regulation of diverse cellular processes and disease pathogenesis. In cancer, loss-of-function of let-7 miRNAs has been linked to tumorigenesis via increased expression of target oncogenes. Excessive proliferation rate of tumor cells is often associated with deregulation of mitotic proteins. Here, we show that let-7b contributes to the maintenance of genomic balance via targeting Aurora B kinase, a key regulator of the spindle assembly checkpoint (SAC). Our results indicate that let-7b binds to Aurora B kinase 3'UTR reducing mRNA and protein expression of the kinase. In cells, excess let-7b induced mitotic defects characteristic to Aurora B perturbation including increased rate of polyploidy and multipolarity, and premature SAC inactivation that leads to forced exit from chemically induced mitotic arrest. Moreover, the frequency of aneuploid HCT-116 cells was significantly increased upon let-7b overexpression compared to controls. Interestingly, together with a chemical Aurora B inhibitor, let-7b had an additive effect on polyploidy induction in HeLa cells. In breast cancer patients, reduced let-7b expression was found to be associated with increased Aurora B expression in grade 3 tumors. Furthermore, let-7b was found downregulated in the most aggressive forms of breast cancer determined by clinicopathological parameters. Together, our findings suggest that let-7b contributes to the fidelity of cell division via regulation of Aurora B. Moreover, the loss of let-7b in aggressive tumors may drive tumorigenesis by up-regulation of Aurora B and other targets of the miRNA, which further supports the role of let-7b in tumor suppression.
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Affiliation(s)
- Jenni Heidi Eveliina Mäki-Jouppila
- VTT Health, VTT Technical Research Centre of Finland, 20520 Turku, Finland; Centre for Biotechnology, University of Turku, 20520 Turku, Finland; Drug Research Doctoral Programme and FinPharma Doctoral Program Drug Discovery, Finland; Department of Pharmacology, Drug Development and Therapeutics, University of Turku, 20520 Turku, Finland
| | - Sofia Pruikkonen
- VTT Health, VTT Technical Research Centre of Finland, 20520 Turku, Finland; Centre for Biotechnology, University of Turku, 20520 Turku, Finland; Turku Doctoral Program of Molecular Medicine, University of Turku, 20520 Finland; Department of Physiology, University of Turku, 20520 Turku, Finland
| | - Mahesh Balasaheb Tambe
- VTT Health, VTT Technical Research Centre of Finland, 20520 Turku, Finland; Centre for Biotechnology, University of Turku, 20520 Turku, Finland; Drug Research Doctoral Programme and FinPharma Doctoral Program Drug Discovery, Finland; Department of Physiology, University of Turku, 20520 Turku, Finland
| | - Miriam Ragle Aure
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, 0310 Oslo, Norway
| | - Tuuli Halonen
- Centre for Biotechnology, University of Turku, 20520 Turku, Finland
| | | | - Leena Laine
- VTT Health, VTT Technical Research Centre of Finland, 20520 Turku, Finland; Centre for Biotechnology, University of Turku, 20520 Turku, Finland
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Marko Johannes Kallio
- VTT Health, VTT Technical Research Centre of Finland, 20520 Turku, Finland; Centre for Biotechnology, University of Turku, 20520 Turku, Finland.
