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Taluri S, Oza VH, Soelter TM, Fisher JL, Lasseigne BN. Inferring chromosomal instability from copy number aberrations as a measure of chromosomal instability across human cancers. Cancer Rep (Hoboken) 2023; 6:e1902. [PMID: 37680168 PMCID: PMC10728508 DOI: 10.1002/cnr2.1902] [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: 05/25/2023] [Revised: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Cancer is a complex disease that is the second leading cause of death in the United States. Despite research efforts, the ability to manage cancer and select optimal therapeutic responses for each patient remains elusive. Chromosomal instability (CIN) is primarily a product of segregation errors wherein one or many chromosomes, in part or whole, vary in number. CIN is an enabling characteristic of cancer, contributes to tumor-cell heterogeneity, and plays a crucial role in the multistep tumorigenesis process, especially in tumor growth and initiation and in response to treatment. AIMS Multiple studies have reported different metrics for analyzing copy number aberrations as surrogates of CIN from DNA copy number variation data. However, these metrics differ in how they are calculated with respect to the type of variation, the magnitude of change, and the inclusion of breakpoints. Here we compared metrics capturing CIN as either numerical aberrations, structural aberrations, or a combination of the two across 33 cancer data sets from The Cancer Genome Atlas (TCGA). METHODS AND RESULTS Using CIN inferred by methods in the CINmetrics R package, we evaluated how six copy number CIN surrogates compared across TCGA cohorts by assessing each across tumor types, as well as how they associate with tumor stage, metastasis, and nodal involvement, and with respect to patient sex. CONCLUSIONS We found that the tumor type impacts how well any two given CIN metrics correlate. While we also identified overlap between metrics regarding their association with clinical characteristics and patient sex, there was not complete agreement between metrics. We identified several cases where only one CIN metric was significantly associated with a clinical characteristic or patient sex for a given tumor type. Therefore, caution should be used when describing CIN based on a given metric or comparing it to other studies.
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Affiliation(s)
- Sasha Taluri
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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Namløs HM, Khelik K, Nakken S, Vodák D, Hovig E, Myklebost O, Boye K, Meza‐Zepeda LA. Chromosomal instability and a deregulated cell cycle are intrinsic features of high-risk gastrointestinal stromal tumours with a metastatic potential. Mol Oncol 2023; 17:2432-2450. [PMID: 37622176 PMCID: PMC10620130 DOI: 10.1002/1878-0261.13514] [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: 02/28/2023] [Revised: 06/22/2023] [Accepted: 08/23/2023] [Indexed: 08/26/2023] Open
Abstract
Patients with localised, high-risk gastrointestinal stromal tumours (GIST) benefit from adjuvant imatinib treatment. Still, approximately 40% of patients relapse within 3 years after adjuvant therapy and the clinical and histopathological features currently used for risk classification cannot precisely predict poor outcomes after standard treatment. This study aimed to identify genomic and transcriptomic profiles that could be associated with disease relapse and thus a more aggressive phenotype. Using a multi-omics approach, we analysed a cohort of primary tumours from patients with untreated, resectable high-risk GISTs. We compared patients who developed metastatic disease within 3 years after finishing adjuvant imatinib treatment and patients without disease relapse after more than 5 years of follow-up. Combining genomics and transcriptomics data, we identified somatic mutations and deregulated mRNA and miRNA genes intrinsic to each group. Our study shows that increased chromosomal instability (CIN), including chromothripsis and deregulated kinetochore and cell cycle signalling, separates high-risk samples according to metastatic potential. The increased CIN seems to be an intrinsic feature for tumours that metastasise and should be further validated as a novel prognostic biomarker for high-risk GIST.
