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Risinskaya N, Gladysheva M, Abdulpatakhov A, Chabaeva Y, Surimova V, Aleshina O, Yushkova A, Dubova O, Kapranov N, Galtseva I, Kulikov S, Obukhova T, Sudarikov A, Parovichnikova E. DNA Copy Number Alterations and Copy Neutral Loss of Heterozygosity in Adult Ph-Negative Acute B-Lymphoblastic Leukemia: Focus on the Genes Involved. Int J Mol Sci 2023; 24:17602. [PMID: 38139431 PMCID: PMC10744257 DOI: 10.3390/ijms242417602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The landscape of chromosomal aberrations in the tumor cells of the patients with B-ALL is diverse and can influence the outcome of the disease. Molecular karyotyping at the onset of the disease using chromosomal microarray (CMA) is advisable to identify additional molecular factors associated with the prognosis of the disease. Molecular karyotyping data for 36 patients with Ph-negative B-ALL who received therapy according to the ALL-2016 protocol are presented. We analyzed copy number alterations and their prognostic significance for CDKN2A/B, DMRTA, DOCK8, TP53, SMARCA2, PAX5, XPA, FOXE1, HEMGN, USP45, RUNX1, NF1, IGF2BP1, ERG, TMPRSS2, CRLF2, FGFR3, FLNB, IKZF1, RUNX2, ARID1B, CIP2A, PIK3CA, ATM, RB1, BIRC3, MYC, IKZF3, ETV6, ZNF384, PTPRJ, CCL20, PAX3, MTCH2, TCF3, IKZF2, BTG1, BTG2, RAG1, RAG2, ELK3, SH2B3, EP300, MAP2K2, EBI3, MEF2D, MEF2C, CEBPA, and TBLXR1 genes, choosing t(4;11) and t(7;14) as reference events. Of the 36 patients, only 5 (13.8%) had a normal molecular karyotype, and 31 (86.2%) were found to have various molecular karyotype abnormalities-104 deletions, 90 duplications or amplifications, 29 cases of cnLOH and 7 biallelic/homozygous deletions. We found that 11q22-23 duplication involving the BIRC3, ATM and MLL genes was the most adverse prognostic event in the study cohort.
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Affiliation(s)
- Natalya Risinskaya
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Maria Gladysheva
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Abdulpatakh Abdulpatakhov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Yulia Chabaeva
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Valeriya Surimova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Olga Aleshina
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Anna Yushkova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Olga Dubova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
- Institute of Biodesign and Modeling of Complex Systems, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Nikolay Kapranov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Irina Galtseva
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Sergey Kulikov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Tatiana Obukhova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Andrey Sudarikov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Elena Parovichnikova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
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2
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Khalil AIS, Muzaki SRBM, Chattopadhyay A, Sanyal A. Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines. BMC Bioinformatics 2020; 21:506. [PMID: 33160308 PMCID: PMC7648276 DOI: 10.1186/s12859-020-03832-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 10/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background Hi-C and its variant techniques have been developed to capture the spatial organization of chromatin. Normalization of Hi-C contact map is essential for accurate modeling and interpretation of high-throughput chromatin conformation capture (3C) experiments. Hi-C correction tools were originally developed to normalize systematic biases of karyotypically normal cell lines. However, a vast majority of available Hi-C datasets are derived from cancer cell lines that carry multi-level DNA copy number variations (CNVs). CNV regions display over- or under-representation of interaction frequencies compared to CN-neutral regions. Therefore, it is necessary to remove CNV-driven bias from chromatin interaction data of cancer cell lines to generate a euploid-equivalent contact map. Results We developed the HiCNAtra framework to compute high-resolution CNV profiles from Hi-C or 3C-seq data of cancer cell lines and to correct chromatin contact maps from systematic biases including CNV-associated bias. First, we introduce a novel ‘entire-fragment’ counting method for better estimation of the read depth (RD) signal from Hi-C reads that recapitulates the whole-genome sequencing (WGS)-derived coverage signal. Second, HiCNAtra employs a multimodal-based hierarchical CNV calling approach, which outperformed OneD and HiNT tools, to accurately identify CNVs of cancer cell lines. Third, incorporating CNV information with other systematic biases, HiCNAtra simultaneously estimates the contribution of each bias and explicitly corrects the interaction matrix using Poisson regression. HiCNAtra normalization abolishes CNV-induced artifacts from the contact map generating a heatmap with homogeneous signal. When benchmarked against OneD, CAIC, and ICE methods using MCF7 cancer cell line, HiCNAtra-corrected heatmap achieves the least 1D signal variation without deforming the inherent chromatin interaction signal. Additionally, HiCNAtra-corrected contact frequencies have minimum correlations with each of the systematic bias sources compared to OneD’s explicit method. Visual inspection of CNV profiles and contact maps of cancer cell lines reveals that HiCNAtra is the most robust Hi-C correction tool for ameliorating CNV-induced bias. Conclusions HiCNAtra is a Hi-C-based computational tool that provides an analytical and visualization framework for DNA copy number profiling and chromatin contact map correction of karyotypically abnormal cell lines. HiCNAtra is an open-source software implemented in MATLAB and is available at https://github.com/AISKhalil/HiCNAtra.