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Song R, Liu Q, Liu T, Li J. Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships. BMC Genomics 2015; 16 Suppl 2:S11. [PMID: 25707620 PMCID: PMC4331711 DOI: 10.1186/1471-2164-16-s2-s11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression relationship is not the only regulatory relationship between miRNAs and their targets, and some miRNAs can positively regulate a mRNA by binding at the 5' UTR of the mRNA. RESULTS This work focuses on the detection of both inverse and positive regulatory relationships from a paired miRNA and mRNA expression data set of HCV patients through a 'change-to-change' method which can derive connected discriminatory rules. Our study uncovered many novel miRNA-mRNA regulatory modules. In particular, it was revealed that GFRA2 is positively regulated by miR-557, miR-765 and miR-17-3p that probably bind at different locations of the 5' UTR of this mRNA. The expression relationship between GFRA2 and any of these three miRNAs has not been studied before, although separate research for this gene and these miRNAs have all drawn conclusions linked to hepatocellular carcinoma. This suggests that the binding of mRNA GFRA2 with miR-557, miR-765, or miR-17-3p, or their combinations, is worthy of further investigation by experimentation. We also report another mRNA QKI which has a strong inverse expression relationship with miR-129 and miR-493-3p which may bind at the 3' UTR of QKI with a perfect sequence match. Furthermore, the interaction between hsa-miR-129-5p (previous ID: hsa-miR-129) and QKI is supported with CLIP-Seq data from starBase. Our method can be easily extended for the expression data analysis of other diseases. CONCLUSION Our rule discovery method is useful for integrating binding information and expression profile for identifying HCV miRNA-mRNA regulatory modules and can be applied to the study of the expression profiles of other complex human diseases.
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Potapenko IO, Lüders T, Russnes HG, Helland Å, Sørlie T, Kristensen VN, Nord S, Lingjærde OC, Børresen-Dale AL, Haakensen VD. Glycan-related gene expression signatures in breast cancer subtypes; relation to survival. Mol Oncol 2015; 9:861-76. [PMID: 25655580 DOI: 10.1016/j.molonc.2014.12.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/27/2014] [Indexed: 01/23/2023] Open
Abstract
Alterations in glycan structures are early signs of malignancy and have recently been proposed to be in part a driving force behind malignant transformation. Here, we explore whether differences in expression of genes related to the process of glycosylation exist between breast carcinoma subtypes - and look for their association to clinical parameters. Five expression datasets of 454 invasive breast carcinomas, 31 ductal carcinomas in situ (DCIS), and 79 non-malignant breast tissue samples were analysed. Results were validated in 1960 breast carcinomas. 419 genes encoding glycosylation-related proteins were selected. The DCIS samples appeared expression-wise similar to carcinomas, showing altered gene expression related to glycosaminoglycans (GAGs) and N-glycans when compared to non-malignant samples. In-situ lesions with different aggressiveness potentials demonstrated changes in glycosaminoglycan sulfation and adhesion proteins. Subtype-specific expression patterns revealed down-regulation of genes encoding glycan-binding proteins in the luminal A and B subtypes. Clustering basal-like samples using a consensus list of genes differentially expressed across discovery datasets produced two clusters with significantly differing prognosis in the validation dataset. Finally, our analyses suggest that glycolipids may play an important role in carcinogenesis of breast tumors - as demonstrated by association of B3GNT5 and UGCG genes to patient survival. In conclusion, most glycan-specific changes occur early in the carcinogenic process. We have identified glycan-related alterations specific to breast cancer subtypes including a prognostic signature for two basal-like subgroups. Future research in this area may potentially lead to markers for better prognostication and treatment stratification of breast cancer patients.
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Affiliation(s)
- Ivan O Potapenko
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Torben Lüders
- Department of Clinical Epidemiology and Molecular Biology (Epi-Gen), Akershus University Hospital, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Hege G Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Åslaug Helland
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Oncology, Oslo University Hospital Radiumhospitalet, Norway
| | - Therese Sørlie
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Clinical Epidemiology and Molecular Biology (Epi-Gen), Akershus University Hospital, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Ole C Lingjærde
- Institute for Informatics, Faculty of Natural Sciences and Mathematics, University of Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vilde D Haakensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
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Bonnans C, Chou J, Werb Z. Remodelling the extracellular matrix in development and disease. Nat Rev Mol Cell Biol 2015; 15:786-801. [PMID: 25415508 DOI: 10.1038/nrm3904] [Citation(s) in RCA: 2749] [Impact Index Per Article: 305.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The extracellular matrix (ECM) is a highly dynamic structure that is present in all tissues and continuously undergoes controlled remodelling. This process involves quantitative and qualitative changes in the ECM, mediated by specific enzymes that are responsible for ECM degradation, such as metalloproteinases. The ECM interacts with cells to regulate diverse functions, including proliferation, migration and differentiation. ECM remodelling is crucial for regulating the morphogenesis of the intestine and lungs, as well as of the mammary and submandibular glands. Dysregulation of ECM composition, structure, stiffness and abundance contributes to several pathological conditions, such as fibrosis and invasive cancer. A better understanding of how the ECM regulates organ structure and function and of how ECM remodelling affects disease progression will contribute to the development of new therapeutics.
