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Scuderi C, Di Bella V, Privitera AP, Giustolisi FM, Barresi V, Condorelli DF. Gain-Type Aneuploidies Influence the Burden of Selective Long Non-Coding Transcripts in Colorectal Cancer. Int J Mol Sci 2024; 25:5538. [PMID: 38791575 PMCID: PMC11122260 DOI: 10.3390/ijms25105538] [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: 02/29/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Chromosomal instability is a hallmark of colorectal carcinogenesis and produces an accumulation of different forms of aneuploidies or broad copy number aberrations. Colorectal cancer is characterized by gain-type broad copy number aberrations, specifically in Chr20, Chr8q, Chr13 and Chr7, but their roles and mechanisms in cancer progression are not fully understood. It has been suggested that broad copy number gains might contribute to tumor development through the so-called caricature transcriptomic effect. We intend to investigate the impact of broad copy number gains on long non-coding RNAs' expression in colorectal cancer, given their well-known role in oncogenesis. The influence of such chromosomal aberrations on lncRNAs' transcriptome profile was investigated by SNP and transcriptome arrays in our series of colorectal cancer samples and cell lines. The correlation between aneuploidies and transcriptomic profiles led us to obtain a class of Over-UpT lncRNAs, which are transcripts upregulated in CRC and further overexpressed in colon tumors bearing specific chromosomal aberrations. The identified lncRNAs can contribute to a wide interaction network to establish the cancer driving effect of gain-type aneuploidies.
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Affiliation(s)
| | | | | | | | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.S.); (V.D.B.); (A.P.P.); (F.M.G.); (D.F.C.)
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2
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Anderson DJ, Pauler FM, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Syst 2022; 13:438-453.e5. [PMID: 35452605 DOI: 10.1016/j.cels.2022.03.006] [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: 05/14/2021] [Revised: 01/21/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans.
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Affiliation(s)
- Donovan J Anderson
- Allen Discovery Center for Lineage Tracing and Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA
| | - Florian M Pauler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | | | - Jay Shendure
- Allen Discovery Center for Lineage Tracing, Department of Genome Sciences, and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Marshall S Horwitz
- Allen Discovery Center for Lineage Tracing and Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA.
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3
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Lee GT, Chung YJ. Comparison of the copy-neutral loss of heterozygosity identified from whole-exome sequencing data using three different tools. Genomics Inform 2022; 20:e4. [PMID: 35399003 PMCID: PMC9001996 DOI: 10.5808/gi.21066] [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: 11/04/2021] [Accepted: 12/31/2001] [Indexed: 11/20/2022] Open
Abstract
Loss of heterozygosity (LOH) is a genomic aberration. In some cases, LOH can be generated without changing the copy number, which is called copy-neutral LOH (CN-LOH). CN-LOH frequently occurs in various human diseases, including cancer. However, the biological and clinical implications of CN-LOH for human diseases have not been well studied. In this study, we compared the performance of CN-LOH determination using three commonly used tools. For an objective comparison, we analyzed CN-LOH profiles from single-nucleotide polymorphism array data from 10 colon adenocarcinoma patients, which were used as the reference for comparison with the CN-LOHs obtained through whole-exome sequencing (WES) data of the same patients using three different analysis tools (FACETS, Nexus, and Sequenza). The majority of the CN-LOHs identified from the WES data were consistent with the reference data. However, some of the CN-LOHs identified from the WES data were not consistent between the three tools, and the consistency with the reference CN-LOH profile was also different. The Jaccard index of the CN-LOHs using FACETS (0.84 ± 0.29; mean value, 0.73) was significantly higher than that of Nexus (0.55 ± 0.29; mean value, 0.50; p = 0.02) or Sequenza (0 ± 0.41; mean value, 0.34; p = 0.04). FACETS showed the highest area under the curve value. Taken together, of the three CN-LOH analysis tools, FACETS showed the best performance in identifying CN-LOHs from The Cancer Genome Atlas colon adenocarcinoma WES data. Our results will be helpful in exploring the biological or clinical implications of CN-LOH for human diseases.
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Affiliation(s)
- Gang-Taik Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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4
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Relation between expression of hMLH1 and p53 mRNA genes, in the feces of patients with colorectal carcinoma. Cross-sectional study. Ann Med Surg (Lond) 2022; 73:103237. [PMID: 35079371 PMCID: PMC8767297 DOI: 10.1016/j.amsu.2021.103237] [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: 10/31/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 11/24/2022] Open
Abstract
Colorectal carcinoma (CRC) is one of the main public health problems. The mortality of CRC is about 8%. Early detection of CRC is very important to prevent death because this cancer could be cured through surgery if the diagnosis can be made as early as possible. Therefore screening strategy for early detection of CRC is critical in reducing mortality. Many investigations supporting the detection of CRC have been developed, including the fecal DNA mutation test using advanced cytological techniques. It is capable of assessing colonocytes for the presence of DNA, RNA, and protein as molecular biomarkers of neoplasia in CRC, including p53 and hMLH1. This study implemented observational approach with a cross-sectional study of the feces of patients with CRC regardless of the stage and grade. The purpose of this study was to determine the expression of the hMLH1 and p53 mRNA genes in the feces of 48 patients with CRC from two hospitals in Indonesia, Siloam Hospitals in Cikarang and Dr. Wahidin Sudirohusodo Hospital in Makassar. The results showed that all adenocarcinoma feces samples with various tumor stages and grades had excess mRNA expression (more than twice the normal amount in Fold Change units) for both the hMLH1 and p53 genes. The average expression of the hMLH1 mRNA gene was the highest at stage two and grade one, while the lowest was at stage four and grade three. In contrast, the average p53 mRNA gene expression was the highest at stage four and grade three, while the lowest was at stage two and grade one. The study suggested that there was a relation between and the expression of hMLH1 and p53 mRNA gene. We concluded that while both hMLH1 and p53 genes in patients’ feces with CRC were overexpressed, they did not significantly affect the grade of CRC. Relation of mRNA expression of hMLH1 and p53 gene in colorectal carcinoma patients feces. mRNA expression in feces colorectal carcinoma by RT-PCR examination. Gene hMLH1 and p53 in feces colorectal carcinoma patients.
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5
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Sivakumar S, San Lucas FA, Jakubek YA, Ozcan Z, Fowler J, Scheet P. Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types. Genetics 2021; 217:1-12. [PMID: 33683368 PMCID: PMC8045738 DOI: 10.1093/genetics/iyaa021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/22/2020] [Indexed: 12/14/2022] Open
Abstract
Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities ("B allele" frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the "B allele" frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.