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Affiliation(s)
- Ahmed Ibrahim Samir Khalil
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | | | - Anupam Chattopadhyay
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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3
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Khalil AIS, Khyriem C, Chattopadhyay A, Sanyal A. Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes. BMC Bioinformatics 2020; 21:147. [PMID: 32299346 PMCID: PMC7160937 DOI: 10.1186/s12859-020-3480-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
Background Detection of DNA copy number alterations (CNAs) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales, and distinct biological origins and functions. Although several computational tools are available to identify CNAs using read depth (RD) signal, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. Additionally, RD signal is affected by overdispersion-driven biases at low coverage, which significantly inflate false detection of CNA regions. Results We have developed CNAtra framework to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from a single whole-genome sequencing (WGS) sample. CNAtra first utilizes a multimodal-based distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We implemented Savitzky-Golay smoothing filter and Modified Varri segmentation to capture the change points of the RD signal. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy numbers. Next, we identified focal alterations in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. Using cancer cell lines and patient datasets, we confirmed CNAtra’s ability to detect and distinguish the segmental aneuploidies and focal alterations. We used realistic simulated data for benchmarking the performance of CNAtra against other single-sample detection tools, where we artificially introduced CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall and f-measure. CNAtra shows the highest sensitivity of 93 and 97% for detecting large-scale and focal alterations respectively. Visual inspection of CNAs revealed that CNAtra is the most robust detection tool for low-coverage cancer data. Conclusions CNAtra is a single-sample CNA detection tool that provides an analytical and visualization framework for CNA profiling without relying on any reference control. It can detect chromosome-level segmental aneuploidies and high-confidence focal alterations, even from low-coverage data. CNAtra is an open-source software implemented in MATLAB®. It is freely available at https://github.com/AISKhalil/CNAtra.
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Affiliation(s)
- Ahmed Ibrahim Samir Khalil
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Costerwell Khyriem
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Anupam Chattopadhyay
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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4
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Singh R, Bassett E, Chakravarti A, Parthun MR. Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function. Nucleic Acids Res 2019; 46:8665-8678. [PMID: 30165676 PMCID: PMC6158624 DOI: 10.1093/nar/gky768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/24/2018] [Indexed: 12/11/2022] Open
Abstract
Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Bassett
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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5
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Fiedler D, Heselmeyer-Haddad K, Hirsch D, Hernandez LS, Torres I, Wangsa D, Hu Y, Zapata L, Rueschoff J, Belle S, Ried T, Gaiser T. Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence. Int J Cancer 2018; 144:1561-1573. [PMID: 30229897 DOI: 10.1002/ijc.31869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence rates are high. We collected formalin-fixed paraffin-embedded tissue of 15 primary adenomas with recurrence, 15 adenomas without recurrence, and 14 matched pair samples (primary adenoma and the corresponding recurrent adenoma). The samples were analysed by array-comparative genomic hybridisation (aCGH) and single-cell multiplex interphase fluorescence in situ hybridisation (miFISH) to understand clonal evolution, to examine the dynamics of copy number alterations (CNAs) and to identify molecular markers for recurrence prediction. The miFISH probe panel consisted of 14 colorectal carcinogenesis-relevant genes (COX2, PIK3CA, APC, CLIC1, EGFR, MYC, CCND1, CDX2, CDH1, TP53, HER2, SMAD7, SMAD4 and ZNF217), and a centromere probe (CEP10). The aCGH analysis confirmed the genetic landscape typical for colorectal tumorigenesis, that is, CNAs of chromosomes 7, 13q, 18 and 20q. Focal aberrations (≤10 Mbp) were mapped to chromosome bands 6p22.1-p21.33 (33.3%), 7q22.1 (31.4%) and 16q21 (29.4%). MiFISH detected gains of EGFR (23.6%), CDX2 (21.8%) and ZNF217 (18.2%). Most adenomas exhibited a major clone population which was accompanied by multiple smaller clone populations. Gains of CDX2 were exclusively seen in primary adenomas with recurrence (25%) compared to primary adenomas without recurrence (0%). Generation of phylogenetic trees for matched pair samples revealed four distinct patterns of clonal dynamics. In conclusion, adenoma development and recurrence are complex genetic processes driven by multiple CNAs whose evaluations by miFISH, with emphasis on CDX2, might serve as a predictor of recurrence.
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Affiliation(s)
- David Fiedler
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniela Hirsch
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Leanora S Hernandez
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.,Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CGR), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Sebastian Belle
- Department of Internal Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Central Interdisciplinary Endoscopy Unit, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Fujita Y, Taguri M, Yamazaki K, Tsurutani J, Sakai K, Tsushima T, Nagase M, Tamagawa H, Ueda S, Tamura T, Tsuji Y, Murata K, Taira K, Denda T, Moriwaki T, Funai S, Nakajima TE, Muro K, Tsuji A, Yoshida M, Suyama K, Kurimoto T, Sugimoto N, Baba E, Seki N, Sato M, Shimura T, Boku N, Hyodo I, Yamanaka T, Nishio K. aCGH Analysis of Predictive Biomarkers for Response to Bevacizumab plus Oxaliplatin- or Irinotecan-Based Chemotherapy in Patients with Metastatic Colorectal Cancer. Oncologist 2018; 24:327-337. [PMID: 30425180 DOI: 10.1634/theoncologist.2018-0119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/05/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The randomized phase III study (WJOG4407G) showed equivalent efficacy between FOLFOX and FOLFIRI in combination with bevacizumab as the first-line treatment for metastatic colorectal cancer (mCRC). We studied whole genome copy number profiles using array-based comparative genomic hybridization (aCGH) analysis of tumor tissue samples obtained in this study. The aim of this study was to identify gene copy number alterations that could aid in selecting either FOLFOX or FOLFIRI in combination with bevacizumab for patients with mCRC. MATERIALS AND METHODS DNA was purified from 154 pretreatment formalin-fixed paraffin-embedded tissue samples (75 from the FOLFOX arm and 79 from the FOLFIRI arm) of 395 patients enrolled in the WJOG4407G trial and analyzed by aCGH. Genomic regions greater than 1.2-fold were regarded as copy number gain (CNG). RESULTS Patient characteristics between the treatment arms were well balanced except for tumor laterality (left side; 64% in FOLFOX arm and 80% in FOLFIRI arm, p = .07). FOLFIRI showed a trend toward better response rate (RR), progression-free survival (PFS) and overall survival (OS) than FOLFOX in the patients with CNG of chromosome 8q24.1 (Fisher's exact test, p = .134 for RR; interaction test, p = .102 for PFS and p = .003 for OS) and 8q24.2 (Fisher's exact test, p = .179 for RR; interaction test, p = .144 for PFS and p = .002 for OS). CONCLUSION Chromosome 8q24.1-q24.2 may contain genes that could potentially serve as predictive markers for selecting either FOLFOX or FOLFIRI in combination with bevacizumab for treatment of patients with mCRC. IMPLICATIONS FOR PRACTICE Bevacizumab has been used as a standard first-line treatment for patients with metastatic colorectal cancer (mCRC) in combination with either oxaliplatin-based or irinotecan-based chemotherapy. Until now, there has been no predictive marker to choose between the two combination chemotherapies. This array-based comparative genomic hybridization analysis revealed that the difference in therapeutic effect between the two combination chemotherapies is prominent in patients with mCRC with gene copy number gain in chromosome 8p24.1-p24.2. Such patients showed more favorable response and survival when treated with irinotecan-based combination chemotherapy. Overlapping genes commonly found in this region may be predictive biomarkers of the efficacy of the combination chemotherapy with bevacizumab.