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Affiliation(s)
- Caroline Bonnans
- 1] Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA. [2] Oncology Department, INSERM U661, Functional Genomic Institute, 141 rue de la Cardonille, 34094 Montpellier, France
| | - Jonathan Chou
- 1] Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA. [2] Department of Medicine, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA
| | - Zena Werb
- Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA
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143
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Steinfeld I, Navon R, Creech ML, Yakhini Z, Tsalenko A. ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types. Bioinformatics 2015; 31:1683-5. [PMID: 25577435 PMCID: PMC4426829 DOI: 10.1093/bioinformatics/btu853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/23/2014] [Indexed: 02/04/2023] Open
Abstract
Summary: ENViz (Enrichment Analysis and Visualization) is a Cytoscape app that performs joint enrichment analysis of two types of sample matched datasets in the context of systematic annotations. Such datasets may be gene expression or any other high-throughput data collected in the same set of samples. The enrichment analysis is done in the context of pathway information, gene ontology or any custom annotation of the data. The results of the analysis consist of significant associations between profiled elements of one of the datasets to the annotation terms (e.g. miR-19 was associated to the cell-cycle process in breast cancer samples). The results of the enrichment analysis are visualized as an interactive Cytoscape network. Availability and implementation: ENViz is publically available in the Cytoscape App Store (http://apps.cytoscape.org/apps/enviz). For additional information please visit the tool website: http://www.agilent.com/labs/research/compbio/enviz/ Contact:israel_steinfeld@agilent.com
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Affiliation(s)
- Israel Steinfeld
- Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA
| | - Roy Navon
- Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA
| | - Michael L Creech
- Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA
| | - Zohar Yakhini
- Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA
| | - Anya Tsalenko
- Agilent Laboratories, Tel-Aviv, Israel, Technion - Israel Institute of Technology, Haifa, Israel, Blue Oak Software and Agilent Laboratories, Santa Clara, CA, USA
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144
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Huang GT, Tsamardinos I, Raghu V, Kaminski N, Benos PV. T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2015; 20:431-442. [PMID: 25592602 PMCID: PMC4299881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Feature selection is used extensively in biomedical research for biomarker identification and patient classification, both of which are essential steps in developing personalized medicine strategies. However, the structured nature of the biological datasets and high correlation of variables frequently yield multiple equally optimal signatures, thus making traditional feature selection methods unstable. Features selected based on one cohort of patients, may not work as well in another cohort. In addition, biologically important features may be missed due to selection of other co-clustered features We propose a new method, Tree-guided Recursive Cluster Selection (T-ReCS), for efficient selection of grouped features. T-ReCS significantly improves predictive stability while maintains the same level of accuracy. T-ReCS does not require an a priori knowledge of the clusters like group-lasso and also can handle "orphan" features (not belonging to a cluster). T-ReCS can be used with categorical or survival target variables. Tested on simulated and real expression data from breast cancer and lung diseases and survival data, T-ReCS selected stable cluster features without significant loss in classification accuracy.