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Affiliation(s)
- Heidi Maria Namløs
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
| | - Ksenia Khelik
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, Institute of Clinical MedicineUniversity of OsloOsloNorway
- Department of InformaticsUniversity of OsloOsloNorway
| | - Daniel Vodák
- Bioinformatics Core Facility, Department of Core Facilities, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
- Department of InformaticsUniversity of OsloOsloNorway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
- Department for Clinical ScienceUniversity of BergenBergenNorway
| | - Kjetil Boye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
- Department of OncologyOslo University HospitalOsloNorway
| | - Leonardo A. Meza‐Zepeda
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalOsloNorway
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer ResearchOslo University HospitalOsloNorway
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3
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Taluri S, Oza VH, Soelter TM, Fisher JL, Lasseigne BN. Inferring chromosomal instability from copy number aberrations as a measure of chromosomal instability across human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542174. [PMID: 37292608 PMCID: PMC10245901 DOI: 10.1101/2023.05.24.542174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Cancer is a complex disease that is the second leading cause of death in the United States. Despite research efforts, the ability to manage cancer and select optimal therapeutic responses for each patient remains elusive. Chromosomal instability (CIN) is primarily a product of segregation errors wherein one or many chromosomes, in part or whole, vary in number. CIN is an enabling characteristic of cancer, contributes to tumor-cell heterogeneity, and plays a crucial role in the multistep tumorigenesis process, especially in tumor growth and initiation and in response to treatment. Aims Multiple studies have reported different metrics for analyzing copy number aberrations as surrogates of CIN from DNA copy number variation data. However, these metrics differ in how they are calculated with respect to the type of variation, the magnitude of change, and the inclusion of breakpoints. Here we compared metrics capturing CIN as either numerical aberrations, structural aberrations, or a combination of the two across 33 cancer data sets from The Cancer Genome Atlas (TCGA). Methods and results Using CIN inferred by methods in the CINmetrics R package, we evaluated how six copy number CIN surrogates compared across TCGA cohorts by assessing each across tumor types, as well as how they associate with tumor stage, metastasis, and nodal involvement, and with respect to patient sex. Conclusions We found that the tumor type impacts how well any two given CIN metrics correlate. While we also identified overlap between metrics regarding their association with clinical characteristics and patient sex, there was not complete agreement between metrics. We identified several cases where only one CIN metric was significantly associated with a clinical characteristic or patient sex for a given tumor type. Therefore, caution should be used when describing CIN based on a given metric or comparing it to other studies.
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Affiliation(s)
- Sasha Taluri
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Wu X, Yan H, Qiu M, Qu X, Wang J, Xu S, Zheng Y, Ge M, Yan L, Liang L. Comprehensive characterization of tumor microenvironment in colorectal cancer via molecular analysis. eLife 2023; 12:e86032. [PMID: 37267125 PMCID: PMC10238095 DOI: 10.7554/elife.86032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/10/2023] [Indexed: 06/04/2023] Open
Abstract
Colorectal cancer (CRC) remains a challenging and deadly disease with high tumor microenvironment (TME) heterogeneity. Using an integrative multi-omics analysis and artificial intelligence-enabled spatial analysis of whole-slide images, we performed a comprehensive characterization of TME in colorectal cancer (CCCRC). CRC samples were classified into four CCCRC subtypes with distinct TME features, namely, C1 as the proliferative subtype with low immunogenicity; C2 as the immunosuppressed subtype with the terminally exhausted immune characteristics; C3 as the immune-excluded subtype with the distinct upregulation of stromal components and a lack of T cell infiltration in the tumor core; and C4 as the immunomodulatory subtype with the remarkable upregulation of anti-tumor immune components. The four CCCRC subtypes had distinct histopathologic and molecular characteristics, therapeutic efficacy, and prognosis. We found that the C1 subtype may be suitable for chemotherapy and cetuximab, the C2 subtype may benefit from a combination of chemotherapy and bevacizumab, the C3 subtype has increased sensitivity to the WNT pathway inhibitor WIKI4, and the C4 subtype is a potential candidate for immune checkpoint blockade treatment. Importantly, we established a simple gene classifier for accurate identification of each CCCRC subtype. Collectively our integrative analysis ultimately established a holistic framework to thoroughly dissect the TME of CRC, and the CCCRC classification system with high biological interpretability may contribute to biomarker discovery and future clinical trial design.
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Affiliation(s)
- Xiangkun Wu
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Hong Yan
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefeiChina
| | - Mingxing Qiu
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Xiaoping Qu
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Jing Wang
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Shaowan Xu
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Yiran Zheng
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Minghui Ge
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Linlin Yan
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Li Liang
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Jinfeng LaboratoryChongqingChina
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Oza VH, Fisher JL, Darji R, Lasseigne BN. CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability. PeerJ 2023; 11:e15244. [PMID: 37123011 PMCID: PMC10143595 DOI: 10.7717/peerj.15244] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.
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Affiliation(s)
- Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL, United States of America
| | - Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL, United States of America
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL, United States of America
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6
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Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome. Sci Rep 2021; 11:23429. [PMID: 34873180 PMCID: PMC8648741 DOI: 10.1038/s41598-021-02787-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022] Open
Abstract
Genomic instability (GI) influences treatment efficacy and resistance, and an accurate measure of it is lacking. Current measures of GI are based on counts of specific structural variation (SV) and mutational signatures. Here, we present a holistic approach to measuring GI based on the quantification of the steady-state equilibrium between DNA damage and repair as assessed by the residual breakpoints (BP) remaining after repair, irrespective of SV type. We use the notion of Hscore, a BP "hotspotness" magnitude scale, to measure the propensity of genomic structural or functional DNA elements to break more than expected by chance. We then derived new measures of transcription- and replication-associated GI that we call iTRAC (transcription-associated chromosomal instability index) and iRACIN (replication-associated chromosomal instability index). We show that iTRAC and iRACIN are predictive of metastatic relapse in Leiomyosarcoma (LMS) and that they may be combined to form a new classifier called MAGIC (mixed transcription- and replication-associated genomic instability classifier). MAGIC outperforms the gold standards FNCLCC and CINSARC in stratifying metastatic risk in LMS. Furthermore, iTRAC stratifies chemotherapeutic response in LMS. We finally show that this approach is applicable to other cancers.
