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Limburg A, Qian X, Brechtefeld B, Hedemann N, Flörkemeier I, Rogmans C, Oliveira-Ferrer L, Maass N, Arnold N, Bauerschlag DO, Weimer JP. Generation of a Specific Fluorescence In Situ Hybridization Test for the Detection of Ovarian Carcinoma Cells. Biomedicines 2024; 12:1171. [PMID: 38927378 PMCID: PMC11201245 DOI: 10.3390/biomedicines12061171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Examinations of ovarian cancer cells require the ability to identify tumor cells. Array-based comparative genome hybridization (aCGH) on 30 ovarian carcinomas (OC) identified three genomic loci (8q24.23; 17p12; 18q22.3) over- or under-represented in OC. A fluorescence in situ hybridization (FISH) probe of these three loci is intended to identify tumor cells by their signal pattern deviating from a diploid pattern. Human DNA from these three loci is isolated from bacterial artificial chromosomes (BAC), amplified and labeled with fluorescent dyes. After a standard FISH procedure, 71 OC suspensions from primary tumors, three OC cell lines, three lymphocyte suspensions, and one mesenchymal cell line LP-3 are analyzed with a fluorescence microscope. On average, 15% of the lymphocytes deviate from the expected diploid signal pattern, giving a cut-off of 36%. If this value is exceeded, tumor cells are detected. The mesenchymal cell line LP-3 shows only 21% as a negative control. The OC cell lines as positive controls exceed this value at 38%, 67%, and 54%. Of the 71 OC primary cultures, four cases fell below this cut-off as false negatives. In the two-sample t-test, the percentages of conspicuous signal patterns differ significantly.
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Affiliation(s)
- Amelie Limburg
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Xueqian Qian
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Bernice Brechtefeld
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Nina Hedemann
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Inken Flörkemeier
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Christoph Rogmans
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | | | - Nicolai Maass
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Dirk O. Bauerschlag
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
| | - Jörg Paul Weimer
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.L.); (N.M.); (N.A.); (D.O.B.)
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Wilczyński J, Paradowska E, Wilczyńska J, Wilczyński M. Prediction of Chemoresistance-How Preclinical Data Could Help to Modify Therapeutic Strategy in High-Grade Serous Ovarian Cancer. Curr Oncol 2023; 31:229-249. [PMID: 38248100 PMCID: PMC10814576 DOI: 10.3390/curroncol31010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is one of the most lethal tumors generally and the most fatal cancer of the female genital tract. The approved standard therapy consists of surgical cytoreduction and platinum/taxane-based chemotherapy, and of targeted therapy in selected patients. The main therapeutic problem is chemoresistance of recurrent and metastatic HGSOC tumors which results in low survival in the group of FIGO III/IV. Therefore, the prediction and monitoring of chemoresistance seems to be of utmost importance for the improvement of HGSOC management. This type of cancer has genetic heterogeneity with several subtypes being characterized by diverse gene signatures and disturbed peculiar epigenetic regulation. HGSOC develops and metastasizes preferentially in the specific intraperitoneal environment composed mainly of fibroblasts, adipocytes, and immune cells. Different HGSOC subtypes could be sensitive to distinct sets of drugs. Moreover, primary, metastatic, and recurrent tumors are characterized by an individual biology, and thus diverse drug responsibility. Without a precise identification of the tumor and its microenvironment, effective treatment seems to be elusive. This paper reviews tumor-derived genomic, mutational, cellular, and epigenetic biomarkers of HGSOC drug resistance, as well as tumor microenvironment-derived biomarkers of chemoresistance, and discusses their possible use in the novel complex approach to ovarian cancer therapy and monitoring.
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Affiliation(s)
- Jacek Wilczyński
- Department of Gynecological Surgery and Gynecological Oncology, Medical University of Lodz, 4 Kosciuszki Str., 90-419 Lodz, Poland
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland;
| | - Justyna Wilczyńska
- Department of Tele-Radiotherapy, Mikolaj Kopernik Provincial Multi-Specialized Oncology and Traumatology Center, 62 Pabianicka Str., 93-513 Lodz, Poland;
| | - Miłosz Wilczyński
- Department of Gynecological, Endoscopic and Oncological Surgery, Polish Mother’s Health Center—Research Institute, 281/289 Rzgowska Str., 93-338 Lodz, Poland;
- Department of Surgical and Endoscopic Gynecology, Medical University of Lodz, 4 Kosciuszki Str., 90-419 Lodz, Poland
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Mo Y, Leung LL, Mak CSL, Wang X, Chan WS, Hui LMN, Tang HWM, Siu MKY, Sharma R, Xu D, Tsui SKW, Ngan HYS, Yung MMH, Chan KKL, Chan DW. Tumor-secreted exosomal miR-141 activates tumor-stroma interactions and controls premetastatic niche formation in ovarian cancer metastasis. Mol Cancer 2023; 22:4. [PMID: 36624516 PMCID: PMC9827705 DOI: 10.1186/s12943-022-01703-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Metastatic colonization is one of the critical steps in tumor metastasis. A pre-metastatic niche is required for metastatic colonization and is determined by tumor-stroma interactions, yet the mechanistic underpinnings remain incompletely understood. METHODS PCR-based miRNome profiling, qPCR, immunofluorescent analyses evaluated the expression of exosomal miR-141 and cell-to-cell communication. LC-MS/MS proteomic profiling and Dual-Luciferase analyses identified YAP1 as the direct target of miR-141. Human cytokine profiling, ChIP, luciferase reporter assays, and subcellular fractionation analyses confirmed YAP1 in modulating GROα production. A series of in vitro tumorigenic assays, an ex vivo model and Yap1 stromal conditional knockout (cKO) mouse model demonstrated the roles of miR-141/YAP1/GROα/CXCR1/2 signaling cascade. RNAi, CRISPR/Cas9 and CRISPRi systems were used for gene silencing. Blood sera, OvCa tumor tissue samples, and tissue array were included for clinical correlations. RESULTS Hsa-miR-141-3p (miR-141), an exosomal miRNA, is highly secreted by ovarian cancer cells and reprograms stromal fibroblasts into proinflammatory cancer-associated fibroblasts (CAFs), facilitating metastatic colonization. A mechanistic study showed that miR-141 targeted YAP1, a critical effector of the Hippo pathway, reducing the nuclear YAP1/TAZ ratio and enhancing GROα production from stromal fibroblasts. Stromal-specific knockout (cKO) of Yap1 in murine models shaped the GROα-enriched microenvironment, facilitating in vivo tumor colonization, but this effect was reversed after Cxcr1/2 depletion in OvCa cells. The YAP1/GROα correlation was demonstrated in clinical samples, highlighting the clinical relevance of this research and providing a potential therapeutic intervention for impeding premetastatic niche formation and metastatic progression of ovarian cancers. CONCLUSIONS This study uncovers miR-141 as an OvCa-derived exosomal microRNA mediating the tumor-stroma interactions and the formation of tumor-promoting stromal niche through activating YAP1/GROα/CXCRs signaling cascade, providing new insight into therapy for OvCa patients with peritoneal metastases.
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Affiliation(s)
- Yulan Mo
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Leanne L. Leung
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Celia S. L. Mak
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Xueyu Wang
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Wai-Sun Chan
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Lynn M. N. Hui
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Hermit W. M. Tang
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Michelle K. Y. Siu
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Rakesh Sharma
- grid.194645.b0000000121742757Centre for PanorOmic Sciences Proteomics and Metabolomics Core, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Dakang Xu
- grid.16821.3c0000 0004 0368 8293Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Stephen K. W. Tsui
- grid.10784.3a0000 0004 1937 0482School of Biomedical Sciences, The Chinese University of Hong Kong, SAR Hong Kong, China
| | - Hextan Y. S. Ngan
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Mingo M. H. Yung
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - Karen K. L. Chan
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China
| | - David W. Chan
- grid.194645.b0000000121742757Department of Obstetrics & Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR China ,grid.10784.3a0000 0004 1937 0482School of Biomedical Sciences, The Chinese University of Hong Kong, SAR Hong Kong, China ,grid.511521.3School of Medicine, The Chinese University of Hong Kong-Shenzhen, Shenzhen, 518172 China
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Du M, Zhang S, Liu X, Xu C, Zhang X. Ploidy Status of Ovarian Cancer Cell Lines and Their Association with Gene Expression Profiles. Biomolecules 2023; 13:biom13010092. [PMID: 36671477 PMCID: PMC9855421 DOI: 10.3390/biom13010092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
As a cancer type potentially dominated by copy number variations, ovarian cancer shows hyperploid karyotypes and large-scale chromosome alterations, which might be promising biomarkers correlated with tumor metastasis and chemoresistance. Experimental studies have provided more information about the roles of aneuploids and polyploids in ovarian cancer. However, ploidy evaluation of ovarian cancer cell lines is still limited, even in some ploidy-related research. Herein, the ploidy landscape of 51 ovarian cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were analyzed, and the ploidy statuses of 13 human ovarian cancer cell lines and 2 murine cell lines were evaluated using G-banding and flow cytometry. Most human ovarian cancer cell lines were aneuploid, with modal numbers of 52-86 and numerical complexity ranging from 5 to 12. A2780, COV434 and TOV21G were screened as diploid cell lines, with a modal number of 46, a low aneuploid score and a near-diploid ploidy value. Two murine cell lines, both OV2944-HM1 and ID-8, were near-tetraploid. Integrated information on karyotypes, aneuploid score and ploidy value supplied references for a nondiploid model construction and a parallel analysis of diploid versus aneuploid. Moreover, the gene expression profiles were compared between diploid and aneuploid cell lines. The functions of differentially expressed genes were mainly enriched in terms of protein function regulation, TGF-β signaling and cell adhesion molecules. Genes downregulated in the aneuploid group were mainly related to metabolism and protein function regulation, and genes upregulated in the aneuploid group were mainly involved in immune regulation. Differentially expressed genes were randomly distributed on all chromosomes, while chromosome 1 alteration might contribute to immune-related alterations in aneuploid cell lines. Chromosome 19 alteration might be potentially significant for aneuploid ovarian cancer cell lines and patients, which needs further verification in ploidy research.
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Affiliation(s)
- Ming Du
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Shuo Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Xiaoxia Liu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, China
- Correspondence: (C.X.); (X.Z.)
| | - Xiaoyan Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, China
- Correspondence: (C.X.); (X.Z.)
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Weng S, Liu Z, Xu H, Ge X, Ren Y, Dang Q, Liu L, Zhang J, Luo P, Ren J, Han X. ALOX12: A Novel Insight in Bevacizumab Response, Immunotherapy Effect, and Prognosis of Colorectal Cancer. Front Immunol 2022; 13:910582. [PMID: 35833141 PMCID: PMC9271859 DOI: 10.3389/fimmu.2022.910582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer is a highly malignant cancer with poor prognosis and mortality rates. As the first biological agent approved for metastatic colorectal cancer (mCRC), bevacizumab was confirmed to exhibit good performance when combined with chemotherapy and immunotherapy. However, the efficacy of both bevacizumab and immunotherapy is highly heterogeneous across CRC patients with different stages. Thus, exploring a novel biomarker to comprehensively assess the prognosis and bevacizumab and immunotherapy response of CRC is of great significance. In our study, weighted gene co-expression network analysis (WGCNA) and the receiver operating characteristic (ROC) curves were employed to identify bevacizumab-related genes. After verification in four public cohorts and our internal cohort, ALOX12 was identified as a key gene related to bevacizumab response. Prognostic analysis and in vitro experiments further demonstrated that ALOX12 was closely associated with the prognosis, tumor proliferation, invasion, and metastasis. Multi-omics data analysis based on mutation and copy number variation (CNV) revealed that RYR3 drove the expression of ALOX12 and the deletion of 17p12 inhibited ALOX12 expression, respectively. Moreover, we interrogated the relationship between ALOX12 and immune cells and checkpoints. The results exhibited that high ALOX12 expression predicted a higher immune infiltration and better immunotherapy response, which was further validated in Tumor Immune Dysfunction and Exclusion (TIDE) and Subclass Mapping (SubMap) methods. Above all, our study provides a stable biomarker for clinical protocol optimization, prognostic assessment, precise treatment, and individualized treatment of CRC.