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Affiliation(s)
- Grace T. Huang
- Department of Computational and Systems Biology, and Joint CMU-Pitt PhD Program in computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Ioannis Tsamardinos
- Department of Computer Science, University of Crete, Heraklion, Crete, Greece
| | - Vineet Raghu
- Department of Computer Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Naftali Kaminski
- School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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145
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Kleivi Sahlberg K, Bottai G, Naume B, Burwinkel B, Calin GA, Børresen-Dale AL, Santarpia L. A serum microRNA signature predicts tumor relapse and survival in triple-negative breast cancer patients. Clin Cancer Res 2014; 21:1207-14. [PMID: 25547678 DOI: 10.1158/1078-0432.ccr-14-2011] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Triple-negative breast cancers (TNBC) are associated with high risk of early tumor recurrence and poor outcome. Common prognostic biomarkers give very restricted predictive information of tumor recurrences in TNBC. Human serum contains stably expressed microRNAs (miRNAs), which have been discovered to predict prognosis in patients with cancer. The purpose of this study was to identify circulating biomarkers able to predict clinical outcome in TNBC. EXPERIMENTAL DESIGN We performed genome-wide serum miRNA expression and real-time PCR analyses to investigate the ability of miRNAs in predicting tumor relapse in serum samples from 60 primary TNBC. Patients were divided into training and testing cohorts. RESULTS By Cox regression analysis, we identified a four-miRNA signature (miR-18b, miR-103, miR-107, and miR-652) that predicted tumor relapse and overall survival. This miRNA signature was further validated in an independent cohort of 70 TNBC. A high-risk signature score was developed and significantly associated with tumor recurrence and reduced survival. Multivariate Cox regression models indicated that the risk score based on the four-miRNA signature was an independent prognostic classifier of patients with TNBC. CONCLUSIONS This signature may serve as a minimally invasive predictor of tumor relapse and overall survival for patients with TNBC. This prediction model may ultimately lead to better treatment options for patients with TNBC.
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Affiliation(s)
- Kristine Kleivi Sahlberg
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway. Department of Research, Vestre Viken, Drammen, Norway
| | - Giulia Bottai
- Oncology Experimental Therapeutics Unit, IRCCS Clinical and Research Institute Humanitas, Rozzano-Milan, Italy
| | - Bjørn Naume
- Department of Oncology, Division of Surgery and Cancer Medicine, Oslo University Hospital-Radiumhospitalet, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Barbara Burwinkel
- Division of Molecular Biology of Breast Cancer, University Women's Clinic, Heidelberg, Germany. Molecular Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway. K.G. Jebsen Centre for Breast Cancer, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Libero Santarpia
- Oncology Experimental Therapeutics Unit, IRCCS Clinical and Research Institute Humanitas, Rozzano-Milan, Italy.
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146
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Chaluvally-Raghavan P, Zhang F, Pradeep S, Hamilton MP, Zhao X, Rupaimoole R, Moss T, Lu Y, Yu S, Pecot CV, Aure MR, Peuget S, Rodriguez-Aguayo C, Han HD, Zhang D, Venkatanarayan A, Krohn M, Kristensen VN, Gagea M, Ram P, Liu W, Lopez-Berestein G, Lorenzi PL, Børresen-Dale AL, Chin K, Gray J, Dusetti NJ, McGuire SE, Flores ER, Sood AK, Mills GB. Copy number gain of hsa-miR-569 at 3q26.2 leads to loss of TP53INP1 and aggressiveness of epithelial cancers. Cancer Cell 2014; 26:863-879. [PMID: 25490449 PMCID: PMC4261159 DOI: 10.1016/j.ccell.2014.10.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 06/13/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
Abstract
Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafter designated as miR569), which is overexpressed in a subset of ovarian and breast cancers, at least in part due to the 3q26.2 amplicon, alters cell survival and proliferation. Downregulation of TP53INP1 expression by miR569 is required for the effects of miR569 on survival and proliferation. Targeting miR569 sensitizes ovarian and breast cancer cells overexpressing miR569 to cisplatin by increasing cell death both in vitro and in vivo. Thus targeting miR569 could potentially benefit patients with the 3q26.2 amplicon and subsequent miR569 elevation.