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Tuna M, Ju Z, Yoshihara K, Amos CI, Tanyi JL, Mills GB. Clinical relevance of TP53 hotspot mutations in high-grade serous ovarian cancers. Br J Cancer 2019; 122:405-412. [PMID: 31780779 PMCID: PMC7000721 DOI: 10.1038/s41416-019-0654-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/28/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
Background Mutation of TP53 is the most frequent genetic alteration in high-grade serous ovarian cancer (HGSOC). The impact of hotspot mutations of TP53 and protein levels on patient outcomes in HGSOC has not been fully elucidated. Methods The study population (n = 791) comprised of HGSOC samples with TP53 mutation from TCGA and other publicly available data. Univariate and multivariate cox proportional hazards regression analyses were used to select variables that were correlated with patient survival. Results We assessed the effects of TP53 mutations based on type and individual hotspot mutations on patient outcomes in HGSOC. Only hotspot mutations were associated with outcomes. Three hotspot mutations: G266, Y163C, and R282, in aggregate were associated with a worsened overall and recurrence-free survival compared with other hotspot mutations (p < 0.0001 and p = 0.001), other non-hotspot missense mutations (p < 0.0001 and p = 0.008), truncated mutations (p < 0.0001 and p = 0.001), and all other mutations (p < 0.0001 and p = 0.001). Specific hotspot mutations were associated with different protein expression patterns consistent with different functions. Conclusions This study provides evidence that individual TP53 hotspot mutations have different impact on HGSOC patient outcomes and potentially TP53 function. Thus the status of particular TP53 aberrations could influence response to therapy and selection of therapeutic agents.
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Affiliation(s)
- Musaffe Tuna
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Precision Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University, Niigata, Japan
| | | | - Janos L Tanyi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gordon B Mills
- Precision Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
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8
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Raab M, Sanhaji M, Zhou S, Rödel F, El-Balat A, Becker S, Strebhardt K. Blocking Mitotic Exit of Ovarian Cancer Cells by Pharmaceutical Inhibition of the Anaphase-Promoting Complex Reduces Chromosomal Instability. Neoplasia 2019; 21:363-375. [PMID: 30851646 PMCID: PMC6407080 DOI: 10.1016/j.neo.2019.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/29/2019] [Indexed: 01/28/2023]
Abstract
Paclitaxel is a frontline drug for the treatment of epithelial ovarian cancer (EOC). However, following paclitaxel-platinum based chemotherapy, tumor recurrence occurs in most ovarian cancer patients. Chromosomal instability (CIN) is a hallmark of cancer and represents genetic variation fueling tumor adaptation to cytotoxic effects of anticancer drugs. In this study, our Kaplan-Meier analysis including 263 ovarian cancer patients (stages I/II) revealed that high Polo-like kinase (PLK) 1 expression correlates with bad prognosis. To evaluate the role of PLK1 as potential cancer target within a combinatorial trial, we induced strong mitotic arrest in ovarian cancer cell lines by synergistically co-targeting microtubules (paclitaxel) and PLK1 (BI6727) followed by pharmaceutical inhibition of the Anaphase-Promoting Complex (APC/C) using proTAME. In short- and long-term experiments, this triple treatment strongly activated apoptosis in cell lines and primary ovarian cells derived from cancer patients. Mechanistically, BI6727/paclitaxel/proTAME stabilize Cyclin B1 and trigger mitotic arrest, which initiates mitochondrial apoptosis by inactivation of antiapoptotic BCL-2 family proteins, followed by activation of caspase-dependent effector pathways. This triple treatment prevented endoreduplication and reduced CIN, two mechanisms that are associated with aggressive tumors and the acquisition of drug resistance. This "two-punch strategy" (strong mitotic arrest followed by blocking mitotic exit) has important implications for developing paclitaxel-based combinatorial treatments in ovarian cancer.
