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Pócza T, Grolmusz VK, Papp J, Butz H, Patócs A, Bozsik A. Germline Structural Variations in Cancer Predisposition Genes. Front Genet 2021; 12:634217. [PMID: 33936164 PMCID: PMC8081352 DOI: 10.3389/fgene.2021.634217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
In addition to single nucleotide variations and small-scale indels, structural variations (SVs) also contribute to the genetic diversity of the genome. SVs, such as deletions, duplications, amplifications, or inversions may also affect coding regions of cancer-predisposing genes. These rearrangements may abrogate the open reading frame of these genes or adversely affect their expression and may thus act as germline mutations in hereditary cancer syndromes. With the capacity of disrupting the function of tumor suppressors, structural variations confer an increased risk of cancer and account for a remarkable fraction of heritability. The development of sequencing techniques enables the discovery of a constantly growing number of SVs of various types in cancer predisposition genes (CPGs). Here, we provide a comprehensive review of the landscape of germline SV types, detection methods, pathomechanisms, and frequency in CPGs, focusing on the two most common cancer syndromes: hereditary breast- and ovarian cancer and gastrointestinal cancers. Current knowledge about the possible molecular mechanisms driving to SVs is also summarized.
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Affiliation(s)
- Tímea Pócza
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
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2
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Boujemaa M, Hamdi Y, Mejri N, Romdhane L, Ghedira K, Bouaziz H, El Benna H, Labidi S, Dallali H, Jaidane O, Ben Nasr S, Haddaoui A, Rahal K, Abdelhak S, Boussen H, Boubaker MS. Germline copy number variations in BRCA1/2 negative families: Role in the molecular etiology of hereditary breast cancer in Tunisia. PLoS One 2021; 16:e0245362. [PMID: 33503040 PMCID: PMC7840007 DOI: 10.1371/journal.pone.0245362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
Hereditary breast cancer accounts for 5-10% of all breast cancer cases. So far, known genetic risk factors account for only 50% of the breast cancer genetic component and almost a quarter of hereditary cases are carriers of pathogenic mutations in BRCA1/2 genes. Hence, the genetic basis for a significant fraction of familial cases remains unsolved. This missing heritability may be explained in part by Copy Number Variations (CNVs). We herein aimed to evaluate the contribution of CNVs to hereditary breast cancer in Tunisia. Whole exome sequencing was performed for 9 BRCA negative cases with a strong family history of breast cancer and 10 matched controls. CNVs were called using the ExomeDepth R-package and investigated by pathway analysis and web-based bioinformatic tools. Overall, 483 CNVs have been identified in breast cancer patients. Rare CNVs affecting cancer genes were detected, of special interest were those disrupting APC2, POU5F1, DOCK8, KANSL1, TMTC3 and the mismatch repair gene PMS2. In addition, common CNVs known to be associated with breast cancer risk have also been identified including CNVs on APOBECA/B, UGT2B17 and GSTT1 genes. Whereas those disrupting SULT1A1 and UGT2B15 seem to correlate with good clinical response to tamoxifen. Our study revealed new insights regarding CNVs and breast cancer risk in the Tunisian population. These findings suggest that rare and common CNVs may contribute to disease susceptibility. Those affecting mismatch repair genes are of interest and require additional attention since it may help to select candidates for immunotherapy leading to better outcomes.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Ben Nasr
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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3
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Behravan H, Hartikainen JM, Tengström M, Kosma VM, Mannermaa A. Predicting breast cancer risk using interacting genetic and demographic factors and machine learning. Sci Rep 2020; 10:11044. [PMID: 32632202 PMCID: PMC7338351 DOI: 10.1038/s41598-020-66907-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022] Open
Abstract
Breast cancer (BC) is a multifactorial disease and the most common cancer in women worldwide. We describe a machine learning approach to identify a combination of interacting genetic variants (SNPs) and demographic risk factors for BC, especially factors related to both familial history (Group 1) and oestrogen metabolism (Group 2), for predicting BC risk. This approach identifies the best combinations of interacting genetic and demographic risk factors that yield the highest BC risk prediction accuracy. In tests on the Kuopio Breast Cancer Project (KBCP) dataset, our approach achieves a mean average precision (mAP) of 77.78 in predicting BC risk by using interacting genetic and Group 1 features, which is better than the mAPs of 74.19 and 73.65 achieved using only Group 1 features and interacting SNPs, respectively. Similarly, using interacting genetic and Group 2 features yields a mAP of 78.00, which outperforms the system based on only Group 2 features, which has a mAP of 72.57. Furthermore, the gene interaction maps built from genes associated with SNPs that interact with demographic risk factors indicate important BC-related biological entities, such as angiogenesis, apoptosis and oestrogen-related networks. The results also show that demographic risk factors are individually more important than genetic variants in predicting BC risk.