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Affiliation(s)
- Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Interventional Institute of Zhengzhou University, Zhengzhou, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Interventional Institute of Zhengzhou University, Zhengzhou, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
- *Correspondence: Xinwei Han, ; Jianzhuang Ren, ; Zaoqu Liu,
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Interventional Institute of Zhengzhou University, Zhengzhou, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianzhuang Ren
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Xinwei Han, ; Jianzhuang Ren, ; Zaoqu Liu,
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Interventional Institute of Zhengzhou University, Zhengzhou, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
- *Correspondence: Xinwei Han, ; Jianzhuang Ren, ; Zaoqu Liu,
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Silva F, Coelho F, Peixoto A, Pinto P, Martins C, Frombach AS, Santo VE, Brito C, Guimarães A, Félix A. Establishment and characterization of a novel ovarian high-grade serous carcinoma cell line-IPO43. Cancer Cell Int 2022; 22:175. [PMID: 35501869 PMCID: PMC9063187 DOI: 10.1186/s12935-022-02600-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/12/2022] [Indexed: 11/26/2022] Open
Abstract
Background Epithelial ovarian cancer (EOC) is an aggressive and lethal malignancy and novel EOC cell lines with detailed characterization are needed, to provide researchers with diverse helpful resources to study EOC biological processes and cancer experimental therapies. Methods The IPO43 cell line was established from the ascitic fluid of a patient with a diagnosis of high-grade serous carcinoma (HGSC) of the ovary, previously treated with chemotherapy. Cell immortalization was achieved in 2D cell culture and growth obtained in 2D and 3D cell cultures. The characterization of immortalized cells was done by immunocytochemistry, flow cytometry, cell proliferation, chromosomal Comparative Genomic Hybridization (cCGH), STR profile and Next Generation Sequencing (NGS). Results Characterization studies confirmed that IPO43 cell line is of EOC origin and maintains morphological and molecular features of the primary tumor. cCGH analysis showed a complex profile with gains and losses of specific DNA regions in both primary ascitic fluid and cell line IPO43. The cell line was successfully grown in a 3D system which allows its future application in more complex assays than those performed in 2D models. IPO43 cell line is resistant to standard drug treatment in vitro. Conclusions IPO43 is available for public research and we hope it can contribute to enrich the in vitro models addressing EOC heterogeneity, being useful to investigate EOC and to develop new therapeutic modalities. IPOLFG-SOC43 cell line represents the heterogeneity of Epithelial Ovarian Cancer Genetic alterations in cancer cells confer a selective advantage 3D cultures preserve the phenotypical features of the original tumor
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Affiliation(s)
- Fernanda Silva
- Chronic Diseases Research Center, (CEDOC-FCM-UNL), NOVA Medical School, NMS, Universidade NOVA de Lisboa, 1169-056, Lisbon, Portugal.
| | - Filipa Coelho
- Chronic Diseases Research Center, (CEDOC-FCM-UNL), NOVA Medical School, NMS, Universidade NOVA de Lisboa, 1169-056, Lisbon, Portugal.,Molecular Pathobiology Research Unit, Portuguese Institute of Oncology Francisco Gentil Lisbon (IPOLFG), 1099-023, Lisbon, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Pedro Pinto
- IPO Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carmo Martins
- Molecular Pathobiology Research Unit, Portuguese Institute of Oncology Francisco Gentil Lisbon (IPOLFG), 1099-023, Lisbon, Portugal
| | - Ann-Sophie Frombach
- IBET, Instituto de Biologia Experimental E Tecnológica PT, 2781-901, Oeiras, Portugal.,Instituto de Tecnologia Química E Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | - Vítor E Santo
- IBET, Instituto de Biologia Experimental E Tecnológica PT, 2781-901, Oeiras, Portugal.,Instituto de Tecnologia Química E Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | - Catarina Brito
- IBET, Instituto de Biologia Experimental E Tecnológica PT, 2781-901, Oeiras, Portugal.,Instituto de Tecnologia Química E Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | | | - Ana Félix
- Chronic Diseases Research Center, (CEDOC-FCM-UNL), NOVA Medical School, NMS, Universidade NOVA de Lisboa, 1169-056, Lisbon, Portugal.,Department of Pathology, IPOLFG, 1099-023, Lisbon, Portugal
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Hannan NJ, Cohen PA, Beard S, Bilic S, Zhang B, Tong S, Whitehead C, Hui L. Transcriptomic analysis of patient plasma reveals circulating miR200c as a potential biomarker for high-grade serous ovarian cancer. Gynecol Oncol Rep 2022; 39:100894. [PMID: 35005155 PMCID: PMC8717717 DOI: 10.1016/j.gore.2021.100894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Background High-grade serous tubo-ovarian cancer (HGSC) is the most common histological subtype of epithelial ovarian cancer, and highly lethal. Currently there is no effective screening test and prognosis is poor as the majority of cases are diagnosed at the advanced stage. Cell free RNAs including microRNAs (miRNAs) are dysregulated in ovarian cancer tissue and are detectable in the circulation. This study aimed to determine whether circulating cell free miRNAs may be potential biomarkers for the detection of HGSC. Methods Plasma was collected from women with HGSC (Grade 3, n = 24), and benign ovarian masses (n = 24). RNA was extracted from patient plasma and subjected to miRNA targeted next generation sequencing (NGS). A subsequent validation cohort was assessed using plasma collected from women with HGSC (n = 14) and controls (with a benign ovarian mass; n = 15). RNA was extracted and assessed using quantitative RT-PCR. Results Differential gene expression (DGE) of the NGS data revealed a significant increase in the miRNA, miR200c, in the circulation of women with HGSC (p less than 0.05) compared to controls. In the validation cohort miR200c expression by qPCR was found to also be increased in the circulation of women with HGSC compared to controls (p = 0.0023). Conclusions Circulating miR200c may be a promising candidate biomarker for the detection of HGSC. Further larger cohort studies exploring earlier stages are needed to determine whether circulating miR200c may be a sensitive and specific biomarker of tubo-ovarian cancer.
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Affiliation(s)
- Natalie J Hannan
- Therapeutics Discovery and Vascular Function Group, University of Melbourne, Heidelberg, Victoria, Australia.,Translational Obstetrics Group, University of Melbourne, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Victoria Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Paul A Cohen
- Division of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, University of Western Australia, Crawley, Western Australia, Australia.,Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, Subiaco, Western Australia, Australia
| | - Sally Beard
- Therapeutics Discovery and Vascular Function Group, University of Melbourne, Heidelberg, Victoria, Australia.,Translational Obstetrics Group, University of Melbourne, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Victoria Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria Australia
| | - Sanela Bilic
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, Subiaco, Western Australia, Australia
| | - Bonnie Zhang
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, Subiaco, Western Australia, Australia
| | - Stephen Tong
- Translational Obstetrics Group, University of Melbourne, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Victoria Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Clare Whitehead
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria Australia
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria Australia
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8
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Salvi A, Young AN, Huntsman AC, Pergande MR, Korkmaz MA, Rathnayake RA, Mize BK, Kinghorn AD, Zhang X, Ratia K, Schirle M, Thomas JR, Brittain SM, Shelton C, Aldrich LN, Cologna SM, Fuchs JR, Burdette JE. PHY34 inhibits autophagy through V-ATPase V0A2 subunit inhibition and CAS/CSE1L nuclear cargo trafficking in high grade serous ovarian cancer. Cell Death Dis 2022; 13:45. [PMID: 35013112 PMCID: PMC8748433 DOI: 10.1038/s41419-021-04495-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/29/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022]
Abstract
PHY34 is a synthetic small molecule, inspired by a compound naturally occurring in tropical plants of the Phyllanthus genus. PHY34 was developed to have potent in vitro and in vivo anticancer activity against high grade serous ovarian cancer (HGSOC) cells. Mechanistically, PHY34 induced apoptosis in ovarian cancer cells by late-stage autophagy inhibition. Furthermore, PHY34 significantly reduced tumor burden in a xenograft model of ovarian cancer. In order to identify its molecular target/s, we undertook an unbiased approach utilizing mass spectrometry-based chemoproteomics. Protein targets from the nucleocytoplasmic transport pathway were identified from the pulldown assay with the cellular apoptosis susceptibility (CAS) protein, also known as CSE1L, representing a likely candidate protein. A tumor microarray confirmed data from mRNA expression data in public databases that CAS expression was elevated in HGSOC and correlated with worse clinical outcomes. Overexpression of CAS reduced PHY34 induced apoptosis in ovarian cancer cells based on PARP cleavage and Annexin V staining. Compounds with a diphyllin structure similar to PHY34 have been shown to inhibit the ATP6V0A2 subunit of V(vacuolar)-ATPase. Therefore, ATP6V0A2 wild-type and ATP6V0A2 V823 mutant cell lines were tested with PHY34, and it was able to induce cell death in the wild-type at 246 pM while the mutant cells were resistant up to 55.46 nM. Overall, our data demonstrate that PHY34 is a promising small molecule for cancer therapy that targets the ATP6V0A2 subunit to induce autophagy inhibition while interacting with CAS and altering nuclear localization of proteins.
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Affiliation(s)
- Amrita Salvi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Alexandria N Young
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Andrew C Huntsman
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Melissa A Korkmaz
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | | | - Brittney K Mize
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - A Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Kiira Ratia
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jason R Thomas
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Scott M Brittain
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Claude Shelton
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Leslie N Aldrich
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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9
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Liu CL, Yuan RH, Mao TL. The Molecular Landscape Influencing Prognoses of Epithelial Ovarian Cancer. Biomolecules 2021; 11:998. [PMID: 34356623 PMCID: PMC8301761 DOI: 10.3390/biom11070998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/26/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the major increasing lethal malignancies of the gynecological tract, mostly due to delayed diagnosis and chemoresistance, as well as its very heterogeneous genetic makeup. Application of high-throughput molecular technologies, gene expression microarrays, and powerful preclinical models has provided a deeper understanding of the molecular characteristics of EOC. Therefore, molecular markers have become a potent tool in EOC management, including prediction of aggressiveness, prognosis, and recurrence, and identification of novel therapeutic targets. In addition, biomarkers derived from genomic/epigenomic alterations (e.g., gene mutations, copy number aberrations, and DNA methylation) enable targeted treatment of affected signaling pathways in advanced EOC, thereby improving the effectiveness of traditional treatments. This review outlines the molecular landscape and discusses the impacts of biomarkers on the detection, diagnosis, surveillance, and therapeutic targets of EOC. These findings focus on the necessity to translate these potential biomarkers into clinical practice.
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Affiliation(s)
- Chao-Lien Liu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Ray-Hwang Yuan
- Department of Surgery, National Taiwan University Hospital, Taipei 10002, Taiwan;
- Department of Surgery, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Tsui-Lien Mao
- Department of Pathology, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Department of Pathology, National Taiwan University Hospital, Taipei 10002, Taiwan
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10
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Li LJ, Chang WM, Hsiao M. Aberrant Expression of microRNA Clusters in Head and Neck Cancer Development and Progression: Current and Future Translational Impacts. Pharmaceuticals (Basel) 2021; 14:ph14030194. [PMID: 33673471 PMCID: PMC7997248 DOI: 10.3390/ph14030194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs are small non-coding RNAs known to negative regulate endogenous genes. Some microRNAs have high sequence conservation and localize as clusters in the genome. Their coordination is regulated by simple genetic and epigenetic events mechanism. In cells, single microRNAs can regulate multiple genes and microRNA clusters contain multiple microRNAs. MicroRNAs can be differentially expressed and act as oncogenic or tumor suppressor microRNAs, which are based on the roles of microRNA-regulated genes. It is vital to understand their effects, regulation, and various biological functions under both normal and disease conditions. Head and neck squamous cell carcinomas are some of the leading causes of cancer-related deaths worldwide and are regulated by many factors, including the dysregulation of microRNAs and their clusters. In disease stages, microRNA clusters can potentially control every field of oncogenic function, including growth, proliferation, apoptosis, migration, and intercellular commutation. Furthermore, microRNA clusters are regulated by genetic mutations or translocations, transcription factors, and epigenetic modifications. Additionally, microRNA clusters harbor the potential to act therapeutically against cancer in the future. Here, we review recent advances in microRNA cluster research, especially relative to head and neck cancers, and discuss their regulation and biological functions under pathological conditions as well as translational applications.