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Affiliation(s)
- Monika Raab
- Department of Gynecology, Goethe-University, Frankfurt am Main
| | - Mourad Sanhaji
- Department of Gynecology, Goethe-University, Frankfurt am Main
| | - Shengtao Zhou
- State Key Laboratory of Biotherapy, Department of Obstetrics and Gynecology, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe University; German Cancer Consortium (DKTK) / German Cancer Research Center, partner site, Frankfurt a. M
| | - Ahmed El-Balat
- Department of Gynecology, Goethe-University, Frankfurt am Main
| | - Sven Becker
- Department of Gynecology, Goethe-University, Frankfurt am Main
| | - Klaus Strebhardt
- Department of Gynecology, Goethe-University, Frankfurt am Main; German Cancer Consortium (DKTK) / German Cancer Research Center, partner site, Frankfurt a. M..
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9
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The expression of miRNAs is associated with tumour genome instability and predicts the outcome of ovarian cancer patients treated with platinum agents. Sci Rep 2017; 7:14736. [PMID: 29116111 PMCID: PMC5677022 DOI: 10.1038/s41598-017-12259-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
miRNAs, a class of short but stable noncoding RNA molecules, have been revealed to play important roles in the DNA damage response (DDR). However, their functions in cancer genome instability and the consequent clinical effect as the response to chemotherapy have not been fully elucidated. In this study, we utilized multidimensional TCGA data and the known miRNAs involved in DDR to identify a miRNA-regulatory network that responds to DNA damage. Additionally, based on the expression of ten miRNAs in this network, we developed a 10-miRNA-score that predicts defects in the homologous recombination (HR) pathway and genome instability in ovarian cancer. Importantly, consistent with the association between HR defects and improved response to chemotherapeutic agents, the 10-miRNA-score predicts the outcome of ovarian cancer patients treated with platinum agents, with a surprisingly better performance than the indexes of DNA damage. Therefore, our study demonstrates the implication of miRNA expression on cancer genome instability and provides an alternative method to identify DDR defects in patients who show the best effect with platinum drug treatment.
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10
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Penner-Goeke S, Lichtensztejn Z, Neufeld M, Ali JL, Altman AD, Nachtigal MW, McManus KJ. The temporal dynamics of chromosome instability in ovarian cancer cell lines and primary patient samples. PLoS Genet 2017; 13:e1006707. [PMID: 28376088 PMCID: PMC5395197 DOI: 10.1371/journal.pgen.1006707] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 04/18/2017] [Accepted: 03/20/2017] [Indexed: 01/12/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the most prevalent form of ovarian cancer and has the highest mortality rate. Novel insight into EOC is required to minimize the morbidity and mortality rates caused by recurrent, drug resistant disease. Although numerous studies have evaluated genome instability in EOC, none have addressed the putative role chromosome instability (CIN) has in disease progression and drug resistance. CIN is defined as an increase in the rate at which whole chromosomes or large parts thereof are gained or lost, and can only be evaluated using approaches capable of characterizing genetic or chromosomal heterogeneity within populations of cells. Although CIN is associated with numerous cancer types, its prevalence and dynamics in EOC is unknown. In this study, we assessed CIN within serial samples collected from the ascites of five EOC patients, and in two well-established ovarian cancer cell models of drug resistance (PEO1/4 and A2780s/cp). We quantified and compared CIN (as measured by nuclear areas and CIN Score (CS) values) within and between serial samples to glean insight into the association and dynamics of CIN within EOC, with a particular focus on resistant and recurrent disease. Using quantitative, single cell analyses we determined that CIN is associated with every sample evaluated and further show that many EOC samples exhibit a large degree of nuclear size and CS value heterogeneity. We also show that CIN is dynamic and generally increases within resistant disease. Finally, we show that both drug resistance models (PEO1/4 and A2780s/cp) exhibit heterogeneity, albeit to a much lesser extent. Surprisingly, the two cell line models exhibit remarkably similar levels of CIN, as the nuclear areas and CS values are largely overlapping between the corresponding paired lines. Accordingly, these data suggest CIN may represent a novel biomarker capable of monitoring changes in EOC progression associated with drug resistance.
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Affiliation(s)
- Signe Penner-Goeke
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Zelda Lichtensztejn
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Megan Neufeld
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Jennifer L. Ali
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Alon D. Altman
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark W. Nachtigal
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
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11
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Salomon-Perzyński A, Salomon-Perzyńska M, Michalski B, Skrzypulec-Plinta V. High-grade serous ovarian cancer: the clone wars. Arch Gynecol Obstet 2017; 295:569-576. [PMID: 28154920 PMCID: PMC5315707 DOI: 10.1007/s00404-017-4292-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND The last 5 years' studies using next-generation sequencing provided evidences that many types of solid tumors present spatial and temporal genetic heterogeneity and are composed of multiple populations of genetically distinct subclones that evolve over time following a pattern of branched evolution. The evolutionary nature of cancer has been proposed as the major contributor to drug resistance and treatment failure. In this review, we present the current state of knowledge about the clonal evolution of high-grade serous ovarian cancer and discuss the challenge that clonal evolution poses for efforts to achieve an optimal cancer control. METHODS A systemic search of peer-reviewed articles published between August 2007 and October 2016 was performed using PUBMED and Google Scholar database. RESULTS AND CONCLUSIONS Recent studies using next-generation sequencing have allowed us to look inside the evolutionary nature of high-grade serous ovarian cancer, which in the light of current evidence can explain the relapsing course of the disease frequently observed in the clinical practice. Since only minimal improvement in the survival of patients treated with standard therapy has been observed in the last decade, novel molecular targeted therapies are of great interest in high-grade serous ovarian cancer. However, both spatial and temporal intratumoral genetic heterogeneity is a major challenge for personalized medicine, and greater knowledge of the molecular rules that drive tumor evolution through space and time is required to achieve a long-term clinical benefit from personalized therapy.