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Affiliation(s)
- Smruthy Sivakumar
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - F Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yasminka A Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zuhal Ozcan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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6
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Haykal MM, Rodrigues-Ferreira S, Nahmias C. Microtubule-Associated Protein ATIP3, an Emerging Target for Personalized Medicine in Breast Cancer. Cells 2021; 10:cells10051080. [PMID: 34062782 PMCID: PMC8147298 DOI: 10.3390/cells10051080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Breast cancer is the leading cause of death by malignancy among women worldwide. Clinical data and molecular characteristics of breast tumors are essential to guide clinician’s therapeutic decisions. In the new era of precision medicine, that aims at personalizing the treatment for each patient, there is urgent need to identify robust companion biomarkers for new targeted therapies. This review focuses on ATIP3, a potent anti-cancer protein encoded by candidate tumor suppressor gene MTUS1, whose expression levels are markedly down-regulated in breast cancer. ATIP3 is a microtubule-associated protein identified both as a prognostic biomarker of patient survival and a predictive biomarker of breast tumors response to taxane-based chemotherapy. We present here recent studies pointing out ATIP3 as an emerging anti-cancer protein and a potential companion biomarker to be combined with future personalized therapy against ATIP3-deficient breast cancer.
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Affiliation(s)
- Maria M. Haykal
- Institut Gustave Roussy, Université Paris-Saclay, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, 94800 Villejuif, France; (M.M.H.); (S.R.-F.)
- LERMIT Laboratory, 92296 Chatenay-Malabry, France
| | - Sylvie Rodrigues-Ferreira
- Institut Gustave Roussy, Université Paris-Saclay, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, 94800 Villejuif, France; (M.M.H.); (S.R.-F.)
- LERMIT Laboratory, 92296 Chatenay-Malabry, France
- Inovarion, 75005 Paris, France
| | - Clara Nahmias
- Institut Gustave Roussy, Université Paris-Saclay, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, 94800 Villejuif, France; (M.M.H.); (S.R.-F.)
- LERMIT Laboratory, 92296 Chatenay-Malabry, France
- Correspondence:
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7
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Augustus GJ, Xicola RM, Llor X, Ellis NA. Decreased copy-neutral loss of heterozygosity in African American colorectal cancers. Genes Chromosomes Cancer 2020; 59:454-464. [PMID: 32293075 DOI: 10.1002/gcc.22851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 11/11/2022] Open
Abstract
Despite improvements over the past 20 years, African Americans continue to have the highest incidence and mortality rates of colorectal cancer (CRC) in the United States. While previous studies have found that copy number variations (CNVs) occur at similar frequency in African American and White CRCs, copy-neutral loss of heterozygosity (cnLOH) has not been investigated. In the present study, we used publicly available data from The Cancer Genome Atlas (TCGA) as well as data from an African American CRC cohort, the Chicago Colorectal Cancer Consortium (CCCC), to compare frequencies of CNVs and cnLOH events in CRCs in the two racial groups. Using genotype microarray data, we analyzed large-scale CNV and cnLOH events from 166 microsatellite stable CRCs-31 and 39 African American CRCs from TCGA and the CCCC, respectively, and 96 White CRCs from TCGA. As reported previously, the frequencies of CNVs were similar between African American and White CRCs; however, there was a significantly lower frequency of cnLOH events in African American CRCs compared to White CRCs, even after adjusting for demographic and clinical covariates. Although larger differences for chromosome 18 were observed, a lower frequency of cnLOH events in African American CRCs was observed for nearly all chromosomes. These results suggest that mechanistic differences, including differences in the frequency of cnLOH, could contribute to clinicopathological disparities between African Americans and Whites. Additionally, we observed a previously uncharacterized phenomenon we refer to as small interstitial cnLOH, in which segments of chromosomes from 1 to 5 Mb long were affected by cnLOH.
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Affiliation(s)
- Gaius J Augustus
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA
| | - Rosa M Xicola
- Department of Internal Medicine and Yale Cancer Center, Yale University, Hew Haven, Connecticut, USA
| | - Xavier Llor
- Department of Internal Medicine and Yale Cancer Center, Yale University, Hew Haven, Connecticut, USA
| | - Nathan A Ellis
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA.,Department of Cellular and Molecular Medicine and University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
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8
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Torabi K, Erola P, Alvarez-Mora MI, Díaz-Gay M, Ferrer Q, Castells A, Castellví-Bel S, Milà M, Lozano JJ, Miró R, Ried T, Ponsa I, Camps J. Quantitative analysis of somatically acquired and constitutive uniparental disomy in gastrointestinal cancers. Int J Cancer 2018; 144:513-524. [PMID: 30350313 PMCID: PMC6635747 DOI: 10.1002/ijc.31936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/31/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022]
Abstract
Somatically acquired uniparental disomies (aUPDs) are frequent events in solid tumors and have been associated with cancer‐related genes. Studies assessing their functional consequences across several cancer types are therefore necessary. Here, we aimed at integrating aUPD profiles with the mutational status of cancer‐related genes in a tumor‐type specific manner. Using TCGA datasets for 1,032 gastrointestinal cancers, including colon (COAD), rectum (READ), stomach (STAD), esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), we show a non‐random distribution of aUPD, suggesting the existence of a cancer‐specific landscape of aUPD events. Our analysis indicates that aUPD acts as a “second hit” in Knudson's model in order to achieve biallelic inactivation of tumor suppressor genes. In particular, APC, ARID1A and NOTCH1 were recurrently inactivated by the presence of homozygous mutation as a consequence of aUPD in COAD and READ, STAD and ESCC, respectively. Furthermore, while TP53 showed inactivation caused by aUPD at chromosome arm 17p across all tumor types, copy number losses at this genomic position were also frequent. By experimental and computationally inferring genome ploidy, we demonstrate that an increased number of aUPD events, both affecting the whole chromosome or segments of it, were present in highly aneuploid genomes compared to near‐diploid tumors. Finally, the presence of mosaic UPD was detected at a higher frequency in DNA extracted from peripheral blood lymphocytes of patients with colorectal cancer compared to healthy individuals. In summary, our study defines specific profiles of aUPD in gastrointestinal cancers and provides unequivocal evidence of their relevance in cancer. What's new? Somatically acquired uniparental disomies (aUPDs), in which two copies of a chromosome originate from the same parent, have been documented in various human cancers. Here, the authors examined the frequency of aUPDs in different gastrointestinal cancer types. Events involving aUPDs were found to occur at high incidence in gastrointestinal cancers and at increased frequency particularly in highly aneuploid genomes. The data also reveal a nonrandom distribution of aUPDs, with evidence of biallelic inactivation of tumor suppressor genes and activation of oncogenes in a tumor type‐specific manner. The findings suggest that aUPDs are functionally relevant in gastrointestinal malignancies.