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Affiliation(s)
- Li-Jie Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - Wei-Min Chang
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-2-2789–8752
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11
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Aboutalebi H, Bahrami A, Soleimani A, Saeedi N, Rahmani F, Khazaei M, Fiuji H, Shafiee M, Ferns GA, Avan A, Hassanian SM. The diagnostic, prognostic and therapeutic potential of circulating microRNAs in ovarian cancer. Int J Biochem Cell Biol 2020; 124:105765. [PMID: 32428568 DOI: 10.1016/j.biocel.2020.105765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/06/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022]
Abstract
Ovarian cancer (OC) is often diagnosed at an advanced stage because of the late onset of symptoms, and this together with the lack of effective treatments, has meant it is associated with a very high mortality. The aberrant expression of MicroRNA (miRNA) contributes to the initiation and development of human tumors including OC. Several miRNAs are secreted by tumor cells and can be identified in body fluids. Serum miRNAs levels are associated with several clinical conditions, and may be used to predict prognosis and response to treatments in some cancers including OC. This review summarizes the current progresses regarding the potential applications of circulating miRNA as innovative biomarkers in OC.
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Affiliation(s)
- Hamideh Aboutalebi
- Department of Anatomy, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Atena Soleimani
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nikoo Saeedi
- Student Research Committee, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Farzad Rahmani
- Iranshahr University of Medical Sciences, Iranshahr, Iran
| | - Majid Khazaei
- Department of Medical Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Department of Biochemistry, Payame-Noor University, Mashhad, Iran
| | - Mojtaba Shafiee
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK.
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12
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Zhou J, Lei J, Wang J, Lian CL, Hua L, He ZY, Wu SG. Bioinformatics-Based Discovery of CKLF-Like MARVEL Transmembrane Member 5 as a Novel Biomarker for Breast Cancer. Front Cell Dev Biol 2020; 7:361. [PMID: 31998718 PMCID: PMC6962189 DOI: 10.3389/fcell.2019.00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Chemokine-like factor (CKLF)-like MARVEL transmembrane members (CMTMs) represent a novel protein family linking the chemokine and transmembrane-4 superfamily families, which potentially play several roles in diverse physiological and pathological processes. The detailed functions and underlying molecular mechanisms of CMTMs remain elusive in breast cancer. Herein, we performed a comprehensive bioinformatic analysis to investigate the prognostic effect, potential functions, and biomolecular regulatory network of CMTMs in breast cancer. The mRNA expression level of CMTM5, in particular, was significantly downregulated in breast cancer; moreover, high mRNA expression level of CMTM5 was significantly associated with better relapse-free survival. DNA promoter hypermethylation of CMTM5 was negatively correlated with its mRNA expression levels. Furthermore, CMTM5 strongly associated with pathway in MARVEL domains, chemotaxis, cytokines, transmembrane structures, and integral component of membrane. For example, genes related to MARVEL domains, transmembrane structures, and chemokines were significantly enriched. Our findings indicate that CMTM5 can be used as a prognostic biomarker and potential therapeutic target for breast cancer.
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Affiliation(s)
- Juan Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, China
| | - Jian Lei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, China
| | - Jun Wang
- Department of Radiation Oncology, Cancer Hospital, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, China
| | - Chen-Lu Lian
- Department of Radiation Oncology, Cancer Hospital, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, China
| | - Li Hua
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, China
| | - Zhen-Yu He
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - San-Gang Wu
- Department of Radiation Oncology, Cancer Hospital, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, China
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13
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Liu G, Ruan G, Huang M, Chen L, Sun P. Genome-wide DNA copy number profiling and bioinformatics analysis of ovarian cancer reveals key genes and pathways associated with distinct invasive/migratory capabilities. Aging (Albany NY) 2020; 12:178-192. [PMID: 31895688 PMCID: PMC6977652 DOI: 10.18632/aging.102608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Ovarian cancer (OC) metastasis presents major hurdles that must be overcome to improve patient outcomes. Recent studies have demonstrated copy number variations (CNVs) frequently contribute to alterations in oncogenic drivers. The present study used a CytoScan HD Array to analyse CNVs and loss of heterozygosity (LOH) in the entire genomes of 6 OC patients and human OC cell lines to determine the genetic target events leading to the distinct invasive/migratory capacities of OC. The results showed that LOH at Xq11.1 and Xp21.1 and gains at 8q21.13 were novel, specific CNVs. Ovarian cancer-related CNVs were then screened by bioinformatics analysis. In addition, transcription factors-target gene interactions were predicted with information from PASTAA analysis. As a result, six genes (i.e., GAB2, AKT1, EGFR, COL6A3, UGT1A1 and UGT1A8) were identified as strong candidates by integrating the above data with gene expression and clinical outcome data. In the transcriptional regulatory network, 4 known cancer-related transcription factors (TFs) interacted with 6 CNV-driven genes. The protein/DNA arrays revealed 3 of these 4 TFs as potential candidate gene-related transcription factors in OC. We then demonstrated that these six genes can serve as potential biomarkers for OC. Further studies are required to elucidate the pathogenesis of OC.
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Affiliation(s)
- GuiFen Liu
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - GuanYu Ruan
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - MeiMei Huang
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - LiLi Chen
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - PengMing Sun
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China.,Department of Gynaecology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
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14
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Reid BM, Permuth JB, Chen YA, Fridley BL, Iversen ES, Chen Z, Jim H, Vierkant RA, Cunningham JM, Barnholtz-Sloan JS, Narod S, Risch H, Schildkraut JM, Goode EL, Monteiro AN, Sellers TA. Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk. Cancer Epidemiol Biomarkers Prev 2019; 28:1117-1126. [PMID: 30948450 DOI: 10.1158/1055-9965.epi-18-0833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/02/2018] [Accepted: 03/28/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Germline DNA copy number variation (CNV) is a ubiquitous source of genetic variation and remains largely unexplored in association with epithelial ovarian cancer (EOC) risk. METHODS CNV was quantified in the DNA of approximately 3,500 cases and controls genotyped with the Illumina 610k and HumanOmni2.5M arrays. We performed a genome-wide association study of common (>1%) CNV regions (CNVRs) with EOC and high-grade serous (HGSOC) risk and, using The Cancer Genome Atlas (TCGA), performed in silico analyses of tumor-gene expression. RESULTS Three CNVRs were associated (P < 0.01) with EOC risk: two large (∼100 kb) regions within the 610k set and one small (<5 kb) region with the higher resolution 2.5M data. Large CNVRs included a duplication at LILRA6 (OR = 2.57; P = 0.001) and a deletion at CYP2A7 (OR = 1.90; P = 0.007) that were strongly associated with HGSOC risk (OR = 3.02; P = 8.98 × 10-5). Somatic CYP2A7 alterations correlated with EGLN2 expression in tumors (P = 2.94 × 10-47). An intronic ERBB4/HER4 deletion was associated with reduced EOC risk (OR = 0.33; P = 9.5 × 10-2), and somatic deletions correlated with ERBB4 downregulation (P = 7.05 × 10-5). Five CNVRs were associated with HGSOC, including two reduced-risk deletions: one at 1p36.33 (OR = 0.28; P = 0.001) that correlated with lower CDKIIA expression in TCGA tumors (P = 2.7 × 10-7), and another at 8p21.2 (OR = 0.52; P = 0.002) that was present somatically where it correlated with lower GNRH1 expression (P = 5.9 × 10-5). CONCLUSIONS Though CNV appears to not contribute largely to EOC susceptibility, a number of low-to-common frequency variants may influence the risk of EOC and tumor-gene expression. IMPACT Further research on CNV and EOC susceptibility is warranted, particularly with CNVs estimated from high-density arrays.
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Affiliation(s)
- Brett M Reid
- Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - Y Ann Chen
- Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | | | - Zhihua Chen
- Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Heather Jim
- Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | | | | | - Steven Narod
- Center for Research in Women's Health, Toronto, Ontario, Canada
| | - Harvey Risch
- Yale School of Public Health, New Haven, Connecticut
| | | | - Ellen L Goode
- Mayo Clinic College of Medicine, Rochester, Minnesota
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15
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Nakabayashi M, Kawashima A, Yasuhara R, Hayakawa Y, Miyamoto S, Iizuka C, Sekizawa A. Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration. Sci Rep 2018; 8:11205. [PMID: 30046040 PMCID: PMC6060170 DOI: 10.1038/s41598-018-29381-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/11/2018] [Indexed: 12/18/2022] Open
Abstract
The discovery of circulating tumour DNA molecules created a paradigm shift in tumour biomarkers as predictors of recurrence. Non-invasive prenatal testing (NIPT) to detect circulating cell-free foetal DNA in maternal plasma is increasingly recognised as a valuable substitute to perceive foetal copy number variation (CNV). This study aimed to determine whether the copy number detection in plasma samples using NIPT platform could be used as a prognostic biomarker in patients with gynaecological cancer. We conducted a prospective study using samples containing preoperative plasma from 100 women with gynaecological cancers. Samples were randomly rearranged and blindly sequenced using a low-coverage whole-genome sequencing plasma DNA, NIPT platform. The NIPT pipeline identified copy number alterations (CNAs) were counted in plasma as a gain or loss if they exceeded 10 Mb from the expected diploid coverage. Progression-free survival (PFS) and overall survival (OS) were analysed according to the presence of CNA in plasma using Kaplan-Meier analyses. The NIPT pipeline detected 19/100 cases of all gynaecological cancers, including 6/36 ovarian cancers, 3/11 cervical cancers, and 10/53 endometrial cancers. Patients with CNA in plasma had a significantly poorer prognosis in all stages concerning PFS and OS. Therefore, low-coverage sequencing NIPT platform could serve as a predictive marker of patient outcome.
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Affiliation(s)
- Makoto Nakabayashi
- Department of Obstetrics and Gynecology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
| | - Akihiro Kawashima
- Department of Obstetrics and Gynecology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan.
| | - Rika Yasuhara
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8666, Japan
| | - Yosuke Hayakawa
- Information System Department GeneTech, Inc. 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Shingo Miyamoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
| | - Chiaki Iizuka
- Department of Obstetrics and Gynecology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
| | - Akihiko Sekizawa
- Department of Obstetrics and Gynecology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
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16
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Circulating tumor cells: potential markers of minimal residual disease in ovarian cancer? a study of the OVCAD consortium. Oncotarget 2017; 8:106415-106428. [PMID: 29290959 PMCID: PMC5739744 DOI: 10.18632/oncotarget.22468] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 10/11/2017] [Indexed: 11/25/2022] Open
Abstract
Purpose In 75% of ovarian cancer patients the tumor mass is completely eradicated by established surgical and cytotoxic treatment; however, the majority of the tumors recur within 24 months. Here we investigated the role of circulating tumor cells (CTCs) indicating occult tumor load, which remains inaccessible by established diagnostics. Experimental design Blood was taken at diagnosis (baseline samples, n = 102) and six months after completion of adjuvant first-line chemotherapy (follow-up samples; n = 78). CTCs were enriched by density gradient centrifugation. A multi-marker immunostaining was established and further complemented by FISH on CTCs and tumor/metastasis tissues using probes for stem-cell like fusion genes MECOM and HHLA1. Results CTCs were observed in 26.5% baseline and 7.7% follow-up blood samples at a mean number of 12.4 and 2.8 CTCs per ml blood, respectively. Baseline CTCs indicated a higher risk of death in R0 patients with complete gross resection (univariate: HR 2.158, 95% CI 1.111–4.191, p = 0.023; multivariate: HR 2.720, 95% CI 1.340–5.522, p = 0.006). At follow-up, the presence of CTCs was associated with response to primary treatment as assessed using RECIST criteria. Chromosomal gains at MECOM and HHLA1 loci suggest that the observed cells were cancer cells and reflect pathophysiological decisive chromosomal aberrations of the primary and metastatic tumors. Conclusions Our data suggest that CTCs detected by the multi-marker protein panel and/or MECOM/HHLA1 FISH represent minimal residual disease in optimally debulked ovarian cancer patients. The role of CTCs cells especially for clinical therapy stratification of the patients has to be validated in consecutive larger studies applying standardized treatment schemes.