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Affiliation(s)
- Yoshihiko Fujita
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Masataka Taguri
- Department of Biostatistics, Yokohama City University School of Medicine, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Junji Tsurutani
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Takahiro Tsushima
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Michitaka Nagase
- Department of Clinical Oncology, Jichi Medical University, Shimotsuke, Japan
| | - Hiroshi Tamagawa
- Department of Surgery, Osaka General Medical Center, Osaka, Japan
| | - Shinya Ueda
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Takao Tamura
- Department of Medical Oncology, Nara Hospital Kindai University Faculty of Medicine, Ikoma, Japan
| | - Yasushi Tsuji
- Department of Medical Oncology, Tonan Hospital, Sapporo, Japan
| | - Kohei Murata
- Department of Surgery, Suita Municipal Hospital, Suita, Japan
| | - Koichi Taira
- Department of Clinical Oncology, Osaka City General Hospital, Osaka, Japan
| | - Tadamichi Denda
- Division of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | | | - Sadao Funai
- Department of Surgery, Sakai Hospital Kindai University Faculty of Medicine, Sakai, Japan
| | - Takako Eguchi Nakajima
- Department of Clinical Oncology, St Marianna University School of Medicine, Kawasaki, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Akihito Tsuji
- Department of Medical Oncology, Kochi Health Sciences Center, Kochi, Japan
| | - Motoki Yoshida
- Division of Cancer Chemotherapy Center, Osaka Medical College Hospital, Takatsuki, Japan
| | - Koichi Suyama
- Department of Medical Oncology, Toranomon Hospital, Tokyo, Japan
| | - Takuya Kurimoto
- Department of Gastrointestinal Oncology, Nagoya Kyoritsu Hospital, Nagoya, Japan
| | - Naotoshi Sugimoto
- Department of Clinical Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Eishi Baba
- Department of Comprehensive Clinical Oncology, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Nobuhiko Seki
- Division of Medical Oncology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Mikio Sato
- Department of Gastroenterology and Hepatology, Ryugasaki Saiseikai Hospital, Ryugasaki, Japan
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Narikazu Boku
- Department of Clinical Oncology, St Marianna University School of Medicine, Kawasaki, Japan
| | - Ichinosuke Hyodo
- Division of Gastroenterology, University of Tsukuba, Tsukuba, Japan
| | - Takeharu Yamanaka
- Department of Biostatistics, Yokohama City University School of Medicine, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
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7
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Oliveira DM, Santamaria G, Laudanna C, Migliozzi S, Zoppoli P, Quist M, Grasso C, Mignogna C, Elia L, Faniello MC, Marinaro C, Sacco R, Corcione F, Viglietto G, Malanga D, Rizzuto A. Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data. Oncotarget 2018; 9:20409-20425. [PMID: 29755661 PMCID: PMC5945505 DOI: 10.18632/oncotarget.24912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 02/28/2018] [Indexed: 01/20/2023] Open
Abstract
The objective of this study was to determine the feasibility to detect copy number alterations in colon cancer samples using Next Generation Sequencing data and to elucidate the association between copy number alterations in specific genes and the development of cancer in different colon segments. We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm. Overall, we have found a total of 748 significant copy number alterations in 230 significant genes, of which 143 showed CN losses and 87 showed CN gains. Validation of results was performed on 20 representative genes by quantitative qPCR and/or immunostaining. By this analysis, we have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments (defined "common genes") and the presence of copy number alterations in 14 genes that were significantly associated to one specific site (defined "site-associated genes"). Finally, copy number alterations in ASXL1, TSC1 and IL7R turned out to be clinically relevant since the loss of TSC1 and IL7R was associated with advanced stages and/or reduced survival whereas copy number gain of ASXL1 was associated with good prognosis.