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Affiliation(s)
- Hamid Behravan
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Jaana M Hartikainen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Maria Tengström
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, P.O. Box 100, FI-70029, Kuopio, Finland
| | - Veli-Matti Kosma
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
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4
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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5
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Kumaran M, Cass CE, Graham K, Mackey JR, Hubaux R, Lam W, Yasui Y, Damaraju S. Germline copy number variations are associated with breast cancer risk and prognosis. Sci Rep 2017; 7:14621. [PMID: 29116104 PMCID: PMC5677082 DOI: 10.1038/s41598-017-14799-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array. Principal component analysis for population stratification revealed 84 outliers leaving 366 cases and 320 controls of Caucasian ancestry for association analysis; CNVs with frequency > 10% and overlapping with protein coding genes were considered for breast cancer risk and prognostic relevance. Coding genes within the CNVs identified were interrogated for gene- dosage effects by correlating copy number status with gene expression profiles in breast tumor tissue. We identified 200 CNVs associated with breast cancer (q-value < 0.05). Of these, 21 CNV regions (overlapping with 22 genes) also showed association with prognosis. We validated representative CNVs overlapping with APOBEC3B and GSTM1 genes using the TaqMan assay. Germline CNVs conferred dosage effects on gene expression in breast tissue. The candidate CNVs identified in this study warrant independent replication.
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Affiliation(s)
- Mahalakshmi Kumaran
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Carol E Cass
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Roland Hubaux
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Wan Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada. .,Cross Cancer Institute, Alberta Health Services, Edmonton, AB, Canada.
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6
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BCIP: a gene-centered platform for identifying potential regulatory genes in breast cancer. Sci Rep 2017; 7:45235. [PMID: 28327601 PMCID: PMC5361122 DOI: 10.1038/srep45235] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks. This platform provides a user-friendly interface integrating comprehensive and flexible analysis tools on differential gene expression, copy number variation, and survival analysis. The prominent characteristic of BCIP is that users can perform analysis by customizing subgroups with single or combined clinical features, including subtypes, histological grades, pathologic stages, metastasis status, lymph node status, ER/PR/HER2 status, TP53 mutation status, menopause status, age, tumor size, therapy responses, and prognosis. BCIP will help to identify regulatory or driver genes and candidate biomarkers for further research in breast cancer.
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Villacis RAR, Basso TR, Canto LM, Nóbrega AF, Achatz MI, Rogatto SR. Germline large genomic alterations on 7q in patients with multiple primary cancers. Sci Rep 2017; 7:41677. [PMID: 28139749 PMCID: PMC5282589 DOI: 10.1038/srep41677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/29/2016] [Indexed: 11/11/2022] Open
Abstract
Patients with multiple primary cancers (MPCs) are suspected to have a hereditary cancer syndrome. However, only a small proportion may be explained by mutations in high-penetrance genes. We investigate two unrelated MPC patients that met Hereditary Breast and Ovaria Cancer criteria, both presenting triple negative breast tumors and no mutations in BRCA1, BRCA2 and TP53 genes. Germline rearrangements on chromosome 7q, involving over 40 Mb of the same region, were found in both patients: one with mosaic loss (80% of cells) and the other with cnLOH (copy-neutral loss of heterozygosity) secondary to maternal allele duplication. Five children tested had no alterations on 7q. The patients shared 330 genes in common on 7q22.1-q34, including several tumor suppressor genes (TSGs) previously related to breast cancer risk and imprinted genes. The analysis of the triple negative BC from one patient revealed a mosaic gain of 7q translated for over-expressed cancer-related genes. The involvement of TSGs and imprinted genes, mapped on 7q, has the potential of being associated to MPC risk, as well as cancer progression. To our knowledge, this is the first description of patients with MPCs that harbor constitutive large alterations on 7q.