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Affiliation(s)
- Keyvan Torabi
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pau Erola
- Bioinformatics Unit, CIBEREHD, Barcelona, Catalonia, Spain.,Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Maria Isabel Alvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Catalonia, Spain
| | - Marcos Díaz-Gay
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Queralt Ferrer
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain
| | - Montserrat Milà
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Catalonia, Spain
| | | | - Rosa Miró
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Immaculada Ponsa
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
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9
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Sugai T, Takahashi Y, Eizuka M, Sugimoto R, Fujita Y, Habano W, Otsuka K, Sasaki A, Yamamoto E, Matsumoto T, Suzuki H. Molecular profiling and genome-wide analysis based on somatic copy number alterations in advanced colorectal cancers. Mol Carcinog 2017; 57:451-461. [PMID: 29230882 PMCID: PMC5814737 DOI: 10.1002/mc.22769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/18/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
Abstract
To characterize somatic alterations in colorectal cancer (CRC), we conducted a genome-scale analysis of 106 CRC specimens. We assessed comprehensive somatic copy number alterations (SCNAs) in these CRC specimens. In addition, we examined microsatellite instability (MSI; low and high), genetic mutations (KRAS, BRAF, TP53, and PIK3CA), and DNA methylation status (classified into low, intermediate, and high type). We stratified molecular alterations in the CRCs using a hierarchical cluster analysis. The examined CRCs could be categorized into three subgroups using hierarchical cluster analysis. Tumors in subgroup 1 were characterized by a low frequency of SCNAs and a high frequency of MSI-high status, whereas tumors in subgroups 2 and 3 were closely associated with a high frequency of SCNAs. Tumors in subgroup 1 were preferentially present in the right-sided colon and showed frequent MSI-high status. Subgroup 3 was distinguished by specific alterations, including gains at 1q23-44, 1p11-36, 10q11-26, 10p11-13, 12q24-24, and 13q33-33. In contrast, tumors in subgroup 2 were characterized by copy-neutral LOH at 12p12-13, 1q24-25, and 10q22. In addition, KRAS mutations were more frequently found in subgroup 3 than in subgroup 1. TP53 mutations and intermediate levels of DNA methylation were common alterations in the three subgroups. SCNAs contributed to sporadic CRC, and there were three subgroups based on SCNAs that played a different role in driving the development of this disease.
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Affiliation(s)
- Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Yayoi Takahashi
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Ryo Sugimoto
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Yasuko Fujita
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Wataru Habano
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Kouki Otsuka
- Department of Surgery, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Akira Sasaki
- Department of Surgery, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, School of Medicine, Sapporo Medical University, Sapporo, Japan
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10
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Druliner BR, Ruan X, Sicotte H, O'Brien D, Liu H, Kocher JPA, Boardman L. Early genetic aberrations in patients with sporadic colorectal cancer. Mol Carcinog 2017; 57:114-124. [PMID: 28926134 DOI: 10.1002/mc.22738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 09/01/2017] [Accepted: 09/18/2017] [Indexed: 01/10/2023]
Abstract
Chromosome instability (CIN) is widely observed in both sporadic and hereditary colorectal cancer (CRC). Defects in APC and WNT signaling are primarily associated with CIN in hereditary CRC, but the genetic causes for CIN in sporadic CRC remain elusive. Using high-density SNP array and exome data from The Cancer Genome Atlas (TCGA), we characterized loss of heterozygosity (LOH) and copy number variation (CNV) in the peripheral blood, normal colon, and corresponding tumor tissue in 15 CRC patients with proficient mismatch repair (MMR) and 24 CRC patients with deficient MMR. We found a high frequency of 18q LOH in tumors and arm-specific enrichment of genetic aberrations on 18q in the normal colon (primarily copy neutral LOH) and blood (primarily copy gain). These aberrations were specific to the sporadic, pMMR CRC. Though in tumor samples genetic aberrations were observed for genes commonly mutated in hereditary CRC (eg, APC, CTNNB1, SMAD4, BRAF), none of them showed LOH or CNV in the normal colon or blood. DCC located on 18q21.1 topped the list of genes with genetic aberrations in the tumor. In an independent cohort of 13 patients subjected to Whole Genome Sequencing (WGS), we found LOH and CNV on 18q in adenomatous polyp and tumor tissues. Our data suggests that patients with sporadic CRC may have genetic aberrations preferentially enriched on 18q in their blood, normal colon epithelium, and non-malignant polyp lesions that may prove useful as a clinical marker for sporadic CRC detection and risk assessment.
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Affiliation(s)
- Brooke R Druliner
- Division of Internal Medicine, Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiaoyang Ruan
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Hugues Sicotte
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Daniel O'Brien
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Hongfang Liu
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Jean-Pierre A Kocher
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Lisa Boardman
- Division of Internal Medicine, Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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11
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Hochman G, Halevi-Tobias K, Kogan Y, Agur Z. Extracellular inhibitors can attenuate tumorigenic Wnt pathway activity in adenomatous polyposis coli mutants: Predictions of a validated mathematical model. PLoS One 2017; 12:e0179888. [PMID: 28708837 PMCID: PMC5510801 DOI: 10.1371/journal.pone.0179888] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Despite considerable investigational efforts, no method to overcome the pathogenesis caused by loss of function (LoF) mutations in tumor suppressor genes has been successfully translated to the clinic. The most frequent LoF mutation in human cancers is Adenomatous polyposis coli (APC), causing aberrant activation of the Wnt pathway. In nearly all colon cancer tumors, the APC protein is truncated, but still retains partial binding abilities. Objective & methods Here, we tested the hypothesis that extracellular inhibitors of the Wnt pathway, although acting upstream of the APC mutation, can restore normal levels of pathway activity in colon cancer cells. To this end, we developed and simulated a mathematical model for the Wnt pathway in different APC mutants, with or without the effects of the extracellular inhibitors, Secreted Frizzled-Related Protein1 (sFRP1) and Dickhopf1 (Dkk1). We compared our model predictions to experimental data in the literature. Results Our model accurately predicts T-cell factor (TCF) activity in mutant cells that vary in APC mutation. Model simulations suggest that both sFRP1 and DKK1 can reduce TCF activity in APC1638N/1572T and Apcmin/min mutants, but restoration of normal activity levels is possible only in the former. When applied in combination, synergism between the two inhibitors can reduce their effective doses to one-fourth of the doses required under single inhibitor application. Overall, re-establishment of normal Wnt pathway activity is predicted for every APC mutant in whom TCF activity is increased by up to 11 fold. Conclusions Our work suggests that extracellular inhibitors can effectively restore normal Wnt pathway activity in APC-truncated cancer cells, even though these LoF mutations occur downstream of the inhibitory action. The insufficient activity of the truncated APC can be quantitatively balanced by the upstream intervention. This new concept of upstream intervention to control the effects of downstream mutations may be considered also for other partial LoF mutations in other signaling pathways.