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Affiliation(s)
- Duarte Mendes Oliveira
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Gianluca Santamaria
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Carmelo Laudanna
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Simona Migliozzi
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Pietro Zoppoli
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Michael Quist
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catie Grasso
- University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Chiara Mignogna
- Dipartimento di Scienze della Salute, Università Magna Graecia, Catanzaro, Italy
| | - Laura Elia
- Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Graecia, Catanzaro, Italy
| | | | - Cinzia Marinaro
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Rosario Sacco
- Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Graecia, Catanzaro, Italy
| | | | - Giuseppe Viglietto
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Donatella Malanga
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Antonia Rizzuto
- Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Graecia, Catanzaro, Italy
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8
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Abstract
Background With one million new cases of colorectal cancer (CRC) diagnosed annually in the world, CRC is the third most commonly diagnosed cancer in the Western world. Patients with stage I-III CRC can be cured with surgery but are at risk for recurrence. Colorectal cancer is characterized by the presence of chromosomal deletions and gains. Large genomic profiling studies have however not been conducted in this disease. The number of a specific genetic aberration in a tumour sample could correlate with recurrence-free survival or overall survival, possibly leading to its use as biomarker for therapeutic decisions. At this point there are not sufficient markers for prediction of disease recurrence in colorectal cancer, which can be used in the clinic to discriminate between stage II patients who will benefit from adjuvant chemotherapy. For instance, the benefit of adjuvant chemotherapy has been most clearly demonstrated in stage III disease with an approximately 30 percent relative reduction in the risk of disease recurrence. The benefits of adjuvant chemotherapy in stage II disease are less certain, the risk for relapse is much smaller in the overall group and the specific patients at risk are hard to identify. Materials and Methods In this study, array-comparative genomic hybridization analysis (array-CGH) was applied to study high-resolution DNA copy number alterations in 93 colon carcinoma samples. These genomic data were combined with parameters like KRAS mutation status, microsatellite status and clinicopathological characteristics. Results Both large and small chromosomal losses and gains were identified in our sample cohort. Recurrent gains were found for chromosome 1q, 7, 8q, 13 and 20 and losses were mostly found for 1p, 4, 8p, 14, 15, 17p, 18, 21 and 22. Data analysis demonstrated that loss of chromosome 4 is linked to a worse prognosis in our patients series. Besides these alterations, two interesting small regions of overlap were identified, which could be associated with disease recurrence. Gain of the 16p13.3 locus (including the RNA binding protein, fox-1 homolog gene, RBFOX1) was linked with a worse recurrence-free survival in our patient cohort. On the other hand, loss of RBFOX1 was only found in patients without disease recurrence. Most interestingly, above mentioned characteristics were also found in stage II patients, for whom there is a high medical need for the identification of new prognostic biomarkers. Conclusions In conclusion, copy number variation of the 16p13.3 locus seems to be an important parameter for prediction of disease recurrence in colon cancer.
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9
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Both J, Krijgsman O, Bras J, Schaap GR, Baas F, Ylstra B, Hulsebos TJM. Focal chromosomal copy number aberrations identify CMTM8 and GPR177 as new candidate driver genes in osteosarcoma. PLoS One 2014; 9:e115835. [PMID: 25551557 PMCID: PMC4281204 DOI: 10.1371/journal.pone.0115835] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/01/2014] [Indexed: 12/04/2022] Open
Abstract
Osteosarcoma is an aggressive bone tumor that preferentially develops in adolescents. The tumor is characterized by an abundance of genomic aberrations, which hampers the identification of the driver genes involved in osteosarcoma tumorigenesis. Our study aims to identify these genes by the investigation of focal copy number aberrations (CNAs, <3 Mb). For this purpose, we subjected 26 primary tumors of osteosarcoma patients to high-resolution single nucleotide polymorphism array analyses and identified 139 somatic focal CNAs. Of these, 72 had at least one gene located within or overlapping the focal CNA, with a total of 94 genes. For 84 of these genes, the expression status in 31 osteosarcoma samples was determined by expression microarray analysis. This enabled us to identify the genes of which the over- or underexpression was in more than 35% of cases in accordance to their copy number status (gain or loss). These candidate genes were subsequently validated in an independent set and furthermore corroborated as driver genes by verifying their role in other tumor types. We identified CMTM8 as a new candidate tumor suppressor gene and GPR177 as a new candidate oncogene in osteosarcoma. In osteosarcoma, CMTM8 has been shown to suppress EGFR signaling. In other tumor types, CMTM8 is known to suppress the activity of the oncogenic protein c-Met and GPR177 is known as an overexpressed upstream regulator of the Wnt-pathway. Further studies are needed to determine whether these proteins also exert the latter functions in osteosarcoma tumorigenesis.
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Affiliation(s)
- Joeri Both
- Department of Genome Analysis, Academic Medical Center, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Johannes Bras
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Gerard R. Schaap
- Department of Orthopedic Surgery, Academic Medical Center, Amsterdam, The Netherlands
| | - Frank Baas
- Department of Genome Analysis, Academic Medical Center, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Theo J. M. Hulsebos
- Department of Genome Analysis, Academic Medical Center, Amsterdam, The Netherlands
- * E-mail:
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10
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Krijgsman O, Benner C, Meijer GA, van de Wiel MA, Ylstra B. FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations. Cancer Inform 2014; 13:153-6. [PMID: 25506197 PMCID: PMC4251178 DOI: 10.4137/cin.s19519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 11/05/2022] Open
Abstract
In order to identify somatic focal copy number aberrations (CNAs) in cancer specimens and to distinguish them from germ-line copy number variations (CNVs), we developed the software package FocalCall. FocalCall enables user-defined size cutoffs to recognize focal aberrations and builds on established array comparative genomic hybridization segmentation and calling algorithms. To distinguish CNAs from CNVs, the algorithm uses matched patient normal signals as references or, if this is not available, a list with known CNVs in a population. Furthermore, FocalCall differentiates between homozygous and heterozygous deletions as well as between gains and amplifications and is applicable to high-resolution array and sequencing data.