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Affiliation(s)
- R. A. R. Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília - UnB, Brasília, DF, Brazil
| | - T. R. Basso
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - L. M. Canto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - A. F. Nóbrega
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - M. I. Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - S. R. Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Clinical Genetics, Vejle Hospital, DK and University of Southern Denmark, Denmark
- Department of Urology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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Sapkota Y, Narasimhan A, Kumaran M, Sehrawat BS, Damaraju S. A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility. Cytogenet Genome Res 2016; 149:156-164. [PMID: 27668787 DOI: 10.1159/000448558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tenn., USA
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WWOX CNV-67048 Functions as a Risk Factor for Epithelial Ovarian Cancer in Chinese Women by Negatively Interacting with Oral Contraceptive Use. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6594039. [PMID: 27190995 PMCID: PMC4842385 DOI: 10.1155/2016/6594039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/22/2016] [Indexed: 12/22/2022]
Abstract
Copy number variations (CNVs) have attracted increasing evidences to represent their roles as cancer susceptibility regulators. However, little is known about the role of CNV in epithelia ovarian cancer (EOC). Recently, the CNV-67048 of WW domain-containing oxidoreductase (WWOX) was reported to alter cancer risks. Considering that WWOX also plays a role in EOC, we hypothesized that the CNV-67048 was associated with EOC risk. In a case-control study of 549 EOC patients and 571 age (±5 years) matched cancer-free controls, we found that the low copy number of CNV-67048 (1-copy and 0-copy) conferred a significantly increased risk of EOC (OR = 1.346, 95% CI = 1.037–1.747) and it determined the risk by means of copy number-dependent dosage effect (P = 0.009). Data from TCGA also confirmed the abovementioned association as the frequency of low copies in EOC group was 3.68 times more than that in healthy group (P = 0.023). The CNV also negatively interacted with oral contraceptive use on EOC risk (P = 0.042). Functional analyses further showed a lower mRNA level of WWOX in tissues with the 0-copy or 1-copy than that in those with the 2-copy (P = 0.045). Our data suggested the CNV-67048 to be a risk factor of EOC in Chinese women.
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Villacis RAR, Abreu FB, Miranda PM, Domingues MAC, Carraro DM, Santos EMM, Andrade VP, Rossi BM, Achatz MI, Rogatto SR. ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients. Tumour Biol 2016; 37:3145-53. [PMID: 26427657 DOI: 10.1007/s13277-015-4145-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/23/2015] [Indexed: 01/22/2023] Open
Abstract
Despite one third of breast (BC) and colorectal cancer (CRC) cases having a hereditary component, only a small proportion can be explained by germline mutations. The aim of this study was to identify potential genomic alterations related to cancer predisposition. Copy number variations (CNVs) were interrogated in 113 unrelated cases fulfilling the criteria for hereditary BC/CRC and presenting non-pathogenic mutations in BRCA1, BRCA2, MLH1, MSH2, TP53, and CHEK2 genes. An identical germline deep intronic deletion of ROBO1 was identified in three index patients using two microarray platforms (Agilent 4x180K and Affymetrix CytoScan HD). The ROBO1 deletion was confirmed by quantitative PCR (qPCR). Six relatives were also evaluated by CytoScan HD Array. Genomic analysis confirmed a co-segregation of the ROBO1 deletion with the occurrence of cancer in two families. Direct sequencing revealed no pathogenic ROBO1 point mutations. Transcriptomic analysis (HTA 2.0, Affymetrix) in two breast carcinomas from a single patient revealed ROBO1 down-expression with no splicing events near the intronic deletion. Deeper in silico analysis showed several enhancer regions and a histone methylation mark in the deleted region. The ROBO1 deletion in a putative transcriptional regulatory region, its down-expression in tumor samples, and the results of the co-segregation analysis revealing the presence of the alteration in affected individuals suggest a pathogenic effect of the ROBO1 in cancer predisposition.
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Affiliation(s)
- Rolando A R Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Francine B Abreu
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Priscila M Miranda
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Maria A C Domingues
- Department of Pathology, Faculty of Medicine, University of São Paulo State (UNESP), Botucatu, SP, Brazil
| | - Dirce M Carraro
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | | | - Victor P Andrade
- Department of Pathology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Maria I Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Silvia R Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil.
- Department of Urology, Faculty of Medicine, University of São Paulo State (UNESP), CEP: 18618-970, Botucatu, SP, Brazil.
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11
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An O, Dall'Olio GM, Mourikis TP, Ciccarelli FD. NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. Nucleic Acids Res 2015; 44:D992-9. [PMID: 26516186 PMCID: PMC4702816 DOI: 10.1093/nar/gkv1123] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022] Open
Abstract
The Network of Cancer Genes (NCG, http://ncg.kcl.ac.uk/) is a manually curated repository of cancer genes derived from the scientific literature. Due to the increasing amount of cancer genomic data, we have introduced a more robust procedure to extract cancer genes from published cancer mutational screenings and two curators independently reviewed each publication. NCG release 5.0 (August 2015) collects 1571 cancer genes from 175 published studies that describe 188 mutational screenings of 13 315 cancer samples from 49 cancer types and 24 primary sites. In addition to collecting cancer genes, NCG also provides information on the experimental validation that supports the role of these genes in cancer and annotates their properties (duplicability, evolutionary origin, expression profile, function and interactions with proteins and miRNAs).
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Affiliation(s)
- Omer An
- Division of Cancer Studies, King's College London, London SE11UL, UK
| | | | - Thanos P Mourikis
- Division of Cancer Studies, King's College London, London SE11UL, UK
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