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Affiliation(s)
- Gili Hochman
- Institute for Medical BioMathematics, Bene Ataroth, Israel
| | | | - Yuri Kogan
- Institute for Medical BioMathematics, Bene Ataroth, Israel
| | - Zvia Agur
- Institute for Medical BioMathematics, Bene Ataroth, Israel
- * E-mail:
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12
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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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13
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Eizuka M, Sugai T, Habano W, Uesugi N, Takahashi Y, Kawasaki K, Yamamoto E, Suzuki H, Matsumoto T. Molecular alterations in colorectal adenomas and intramucosal adenocarcinomas defined by high-density single-nucleotide polymorphism arrays. J Gastroenterol 2017; 52:1158-1168. [PMID: 28197804 PMCID: PMC5666076 DOI: 10.1007/s00535-017-1317-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/30/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND We examined colorectal adenomas and intramucosal adenocarcinomas (IMAs) to develop a genome-wide overview of copy number alterations (CNAs) during colorectal tumorigenesis. METHODS We analysed CNAs using a high-resolution SNP array of isolated tumour glands obtained from 55 colorectal adenomas (35 low-grade adenomas and 20 high-grade adenomas) and 30 IMAs. Next, we examined whether frequent CNAs differed between low-grade and high-grade adenomas or high-grade adenomas and IMAs. Finally, we investigated the total lengths of the CNAs in low-grade adenomas, high-grade adenomas, and IMAs. RESULTS Although no frequent CNAs were found in low-grade adenomas, the most frequent alterations of high-grade adenomas were gains of 7q11, 7q21 and 9p13 and loss of 5q14.3-35. High levels of gains were detected at 13q, 7q, 8p, 20q, 7p, 18p and 17p in IMAs. Although no frequent alteration differed between low-grade and high-grade adenomas, significant differences of gains at 13q, 17p and 18p were found between high-grade adenoma and IMAs. Although the total lengths of all CNAs (gains and losses), copy number gains, and losses of heterozygosity were significantly greater in high-grade adenomas than in low-grade adenomas, no significant differences in the lengths of CNAs were found between high-grade adenomas and IMAs. CONCLUSIONS Genomic alterations play an essential role in early colorectal carcinogenesis. CNAs in colorectal tumours provide new insights for evaluation of colorectal tumorigenesis.
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Affiliation(s)
- Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, 19-1, Uchimaru, Morioka, 020-8505 Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, 19-1, Uchimaru, Morioka, 020-8505 Japan
| | - Wataru Habano
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Noriyuki Uesugi
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, 19-1, Uchimaru, Morioka, 020-8505 Japan
| | - Yayoi Takahashi
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, 19-1, Uchimaru, Morioka, 020-8505 Japan
| | - Keisuke Kawasaki
- Division of Gastroenterology, Department of Internal Medicine, Iwate Medical University, Morioka, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, Iwate Medical University, Morioka, Japan
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14
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Barresi V, Castorina S, Musso N, Capizzi C, Luca T, Privitera G, Condorelli DF. Chromosomal instability analysis and regional tumor heterogeneity in colon cancer. Cancer Genet 2016; 210:9-21. [PMID: 28212810 DOI: 10.1016/j.cancergen.2016.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/11/2016] [Accepted: 11/14/2016] [Indexed: 01/24/2023]
Abstract
Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively). In 15 tumors, two samples, separated by at least 1 cm, were taken from the same tumor mass (double-sampling pairs) in order to evaluate differences in detection of chromosomal abnormalities between distant regions of the same tumor and their influence on CIN quantitative and qualitative analysis. Our data show a high degree of correlation of the quantitative CIN index (somatic BCNA number) between distant tumor regions. On the contrary, a lower correlation is observed in terms of chromosomal distribution of BCNAs, as summarized by a simplified cytogenetic table. Quantitative or qualitative analysis of FCNAs, including homozygous deletions and high level amplifications, did not add further information on the CIN status. The use of the index "somatic BCNA number" can be proposed for a robust classification of tumors as CIN positive or negative even in the presence of a significant tumor regional heterogeneity.
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Affiliation(s)
- Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Italy; Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy
| | - Sergio Castorina
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, University of Catania, Italy; Fondazione Mediterranea G.B. Morgagni, Catania, Italy
| | - Nicolò Musso
- Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy
| | - Carmela Capizzi
- Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy
| | - Tonia Luca
- Fondazione Mediterranea G.B. Morgagni, Catania, Italy
| | | | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Italy; Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy.
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15
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Perez RE, Shen H, Duan L, Kim RH, Kim T, Park NH, Maki CG. Modeling the Etiology of p53-mutated Cancer Cells. J Biol Chem 2016; 291:10131-47. [PMID: 27022024 DOI: 10.1074/jbc.m116.724781] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 12/23/2022] Open
Abstract
p53 gene mutations are among the most common alterations in cancer. In most cases, missense mutations in one TP53 allele are followed by loss-of-heterozygosity (LOH), so tumors express only mutant p53. TP53 mutations and LOH have been linked, in many cases, with poor therapy response and worse outcome. Despite this, remarkably little is known about how TP53 point mutations are acquired, how LOH occurs, or the cells involved. Nutlin-3a occupies the p53-binding site in MDM2 and blocks p53-MDM2 interaction, resulting in the stabilization and activation of p53 and subsequent growth arrest or apoptosis. We leveraged the powerful growth inhibitory activity of Nutlin-3a to select p53-mutated cells and examined how TP53 mutations arise and how the remaining wild-type allele is lost or inactivated. Mismatch repair (MMR)-deficient colorectal cancer cells formed heterozygote (p53 wild-type/mutant) colonies when cultured in low doses of Nutlin-3a, whereas MMR-corrected counterparts did not. Placing these heterozygotes in higher Nutlin-3a doses selected clones in which the remaining wild-type TP53 was silenced. Our data suggest silencing occurred through a novel mechanism that does not involve DNA methylation, histone methylation, or histone deacetylation. These data indicate MMR deficiency in colorectal cancer can give rise to initiating TP53 mutations and that TP53 silencing occurs via a copy-neutral mechanism. Moreover, the data highlight the use of MDM2 antagonists as tools to study mechanisms of TP53 mutation acquisition and wild-type allele loss or silencing in cells with defined genetic backgrounds.