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Affiliation(s)
| | - Fan Zhang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sunila Pradeep
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Mark P Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi Zhao
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, 0424 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Rajesha Rupaimoole
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Tyler Moss
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chad V Pecot
- Department of Thoracic, Head and Neck Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Miriam R Aure
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, 0424 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Sylvain Peuget
- INSERM U1068, CRCM, Cell Stress, Marseille F-13009, France; Institut Paoli-Calmettes, 13273 Marseille Cedex 9, France; UMR7258, CNRS, Aix-Marseille University, Marseille F-13009, France
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hee-Dong Han
- Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dong Zhang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Avinashnarayan Venkatanarayan
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Marit Krohn
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, 0424 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, 0424 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Prahlad Ram
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Wenbin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, 0424 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Koei Chin
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - Joe Gray
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nelson J Dusetti
- INSERM U1068, CRCM, Cell Stress, Marseille F-13009, France; Institut Paoli-Calmettes, 13273 Marseille Cedex 9, France; UMR7258, CNRS, Aix-Marseille University, Marseille F-13009, France
| | - Sean E McGuire
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elsa R Flores
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Anil K Sood
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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Maltseva DV, Galatenko VV, Samatov TR, Zhikrivetskaya SO, Khaustova NA, Nechaev IN, Shkurnikov MU, Lebedev AE, Mityakina IA, Kaprin AD, Schumacher U, Tonevitsky AG. miRNome of inflammatory breast cancer. BMC Res Notes 2014; 7:871. [PMID: 25471792 PMCID: PMC4289319 DOI: 10.1186/1756-0500-7-871] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/28/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) is an extremely malignant form of breast cancer which can be easily misdiagnosed. Conclusive prognostic IBC molecular biomarkers which are also providing the perspectives for targeted therapy are lacking so far. The aim of this study was to reveal the IBC-specific miRNA expression profile and to evaluate its association with clinicopathological parameters. METHODS miRNA expression profiles of 13 IBC and 17 non-IBC patients were characterized using comprehensive Affymetrix GeneChip miRNA 3.0 microarray platform. Bioinformatic analysis was used to reveal IBC-specific miRNAs, deregulated pathways and potential miRNA targets. RESULTS 31 differentially expressed miRNAs characterize IBC and mRNAs regulated by them and their associated pathways can functionally be attributed to IBC progression. In addition, a minimal predictive set of 4 miRNAs characteristic for the IBC phenotype and associated with the TP53 mutational status in breast cancer patients was identified. CONCLUSIONS We have characterized the complete miRNome of inflammatory breast cancer and found differentially expressed miRNAs which reliably classify the patients to IBC and non-IBC groups. We found that the mRNAs and pathways likely regulated by these miRNAs are highly relevant to cancer progression. Furthermore a minimal IBC-related predictive set of 4 miRNAs associated with the TP53 mutational status and survival for breast cancer patients was identified.
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Affiliation(s)
| | | | - Timur R Samatov
- SRC Bioclinicum, Ugreshskaya str 2/85, 115088 Moscow, Russia.
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148
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Bonnans C, Chou J, Werb Z. Remodelling the extracellular matrix in development and disease. Nat Rev Mol Cell Biol 2014; 15:786-801. [PMID: 25415508 DOI: 10.1038/nrm3904.remodelling] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The extracellular matrix (ECM) is a highly dynamic structure that is present in all tissues and continuously undergoes controlled remodelling. This process involves quantitative and qualitative changes in the ECM, mediated by specific enzymes that are responsible for ECM degradation, such as metalloproteinases. The ECM interacts with cells to regulate diverse functions, including proliferation, migration and differentiation. ECM remodelling is crucial for regulating the morphogenesis of the intestine and lungs, as well as of the mammary and submandibular glands. Dysregulation of ECM composition, structure, stiffness and abundance contributes to several pathological conditions, such as fibrosis and invasive cancer. A better understanding of how the ECM regulates organ structure and function and of how ECM remodelling affects disease progression will contribute to the development of new therapeutics.