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Affiliation(s)
- Aleksander Salomon-Perzyński
- Department of Internal Medicine and Oncological Chemotherapy, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Magdalena Salomon-Perzyńska
- Department of Gynaecology Oncological, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland.
| | - Bogdan Michalski
- Department of Gynaecology Oncological, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland
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Cerrato A, Morra F, Celetti A. Use of poly ADP-ribose polymerase [PARP] inhibitors in cancer cells bearing DDR defects: the rationale for their inclusion in the clinic. J Exp Clin Cancer Res 2016; 35:179. [PMID: 27884198 PMCID: PMC5123312 DOI: 10.1186/s13046-016-0456-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/09/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA damage response (DDR) defects imply genomic instability and favor tumor progression but make the cells vulnerable to the pharmacological inhibition of the DNA repairing enzymes. Targeting cellular proteins like PARPs, which cooperate and complement molecular defects of the DDR process, induces a specific lethality in DDR defective cancer cells and represents an anti-cancer strategy. Normal cells can tolerate the DNA damage generated by PARP inhibition because of an efficient homologous recombination mechanism (HR); in contrast, cancer cells with a deficient HR are unable to manage the DSBs and appear especially sensitive to the PARP inhibitors (PARPi) effects. MAIN BODY In this review we discuss the proof of concept for the use of PARPi in different cancer types and the success and failure of their inclusion in clinical trials. The PARP inhibitor Olaparib [AZD2281] has been approved by the FDA for use in pretreated ovarian cancer patients with defective BRCA1/2 genes, and by the EMEA for maintenance therapy in platinum sensitive ovarian cancer patients with defective BRCA1/2 genes. BRCA mutations are now recognised as the molecular targets for PARPi sensitivity in several tumors. However, it is noteworthy that the use of PARPi has shown its efficacy also in non-BRCA related tumors. Several trials are ongoing to test different PARPi in different cancer types. Here we review the concept of BRCAness and the functional loss of proteins involved in DDR/HR mechanisms in cancer, including additional molecules that can influence the cancer cells sensitivity to PARPi. Given the complexity of the existing crosstalk between different DNA repair pathways, it is likely that a single biomarker may not be sufficient to predict the benefit of PARP inhibitors therapies. Novel general assays able to predict the DDR/HR proficiency in cancer cells and the PARPi sensitivity represent a challenge for a personalized therapy. CONCLUSIONS PARP inhibition is a potentially important strategy for managing a significant subset of tumors. The discovery of both germline and somatic DNA repair deficiencies in different cancer patients, together with the development of new PARP inhibitors that can kill selectively cancer cells is a potent example of targeting therapy to molecularly defined tumor subtypes.
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13
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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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14
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Galdiero F, Romano A, Pasquinelli R, Pignata S, Greggi S, Vuttariello E, Bello AM, Calise C, Scaffa C, Pisano C, Losito NS, Fusco A, Califano D, Chiappetta G. Detection of high mobility group A2 specific mRNA in the plasma of patients affected by epithelial ovarian cancer. Oncotarget 2016; 6:19328-35. [PMID: 25749380 PMCID: PMC4662494 DOI: 10.18632/oncotarget.2896] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer is the most lethal gynecological malignancy and the high mortality rate is associated with advanced-stage disease at the time of the diagnosis. In order to find new tools to make diagnosis of Epithelial Ovarian Cancer (EOC) at early stages we have analyzed the presence of specific HMGA2 mRNA in the plasma of patients affected by this neoplasm. HMGA2 overexpression represents a feature of several malignances including ovarian carcinomas. Notably, we detected HMGA2 specific mRNA in the plasma of 40 out 47 patients with EOC, but not in the plasma of healthy donors. All cases found positive for HMGA2 mRNA in the plasma showed HMGA2 protein expression in EOC tissues. Therefore, on the basis of these results, the analysis of circulating HMGA2 specific mRNA might be considered a very promising tool for the early diagnosis of EOC.