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Affiliation(s)
- Ricardo E Perez
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| | - Hong Shen
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| | - Lei Duan
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
| | - Reuben H Kim
- The Shapiro Family Laboratory of Viral Oncology and Aging Research, UCLA School of Dentistry and David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Terresa Kim
- The Shapiro Family Laboratory of Viral Oncology and Aging Research, UCLA School of Dentistry and David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - No-Hee Park
- The Shapiro Family Laboratory of Viral Oncology and Aging Research, UCLA School of Dentistry and David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Carl G Maki
- From the Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois 60612 and
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16
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Abdel-Rahman WM, Lotsari-Salomaa JE, Kaur S, Niskakoski A, Knuutila S, Järvinen H, Mecklin JP, Peltomäki P. The Role of Chromosomal Instability and Epigenetics in Colorectal Cancers Lacking β-Catenin/TCF Regulated Transcription. Gastroenterol Res Pract 2016; 2016:6089658. [PMID: 27047543 PMCID: PMC4800109 DOI: 10.1155/2016/6089658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/15/2022] Open
Abstract
All colorectal cancer cell lines except RKO displayed active β-catenin/TCF regulated transcription. This feature of RKO was noted in familial colon cancers; hence our aim was to dissect its carcinogenic mechanism. MFISH and CGH revealed distinct instability of chromosome structure in RKO. Gene expression microarray of RKO versus 7 colon cancer lines (with active Wnt signaling) and 3 normal specimens revealed 611 differentially expressed genes. The majority of the tested gene loci were susceptible to LOH in primary tumors with various β-catenin localizations as a surrogate marker for β-catenin activation. The immunohistochemistry of selected genes (IFI16, RGS4, MCTP1, DGKI, OBCAM/OPCML, and GLIPR1) confirmed that they were differentially expressed in clinical specimens. Since epigenetic mechanisms can contribute to expression changes, selected target genes were evaluated for promoter methylation in patient specimens from sporadic and hereditary colorectal cancers. CMTM3, DGKI, and OPCML were frequently hypermethylated in both groups, whereas KLK10, EPCAM, and DLC1 displayed subgroup specificity. The overall fraction of hypermethylated genes was higher in tumors with membranous β-catenin. We identified novel genes in colorectal carcinogenesis that might be useful in personalized tumor profiling. Tumors with inactive Wnt signaling are a heterogeneous group displaying interaction of chromosomal instability, Wnt signaling, and epigenetics.
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Affiliation(s)
- Wael M. Abdel-Rahman
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research (SIMR), University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
| | | | - Sippy Kaur
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
| | - Anni Niskakoski
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland
| | - Heikki Järvinen
- Second Department of Surgery, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, 40620 Jyväskylä, Finland
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
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17
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Torabi K, Miró R, Fernández-Jiménez N, Quintanilla I, Ramos L, Prat E, del Rey J, Pujol N, Killian JK, Meltzer PS, Fernández PL, Ried T, Lozano JJ, Camps J, Ponsa I. Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer. Carcinogenesis 2015; 36:1103-10. [PMID: 26243311 PMCID: PMC4598814 DOI: 10.1093/carcin/bgv115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/06/2015] [Accepted: 07/29/2015] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer (CRC) is characterized by specific patterns of copy number alterations (CNAs), which helped with the identification of driver oncogenes and tumor suppressor genes (TSGs). More recently, the usage of single nucleotide polymorphism arrays provided information of copy number neutral loss of heterozygosity, thus suggesting the occurrence of somatic uniparental disomy (UPD) and uniparental polysomy (UPP) events. The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs and CNAs in sporadic CRC. Our results indicate that regions showing high frequencies of UPD/UPP mostly coincide with regions typically involved in genomic losses. Among them, chromosome arms 3p, 5q, 9q, 10q, 14q, 17p, 17q, 20p, 21q and 22q preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. Several regions affected by recurrent UPDs/UPPs contain well-known TSGs, as well as novel candidates such as ARID1A, DLC1, TCF7L2 and DMBT1. In addition, VCAN, FLT4, SFRP1 and GAS7 were also frequently involved in regions of UPD/UPP and displayed high levels of methylation. Finally, sequencing and fluorescence in situ hybridization analysis of the gene APC underlined that a somatic UPD event might represent the second hit to achieve biallelic inactivation of this TSG in colorectal tumors. In summary, our data define a profile of somatic UPDs/UPPs in sporadic CRC and highlights the importance of these events as a mechanism to achieve the inactivation of TSGs.
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Affiliation(s)
- Keyvan Torabi
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - Rosa Miró
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - Nora Fernández-Jiménez
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Present address: Epigenetics Group, International Agency for Research on Cancer 69008, Lyon, France
| | - Isabel Quintanilla
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Catalonia 08036, Spain
| | - Laia Ramos
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Present address: Unitat de Genòmica i Bioinformàtica, Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Catalonia 08916, Spain
| | - Esther Prat
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Present address: Laboratori de Genètica Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Catalonia 08908, Spain
| | - Javier del Rey
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - Núria Pujol
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain
| | - J Keith Killian
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro Luis Fernández
- Department of Pathology, Hospital Clínic/IDIBAPS, Universitat de Barcelona, Barcelona, Catalonia 08036, Spain and
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan José Lozano
- Bioinformatics Unit, CIBERehd, Barcelona, Catalonia 08036, Spain
| | - Jordi Camps
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Catalonia 08036, Spain, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Immaculada Ponsa
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia 08193, Spain,
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18
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Zarzour P, Boelen L, Luciani F, Beck D, Sakthianandeswaren A, Mouradov D, Sieber OM, Hawkins NJ, Hesson LB, Ward RL, Wong JWH. Single nucleotide polymorphism array profiling identifies distinct chromosomal aberration patterns across colorectal adenomas and carcinomas. Genes Chromosomes Cancer 2015; 54:303-14. [PMID: 25726927 DOI: 10.1002/gcc.22243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/11/2015] [Indexed: 11/07/2022] Open
Abstract
The progression of benign colorectal adenomas into cancer is associated with the accumulation of chromosomal aberrations. Even though patterns and frequencies of chromosomal aberrations have been well established in colorectal carcinomas, corresponding patterns of aberrations in adenomas are less well documented. The aim of this study was to profile chromosomal aberrations across colorectal adenomas and carcinomas to provide a better insight into key changes during tumor initiation and progression. Single nucleotide polymorphism array analysis was performed on 216 colorectal tumor/normal matched pairs, comprising 60 adenomas and 156 carcinomas. While many chromosomal aberrations were specific to carcinomas, those with the highest frequency in carcinomas (amplification of chromosome 7, 13q, and 20q; deletion of 17p and chromosome 18; LOH of 1p, chromosome 4, 5q, 8p, 17p, chromosome 18, and 20p) were also identified in adenomas. Hierarchical clustering using chromosomal aberrations revealed three distinct subtypes. Interestingly, these subtypes were only partially dependent on tumor staging. A cluster of colorectal cancer patients with frequent chromosomal deletions had the least favorable prognosis, and a number of adenomas (n = 9) were also present in the cluster suggesting that, at least in some tumors, the chromosomal aberration pattern is determined at a very early stage of tumor formation. Finally, analysis of LOH events revealed that copy-neutral/gain LOH (CN/G-LOH) is frequent (>10%) in carcinomas at 5q, 11q, 15q, 17p, chromosome 18, 20p, and 22q. Deletion of the corresponding region is sometimes present in adenomas, suggesting that LOH at these loci may play an important role in tumor initiation.