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17
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Li L, Bai H, Yang J, Cao D, Shen K. Genome-wide DNA copy number analysis in clonally expanded human ovarian cancer cells with distinct invasive/migratory capacities. Oncotarget 2017; 8:15136-15148. [PMID: 28122348 PMCID: PMC5362473 DOI: 10.18632/oncotarget.14767] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/10/2017] [Indexed: 01/26/2023] Open
Abstract
Ovarian cancer has the worst prognosis of any gynecological malignancy, and generally presents with metastasis at advanced stages. Copy number variation (CNV) frequently contributes to the alteration of oncogenic drivers. In this study, we sought to identify genetic targets in heterogeneous clones from human ovarian cancers cells. We used array-based technology to systematically assess all the genes with CNVs in cell models clonally expanded from A2780 and SKOV3 ovarian cancer cell lines with distinct highly and minimally invasive/migratory capacities. We found that copy number alterations differed between matched highly and minimally invasive/migratory subclones, differentially affecting specific functional processes including immune response processes, DNA damage repair, cell cycle and cell proliferation. We also identified seven genes as strong candidates, including DDB1, ERCC1, ERCC2, PRPF19, BCAT1, CDKN1B and MARK4, by integrating the above data with gene expression and clinical outcome data. Thus, by determining the molecular signatures of heterogeneous invasive/migratory ovarian cancer cells, we identified genes that could be specifically targeted for the treatment and prognosis of advanced ovarian cancers.
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Affiliation(s)
- Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Huimin Bai
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiaxin Yang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Keng Shen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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18
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Koutsaki M, Libra M, Spandidos DA, Zaravinos A. The miR-200 family in ovarian cancer. Oncotarget 2017; 8:66629-66640. [PMID: 29029543 PMCID: PMC5630443 DOI: 10.18632/oncotarget.18343] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecological malignancy. Its insidious nature, manifesting with little to no symptoms until the disease progresses to metastasis, along with a wide diversity of histological subtypes and corresponding clinical behavior, poses significant therapeutic challenges. The genetic profiling of this aggressive tumor and its subtypes has led to the identification of various molecular markers of prognosis. Among these, the miR-200 family of miRNAs appears to play an important role. The deregulated expression of the miR-200 family members has been detected in a variety of OC studies. The present review examines the potential usefulness of the miR-200 family members as prognostic indicators in ovarian cancer and their impact across different OC publications, with a particular focus on prognostic features, such as disease stage, tumor histology, survival and response to chemotherapy. We present the potential usefulness of the miR-200 family genes as prognostic indicators in OC and highlight the tendency that miR-200 overexpression corresponds with an advanced cancer stage.
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Affiliation(s)
- Maria Koutsaki
- 3rd Department of Pediatrics of the National and Kapodistrian University of Athens, Attikon University Hospital, 12462 Athens, Greece
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, Laboratory of Translational Oncology and Functional Genomics, Section of General and Clinical Pathology and Oncology, University of Catania, 95124 Catania, Italy
| | - Demetrios A Spandidos
- Laboratory of Virology, Medical School, University of Crete, 71110 Heraklion, Crete, Greece
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus
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19
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Pendlebury A, Hannan NJ, Binder N, Beard S, Mcgauran M, Grant P, Tong S, Whitehead CL. The circulating microRNA-200 family in whole blood are potential biomarkers for high-grade serous epithelial ovarian cancer. Biomed Rep 2017; 6:319-322. [PMID: 28451393 PMCID: PMC5403187 DOI: 10.3892/br.2017.847] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/30/2016] [Indexed: 12/14/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the leading cause of mortality with regard to gynaecological cancer. There is no effective biomarker and therefore prognosis is poor as the majority of cases are not diagnosed until advanced disease is present. MicroRNAs (miRs) are dysregulated in ovarian cancer tissue and are present in the circulation. The aim of the present study was to investigate whether circulating miRs from the miR-200 family served as potential candidate biomarkers for the early detection of EOC. Whole blood and ovarian tissue were collected from women with early (stage I/II, n=4), advanced EOC (stage III/IV, n=4), and women with benign ovarian masses (n=5). A panel of 5 miRs were studied in whole blood and ovarian tissue using Taqman RT-PCR miR assays. The expression of circulating miR-200a, miR-200b and miR-200c were upregulated (P<0.05) in ovarian cancer compared to controls, correlated with the stage of disease and reflected tissue expression. Despite a trend, there was no significant increase in the expression of miR-21 and miR-210 in the present study. In conclusion, the circulating miR-200 family may be promising candidate biomarkers for EOC that require validation in a larger study.
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Affiliation(s)
- Adam Pendlebury
- Department of Gynaecological Oncology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Natalie J. Hannan
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Natalie Binder
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Sally Beard
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Monica Mcgauran
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Peter Grant
- Department of Gynaecological Oncology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Stephen Tong
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
| | - Clare L. Whitehead
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Vic 3084, Australia
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20
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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21
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Kaveh F, Baumbusch LO, Nebdal D, Børresen-Dale AL, Lingjærde OC, Edvardsen H, Kristensen VN, Solvang HK. A systematic comparison of copy number alterations in four types of female cancer. BMC Cancer 2016; 16:913. [PMID: 27876019 PMCID: PMC5120489 DOI: 10.1186/s12885-016-2899-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/30/2016] [Indexed: 01/06/2023] Open
Abstract
Background Detection and localization of genomic alterations and breakpoints are crucial in cancer research. The purpose of this study was to investigate, in a methodological and biological perspective, different female, hormone-dependent cancers to identify common and diverse DNA aberrations, genes, and pathways. Methods In this work, we analyzed tissue samples from patients with breast (n = 112), ovarian (n = 74), endometrial (n = 84), or cervical (n = 76) cancer. To identify genomic aberrations, the Circular Binary Segmentation (CBS) and Piecewise Constant Fitting (PCF) algorithms were used and segmentation thresholds optimized. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was applied to the segmented data to identify significantly altered regions and the associated genes were analyzed by Ingenuity Pathway Analysis (IPA) to detect over-represented pathways and functions within the identified gene sets. Results and Discussion Analyses of high-resolution copy number alterations in four different female cancer types are presented. For appropriately adjusted segmentation parameters the two segmentation algorithms CBS and PCF performed similarly. We identified one region at 8q24.3 with focal aberrations that was altered at significant frequency across all four cancer types. Considering both, broad regions and focal peaks, three additional regions with gains at significant frequency were revealed at 1p21.1, 8p22, and 13q21.33, respectively. Several of these events involve known cancer-related genes, like PPP2R2A, PSCA, PTP4A3, and PTK2. In the female reproductive system (ovarian, endometrial, and cervix [OEC]), we discovered three common events: copy number gains at 5p15.33 and 15q11.2, further a copy number loss at 8p21.2. Interestingly, as many as 75% of the aberrations (75% amplifications and 86% deletions) identified by GISTIC were specific for just one cancer type and represented distinct molecular pathways. Conclusions Our results disclose that some prominent copy number changes are shared in the four examined female, hormone-dependent cancer whereas others are definitive to specific cancer types. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2899-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fatemeh Kaveh
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Medical Genetics Department, Oslo University Hospital Ullevål, Oslo, Norway.,Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Lars O Baumbusch
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Daniel Nebdal
- 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
| | - Ole Christian Lingjærde
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Department of Computer Science, University of Oslo, Oslo, Norway
| | - Hege Edvardsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. .,Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway.
| | - Hiroko K Solvang
- Marine Mammals Research Group, Institute of Marine Research, Bergen, Norway
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22
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Kadioglu O, Cao J, Kosyakova N, Mrasek K, Liehr T, Efferth T. Genomic and transcriptomic profiling of resistant CEM/ADR-5000 and sensitive CCRF-CEM leukaemia cells for unravelling the full complexity of multi-factorial multidrug resistance. Sci Rep 2016; 6:36754. [PMID: 27824156 PMCID: PMC5099876 DOI: 10.1038/srep36754] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
We systematically characterised multifactorial multidrug resistance (MDR) in CEM/ADR5000 cells, a doxorubicin-resistant sub-line derived from drug-sensitive, parental CCRF-CEM cells developed in vitro. RNA sequencing and network analyses (Ingenuity Pathway Analysis) were performed. Chromosomal aberrations were identified by array-comparative genomic hybridisation (aCGH) and multicolour fluorescence in situ hybridisation (mFISH). Fifteen ATP-binding cassette transporters and numerous new genes were overexpressed in CEM/ADR5000 cells. The basic karyotype in CCRF-CEM cells consisted of 47, XX, der(5)t(5;14) (q35.33;q32.3), del(9) (p14.1), +20. CEM/ADR5000 cells acquired additional aberrations, including X-chromosome loss, 4q and 14q deletion, chromosome 7 inversion, balanced and unbalanced two and three way translocations: t(3;10), der(3)t(3;13), der(5)t(18;5;14), t(10;16), der(18)t(7;18), der(18)t(21;18;5), der(21;21;18;5) and der(22)t(9;22). CCRF-CEM consisted of two and CEM/ADR5000 of five major sub-clones, indicating genetic tumor heterogeneity. Loss of 3q27.1 in CEM/ADR5000 caused down-regulation of ABCC5 and ABCF3 expression, Xq28 loss down-regulated ABCD1 expression. ABCB1, the most well-known MDR gene, was 448-fold up-regulated due to 7q21.12 amplification. In addition to well-known drug resistance genes, numerous novel genes and genomic aberrations were identified. Transcriptomics and genetics in CEM/AD5000 cells unravelled a range of MDR mechanisms, which is much more complex than estimated thus far. This may have important implications for future treatment strategies.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jingming Cao
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
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23
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Dong A, Lu Y, Lu B. Genomic/Epigenomic Alterations in Ovarian Carcinoma: Translational Insight into Clinical Practice. J Cancer 2016; 7:1441-51. [PMID: 27471560 PMCID: PMC4964128 DOI: 10.7150/jca.15556] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/24/2016] [Indexed: 12/22/2022] Open
Abstract
Ovarian carcinoma is the most lethal gynecological malignancy worldwide. Recent advance in genomic/epigenomic researches will impact on our prevention, detection and intervention on ovarian carcinoma. Detection of germline mutations in BRCA1/BRCA2, mismatch repair genes, and other genes in the homologous recombination/DNA repair pathway propelled the genetic surveillance of most hereditary ovarian carcinomas. Germline or somatic mutations in SMARCA4 in familial and sporadic small cell carcinoma of the ovary, hypercalcemia type, lead to our recognition on this rare aggressive tumor as a new entity of the atypical teratoma/rhaboid tumor family. Genome-wide association studies have identified many genetic variants that will contribute to the evaluation of ovarian carcinoma risk and prognostic prediction. Whole exome sequencing and whole genome sequencing discovered rare mutations in other drive mutations except p53, but demonstrated the presence of high genomic heterogeneity and adaptability in the genetic evolution of high grade ovarian serous carcinomas that occurs in cancer progression and chemotherapy. Gene mutations, copy number aberrations and DNA methylations provided promising biomarkers for the detection, diagnosis, prognosis, therapy response and targets of ovarian cancer. These findings underscore the necessity to translate these potential biomarkers into clinical practice.