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Affiliation(s)
- Francesca Galdiero
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Annunciata Romano
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Rosa Pasquinelli
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Sandro Pignata
- Dipartimento di Oncologia Uroginecologica, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Stefano Greggi
- Dipartimento di Oncologia Uroginecologica, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Emilia Vuttariello
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Anna Maria Bello
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Celeste Calise
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Cono Scaffa
- Dipartimento di Oncologia Uroginecologica, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Carmela Pisano
- Dipartimento di Oncologia Uroginecologica, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Nunzia Simona Losito
- Anatomia Patologica, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Daniela Califano
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
| | - Gennaro Chiappetta
- Genomica Funzionale, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, Naples, Italy
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15
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Jamal-Hanjani M, A'Hern R, Birkbak NJ, Gorman P, Grönroos E, Ngang S, Nicola P, Rahman L, Thanopoulou E, Kelly G, Ellis P, Barrett-Lee P, Johnston SRD, Bliss J, Roylance R, Swanton C. Extreme chromosomal instability forecasts improved outcome in ER-negative breast cancer: a prospective validation cohort study from the TACT trial. Ann Oncol 2015; 26:1340-6. [PMID: 26003169 DOI: 10.1093/annonc/mdv178] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/28/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chromosomal instability (CIN) has been shown to be associated with drug resistance and poor clinical outcome in several cancer types. However, in oestrogen receptor (ER)-negative breast cancer we have previously demonstrated that extreme CIN is associated with improved clinical outcome, consistent with a negative impact of CIN on tumour fitness and growth. The aim of this current study was to validate this finding using previously defined CIN thresholds in a much larger prospective cohort from a randomised, controlled, clinical trial. PATIENTS AND METHODS As a surrogate measurement of CIN, dual centromeric fluorescence in situ hybridisation was performed for both chromosomes 2 and 15 on 1173 tumours from the breast cancer TACT trial (CRUK01/001). Each tumour was scored manually and the mean percentage of cells deviating from the modal centromere number was used to define four CIN groups (MCD1-4), where tumours in the MCD4 group were defined as having extreme CIN. RESULTS In a multivariate analysis of disease-free survival, with a median follow-up of 91 months, increasing CIN was associated with improved outcome in patients with ER-negative cancer (P trend = 0.03). A similar pattern was seen in ER-negative/HER2-negative cancers (Ptrend = 0.007). CONCLUSIONS This prospective validation cohort study further substantiated the association between extreme CIN and improved outcome in ER-negative breast cancers. Identifying such patients with extreme CIN may help distinguish good from poor prognostic groups, and therefore support treatment and risk stratification in this aggressive breast cancer subtype.
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Affiliation(s)
- M Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - R A'Hern
- ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London
| | - N J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - P Gorman
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - E Grönroos
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - S Ngang
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - P Nicola
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - L Rahman
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - E Thanopoulou
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - G Kelly
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - P Ellis
- Guy's and St Thomas' NHS Trust, London
| | | | | | - J Bliss
- ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London
| | - R Roylance
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - C Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London The Francis Crick Institute, 44 Lincoln's Inn Fields, London
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16
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Zhang S, Yuan Y, Hao D. A genomic instability score in discriminating nonequivalent outcomes of BRCA1/2 mutations and in predicting outcomes of ovarian cancer treated with platinum-based chemotherapy. PLoS One 2014; 9:e113169. [PMID: 25437005 PMCID: PMC4249855 DOI: 10.1371/journal.pone.0113169] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 10/24/2014] [Indexed: 12/15/2022] Open
Abstract
Detecting mutation in BRCA1/2 is a generally accepted strategy for screening ovarian cancers that have impaired homologous recombination (HR) ability and improved sensitivity to PARP inhibitor. However, a substantial subset of BRCA-mutant ovarian cancer patients shows less impaired or unimpaired HR ability, resulting in nonequivalent outcome after ovarian cancer development. We hypothesize that genomic instability provides a lifetime record of DNA repair deficiency and predicts ovarian cancer outcome. Based on the multi-dimensional TCGA ovarian cancer data, we developed a biological rationale-driven genomic instability score integrating somatic mutation and copy number change in a tumor genome. The score successfully divided BRCA-mutant ovarian tumors into cases of significantly improved outcome and cases of unimproved outcome. The score was also capable of discriminating HR-deficiency indicated by BRCA1 epigenetically silencing, EMSY amplification and homozygous deletion of core HR genes. We further found that the score was positively correlated with the complete response rate of chemotherapy and the rate of platinum-sensitivity, and predicted improved outcome of ovarian cancer, regardless of BRCA-mutation status. The score may have important value in outcome prediction and clinical trial design.