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Affiliation(s)
- Caroline Bonnans
- 1] Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA. [2] Oncology Department, INSERM U661, Functional Genomic Institute, 141 rue de la Cardonille, 34094 Montpellier, France
| | - Jonathan Chou
- 1] Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA. [2] Department of Medicine, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA
| | - Zena Werb
- Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, California 94143-0452, USA
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149
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Miller PC, Clarke J, Koru-Sengul T, Brinkman J, El-Ashry D. A novel MAPK-microRNA signature is predictive of hormone-therapy resistance and poor outcome in ER-positive breast cancer. Clin Cancer Res 2014; 21:373-85. [PMID: 25370469 DOI: 10.1158/1078-0432.ccr-14-2053] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Hyperactivation of ERK1/2 MAPK (hMAPK) leads to loss of estrogen receptor (ER) expression and poor outcome in breast cancer. microRNAs (miRNA) play important regulatory roles and serve as biomarkers of disease. Here, we describe molecular, pathologic, and clinical outcome associations of an hMAPK-miRNA expression signature in breast cancer. EXPERIMENTAL DESIGN An hMAPK-miRNA signature was identified, and associations of this signature with molecular and genetic alterations, gene expression, pathologic features, and clinical outcomes were determined in primary breast cancers from training data and validated using independent datasets. Univariate and multivariate analyses identified subsignatures associated with increased disease recurrence and poorer disease survival among ER-positive (ER(+)) patients, respectively. RESULTS High-hMAPK-miRNA status significantly correlated with ER-negativity, enrichment for basal and HER2-subtypes, and reduced recurrence-free and disease-specific survival in publicly available datasets. A robust determination of a recurrence signature and a survival signature identified hMAPK-miRNAs commonly associated with poor clinical outcome, and specific subsets associated more closely with either disease recurrence or disease survival, especially among ER(+) cancers of both luminal A and luminal B subtypes. Multivariate analyses indicated that these recurrence and survival signatures significantly associated with increased risk of disease-specific death and disease recurrence in ER(+) cancer and ER(+) cancers treated with hormone therapy. CONCLUSIONS We report an hMAPK-miRNA signature and two subsignatures derived from it that associate significantly with adverse clinical features, poor clinical outcome, and poor response to hormone therapy in breast cancer, thus identifying potential effectors of MAPK signaling, and novel predictive and prognostic biomarkers or therapeutic targets in breast cancer.
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Affiliation(s)
- Philip C Miller
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida. Braman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Jennifer Clarke
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida. Braman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, Florida. Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida. Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida. Department of Statistics, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Tulay Koru-Sengul
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida. Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Joeli Brinkman
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Dorraya El-Ashry
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida. Braman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, Florida. Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida.
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150
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Mining cancer gene expression databases for latent information on intronic microRNAs. Mol Oncol 2014; 9:473-87. [PMID: 25459350 DOI: 10.1016/j.molonc.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/23/2014] [Accepted: 10/02/2014] [Indexed: 12/19/2022] Open
Abstract
Around 50% of all human microRNAs reside within introns of coding genes and are usually co-transcribed. Gene expression datasets, therefore, should contain a wealth of miRNA-relevant latent information, exploitable for many basic and translational research aims. The present study was undertaken to investigate this possibility. We developed an in silico approach to identify intronic-miRNAs relevant to breast cancer, using public gene expression datasets. This led to the identification of a miRNA signature for aggressive breast cancer, and to the characterization of novel roles of selected miRNAs in cancer-related biological phenotypes. Unexpectedly, in a number of cases, expression regulation of the intronic-miRNA was more relevant than the expression of their host gene. These results provide a proof of principle for the validity of our intronic miRNA mining strategy, which we envision can be applied not only to cancer research, but also to other biological and biomedical fields.
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