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Affiliation(s)
- Anliang Dong
- 1. Women's Hospital & Institute of Translational Medicine, School of Medicine, Zhejiang University, China
| | - Yan Lu
- 1. Women's Hospital & Institute of Translational Medicine, School of Medicine, Zhejiang University, China
| | - Bingjian Lu
- 2. Department of Surgical Pathology, Women's Hospital, School of Medicine, Zhejiang University, China
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24
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English DP, Menderes G, Black J, Schwab CL, Santin AD. Molecular diagnosis and molecular profiling to detect treatment-resistant ovarian cancer. Expert Rev Mol Diagn 2016; 16:769-82. [PMID: 27169329 DOI: 10.1080/14737159.2016.1188692] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Epithelial ovarian cancer remains the gynecologic tumor with the highest rate of recurrence after initial optimal cytoreductive surgery followed by adjuvant chemotherapy. Unfortunately, with the development of recurrent ovarian cancer often comes the discovery of chemo-resistant disease. The absence of improvement in long term survival, notwithstanding the use of newer agents as is seen in other cancers, emphasizes the need for improved understanding of the processes that lead to chemo-resistant disease. AREAS COVERED This review will cover the following topics: 1. Molecular and cellular mechanisms in platinum and paclitaxel resistance 2. Other molecular mediators of chemo-resistance 3. Expression of stem cell markers in ovarian cancer and relationship to chemo-resistance 4. MicroRNA and long non-coding RNA expression in chemo-resistant ovarian cancer 5. Determination of chromosomal aberrations as markers of chemo-resistance 6. Molecular profiling in chemo-resistant disease. A standard MEDLINE search was performed using the key words; ovarian cancer, chemo-resistant disease, molecular profiling, cancer stem cells and chemotherapy. Expert Commentary: Over the next few years the challenge remains to precisely determine the mechanisms responsible for the onset and maintenance of chemo-resistance and to effectively target these mechanisms.
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Affiliation(s)
- Diana P English
- a Department of Obstetrics and Gynecology, Division of Gynecologic Oncology , Stanford University , Stanford , CA , USA
| | - Gulden Menderes
- b Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Gynecologic Oncology , Yale University School of Medicine , New Haven , CT , USA
| | - Jonathan Black
- a Department of Obstetrics and Gynecology, Division of Gynecologic Oncology , Stanford University , Stanford , CA , USA
| | - Carlton L Schwab
- b Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Gynecologic Oncology , Yale University School of Medicine , New Haven , CT , USA
| | - Alessandro D Santin
- b Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Gynecologic Oncology , Yale University School of Medicine , New Haven , CT , USA
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25
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Genomic approach to understand association between single nucleotide polymorphisms and risk of Korean serous ovarian cancer at stage IIIc. Mol Cell Toxicol 2016. [DOI: 10.1007/s13273-016-0004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Zhang J, Zhang H, Xu X, Wang M, Yu Z. Comparative genomic hybridization analysis of invasive ductal breast carcinomas in the Chinese population. Oncol Lett 2015; 10:2100-2106. [PMID: 26622803 PMCID: PMC4579858 DOI: 10.3892/ol.2015.3608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 03/31/2015] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is the most common malignancy in Chinese women. The aim of the present study was to investigate the genetic alterations that occur in breast cancer cells in Chinese women. Comparative genomic hybridization (CGH) analysis was performed on 34 tumors obtained from patients with primary invasive ductal breast carcinoma (IDC). Recurrent genetic alterations in breast cancer include gains on chromosomes 1q (59%), 16p (50%), 17q (44%), 8q (38%), 11q (32%), 20q (32%), 1p (24%), 20p (24%), 19q (21%) and 19p (18%). Losses are common on chromosomes 6q (15%), 8p (12%), 18 (12%), 4q (9%), X (9%) and 17p (9%). In the present study, high-level amplifications were observed on chromosomes 1q32, 8p, 11q13, 17q and 20q. Overall, the chromosomal DNA gains observed were consistent with the changes reported in Caucasian populations. However, the incidence of chromosomal DNA loss was lower in the present study compared with the incidence reported in the literature. The present results demonstrate the pattern of chromosomal imbalances in the invasive ductal breast carcinomas of Chinese females.
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Affiliation(s)
- Jianwei Zhang
- Department of Oncology, Beijing Army General Hospital, Beijing 100700, P.R. China
| | - Hongyan Zhang
- Department of Oncology, Beijing Army General Hospital, Beijing 100700, P.R. China
| | - Xin Xu
- National Laboratory of Molecular Oncology, Cancer Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Mingrong Wang
- National Laboratory of Molecular Oncology, Cancer Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Zhonghe Yu
- Department of Oncology, Beijing Army General Hospital, Beijing 100700, P.R. China
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27
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Lin WH, Asmann YW, Anastasiadis PZ. Expression of polarity genes in human cancer. Cancer Inform 2015; 14:15-28. [PMID: 25991909 PMCID: PMC4390136 DOI: 10.4137/cin.s18964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 01/01/2023] Open
Abstract
Polarity protein complexes are crucial for epithelial apical–basal polarity and directed cell migration. Since alterations of these processes are common in cancer, polarity proteins have been proposed to function as tumor suppressors or oncogenic promoters. Here, we review the current understanding of polarity protein functions in epithelial homeostasis, as well as tumor formation and progression. As most previous studies focused on the function of single polarity proteins in simplified model systems, we used a genomics approach to systematically examine and identify the expression profiles of polarity genes in human cancer. The expression profiles of polarity genes were distinct in different human tissues and classified cancer types. Additionally, polarity expression profiles correlated with disease progression and aggressiveness, as well as with identified cancer types, where specific polarity genes were commonly altered. In the case of Scribble, gene expression analysis indicated its common amplification and upregulation in human cancer, suggesting a tumor promoting function.
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Affiliation(s)
- Wan-Hsin Lin
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
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28
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Johnson N, Zhang H, Fang G, Kumar V, Kuang R. SubPatCNV: approximate subspace pattern mining for mapping copy-number variations. BMC Bioinformatics 2015; 16:16. [PMID: 25591662 PMCID: PMC4305219 DOI: 10.1186/s12859-014-0426-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/11/2014] [Indexed: 11/16/2022] Open
Abstract
Background Many DNA copy-number variations (CNVs) are known to lead to phenotypic variations and pathogenesis. While CNVs are often only common in a small number of samples in the studied population or patient cohort, previous work has not focused on customized identification of CNV regions that only exhibit in subsets of samples with advanced data mining techniques to reliably answer questions such as “Which are all the chromosomal fragments showing nearly identical deletions or insertions in more than 30% of the individuals?”. Results We introduce a tool for mining CNV subspace patterns, namely SubPatCNV, which is capable of identifying all aberrant CNV regions specific to arbitrary sample subsets larger than a support threshold. By design, SubPatCNV is the implementation of a variation of approximate association pattern mining algorithm under a spatial constraint on the positional CNV probe features. In benchmark test, SubPatCNV was applied to identify population specific germline CNVs from four populations of HapMap samples. In experiments on the TCGA ovarian cancer dataset, SubPatCNV discovered many large aberrant CNV events in patient subgroups, and reported regions enriched with cancer relevant genes. In both HapMap data and TCGA data, it was observed that SubPatCNV employs approximate pattern mining to more effectively identify CNV subspace patterns that are consistent within a subgroup from high-density array data. Conclusions SubPatCNV available through http://sourceforge.net/projects/subpatcnv/is a unique scalable open-source software tool that provides the flexibility of identifying CNV regions specific to sample subgroups of different sizes from high-density CNV array data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0426-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas Johnson
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Huanan Zhang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Gang Fang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota. .,Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York.
| | - Vipin Kumar
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Rui Kuang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
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29
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Despierre E, Moisse M, Yesilyurt B, Sehouli J, Braicu I, Mahner S, Castillo-Tong DC, Zeillinger R, Lambrechts S, Leunen K, Amant F, Moerman P, Lambrechts D, Vergote I. Somatic copy number alterations predict response to platinum therapy in epithelial ovarian cancer. Gynecol Oncol 2014; 135:415-22. [PMID: 25281495 DOI: 10.1016/j.ygyno.2014.09.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Platinum resistance remains an obstacle in the treatment of epithelial ovarian cancer (EOC). The goal of this study was to profile EOCs for somatic copy number alterations (SCNAs) as predictive markers of platinum response. METHODS SCNAs were assessed in a discovery (n=86) and validation cohort (n=115) of high risk stage I or stage II-IV EOCs using high-resolution SNP arrays. ASCAT and GISTIC identified all significantly overrepresented amplified or deleted chromosomal regions. Cox regression and univariate analysis assessed which SCNAs correlated with overall survival (OS), progression-free survival (PFS), platinum-free interval (PFI) and platinum response. Relevant SCNAs were also assessed in a pooled analysis involving both cohorts and published SCNA data from The Cancer Genome Atlas (TCGA; n=227). RESULTS We identified 53 regions to be significantly overrepresented in EOC. Of these, 6 were associated with OS, PFS or PFI in the discovery cohort at P<0.05. In the validation cohort, amplifications of chromosomal region 14q32.33, which contains AKT1 as a potential driver gene, also correlated with OS (OR=1.670; P=0.018). In a pooled analysis of 428 tumors, involving the discovery, validation and TCGA cohorts, 14q32.33 amplifications significantly reduced OS, PFS and PFI (HR=2.69, P=1.7×10(-4); HR=1.82, P=1.9×10(-2) and HR=1.80, P=2.2×10(-2) respectively). Moreover, AKT1 mRNA expression correlated with the number of chromosomal copies of the 14q32.33 region (P=2.8×10(-11);R(2)=0.26). CONCLUSIONS We established that amplifications in 14q32.33 were associated with reduced OS, PFS, PFI and platinum resistance in three independent cohorts, suggesting that AKT1 amplifications act as a potentially predictive marker for EOC treated with platinum-based chemotherapy.
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Affiliation(s)
- Evelyn Despierre
- Gynecologic Oncology, University Hospitals Leuven, Leuven, Belgium; Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
| | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium; Vesalius Research Center, VIB, Leuven, Belgium
| | - Betül Yesilyurt
- Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium; Vesalius Research Center, VIB, Leuven, Belgium
| | - Jalid Sehouli
- Department of Gynecology, Campus Virchow-Klinikum, Charité University Hospital, European Competence Center for Ovarian Cancer Berlin, Germany
| | - Ioana Braicu
- Department of Gynecology, Campus Virchow-Klinikum, Charité University Hospital, European Competence Center for Ovarian Cancer Berlin, Germany
| | - Sven Mahner
- Department of Gynecology, Hamburg-Eppendorf University Medical Center, University Cancer Center Hamburg-Eppendorf (UCCH), Germany
| | - Dan Cacsire Castillo-Tong
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Gynecologic Cancer Unit, Medical University of Vienna, Austria
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Gynecologic Cancer Unit, Medical University of Vienna, Austria
| | - Sandrina Lambrechts
- Gynecologic Oncology, University Hospitals Leuven, Leuven, Belgium; Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Karin Leunen
- Gynecologic Oncology, University Hospitals Leuven, Leuven, Belgium; Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Frédéric Amant
- Gynecologic Oncology, University Hospitals Leuven, Leuven, Belgium; Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Philippe Moerman
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium; Vesalius Research Center, VIB, Leuven, Belgium.
| | - Ignace Vergote
- Gynecologic Oncology, University Hospitals Leuven, Leuven, Belgium; Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
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Thériault BL, Basavarajappa HD, Lim H, Pajovic S, Gallie BL, Corson TW. Transcriptional and epigenetic regulation of KIF14 overexpression in ovarian cancer. PLoS One 2014; 9:e91540. [PMID: 24626475 PMCID: PMC3953446 DOI: 10.1371/journal.pone.0091540] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 02/13/2014] [Indexed: 02/06/2023] Open
Abstract
KIF14 (kinesin family member 14) is a mitotic kinesin and an important oncogene in several cancers. Tumor KIF14 expression levels are independently predictive of poor outcome, and in cancer cells KIF14 can modulate metastatic behavior by maintaining appropriate levels of cell adhesion and migration proteins at the cell membrane. Thus KIF14 is an exciting potential therapeutic target. Understanding KIF14's regulation in cancer cells is crucial to the development of effective and selective therapies to block its tumorigenic function(s). We previously determined that close to 30% of serous ovarian cancers (OvCa tumors) exhibit low-level genomic gain, indicating one mechanism of KIF14 overexpression in tumors. We now report on transcriptional and epigenetic regulation of KIF14. Through promoter deletion analyses, we identified one cis-regulatory region containing binding sites for Sp1, HSF1 and YY1. siRNA-mediated knockdown of these transcription factors demonstrated endogenous regulation of KIF14 overexpression by Sp1 and YY1, but not HSF1. ChIP experiments confirmed an enrichment of both Sp1 and YY1 binding to the endogenous KIF14 promoter in OvCa cell lines with high KIF14 expression. A strong correlation was seen in primary serous OvCa tumors between Sp1, YY1 and KIF14 expression, further evidence that these transcription factors are important players in KIF14 overexpression. Hypomethylation patterns were observed in primary serous OvCa tumors, suggesting a minor role for promoter methylation in the control of KIF14 gene expression. miRNA expression analysis determined that miR-93, miR-144 and miR-382 had significantly lower levels of expression in primary serous OvCa tumors than normal tissues; treatment of an OvCa cell line with miRNA mimics and inhibitors specifically modulated KIF14 mRNA levels, pointing to potential novel mechanisms of KIF14 overexpression in primary tumors. Our findings reveal multiple mechanisms of KIF14 upregulation in cancer cells, offering new targets for therapeutic interventions to reduce KIF14 in tumors, aiming at improved prognosis.