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Affiliation(s)
- Oscar Krijgsman
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Christian Benner
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands. ; Department of Mathematics, VU University Amsterdam, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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11
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Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJM, van de Wiel MA, Israeli D, van Essen HF, van Grieken NCT, Voorham QJM, Bosch LJW, Qu X, Kabbarah O, Verheul HMW, Nagtegaal ID, Punt CJA, Ylstra B, Meijer GA. Genomic landscape of metastatic colorectal cancer. Nat Commun 2014; 5:5457. [PMID: 25394515 PMCID: PMC4243240 DOI: 10.1038/ncomms6457] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022] Open
Abstract
Response to drug therapy in individual colorectal cancer (CRC) patients is associated with tumour biology. Here we describe the genomic landscape of tumour samples of a homogeneous well-annotated series of patients with metastatic CRC (mCRC) of two phase III clinical trials, CAIRO and CAIRO2. DNA copy number aberrations of 349 patients are determined. Within three treatment arms, 194 chromosomal subregions are associated with progression-free survival (PFS; uncorrected single-test P-values <0.005). These subregions are filtered for effect on messenger RNA expression, using an independent data set from The Cancer Genome Atlas which returned 171 genes. Three chromosomal regions are associated with a significant difference in PFS between treatment arms with or without irinotecan. One of these regions, 6q16.1–q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of mCRC reveals a number of DNA copy number aberrations associated with response to drug therapy. Response to drug therapy in colorectal cancer (CRC) patients has been associated with tumour heterogeneity. Here the authors analyse DNA copy number aberrations in primary tumours from CRC patients and identify genetic variants that influence drug response.
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Affiliation(s)
- Josien C Haan
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jolien Tol
- Department of Medical Oncology, Radboud University Medical Centre, Route 452, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Leonie J M Mekenkamp
- Department of Pathology, Radboud University Medical Centre, Huispost 824, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Danielle Israeli
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Hendrik F van Essen
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Quirinus J M Voorham
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Linda J W Bosch
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Xueping Qu
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 USA
| | - Omar Kabbarah
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 USA
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Centre, Huispost 824, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, PO Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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12
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Orsetti B, Selves J, Bascoul-Mollevi C, Lasorsa L, Gordien K, Bibeau F, Massemin B, Paraf F, Soubeyran I, Hostein I, Dapremont V, Guimbaud R, Cazaux C, Longy M, Theillet C. Impact of chromosomal instability on colorectal cancer progression and outcome. BMC Cancer 2014; 14:121. [PMID: 24559140 PMCID: PMC4233623 DOI: 10.1186/1471-2407-14-121] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/07/2014] [Indexed: 01/16/2023] Open
Abstract
Background It remains presently unclear whether disease progression in colorectal carcinoma (CRC), from early, to invasive and metastatic forms, is associated to a gradual increase in genetic instability and to a scheme of sequentially occurring Copy Number Alterations (CNAs). Methods In this work we set to determine the existence of such links between CRC progression and genetic instability and searched for associations with patient outcome. To this aim we analyzed a set of 162 Chromosomal Instable (CIN) CRCs comprising 131 primary carcinomas evenly distributed through stage 1 to 4, 31 metastases and 14 adenomas by array-CGH. CNA profiles were established according to disease stage and compared. We, also, asked whether the level of genomic instability was correlated to disease outcome in stage 2 and 3 CRCs. Two metrics of chromosomal instability were used; (i) Global Genomic Index (GGI), corresponding to the fraction of the genome involved in CNA, (ii) number of breakpoints (nbBP). Results Stage 1, 2, 3 and 4 tumors did not differ significantly at the level of their CNA profiles precluding the conventional definition of a progression scheme based on increasing levels of genetic instability. Combining GGI and nbBP,we classified genomic profiles into 5 groups presenting distinct patterns of chromosomal instability and defined two risk classes of tumors, showing strong differences in outcome and hazard risk (RFS: p = 0.012, HR = 3; OS: p < 0.001, HR = 9.7). While tumors of the high risk group were characterized by frequent fractional CNAs, low risk tumors presented predominantly whole chromosomal arm CNAs. Searching for CNAs correlating with negative outcome we found that losses at 16p13.3 and 19q13.3 observed in 10% (7/72) of stage 2–3 tumors showed strong association with early relapse (p < 0.001) and death (p < 0.007, p < 0.016). Both events showed frequent co-occurrence (p < 1x10-8) and could, therefore, mark for stage 2–3 CRC susceptible to negative outcome. Conclusions Our data show that CRC disease progression from stage 1 to stage 4 is not paralleled by increased levels of genetic instability. However, they suggest that stage 2–3 CRC with elevated genetic instability and particularly profiles with fractional CNA represent a subset of aggressive tumors.
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13
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Mekenkamp LJM, Haan JC, Israeli D, van Essen HFB, Dijkstra JR, van Cleef P, Punt CJA, Meijer GA, Nagtegaal ID, Ylstra B. Chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts and differences are typically non-recurrent. PLoS One 2014; 9:e86833. [PMID: 24505270 PMCID: PMC3914793 DOI: 10.1371/journal.pone.0086833] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/16/2013] [Indexed: 12/22/2022] Open
Abstract
The metastatic process is complex and remains a major obstacle in the management of colorectal cancer. To gain a better insight into the pathology of metastasis, we investigated genomic aberrations in a large cohort of matched colorectal cancer primaries and distant metastases from various sites by high resolution array comparative genomic hybridization. In total, 62 primary colorectal cancers, and 68 matched metastases (22 liver, 11 lung, 12 ovary, 12 omentum, and 11 distant lymph nodes) were analyzed. Public datasets were used for validation purposes. Metastases resemble their matched primary tumors in the majority of the patients. This validates the significant overlap in chromosomal aberrations between primary tumors and corresponding metastases observed previously. We observed 15 statistically significant different regions between the primary tumors and their matched metastases, of which only one recurrent event in metastases was observed. We conclude, based on detailed analysis and large independent datasets, that chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts, and differences are typically non-recurrent.