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Affiliation(s)
- Shaojun Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P.R. China
| | - Yuan Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P.R. China; Department of Gynecology and Obstetrics, The Forth Affiliated Hospital of Harbin Medical University, Department of Gynecology and Obstetrics, Harbin 150081, P.R. China
| | - Dapeng Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P.R. China
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17
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Kamieniak MM, Rico D, Milne RL, Muñoz-Repeto I, Ibáñez K, Grillo MA, Domingo S, Borrego S, Cazorla A, García-Bueno JM, Hernando S, García-Donas J, Hernández-Agudo E, Y Cajal TR, Robles-Díaz L, Márquez-Rodas I, Cusidó M, Sáez R, Lacambra-Calvet C, Osorio A, Urioste M, Cigudosa JC, Paz-Ares L, Palacios J, Benítez J, García MJ. Deletion at 6q24.2-26 predicts longer survival of high-grade serous epithelial ovarian cancer patients. Mol Oncol 2014; 9:422-36. [PMID: 25454820 PMCID: PMC5528660 DOI: 10.1016/j.molonc.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/12/2014] [Accepted: 09/25/2014] [Indexed: 12/15/2022] Open
Abstract
Standard treatments for advanced high-grade serous ovarian carcinomas (HGSOCs) show significant side-effects and provide only short-term survival benefits due to disease recurrence. Thus, identification of novel prognostic and predictive biomarkers is urgently needed. We have used 42 paraffin-embedded HGSOCs, to evaluate the utility of DNA copy number alterations, as potential predictors of clinical outcome. Copy number-based unsupervised clustering stratified HGSOCs into two clusters of different immunohistopathological features and survival outcome (HR = 0.15, 95%CI = 0.03-0.81; Padj = 0.03). We found that loss at 6q24.2-26 was significantly associated with the cluster of longer survival independently from other confounding factors (HR = 0.06, 95%CI = 0.01-0.43, Padj = 0.005). The prognostic value of this deletion was validated in two independent series, one consisting of 36 HGSOCs analyzed by fluorescent in situ hybridization (P = 0.04) and another comprised of 411 HGSOCs from the Cancer Genome Atlas study (TCGA) (HR = 0.67, 95%CI = 0.48-0.93, Padj = 0.019). In addition, we confirmed the association of low expression of the genes from the region with longer survival in 799 HGSOCs (HR = 0.74, 95%CI = 0.61-0.90, log-rank P = 0.002) and 675 high-FIGO stage HGSOCs (HR = 0.76, 95%CI = 0.61-0.96, log-rank P = 0.02) available from the online tool KM-plotter. Finally, by integrating copy number, RNAseq and survival data of 296 HGSOCs from TCGA we propose a few candidate genes that can potentially explain the association. Altogether our findings indicate that the 6q24.2-26 deletion is an independent marker of favorable outcome in HGSOCs with potential clinical value as it can be analyzed by FISH on tumor sections and guide the selection of patients towards more conservative therapeutic strategies in order to reduce side-effects and improve quality of life.
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Affiliation(s)
- Marta M Kamieniak
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel Rico
- Structural Computational Biology Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3 28029, Madrid, Spain
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne 3004, Australia; Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street Carlton, Melbourne 3010, Victoria, Australia
| | - Ivan Muñoz-Repeto
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Kristina Ibáñez
- Structural Computational Biology Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3 28029, Madrid, Spain
| | - Miguel A Grillo
- Molecular Cytogenetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Samuel Domingo
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Salud Borrego
- Departments of Genetics, Reproduction, and Fetal Medicine, IBIS, University Hospital Virgen del Rocio/CSIC/University of Seville, Avda. Manuel Siurot, s/n., 41013 Sevilla, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Alicia Cazorla
- Pathology Department, Fundación Jiménez Díaz, Avda. Reyes Católicos, 2, 28040 Madrid, Spain
| | - José M García-Bueno
- Oncology Department, Hospital General de Albacete, Calle Hermanos Falco, 37, 02006 Albacete, Spain
| | - Susana Hernando
- Oncology Department, Fundación Hospital Alcorcón, Calle Valdelaguna, 1, 28922 Alcorcón, Spain
| | - Jesús García-Donas
- Medical Oncology Service, Oncologic Center Clara Campal, Calle Oña, 10, 28050 Madrid, Spain
| | - Elena Hernández-Agudo
- Breast Cancer Clinical Research Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Teresa Ramón Y Cajal
- Medical Oncology Service, Hospital Sant Pau, Carrer de Sant Quintí, 89, 08026 Barcelona, Spain
| | - Luis Robles-Díaz
- Familial Cancer Unit and Medical Oncology Department, Hospital 12 de Octubre, Avda de Córdoba, s/n, 28041 Madrid, Spain
| | - Ivan Márquez-Rodas
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, Calle Doctor Esquerdo, 46, 28007 Madrid, Spain
| | - Maite Cusidó
- Obstetrics and Gynecology Department, Institut Universitari Dexeus, Carrer de Sabino Arana, 5, 08028 Barcelona, Spain
| | - Raquel Sáez
- Laboratory of Genetics, Hospital Donostia, Calle Doctor Begiristain, 117, 20080 San Sebastián, Spain
| | - Carmen Lacambra-Calvet
- Department of Internal Medicine, Hospital Severo Ochoa, Avd. de Orellana, s/n., 28911 Madrid, Spain
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Juan C Cigudosa
- Molecular Cytogenetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Luis Paz-Ares
- Medical Oncology Department, University Hospital Virgen del Rocio, Avda. Manuel Siurot s/n., 41013 Sevilla, Spain
| | - José Palacios
- Pathology Department, Hospital Universitario Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, 28034 Madrid, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - María J García
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain.