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Affiliation(s)
- Peter Zarzour
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
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19
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Sapkota Y. Germline DNA variations in breast cancer predisposition and prognosis: a systematic review of the literature. Cytogenet Genome Res 2014; 144:77-91. [PMID: 25401968 DOI: 10.1159/000369045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is the most common cancer and the second leading cause of death in women worldwide. The disease is caused by a combination of genetic, environmental, lifestyle, and reproductive risk factors. Linkage and family-based studies have identified many pathological germline mutations, which account for around 20% of the genetic risk of familial breast cancer. In recent years, single nucleotide polymorphism-based genetic association studies, especially genome-wide association studies (GWASs), have been very successful in uncovering low-penetrance common variants associated with breast cancer risk. These common variants alone may explain up to an additional 30% of the familial risk of breast cancer. With the advent of available genetic resources and growing collaborations among researchers across the globe, the much needed large sample size to capture variants with small effect sizes and low population frequencies is being addressed, and hence many more common variants are expected to be discovered in the coming days. Here, major GWASs conducted for breast cancer predisposition and prognosis until 2013 are summarized. Few studies investigating other forms of genetic variations contributing to breast cancer predisposition and disease outcomes are also discussed. Finally, the potential utility of the GWAS-identified variants in disease risk models and some future perspectives are presented.
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Affiliation(s)
- Yadav Sapkota
- The Neurogenetics Laboratory, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Qld., Australia
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Lourenço N, Hélias-Rodzewicz Z, Bachet JB, Brahimi-Adouane S, Jardin F, Tran van Nhieu J, Peschaud F, Martin E, Beauchet A, Chibon F, Emile JF. Copy-neutral loss of heterozygosity and chromosome gains and losses are frequent in gastrointestinal stromal tumors. Mol Cancer 2014; 13:246. [PMID: 25373456 PMCID: PMC4417285 DOI: 10.1186/1476-4598-13-246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Background A KIT gain of function mutation is present in 70% of gastrointestinal stromal tumors (GISTs) and the wild-type (WT) allele is deleted in 5 to 15% of these cases. The WT KIT is probably deleted during GIST progression. We aimed to identify the mechanism of WT KIT loss and to determine whether other genes are involved or affected. Methods Whole-genome SNP array analyses were performed in 22 GISTs with KIT exon 11 mutations, including 11 with WT loss, to investigate the mechanisms of WT allele deletion. CGH arrays and FISH were performed in some cases. Common genetic events were identified by SNP data analysis. The 9p21.3 locus was studied by multiplex quantification of genomic DNA. Results Chromosome instability involving the whole chromosome/chromosome arm (whole C/CA) was detected in 21/22 cases. The GISTs segregated in two groups based on their chromosome number: polyGISTs had numerous whole C/CA gains (mean 23, range [9 to 43]/3.11 [1 to 5]), whereas biGISTs had fewer aberrations. Whole C/CA losses were also frequent and found in both groups. There were numerous copy-neutral losses of heterozygosity (cnLOH) of whole C/CA in both polyGIST (7/9) and biGIST (9/13) groups. cnLOH were frequent on 4q, 11p, 11q, 1p, 2q, 3p and 10, and never involved 12p, 12q, 20p, 20q or 19q. Other genetic alterations included segmental chromosome abnormalities, complete bi-allelic deletions (homozygous deletions) and, more rarely, amplifications. Nine of 11 GISTs with homozygous KIT exon 11 mutations had cnLOH of chromosome 4. Conclusion The cnLOH of whole C/CA is a frequent genetic alteration in GISTs and is closely associated with homozygous mutations of KIT and WT allele deletion. Electronic supplementary material The online version of this article (doi:10.1186/1476-4598-13-246) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nelson Lourenço
- EA4340, Versailles University, Boulogne-Billancourt, France. .,Digestive Oncology Unit, Saint Louis Hospital, APHP, Paris, France.
| | - Zofia Hélias-Rodzewicz
- EA4340, Versailles University, Boulogne-Billancourt, France. .,Department of Pathology, Ambroise Paré Hospital, APHP, 9 Avenue Charles de Gaulle, Boulogne-Billancourt, France.
| | - Jean-Baptiste Bachet
- EA4340, Versailles University, Boulogne-Billancourt, France. .,Digestive Oncology Unit, Pitié Salpétrière Hospital, APHP, Paris, France.
| | | | - Fabrice Jardin
- Centre Henri Becquerel, INSERM U918, Université de Rouen, Rouen, France.
| | | | - Frédérique Peschaud
- EA4340, Versailles University, Boulogne-Billancourt, France. .,Department of Surgery, Ambroise Paré Hospital, APHP, Boulogne-Billancourt, France.
| | | | - Alain Beauchet
- EA4340, Versailles University, Boulogne-Billancourt, France. .,Clinical Research Unit, Ambroise Paré Hospital, APHP, Boulogne-Billancourt, France.
| | | | - Jean-François Emile
- EA4340, Versailles University, Boulogne-Billancourt, France. .,Department of Pathology, Ambroise Paré Hospital, APHP, 9 Avenue Charles de Gaulle, Boulogne-Billancourt, France.