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Affiliation(s)
- Leonie J. M. Mekenkamp
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Josien C. Haan
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Daniëlle Israeli
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Jeroen R. Dijkstra
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Patricia van Cleef
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Cornelis J. A. Punt
- Department of Medical Oncology, Academic Medical Center, Amsterdam, The Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Iris D. Nagtegaal
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail:
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14
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Labots M, Buffart TE, Haan JC, van Grieken NCT, Tijssen M, van de Velde CJH, Grabsch HI, Ylstra B, Carvalho B, Fijneman RJA, Verheul HMW, Meijer GA. High-level copy number gains of established and potential drug target genes in gastric cancer as a lead for treatment development and selection. Cell Oncol (Dordr) 2013; 37:41-52. [PMID: 24379144 DOI: 10.1007/s13402-013-0162-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2013] [Indexed: 01/20/2023] Open
Abstract
PURPOSE The overall survival rate of patients with advanced gastric cancer is poor. Therefore, there is an urgent need for new treatment options for these patients. The identification of drug target genes located on DNA regions exhibiting high-level copy number gains (CNG) may be an effective approach, as has e.g. previously been shown for HER2. The aim of the present study was to identify putative drug targets in patients with gastric cancer by applying this strategy. METHODS Genome-wide array comparative genomic hybridization (array CGH) data available from 183 primary gastric cancer samples were analyzed through Ingenuity Pathway Analysis (IPA) to assess whether any established or potential anticancer drug target genes showed high-level CNG, including focal amplifications. RESULTS A total of 147 high-level gained regions were identified in the gastric cancer samples, harboring 167 genes that had previously been annotated as drug target genes. Thirty (18 %) of these genes showed high-level gains in at least 2 % of the tumors. The identified drug target genes included those for drugs known to be active in advanced (gastric) cancer, targets for targeted therapies in clinical development, as well as targets for drugs currently used for other indications but of potential interest for anticancer treatment. In addition, 12 potential drug target genes were identified, including genes involved in growth factor signaling and cell cycle regulation. CONCLUSION The majority of gastric cancers carried one or more high-level CNGs or focal amplifications encompassing putative drug target genes. A number of the associated drugs are currently not being considered for treatment of gastric cancer. Based on these results we hypothesize that DNA copy number profiling may be a useful tool to identify new drug targets and to guide individualized treatment strategies in patients with gastric cancer.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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15
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Identification of candidate driver genes in common focal chromosomal aberrations of microsatellite stable colorectal cancer. PLoS One 2013; 8:e83859. [PMID: 24367615 PMCID: PMC3867468 DOI: 10.1371/journal.pone.0083859] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/08/2013] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Chromosomal instability (CIN) is a major driving force of microsatellite stable (MSS) sporadic CRC. CIN tumours are characterised by a large number of somatic chromosomal copy number aberrations (SCNA) that frequently affect oncogenes and tumour suppressor genes. The main aim of this work was to identify novel candidate CRC driver genes affected by recurrent and focal SCNA. High resolution genome-wide comparative genome hybridisation (CGH) arrays were used to compare tumour and normal DNA for 53 sporadic CRC cases. Context corrected common aberration (COCA) analysis and custom algorithms identified 64 deletions and 32 gains of focal minimal common regions (FMCR) at high frequency (>10%). Comparison of these FMCR with published genomic profiles from CRC revealed common overlap (42.2% of deletions and 34.4% of copy gains). Pathway analysis showed that apoptosis and p53 signalling pathways were commonly affected by deleted FMCR, and MAPK and potassium channel pathways by gains of FMCR. Candidate tumour suppressor genes in deleted FMCR included RASSF3, IFNAR1, IFNAR2 and NFKBIA and candidate oncogenes in gained FMCR included PRDM16, TNS1, RPA3 and KCNMA1. In conclusion, this study confirms some previously identified aberrations in MSS CRC and provides in silico evidence for some novel candidate driver genes.
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16
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Abstract
MOTIVATION Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses. METHOD We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes. RESULTS Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets. CONTACT lzhangli@mdanderson.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liangcai Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA and Department of Biophysics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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17
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Krijgsman O, Gonzalez P, Ponz OB, Roemer MGM, Slot S, Broeks A, Braaf L, Kerkhoven RM, Bot F, van Groningen K, Beijert M, Ylstra B, de Jong D. Dissecting the gray zone between follicular lymphoma and marginal zone lymphoma using morphological and genetic features. Haematologica 2013; 98:1921-9. [PMID: 23850804 DOI: 10.3324/haematol.2013.085118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Nodal marginal zone lymphoma is a poorly defined entity in the World Health Organization classification, based largely on criteria of exclusion and the diagnosis often remains subjective. Follicular lymphoma lacking t(14;18) has similar characteristics which results in a major potential diagnostic overlap which this study aims to dissect. Four subgroups of lymphoma samples (n=56) were analyzed with high-resolution array comparative genome hybridization: nodal marginal zone lymphoma, t(14;18)-negative follicular lymphoma, localized t(14:18)-positive follicular lymphoma and disseminated t(14;18)-positive follicular lymphoma. Gains on chromosomes 7, 8 and 12 were observed in all subgroups. The mean number of aberrations was higher in disseminated t(14;18)-positive follicular lymphoma than in localized t(14:18)-positive follicular lymphoma (P<0.01) and the majority of alterations in localized t(14:18)-positive follicular lymphoma were also found in disseminated t(14;18)-positive follicular lymphoma. Nodal marginal zone lymphoma was marked by 3q gains with amplifications of four genes. A different overall pattern of aberrations was seen in t(14;18)-negative follicular lymphoma compared to t(14;18)-positive follicular lymphoma. t(14;18)-negative follicular lymphoma is characterized by specific (focal) gains on chromosome 3, as observed in nodal marginal zone lymphoma. Our results support the notion that localized t(14:18)-positive follicular lymphoma represents an early phase of disseminated t(14;18)-positive follicular lymphoma. t(14;18)-negative follicular lymphoma bears aberrations that are more like those in nodal marginal zone lymphoma, suggesting a relation between these groups.