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Affiliation(s)
- Brigitte L. Thériault
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Halesha D. Basavarajappa
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Harvey Lim
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sanja Pajovic
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Brenda L. Gallie
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Visual Science, Toronto Western Hospital Research Institute, Toronto, Ontario, Canada
- Departments of Molecular Genetics and Ophthalmology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy W. Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
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31
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Wang L, Wenners A, Hilpert F, Fredrik R, Micci F, Onkes W, Caliebe A, Maass N, Weimer J, Arnold N. Frequent translocations of 11q13.2 and 19p13.2 in ovarian cancer. Genes Chromosomes Cancer 2014; 53:447-53. [PMID: 24615723 DOI: 10.1002/gcc.22152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 01/17/2014] [Accepted: 01/19/2014] [Indexed: 01/12/2023] Open
Abstract
Aberrations of chromosome arm 19p in ovarian cancer were first described decades ago and have been confirmed in recent publications, which have focused on chromosome 11 as a translocation partner. Recently, genetic analysis of the ovarian cancer cell line SKOV3 revealed a rearrangement described as der(19)t(11;19)(q13.2;p13.2), which lead to a fusion protein containing parts of HOOK2 and frame shifted ACTN3 that had unknown functionality. To evaluate the frequency of these breakpoints, we used fluorescence in situ hybridization (FISH) probes flanking these genes for interphase analysis of ovarian cancer cells. We analyzed 49 primary cell cultures of ovarian cancers using FISH probes next to these breakpoints on chromosomes 11 and 19 defined in SKOV3. Co-localizations of the signals in interphase nuclei were considered to be positive fusions when the frequency was over the experimentally calculated cutoff of 24.3% (mean average value for normal ovary cells plus three times the standard deviation). Fusions between 11q13.2 and 19p13.2 were confirmed in 22 (45%) primary cell cultures of ovarian cancers. However, by PCR, the fusion originally described in SKOV3 was not detected in any of the primary cell cultures. Our results confirm other reports and show that these regions are very frequently involved in chromosomal rearrangements in ovarian cancer. Furthermore, they reveal a significant correlation (P = 0.023) of co-localized signals of 11q13.2 and 19p13.2 with low and intermediate grades in ovarian cancer.
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Affiliation(s)
- Liang Wang
- Department of Gynecology, Zhejiang University School of Medicine, The 2nd Affiliated Hospital, Hangzhou, Zhejiang, China; Clinic of Gynecology and Obstetrics, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
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Aure MR, Leivonen SK, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GIG, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale AL, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol 2013; 14:R126. [PMID: 24257477 PMCID: PMC4053776 DOI: 10.1186/gb-2013-14-11-r126] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/20/2013] [Indexed: 01/31/2023] Open
Abstract
Background The global effect of copy number and epigenetic alterations on miRNA expression in cancer is poorly understood. In the present study, we integrate genome-wide DNA methylation, copy number and miRNA expression and identify genetic mechanisms underlying miRNA dysregulation in breast cancer. Results We identify 70 miRNAs whose expression was associated with alterations in copy number or methylation, or both. Among these, five miRNA families are represented. Interestingly, the members of these families are encoded on different chromosomes and are complementarily altered by gain or hypomethylation across the patients. In an independent breast cancer cohort of 123 patients, 41 of the 70 miRNAs were confirmed with respect to aberration pattern and association to expression. In vitro functional experiments were performed in breast cancer cell lines with miRNA mimics to evaluate the phenotype of the replicated miRNAs. let-7e-3p, which in tumors is found associated with hypermethylation, is shown to induce apoptosis and reduce cell viability, and low let-7e-3p expression is associated with poorer prognosis. The overexpression of three other miRNAs associated with copy number gain, miR-21-3p, miR-148b-3p and miR-151a-5p, increases proliferation of breast cancer cell lines. In addition, miR-151a-5p enhances the levels of phosphorylated AKT protein. Conclusions Our data provide novel evidence of the mechanisms behind miRNA dysregulation in breast cancer. The study contributes to the understanding of how methylation and copy number alterations influence miRNA expression, emphasizing miRNA functionality through redundant encoding, and suggests novel miRNAs important in breast cancer.
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Candidate microRNA biomarkers in human epithelial ovarian cancer: systematic review profiling studies and experimental validation. Cancer Cell Int 2013; 13:86. [PMID: 23978303 PMCID: PMC3765519 DOI: 10.1186/1475-2867-13-86] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/23/2013] [Indexed: 12/13/2022] Open
Abstract
Despite advances in detection and therapy, epithelial ovarian cancer (EOC) still represents the most lethal gynecologic malignancy in women worldwide. The high mortality of EOC is mainly due to late-stage diagnosis for more than 70% of patients. There is an urgent need to search for specific and sensitive biomarkers for early diagnosis of EOC. Recently, the cumulative data indicated an essential role for microRNA (miRNA), a class of small non-coding RNAs targeting multiple mRNAs and triggering translation repression and/or RNA degradation, in ovarian caner carcinogenesis and progression. Here, we reviewed the published miRNA expression profiling studies that compared the miRNA expression profiles between EOC tissues or cell lines and normal ovarian tissues or benign ovarian tumor or human primary cultured ovarian surface epithelial cells. A miRNA ranking system that takes the number of comparisons in agreement and direction of differential expression into the consideration was devised and used. Finally, five promising differentially miRNAs (miR-200a, miR-100, miR-141, miR-200b, and miR-200c) were reported with the consistent direction in four or more studies. MiR-200a, miR-200b, miR-200c, and miR-141, all of them belong to miR-200 family, were reported with consistently up-regulated in at least 4 studies, whereas miR-100 was reported with down-regulated in 4 studies. Furthermore, we validated these miRNAs in a clinical setting using qRT-PCR and their dysregulations in EOC tissues confirmed the findings. Conclusively, the five most consistently expressed miRNAs might provide some clues of the potential biomarkers in EOC. Further mechanistic and precise validation studies are needed for their clinical significances and roles in the progression of EOC.
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Rinella ES, Shao Y, Yackowski L, Pramanik S, Oratz R, Schnabel F, Guha S, LeDuc C, Campbell CL, Klugman SD, Terry MB, Senie RT, Andrulis IL, Daly M, John EM, Roses D, Chung WK, Ostrer H. Genetic variants associated with breast cancer risk for Ashkenazi Jewish women with strong family histories but no identifiable BRCA1/2 mutation. Hum Genet 2013; 132:523-36. [PMID: 23354978 DOI: 10.1007/s00439-013-1269-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 01/13/2013] [Indexed: 01/26/2023]
Abstract
The ability to establish genetic risk models is critical for early identification and optimal treatment of breast cancer. For such a model to gain clinical utility, more variants must be identified beyond those discovered in previous genome-wide association studies (GWAS). This is especially true for women at high risk because of family history, but without BRCA1/2 mutations. This study incorporates three datasets in a GWAS analysis of women with Ashkenazi Jewish (AJ) homogeneous ancestry. Two independent discovery cohorts comprised 239 and 238 AJ women with invasive breast cancer or preinvasive ductal carcinoma in situ and strong family histories of breast cancer, but lacking the three BRCA1/2 founder mutations, along with 294 and 230 AJ controls, respectively. An independent, third cohort of 203 AJ cases with familial breast cancer history and 263 healthy controls of AJ women was used for validation. A total of 19 SNPs were identified as associated with familial breast cancer risk in AJ women. Among these SNPs, 13 were identified from a panel of 109 discovery SNPs, including an FGFR2 haplotype. In addition, six previously identified breast cancer GWAS SNPs were confirmed in this population. Seven of the 19 markers were significant in a multivariate predictive model of familial breast cancer in AJ women, three novel SNPs [rs17663555(5q13.2), rs566164(6q21), and rs11075884(16q22.2)], the FGFR2 haplotype, and three previously published SNPs [rs13387042(2q35), rs2046210(ESR1), and rs3112612(TOX3)], yielding moderate predictive power with an area under the curve (AUC) of the ROC (receiver-operator characteristic curve) of 0.74. Population-specific genetic variants in addition to variants shared with populations of European ancestry may improve breast cancer risk prediction among AJ women from high-risk families without founder BRCA1/2 mutations.
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Affiliation(s)
- Erica S Rinella
- Department of Surgery, New York University Langone Medical Center, New York, NY, USA
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Abstract
During development and tissue homeostasis, patterns of cellular organization, proliferation and movement are highly choreographed. Receptor tyrosine kinases (RTKs) have a crucial role in establishing these patterns. Individual cells and tissues exhibit tight spatial control of the RTKs that they express, enabling tissue morphogenesis and function, while preventing unwarranted cell division and migration that can contribute to tumorigenesis. Indeed, RTKs are deregulated in most human cancers and are a major focus of targeted therapeutics. A growing appreciation of the essential role of spatial RTK regulation during development prompts the realization that spatial deregulation of RTKs is likely to contribute broadly to cancer development and may affect the sensitivity and resistance of cancer to pharmacological RTK inhibitors.
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Affiliation(s)
- Jessica B. Casaletto
- MGH Center for Cancer Research and Harvard Medical School Department of Pathology, 149 13th Street Charlestown, MA 02129 United States
| | - Andrea I. McClatchey
- MGH Center for Cancer Research and Harvard Medical School Department of Pathology, 149 13th Street Charlestown, MA 02129 United States
- To whom correspondence should be addressed:
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36
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Engler DA, Gupta S, Growdon WB, Drapkin RI, Nitta M, Sergent PA, Allred SF, Gross J, Deavers MT, Kuo WL, Karlan BY, Rueda BR, Orsulic S, Gershenson DM, Birrer MJ, Gray JW, Mohapatra G. Genome wide DNA copy number analysis of serous type ovarian carcinomas identifies genetic markers predictive of clinical outcome. PLoS One 2012; 7:e30996. [PMID: 22355333 PMCID: PMC3280266 DOI: 10.1371/journal.pone.0030996] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/28/2011] [Indexed: 01/09/2023] Open
Abstract
Ovarian cancer is the fifth leading cause of cancer death in women. Ovarian cancers display a high degree of complex genetic alterations involving many oncogenes and tumor suppressor genes. Analysis of the association between genetic alterations and clinical endpoints such as survival will lead to improved patient management via genetic stratification of patients into clinically relevant subgroups. In this study, we aim to define subgroups of high-grade serous ovarian carcinomas that differ with respect to prognosis and overall survival. Genome-wide DNA copy number alterations (CNAs) were measured in 72 clinically annotated, high-grade serous tumors using high-resolution oligonucleotide arrays. Two clinically annotated, independent cohorts were used for validation. Unsupervised hierarchical clustering of copy number data derived from the 72 patient cohort resulted in two clusters with significant difference in progression free survival (PFS) and a marginal difference in overall survival (OS). GISTIC analysis of the two clusters identified altered regions unique to each cluster. Supervised clustering of two independent large cohorts of high-grade serous tumors using the classification scheme derived from the two initial clusters validated our results and identified 8 genomic regions that are distinctly different among the subgroups. These 8 regions map to 8p21.3, 8p23.2, 12p12.1, 17p11.2, 17p12, 19q12, 20q11.21 and 20q13.12; and harbor potential oncogenes and tumor suppressor genes that are likely to be involved in the pathogenesis of ovarian carcinoma. We have identified a set of genetic alterations that could be used for stratification of high-grade serous tumors into clinically relevant treatment subgroups.