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Geurts-Giele WRR, Leenen CHM, Dubbink HJ, Meijssen IC, Post E, Sleddens HFBM, Kuipers EJ, Goverde A, van den Ouweland AMW, van Lier MGF, Steyerberg EW, van Leerdam ME, Wagner A, Dinjens WNM. Somatic aberrations of mismatch repair genes as a cause of microsatellite-unstable cancers. J Pathol 2014; 234:548-59. [PMID: 25111426 DOI: 10.1002/path.4419] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/28/2014] [Accepted: 08/06/2014] [Indexed: 12/17/2022]
Abstract
Lynch syndrome (LS) is caused by germline mutations in mismatch repair (MMR) genes, resulting in microsatellite-unstable tumours. Approximately 35% of suspected LS (sLS) patients test negative for germline MMR gene mutations, hampering conclusive LS diagnosis. The aim of this study was to investigate somatic MMR gene aberrations in microsatellite-unstable colorectal and endometrial cancers of sLS patients negative for germline MMR gene mutations. Suspected LS cases were selected from a retrospective Clinical Genetics Department diagnostic cohort and from a prospective multicentre population-based study on LS in The Netherlands. In total, microsatellite-unstable tumours of 40 sLS patients (male/female 20/20, median age 57 years) were screened for somatic MMR gene mutations by next-generation sequencing. In addition, loss of heterozygosity (LOH) of the affected MMR genes in these tumours as well as in 68 LS-associated tumours and 27 microsatellite-unstable tumours with MLH1 promoter hypermethylation was studied. Of the sLS cases, 5/40 (13%) tumours had two pathogenic somatic mutations and 16/40 (40%) tumours had a (likely) pathogenic mutation and LOH. Overall, LOH of the affected MMR gene locus was observed in 24/39 (62%) tumours with informative LOH markers. Of the LS cases and the tumours with MLH1 promoter hypermethylation, 39/61 (64%) and 2/21 (10%) tumours, respectively, demonstrated LOH. Half of microsatellite-unstable tumours of sLS patients without germline MMR gene mutations had two (likely) deleterious somatic MMR gene aberrations, indicating their sporadic origin. Therefore, we advocate adding somatic mutation and LOH analysis of the MMR genes to the molecular diagnostic workflow of LS.
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Affiliation(s)
- Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre, Rotterdam, The Netherlands
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Bond CE, Nancarrow DJ, Wockner LF, Wallace L, Montgomery GW, Leggett BA, Whitehall VLJ. Microsatellite stable colorectal cancers stratified by the BRAF V600E mutation show distinct patterns of chromosomal instability. PLoS One 2014; 9:e91739. [PMID: 24651849 PMCID: PMC3961279 DOI: 10.1371/journal.pone.0091739] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/13/2014] [Indexed: 02/07/2023] Open
Abstract
The BRAF (V600E) mutation in colorectal cancers that are microsatellite stable (MSS) confers a poor patient prognosis, whereas BRAF mutant microsatellite-unstable (MSI) colorectal cancers have an excellent prognosis. BRAF wild type cancers are typically MSS and display chromosomal instability (CIN). CIN has not been extensively studied on a genome-wide basis in relation to BRAF mutational status in colorectal cancer. BRAF mutant/MSS (BRAFmut/MSS) cancers (n = 33) and BRAF mutant/MSI (BRAFmut/MSI) cancers (n = 30) were compared for presence of copy number aberrations (CNAs) indicative of CIN, with BRAF wild type/MSS (BRAFwt/MSS) cancers (n = 18) using Illumina CytoSNP-12 arrays. BRAFmut/MSS and BRAFwt/MSS cancers showed comparable numbers of CNAs/cancer at 32.8 and 29.8 respectively. However, there were differences in patterns of CNA length between MSS cohorts, with BRAFmut/MSS cancers having significantly greater proportions of focal CNAs compared to BRAFwt/MSS cancers (p<0.0001); whereas whole chromosomal arm CNAs were more common in BRAFwt/MSS cancers (p<0.0001). This related to a reduced average CNA length in BRAFmut/MSS compared to BRAFwt/MSS cancers (20.7 Mb vs 33.4 Mb;p<0.0001); and a smaller average percent of CIN affected genomes in BRAFmut/MSS compared to BRAFwt/MSS cancers (23.9% vs 34.9% respectively). BRAFmut/MSI cancers were confirmed to have low CNA rates (5.4/cancer) and minimal CIN-affected genomes (average of 4.5%) compared to MSS cohorts (p<0.0001). BRAFmut/MSS cancers had more frequent deletion CNAs compared to BRAFwt/MSS cancers on 6p and 17q at loci not typically correlated with colorectal cancer, and greater amplification CNAs on 8q and 18q compared to BRAFwt/MSS cancers. These results indicate that comparable rates of CIN occur between MSS subgroups, however significant differences in their patterns of instability exist, with BRAFmut/MSS cancers showing a ‘focal pattern’ and BRAFwt/MSS cancers having a ‘whole arm pattern’ of CIN. This and the genomic loci more frequently affected in BRAFmut/MSS cancers provides further evidence of the biological distinctions of this important cancer subgroup.
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Affiliation(s)
- Catherine E. Bond
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| | - Derek J. Nancarrow
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leesa F. Wockner
- Cancer and Population Studies Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leanne Wallace
- Molecular Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W. Montgomery
- Molecular Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Barbara A. Leggett
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vicki L. J. Whitehall
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Pathology Queensland, Brisbane, Queensland, Australia
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Bundschu K, Schuh K. Cardiovascular ATIP (Angiotensin receptor type 2 interacting protein) expression in mouse development. Dev Dyn 2014; 243:699-711. [DOI: 10.1002/dvdy.24102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/13/2013] [Accepted: 11/21/2013] [Indexed: 12/23/2022] Open
Affiliation(s)
- Karin Bundschu
- Institute of Biochemistry and Molecular Biology; University of Ulm; Ulm Germany
| | - Kai Schuh
- Institute of Physiology; University of Würzburg; Würzburg Germany
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Loo LWM, Tiirikainen M, Cheng I, Lum-Jones A, Seifried A, Church JM, Gryfe R, Weisenberger DJ, Lindor NM, Gallinger S, Haile RW, Duggan DJ, Thibodeau SN, Casey G, Le Marchand L. Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer. Genes Chromosomes Cancer 2013; 52:450-66. [PMID: 23341073 DOI: 10.1002/gcc.22043] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/04/2012] [Accepted: 12/16/2012] [Indexed: 12/11/2022] Open
Abstract
Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)-negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome-wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12-11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15-12, 4q12-35, 5q21-22, 6q26, 8p, 14q, 15q11-12, 17p, 18p, 18q, 21q21-22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P < 0.0001 and ±1.5-fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11-20q13 contained several cancer-related genes (AHCY, POFUT1, RPN2, TH1L, and PRPF6) that were upregulated and demonstrated a significant linear correlation (P < 0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer.