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18
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Rao CV, Yamada HY. Genomic instability and colon carcinogenesis: from the perspective of genes. Front Oncol 2013; 3:130. [PMID: 23734346 PMCID: PMC3659308 DOI: 10.3389/fonc.2013.00130] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/07/2013] [Indexed: 12/12/2022] Open
Abstract
Colon cancer is the second most lethal cancer; approximately 600,000 people die of it annually in the world. Colon carcinogenesis generally follows a slow and stepwise process of accumulation of mutations under the influence of environmental and epigenetic factors. To adopt a personalized (tailored) cancer therapy approach and to improve current strategies for prevention, diagnosis, prognosis, and therapy overall, advanced understanding of molecular events associated with colon carcinogenesis is necessary. A contemporary approach that combines genetics, epigenomics, and signaling pathways has revealed many genetic/genomic alterations associated with colon cancer progression and their relationships to a genomic instability phenotype prevalent in colon cancer. In this review, we describe the relationship between gene mutations associated with colon carcinogenesis and a genomic instability phenotype, and we discuss possible clinical applications of genomic instability studies. Colon carcinogenesis is associated with frequent mutations in several pathways that include phosphatidylinositol 3-kinase, adenomatous polyposis coli, p53 (TP53), F-box and WD repeat domain containing 7, transforming growth factor-β, chromosome cohesion, and K-RAS. These genes frequently mutated in pathways affecting colon cancer were designated colon cancer (CAN) genes. Aberrations in major colon CAN genes have a causal relationship to genomic instability. Conversely, genomic instability itself plays a role in colon carcinogenesis in experimental settings, as demonstrated in transgenic mouse models with high genomic instability. Thus, there is a feedback-type relationship between CAN gene mutations and genomic instability. These genetic/genomic studies have led to emerging efforts to apply the knowledge to colon cancer prognosis and to targeted therapy.
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Affiliation(s)
- Chinthalapally V Rao
- Department of Medicine, University of Oklahoma Health Sciences Center Oklahoma City, OK, USA
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19
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Camps J, Pitt JJ, Emons G, Hummon AB, Case CM, Grade M, Jones TL, Nguyen QT, Ghadimi BM, Beissbarth T, Difilippantonio MJ, Caplen NJ, Ried T. Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer. Cancer Res 2013; 73:2003-13. [PMID: 23319804 DOI: 10.1158/0008-5472.can-12-3159] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromosomal copy number alterations (aneuploidy) define the genomic landscape of most cancer cells, but identification of the oncogenic drivers behind these imbalances remains an unfinished task. In this study, we conducted a systematic analysis of colorectal carcinomas that integrated genomic copy number changes and gene expression profiles. This analysis revealed 44 highly overexpressed genes mapping to localized amplicons on chromosome 13, gains of which occur often in colorectal cancers (CRC). RNA interference (RNAi)-mediated silencing identified eight candidates whose loss-of-function reduced cell viability 20% or more in CRC cell lines. The functional space of the genes NUPL1, LNX2, POLR1D, POMP, SLC7A1, DIS3, KLF5, and GPR180 was established by global expression profiling after RNAi exposure. One candidate, LNX2, not previously known as an oncogene, was involved in regulating NOTCH signaling. Silencing LNX2 reduced NOTCH levels but also downregulated the transcription factor TCF7L2 and markedly reduced WNT signaling. LNX2 overexpression and chromosome 13 amplification therefore constitutively activates the WNT pathway, offering evidence of an aberrant NOTCH-WNT axis in CRC.
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Affiliation(s)
- Jordi Camps
- Cancer Genomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20893, USA.
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20
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Xie T, d’ Ario G, Lamb JR, Martin E, Wang K, Tejpar S, Delorenzi M, Bosman FT, Roth AD, Yan P, Bougel S, Di Narzo AF, Popovici V, Budinská E, Mao M, Weinrich SL, Rejto PA, Hodgson JG. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS One 2012; 7:e42001. [PMID: 22860045 PMCID: PMC3409212 DOI: 10.1371/journal.pone.0042001] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/28/2012] [Indexed: 12/18/2022] Open
Abstract
To develop a comprehensive overview of copy number aberrations (CNAs) in stage-II/III colorectal cancer (CRC), we characterized 302 tumors from the PETACC-3 clinical trial. Microsatellite-stable (MSS) samples (n = 269) had 66 minimal common CNA regions, with frequent gains on 20 q (72.5%), 7 (41.8%), 8 q (33.1%) and 13 q (51.0%) and losses on 18 (58.6%), 4 q (26%) and 21 q (21.6%). MSS tumors have significantly more CNAs than microsatellite-instable (MSI) tumors: within the MSI tumors a novel deletion of the tumor suppressor WWOX at 16 q23.1 was identified (p<0.01). Focal aberrations identified by the GISTIC method confirmed amplifications of oncogenes including EGFR, ERBB2, CCND1, MET, and MYC, and deletions of tumor suppressors including TP53, APC, and SMAD4, and gene expression was highly concordant with copy number aberration for these genes. Novel amplicons included putative oncogenes such as WNK1 and HNF4A, which also showed high concordance between copy number and expression. Survival analysis associated a specific patient segment featured by chromosome 20 q gains to an improved overall survival, which might be due to higher expression of genes such as EEF1B2 and PTK6. The CNA clustering also grouped tumors characterized by a poor prognosis BRAF-mutant-like signature derived from mRNA data from this cohort. We further revealed non-random correlation between CNAs among unlinked loci, including positive correlation between 20 q gain and 8 q gain, and 20 q gain and chromosome 18 loss, consistent with co-selection of these CNAs. These results reinforce the non-random nature of somatic CNAs in stage-II/III CRC and highlight loci and genes that may play an important role in driving the development and outcome of this disease.