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18
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Correlation between gene expression and mutator phenotype predicts homologous recombination deficiency and outcome in ovarian cancer. J Mol Med (Berl) 2014; 92:1159-68. [PMID: 25062964 DOI: 10.1007/s00109-014-1191-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED New strategies are needed to predict response to platinum-based chemotherapy and outcome of ovarian cancers. We hypothesized that the mutator phenotype in the cancer genome represents the overuse of alternative DNA repair mechanisms, which might be a sign of homologous recombination (HR) deficiency and can be captured by gene expression. Multidimensional data of ovarian cancer patients and breast cancer patients from The Cancer Genome Atlas (TCGA) database were used for the development and validation of a potential clinical information-independent score that correlates with HR deficiency and predicts outcome. Correlation of the score with platinum response, outcome, and BRCA mutations was assessed. The score correlated with increased genomic mutation rate in both ovarian cancer and breast cancer cases that harbored a substantial subset of HR-deficient samples. Significantly improved outcomes were observed in the high-scoring group versus the low-scoring group in the TCGA dataset and in three large gene expression microarray datasets. A strong correlation was found between the score and the likelihood of achieving complete response to chemotherapy. The score was also found to be highly robust to noises in genomic mutations. Sixty-four patients harboring BRCA mutations were successfully divided into two groups based on scores, with the high-scoring group showing significantly improved outcomes compared with wild-type cases and the low-scoring group showing no significance in all the same analyses. The score was significantly correlated with the response to platinum therapy and outcome. Evaluation of the score as a prognostic tool in ovarian cancer patients is warranted. KEY MESSAGE We develop a diagnostic signature for the HR-deficiency based on a novel hypothesis. HR-deficiency score is significantly correlated to platinum therapy and outcomes. HRDS was validated by its association with OS, PFS, DFS and CR in validation datasets. Evaluation of the score as a prognostic tool in ovarian cancer patients is warranted.
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19
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The degree of segmental aneuploidy measured by total copy number abnormalities predicts survival and recurrence in superficial gastroesophageal adenocarcinoma. PLoS One 2014; 9:e79079. [PMID: 24454681 PMCID: PMC3894223 DOI: 10.1371/journal.pone.0079079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/26/2013] [Indexed: 01/23/2023] Open
Abstract
Background Prognostic biomarkers are needed for superficial gastroesophageal adenocarcinoma (EAC) to predict clinical outcomes and select therapy. Although recurrent mutations have been characterized in EAC, little is known about their clinical and prognostic significance. Aneuploidy is predictive of clinical outcome in many malignancies but has not been evaluated in superficial EAC. Methods We quantified copy number changes in 41 superficial EAC using Affymetrix SNP 6.0 arrays. We identified recurrent chromosomal gains and losses and calculated the total copy number abnormality (CNA) count for each tumor as a measure of aneuploidy. We correlated CNA count with overall survival and time to first recurrence in univariate and multivariate analyses. Results Recurrent segmental gains and losses involved multiple genes, including: HER2, EGFR, MET, CDK6, KRAS (recurrent gains); and FHIT, WWOX, CDKN2A/B, SMAD4, RUNX1 (recurrent losses). There was a 40-fold variation in CNA count across all cases. Tumors with the lowest and highest quartile CNA count had significantly better overall survival (p = 0.032) and time to first recurrence (p = 0.010) compared to those with intermediate CNA counts. These associations persisted when controlling for other prognostic variables. Significance SNP arrays facilitate the assessment of recurrent chromosomal gain and loss and allow high resolution, quantitative assessment of segmental aneuploidy (total CNA count). The non-monotonic association of segmental aneuploidy with survival has been described in other tumors. The degree of aneuploidy is a promising prognostic biomarker in a potentially curable form of EAC.
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