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Affiliation(s)
- Lenora W M Loo
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
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Sapkota Y, Ghosh S, Lai R, Coe BP, Cass CE, Yasui Y, Mackey JR, Damaraju S. Germline DNA copy number aberrations identified as potential prognostic factors for breast cancer recurrence. PLoS One 2013; 8:e53850. [PMID: 23342018 PMCID: PMC3547038 DOI: 10.1371/journal.pone.0053850] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/05/2012] [Indexed: 11/30/2022] Open
Abstract
Breast cancer recurrence (BCR) is a common treatment outcome despite curative-intent primary treatment of non-metastatic breast cancer. Currently used prognostic and predictive factors utilize tumor-based markers, and are not optimal determinants of risk of BCR. Germline-based copy number aberrations (CNAs) have not been evaluated as determinants of predisposition to experience BCR. In this study, we accessed germline DNA from 369 female breast cancer subjects who received curative-intent primary treatment following diagnosis. Of these, 155 experienced BCR and 214 did not, after a median duration of follow up after breast cancer diagnosis of 6.35 years (range = 0.60–21.78) and 8.60 years (range = 3.08–13.57), respectively. Whole genome CNA genotyping was performed on the Affymetrix SNP array 6.0 platform. CNAs were identified using the SNP-Fast Adaptive States Segmentation Technique 2 algorithm implemented in Nexus Copy Number 6.0. Six samples were removed due to poor quality scores, leaving 363 samples for further analysis. We identified 18,561 CNAs with ≥1 kb as a predefined cut-off for observed aberrations. Univariate survival analyses (log-rank tests) identified seven CNAs (two copy number gains and five copy neutral-loss of heterozygosities, CN-LOHs) showing significant differences (P<2.01×10−5) in recurrence-free survival (RFS) probabilities with and without CNAs.We also observed three additional but distinct CN-LOHs showing significant differences in RFS probabilities (P<2.86×10−5) when analyses were restricted to stratified cases (luminal A, n = 208) only. After adjusting for tumor stage and grade in multivariate analyses (Cox proportional hazards models), all the CNAs remained strongly associated with the phenotype of BCR. Of these, we confirmed three CNAs at 17q11.2, 11q13.1 and 6q24.1 in representative samples using independent genotyping platforms. Our results suggest further investigations on the potential use of germline DNA variations as prognostic markers in cancer-associated phenotypes.
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Affiliation(s)
- Yadav Sapkota
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sunita Ghosh
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Raymond Lai
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington, School of Medicine, Seattle, Washington, United States of America
| | - Carol E. Cass
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Yutaka Yasui
- Department of Public Health Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John R. Mackey
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Chromosomal instability in BRAF mutant, microsatellite stable colorectal cancers. PLoS One 2012; 7:e47483. [PMID: 23110075 PMCID: PMC3478278 DOI: 10.1371/journal.pone.0047483] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/12/2012] [Indexed: 01/05/2023] Open
Abstract
The BRAF oncogene is mutated in 15% of sporadic colorectal cancers. Approximately half of these BRAF mutant cancers demonstrate frequent frameshift mutations termed microsatellite instability (MSI), but are diploid and chromosomally stable. BRAF wild type cancers are typically microsatellite stable (MSS) and instead acquire chromosomal instability (CIN). In these cancers, CIN is associated with a poor outcome. BRAF mutant cancers that are MSS, typically present at an advanced stage and have a particularly poor prognosis. We have previously demonstrated clinical and molecular similarities between MSS cancers with or without a BRAF mutation, and therefore hypothesised that CIN may also be frequent in BRAF mutant/MSS cancers. BRAF mutant/MSS (n = 60), and BRAF wild type/MSS CRCs (n = 90) were investigated for CIN using loss of heterozygosity analysis over twelve loci encompassing chromosomal regions 5q, 8p, 17p and 18q. CIN was frequent in BRAF mutant/MSS cancers (41/57, 72%), which was comparable to the rate found in BRAF wild type/MSS cancers (74/90, 82%). The greatest loss in BRAF mutant/MSS cancers occurred at 8p (26/44, 59%), and the least at 5q (19/49, 39%). CIN in BRAF mutant/MSS cancers correlated with advanced stage (AJCC III/IV: 15/17, 88%; p = 0.02); showed high rates of co-occurrence with the CpG Island Methylator Phenotype (17/23, 74%); and CIN at 18q and 8p associated with worse survival (p = 0.02, p<0.05). This study demonstrates that CIN commonly occurs in advanced BRAF mutant/MSS colorectal cancers where it may contribute to poorer survival, and further highlights molecular similarities occurring between these and BRAF wild type cancers.
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Kanthan R, Senger JL, Kanthan SC. Molecular events in primary and metastatic colorectal carcinoma: a review. PATHOLOGY RESEARCH INTERNATIONAL 2012; 2012:597497. [PMID: 22997602 PMCID: PMC3357597 DOI: 10.1155/2012/597497] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 02/23/2012] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease, developing through a multipathway sequence of events guided by clonal selections. Pathways included in the development of CRC may be broadly categorized into (a) genomic instability, including chromosomal instability (CIN), microsatellite instability (MSI), and CpG island methylator phenotype (CIMP), (b) genomic mutations including suppression of tumour suppressor genes and activation of tumour oncogenes, (c) microRNA, and (d) epigenetic changes. As cancer becomes more advanced, invasion and metastases are facilitated through the epithelial-mesenchymal transition (EMT), with additional genetic alterations. Despite ongoing identification of genetic and epigenetic markers and the understanding of alternative pathways involved in the development and progression of this disease, CRC remains the second highest cause of malignancy-related mortality in Canada. The molecular events that underlie the tumorigenesis of primary and metastatic colorectal carcinoma are detailed in this manuscript.
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Affiliation(s)
- Rani Kanthan
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada S7N 0W8
- Royal University Hospital, Room 2868 G-Wing, 103 Hospital Drive, Saskatoon, SK, Canada S7N 0W8
| | - Jenna-Lynn Senger
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada S7N 0W8
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de Miranda NFCC, Hes FJ, van Wezel T, Morreau H. Role of the microenvironment in the tumourigenesis of microsatellite unstable and MUTYH-associated polyposis colorectal cancers. Mutagenesis 2012; 27:247-53. [DOI: 10.1093/mutage/ger077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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