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Affiliation(s)
- Tao Xie
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
- * E-mail: (TX); (JGH)
| | | | - John R. Lamb
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Eric Martin
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Kai Wang
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Sabine Tejpar
- University Hospital Gasthuisberg, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Lausanne University Medical Center, Lausanne, Switzerland
| | - Fred T. Bosman
- Lausanne University Medical Center, Lausanne, Switzerland
| | | | - Pu Yan
- Lausanne University Medical Center, Lausanne, Switzerland
| | | | | | - Vlad Popovici
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eva Budinská
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mao Mao
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Scott L. Weinrich
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Paul A. Rejto
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - J. Graeme Hodgson
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
- * E-mail: (TX); (JGH)
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Zaal A, Peyrot WJ, Berns PMJJ, van der Burg MEL, Veerbeek JHW, Trimbos JB, Cadron I, van Diest PJ, van Wieringen WN, Krijgsman O, Meijer GA, Piek JMJ, Timmers PJ, Vergote I, Verheijen RHM, Ylstra B, Zweemer RP. Genomic aberrations relate early and advanced stage ovarian cancer. Cell Oncol (Dordr) 2012; 35:181-8. [PMID: 22581446 PMCID: PMC3396335 DOI: 10.1007/s13402-012-0077-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2012] [Indexed: 11/29/2022] Open
Abstract
Background Because of the distinct clinical presentation of early and advanced stage ovarian cancer, we aim to clarify whether these disease entities are solely separated by time of diagnosis or whether they arise from distinct molecular events. Methods Sixteen early and sixteen advanced stage ovarian carcinomas, matched for histological subtype and differentiation grade, were included. Genomic aberrations were compared for each early and advanced stage ovarian cancer by array comparative genomic hybridization. To study how the aberrations correlate to the clinical characteristics of the tumors we clustered tumors based on the genomic aberrations. Results The genomic aberration patterns in advanced stage cancer equalled those in early stage, but were more frequent in advanced stage (p = 0.012). Unsupervised clustering based on genomic aberrations yielded two clusters that significantly discriminated early from advanced stage (p = 0.001), and that did differ significantly in survival (p = 0.002). These clusters however did give a more accurate prognosis than histological subtype or differentiation grade. Conclusion This study indicates that advanced stage ovarian cancer either progresses from early stage or from a common precursor lesion but that they do not arise from distinct carcinogenic molecular events. Furthermore, we show that array comparative genomic hybridization has the potential to identify clinically distinct patients. Electronic supplementary material The online version of this article (doi:10.1007/s13402-012-0077-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Afra Zaal
- Department of Gynaecological Oncology, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands.
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Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism. Cell Oncol (Dordr) 2012; 35:53-63. [PMID: 22278361 PMCID: PMC3308003 DOI: 10.1007/s13402-011-0065-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2011] [Indexed: 02/08/2023] Open
Abstract
Background Colorectal cancer develops in a multi-step manner from normal epithelium, through a pre-malignant lesion (so-called adenoma), into a malignant lesion (carcinoma), which invades surrounding tissues and eventually can spread systemically (metastasis). It is estimated that only about 5% of adenomas do progress to a carcinoma. Aim The present study aimed to unravel the biology of adenoma to carcinoma progression by mRNA expression profiling, and to identify candidate biomarkers for adenomas that are truly at high risk of progression. Methods Genome-wide mRNA expression profiles were obtained from a series of 37 colorectal adenomas and 31 colorectal carcinomas using oligonucleotide microarrays. Differentially expressed genes were validated in an independent colorectal gene expression data set. Gene Set Enrichment Analysis (GSEA) was used to identify altered expression of sets of genes associated with specific biological processes, in order to better understand the biology of colorectal adenoma to carcinoma progression. Results mRNA expression of 248 genes was significantly different, of which 96 were upregulated and 152 downregulated in carcinomas compared to adenomas. Classification of adenomas and carcinomas using the expression of these genes showed to be very accurate, also when tested in an independent expression data set. Gene-sets associated with ageing (which is related to senescence) and chromosomal instability were upregulated, and a gene-set associated with fatty acid metabolism was downregulated in carcinomas compared to adenomas. Moreover, gene-sets associated with chromosomal location revealed chromosome 4q22 loss and chromosome 20q gain of gene-set expression as being relevant in this progression. Concluding remark These data are consistent with the notion that adenomas and carcinomas are distinct biological entities. Disruption of specific biological processes like senescence (ageing), maintenance of chromosomal instability and altered metabolism, are key factors in the progression from adenoma to carcinoma. Electronic supplementary material The online version of this article (doi:10.1007/s13402-011-0065-1) contains supplementary material, which is available to authorized users.
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