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Affiliation(s)
- David A. Engler
- Department of Statistics, Brigham Young University, Provo, Utah, United States of America
| | - Sumeet Gupta
- Whitehead Institute of Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Whitfield B. Growdon
- Department of Vincent Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ronny I. Drapkin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Mai Nitta
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Petra A. Sergent
- Department of Vincent Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Serena F. Allred
- Department of Statistics, Brigham Young University, Provo, Utah, United States of America
| | - Jenny Gross
- Women's Cancer Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Michael T. Deavers
- Department of Pathology and Gynecology Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Wen-Lin Kuo
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Beth Y. Karlan
- Women's Cancer Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Bo R. Rueda
- Department of Vincent Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sandra Orsulic
- Women's Cancer Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - David M. Gershenson
- Department of Pathology and Gynecology Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Michael J. Birrer
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Joe W. Gray
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gayatry Mohapatra
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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Vaira V, Faversani A, Dohi T, Montorsi M, Augello C, Gatti S, Coggi G, Altieri DC, Bosari S. miR-296 regulation of a cell polarity-cell plasticity module controls tumor progression. Oncogene 2012; 31:27-38. [PMID: 21643016 PMCID: PMC3252463 DOI: 10.1038/onc.2011.209] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/11/2011] [Accepted: 04/11/2011] [Indexed: 01/02/2023]
Abstract
The expression of small, non-coding RNA or microRNAs (miR), is frequently deregulated in human cancer, but how these pathways affect disease progression is still largely elusive. Here, we report on a miR, miR-296, which is progressively lost during tumor progression and correlates with metastatic disease in colorectal, breast, lung, gastric, parathyroid, liver and bile ducts cancers. Functionally, miR-296 controls a global cell motility gene signature in epithelial cells by transcriptionally repressing the cell polarity-cell plasticity module, Scribble (Scrib). In turn, loss of miR-296 causes aberrantly increased and mislocalized Scrib in human tumors, resulting in exaggerated random cell migration and tumor cell invasiveness. Re-expression of miR-296 in MDA-MB231 cells inhibits tumor growth in vivo. Finally, miR-296 or Scrib levels predict tumor relapse in hepatocellular carcinoma patients. These data identify miR-296 as a global repressor of tumorigenicity and uncover a previously unexplored exploitation of Scrib in tumor progression in humans.
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Affiliation(s)
- Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20135, Milan, Italy
| | - Alice Faversani
- Division of Pathology, Department of Medicine, Surgery and Dentistry, University of Milan Medical School, and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20135, Milan, Italy
| | - Takehiko Dohi
- Prostate Cancer Discovery and Development Program, The Wistar Institute Cancer Center, Philadelphia, PA 19104
| | - Marco Montorsi
- Third division of General Surgery, University of Milan School of Medicine, Istituto Clinico Humanitas IRCCS, 20089, Rozzano, Italy
| | - Claudia Augello
- Division of Pathology, Department of Medicine, Surgery and Dentistry, University of Milan Medical School, and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20135, Milan, Italy
| | - Stefano Gatti
- Center for Surgical Research, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Guido Coggi
- Division of Pathology, Department of Medicine, Surgery and Dentistry, University of Milan Medical School, and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20135, Milan, Italy
| | - Dario C. Altieri
- Prostate Cancer Discovery and Development Program, The Wistar Institute Cancer Center, Philadelphia, PA 19104
| | - Silvano Bosari
- Division of Pathology, Department of Medicine, Surgery and Dentistry, University of Milan Medical School, and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20135, Milan, Italy
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Han W, Woo JH, Jeon YK, Yang SJ, Cho J, Ko E, Kim TY, Im SA, Oh DOY, Park IA, Hwang KT, Moon HG, Yang KS, Noh DY. 17p12 deletion in breast cancer predicts resistance to neoadjuvant chemotherapy. Exp Ther Med 2011; 2:799-804. [PMID: 22977578 DOI: 10.3892/etm.2011.299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 06/16/2011] [Indexed: 12/16/2022] Open
Abstract
Numerous studies have attempted to identify gene expression profiles which can be utilized to predict responses to neoadjuvant chemotherapy (NAC), but their findings are not clinically applicable at present. In the present study, we sought to determine DNA copy number alterations (CNAs) in breast cancer tissues which are associated with the response to NAC. Frozen tumor tissues from 63 breast cancer patients were obtained using core needle biopsy prior to NAC (3 cycles of docetaxel plus adriamycin) and were microdissected. Array comparative genomic hybridization (array CGH) with 4,045 bacterial artificial chromosome (BAC) probes was performed to identify the CNAs. Changes in tumor size in response to NAC were measured via magnetic resonance imaging. Fluorescence in situ hybridization (FISH) was conducted to verify array CGH results and for independent validation studies. CNAs at eight chromosomal loci encompassing 24 clones were correlated with changes in tumor size after NAC (p<0.05; t-test). Two CNAs were selected, 17p12 deletion and 17q21.32-33 gain, which were significantly associated with a smaller reduction in tumor size following NAC, via prioritization of the regions containing the candidate genes. In an independent validation set of samples from 39 patients, FISH assay further showed that the 17p12 deletion was markedly associated with smaller changes in tumor size (p=0.006), while the 17q21.32-33 gain was not significant (p=0.309). In conclusion, we successfully identified a 17p12 deletion in breast cancer tissue which can be applied in predicting tumor resistance to NAC.
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Vaira V, Faversani A, Dohi T, Maggioni M, Nosotti M, Tosi D, Altieri DC, Bosari S. Aberrant overexpression of the cell polarity module scribble in human cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:2478-83. [PMID: 21549346 DOI: 10.1016/j.ajpath.2011.02.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/24/2011] [Accepted: 02/22/2011] [Indexed: 11/17/2022]
Abstract
Human Scribble (Scrib) is an evolutionary-conserved cell polarity protein, but its potential role in human cancer is controversial. Herein, we show that Scrib is nearly universally overexpressed in cultured tumor cell lines and genetically disparate cancer patient series compared with matched normal tissues in vivo. Instead of a membrane association seen in normal epithelia, tumor-associated Scrib is mislocalized and found predominantly in the cytosol. Small-interfering RNA silencing of Scrib in model lung adenocarcinoma A549 cells inhibited cell migration in wound-healing assays, suppressed tumor cell invasion across Matrigel-coated inserts, and down-regulated the expression of cell motility markers and mediators of epithelial-mesenchymal transition. These data uncover a previously unrecognized exploitation of Scrib for aberrant tumor cell motility and invasion, thus potentially contributing to disease progression in humans.
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Affiliation(s)
- Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Kim SW, Kim S, Nam EJ, Jeong YW, Lee SH, Paek JH, Kim JH, Kim JW, Kim YT. Comparative Proteomic Analysis of Advanced Serous Epithelial Ovarian Carcinoma: Possible Predictors of Chemoresistant Disease. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:281-92. [DOI: 10.1089/omi.2010.0012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sang Wun Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Sunghoon Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Ji Nam
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Yong Wook Jeong
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - San Hui Lee
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Heum Paek
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Hoon Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Wook Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Kwandong University College of Medicine, Kyunggi-do, Korea
| | - Young Tae Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
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Recognition of potential predictive markers for diagnosis in Korean serous ovarian cancer patients at stage IIIc using array comparative genomic hybridization with high resolution. Mol Cell Toxicol 2011. [DOI: 10.1007/s13273-011-0011-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Seo HW, Choi JW, Yun TW, Lee HJ, Kim HS, Song YS, Song GH, Han JY. Large-Scale Copy-Number Alterations in Chicken Ovarian Cancer. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2010. [DOI: 10.5187/jast.2010.52.6.491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Li C, Xin W, Sy MS. Binding of pro-prion to filamin A: by design or an unfortunate blunder. Oncogene 2010; 29:5329-45. [PMID: 20697352 DOI: 10.1038/onc.2010.307] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the last decades, cancer research has focused on tumor suppressor genes and oncogenes. Genes in other cellular pathways has received less attention. Between 0.5% to 1% of the mammalian genome encodes for proteins that are tethered on the cell membrane via a glycosylphosphatidylinositol (GPI)-anchor. The GPI modification pathway is complex and not completely understood. Prion (PrP), a GPI-anchored protein, is infamous for being the only normal protein that when misfolded can cause and transmit a deadly disease. Though widely expressed and highly conserved, little is known about the functions of PrP. Pancreatic cancer and melanoma cell lines express PrP. However, in these cell lines the PrP exists as a pro-PrP as defined by retaining its GPI anchor peptide signal sequence (GPI-PSS). Unexpectedly, the GPI-PSS of PrP has a filamin A (FLNA) binding motif and binds FLNA. FLNA is a cytolinker protein, and an integrator of cell mechanics and signaling. Binding of pro-PrP to FLNA disrupts the normal FLNA functions. Although normal pancreatic ductal cells lack PrP, about 40% of patients with pancreatic ductal cell adenocarcinoma express PrP in their cancers. These patients have significantly shorter survival time compared with patients whose cancers lack PrP. Pro-PrP is also detected in melanoma in situ but is undetectable in normal melanocyte, and invasive melanoma expresses more pro-PrP. In this review, we will discuss the underlying mechanisms by which binding of pro-PrP to FLNA disrupts normal cellular physiology and contributes to tumorigenesis, and the potential mechanisms that cause the accumulation of pro-PrP in cancer cells.
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Affiliation(s)
- C Li
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-7288, USA
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He L, Ingram A, Rybak AP, Tang D. Shank-interacting protein-like 1 promotes tumorigenesis via PTEN inhibition in human tumor cells. J Clin Invest 2010; 120:2094-108. [PMID: 20458142 DOI: 10.1172/jci40778] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 03/17/2010] [Indexed: 01/26/2023] Open
Abstract
Inactivation of phosphatase and tensin homolog (PTEN) is a critical step during tumorigenesis, and PTEN inactivation by genetic and epigenetic means has been well studied. There is also evidence suggesting that PTEN negative regulators (PTEN-NRs) have a role in PTEN inactivation during tumorigenesis, but their identity has remained elusive. Here we have identified shank-interacting protein-like 1 (SIPL1) as a PTEN-NR in human tumor cell lines and human primary cervical cancer cells. Ectopic SIPL1 expression protected human U87 glioma cells from PTEN-mediated growth inhibition and promoted the formation of HeLa cell-derived xenograft tumors in immunocompromised mice. Conversely, siRNA-mediated knockdown of SIPL1 expression inhibited the growth of both HeLa cells and DU145 human prostate carcinoma cells in vitro and in vivo in a xenograft tumor model. These inhibitions were reversed by concomitant knockdown of PTEN, demonstrating that SIPL1 affects tumorigenesis via inhibition of PTEN function. Mechanistically, SIPL1 was found to interact with PTEN through its ubiquitin-like domain (UBL), inhibiting the phosphatidylinositol 3,4,5-trisphosphate (PIP3) phosphatase activity of PTEN. Furthermore, SIPL1 expression correlated with loss of PTEN function in PTEN-positive human primary cervical cancer tissue. Taken together, these observations indicate that SIPL1 is a PTEN-NR and that it facilitates tumorigenesis, at least in part, through its PTEN inhibitory function.
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Affiliation(s)
- Lizhi He
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
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Sung JS, Park KH, Kim YH. Genomic alterations of chromosome region 11p as predictive marker by array comparative genomic hybridization in lung adenocarcinoma patients. ACTA ACUST UNITED AC 2010; 198:27-34. [PMID: 20303011 DOI: 10.1016/j.cancergencyto.2009.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 11/10/2009] [Accepted: 12/05/2009] [Indexed: 10/19/2022]
Abstract
Array comparative genomic hybridization (aCGH) provides a method to quantitatively measure the changes of DNA copy number with an extremely high resolution and to map them directly onto the complete linear genome sequences. In this study, we used aCGH to compare genomic alterations in fresh-frozen lung cancer tissues of 21 adenocarcinomas (AdCCs) (11 early relapse and 10 nonrelapse) and identified genomic alterations that showed significant by different frequency between early relapse and nonrelapse AdCCs. Twelve clones were identified by the false discovery rate (FDR) test, and Kaplan-Meier analyses were selected as predictive markers. The significant gain clones were found in 11p (11p15.4, 11p15.1, and 11p13). When the cutoff value was 2, study of the association between candidate clones and relapse prediction revealed that early relapse and nonrelapse groups were most effectively separated. To further validate the gain of chromosome 11p region that was identified by array CGH, fluorescence in situ hybridization (FISH) was performed. To further confirm the results of aCGH, copy number changes of cancer-related candidate genes in AdCC patients were compared by real-time quantitative polymerase chain reaction. Array CGH and real-time quantitative polymerase chain reaction data were found to correspond to delineated DNA copy number changes. Genomic alterations of chromosome 11p region in AdCC patients were observed with aCGH, and a relapsable marker was identified in the nonrelapse group. This marker could be useful in stratifying patient groups according to likelihood of relapse for adjuvant treatment after surgical resection.
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Affiliation(s)
- Jae Sook Sung
- Genomic Research Center for Lung and Breast/Ovarian Cancers, Korea University Anam Hospital, Seongbuk-gu, Seoul, Republic of Korea
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Ding J, Huang S, Wu S, Zhao Y, Liang L, Yan M, Ge C, Yao J, Chen T, Wan D, Wang H, Gu J, Yao M, Li J, Tu H, He X. Gain of miR-151 on chromosome 8q24.3 facilitates tumour cell migration and spreading through downregulating RhoGDIA. Nat Cell Biol 2010; 12:390-9. [PMID: 20305651 DOI: 10.1038/ncb2039] [Citation(s) in RCA: 258] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 03/01/2010] [Indexed: 02/07/2023]
Abstract
Recurrent chromosomal aberrations are often observed in hepatocellular carcinoma (HCC), but little is known about the functional non-coding sequences, particularly microRNAs (miRNAs), at the chromosomal breakpoints in HCC. Here we show that 22 miRNAs are often amplified or deleted in HCC. MicroRNA-151 (miR-151), a frequently amplified miRNA on 8q24.3, is correlated with intrahepatic metastasis of HCC. We further show that miR-151, which is often expressed together with its host gene FAK, encoding focal adhesion kinase, significantly increases HCC cell migration and invasion in vitro and in vivo, mainly through miR-151-5p, but not through miR-151-3p. Moreover, miR-151 exerts this function by directly targeting RhoGDIA, a putative metastasis suppressor in HCC, thus leading to the activation of Rac1, Cdc42 and Rho GTPases. In addition, miR-151 can function synergistically with FAK to enhance HCC cell motility and spreading. Thus, our findings indicate that chromosome gain of miR-151 is a crucial stimulus for tumour invasion and metastasis of HCC.
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Affiliation(s)
- Jie Ding
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
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Huang J, Zheng DL, Qin FS, Cheng N, Chen H, Wan BB, Wang YP, Xiao HS, Han ZG. Genetic and epigenetic silencing of SCARA5 may contribute to human hepatocellular carcinoma by activating FAK signaling. J Clin Invest 2009; 120:223-41. [PMID: 20038795 DOI: 10.1172/jci38012] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 10/14/2009] [Indexed: 01/16/2023] Open
Abstract
The epigenetic silencing of tumor suppressor genes is a crucial event during carcinogenesis and metastasis. Here, in a human genome-wide survey, we identified scavenger receptor class A, member 5 (SCARA5) as a candidate tumor suppressor gene located on chromosome 8p. We found that SCARA5 expression was frequently downregulated as a result of promoter hypermethylation and allelic imbalance and was associated with vascular invasion in human hepatocellular carcinoma (HCC). Furthermore, SCARA5 knockdown via RNAi markedly enhanced HCC cell growth in vitro, colony formation in soft agar, and invasiveness, tumorigenicity, and lung metastasis in vivo. By contrast, SCARA5 overexpression suppressed these malignant behaviors. Interestingly, SCARA5 was found to physically associate with focal adhesion kinase (FAK) and inhibit the tyrosine phosphorylation cascade of the FAK-Src-Cas signaling pathway. Conversely, silencing SCARA5 stimulated the signaling pathway via increased phosphorylation of certain tyrosine residues of FAK, Src, and p130Cas; it was also associated with activation of MMP9, a tumor metastasis-associated enzyme. Taken together, these data suggest that the plasma membrane protein SCARA5 can contribute to HCC tumorigenesis and metastasis via activation of the FAK signaling pathway.
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Affiliation(s)
- Jian Huang
- National Human Genome Center, Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, 351 Guo Shou-Jing Road, Shanghai, People's Republic of China
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Österberg L, Levan K, Partheen K, Delle U, Olsson B, Sundfeldt K, Horvath G. Potential predictive markers of chemotherapy resistance in stage III ovarian serous carcinomas. BMC Cancer 2009; 9:368. [PMID: 19835627 PMCID: PMC2770569 DOI: 10.1186/1471-2407-9-368] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 10/18/2009] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Chemotherapy resistance remains a major obstacle in the treatment of women with ovarian cancer. Establishing predictive markers of chemoresponse would help to individualize therapy and improve survival of ovarian cancer patients. Chemotherapy resistance in ovarian cancer has been studied thoroughly and several non-overlapping single genes, gene profiles and copy number alterations have been suggested as potential markers. The objective of this study was to explore genetic alterations behind chemotherapy resistance in ovarian cancer with the ultimate aim to find potential predictive markers. METHODS To create the best opportunities for identifying genetic alterations of importance for resistance, we selected a homogenous tumor material concerning histology, stage and chemotherapy. Using high-resolution whole genome array comparative genomic hybridization (CGH), we analyzed the tumor genomes of 40 fresh-frozen stage III ovarian serous carcinomas, all uniformly treated with combination therapy paclitaxel/carboplatin. Fisher's exact test was used to identify significant differences. Subsequently, we examined four genes in the significant regions (EVI1, MDS1, SH3GL2, SH3KBP1) plus the ABCB1 gene with quantitative real-time polymerase chain reaction (QPCR) to evaluate the impact of DNA alterations on the transcriptional level. RESULTS We identified gain in 3q26.2, and losses in 6q11.2-12, 9p22.3, 9p22.2-22.1, 9p22.1-21.3, Xp22.2-22.12, Xp22.11-11.3, and Xp11.23-11.1 to be significantly associated with chemotherapy resistance. In the gene expression analysis, EVI1 expression differed between samples with gain versus without gain, exhibiting higher expression in the gain group. CONCLUSION In conclusion, we detected specific genetic alterations associated with resistance, of which some might be potential predictive markers of chemotherapy resistance in advanced ovarian serous carcinomas. Thus, further studies are required to validate these findings in an independent ovarian tumor series.
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Affiliation(s)
- Lovisa Österberg
- Department of Oncology, Institute of Clinical Sciences, University of Gothenburg, Sweden
| | - Kristina Levan
- Department of Oncology, Institute of Clinical Sciences, University of Gothenburg, Sweden
| | - Karolina Partheen
- Department of Oncology, Institute of Clinical Sciences, University of Gothenburg, Sweden
| | - Ulla Delle
- Department of Oncology, Institute of Clinical Sciences, University of Gothenburg, Sweden
| | - Björn Olsson
- School of Life Sciences, University College of Skövde, Sweden
| | - Karin Sundfeldt
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, University of Gothenburg, Sweden
| | - György Horvath
- Department of Oncology, Institute of Clinical Sciences, University of Gothenburg, Sweden
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Dykxhoorn DM, Wu Y, Xie H, Yu F, Lal A, Petrocca F, Martinvalet D, Song E, Lim B, Lieberman J. miR-200 enhances mouse breast cancer cell colonization to form distant metastases. PLoS One 2009; 4:e7181. [PMID: 19787069 PMCID: PMC2749331 DOI: 10.1371/journal.pone.0007181] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/05/2009] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The development of metastases involves the dissociation of cells from the primary tumor to penetrate the basement membrane, invade and then exit the vasculature to seed, and colonize distant tissues. The last step, establishment of macroscopic tumors at distant sites, is the least well understood. Four isogenic mouse breast cancer cell lines (67NR, 168FARN, 4TO7, and 4T1) that differ in their ability to metastasize when implanted into the mammary fat pad are used to model the steps of metastasis. Only 4T1 forms macroscopic lung and liver metastases. Because some miRNAs are dysregulated in cancer and affect cellular transformation, tumor formation, and metastasis, we examined whether changes in miRNA expression might explain the differences in metastasis of these cells. METHODOLOGY/PRINCIPAL FINDINGS miRNA expression was analyzed by miRNA microarray and quantitative RT-PCR in isogenic mouse breast cancer cells with distinct metastatic capabilities. 4T1 cells that form macroscopic metastases had elevated expression of miR-200 family miRNAs compared to related cells that invade distant tissues, but are unable to colonize. Moreover, over-expressing miR-200 in 4TO7 cells enabled them to metastasize to lung and liver. These findings are surprising since the miR-200 family was previously shown to promote epithelial characteristics by inhibiting the transcriptional repressor Zeb2 and thereby enhancing E-cadherin expression. We confirmed these findings in these cells. The most metastatic 4T1 cells acquired epithelial properties (high expression of E-cadherin and cytokeratin-18) compared to the less metastatic cells. CONCLUSIONS/SIGNIFICANCE Expression of miR-200, which promotes a mesenchymal to epithelial cell transition (MET) by inhibiting Zeb2 expression, unexpectedly enhances macroscopic metastases in mouse breast cancer cell lines. These results suggest that for some tumors, tumor colonization at metastatic sites might be enhanced by MET. Therefore the epithelial nature of a tumor does not predict metastatic outcome.
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Affiliation(s)
- Derek M. Dykxhoorn
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- The John T. Macdonald Foundation of Human Genetics and the Department of Microbiology and Immunology, Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail: (JL); (DMD)
| | - Yichao Wu
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huangming Xie
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Fengyan Yu
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Breast Surgery, No. 2 Affiliated Hospital, Sun-Yat-Sen University, Guangzhou, People's Republic of China
| | - Ashish Lal
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Fabio Petrocca
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Denis Martinvalet
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erwei Song
- Department of Breast Surgery, No. 2 Affiliated Hospital, Sun-Yat-Sen University, Guangzhou, People's Republic of China
| | - Bing Lim
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Judy Lieberman
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JL); (DMD)
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Haverty PM, Hon LS, Kaminker JS, Chant J, Zhang Z. High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Med Genomics 2009; 2:21. [PMID: 19419571 PMCID: PMC2694826 DOI: 10.1186/1755-8794-2-21] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 05/06/2009] [Indexed: 02/06/2023] Open
Abstract
Background DNA copy number alterations are frequently observed in ovarian cancer, but it remains a challenge to identify the most relevant alterations and the specific causal genes in those regions. Methods We obtained high-resolution 500K SNP array data for 52 ovarian tumors and identified the most statistically significant minimal genomic regions with the most prevalent and highest-level copy number alterations (recurrent CNAs). Within a region of recurrent CNA, comparison of expression levels in tumors with a given CNA to tumors lacking that CNA and to whole normal ovary samples was used to select genes with CNA-specific expression patterns. A public expression array data set of laser capture micro-dissected (LCM) non-malignant fallopian tube epithelia and LCM ovarian serous adenocarcinoma was used to evaluate the effect of cell-type mixture biases. Results Fourteen recurrent deletions were detected on chromosomes 4, 6, 9, 12, 13, 15, 16, 17, 18, 22 and most prevalently on X and 8. Copy number and expression data suggest several apoptosis mediators as candidate drivers of the 8p deletions. Sixteen recurrent gains were identified on chromosomes 1, 2, 3, 5, 8, 10, 12, 15, 17, 19, and 20, with the most prevalent gains localized to 8q and 3q. Within the 8q amplicon, PVT1, but not MYC, was strongly over-expressed relative to tumors lacking this CNA and showed over-expression relative to normal ovary. Likewise, the cell polarity regulators PRKCI and ECT2 were identified as putative drivers of two distinct amplicons on 3q. Co-occurrence analyses suggested potential synergistic or antagonistic relationships between recurrent CNAs. Genes within regions of recurrent CNA showed an enrichment of Cancer Census genes, particularly when filtered for CNA-specific expression. Conclusion These analyses provide detailed views of ovarian cancer genomic changes and highlight the benefits of using multiple reference sample types for the evaluation of CNA-specific expression changes.
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Affiliation(s)
- Peter M Haverty
- Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA.
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