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Liu Z, Hu Y, Xie H, Chen K, Wen L, Fu W, Zhou X, Tang F. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers. Cancer Discov 2024; 14:1082-1105. [PMID: 38445965 DOI: 10.1158/2159-8290.cd-23-1445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. SIGNIFICANCE Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Zhenyu Liu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqiong Hu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Haoling Xie
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kexuan Chen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Wei Fu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Xin Zhou
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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Viswanathan R, Cheruba E, Wong PM, Yi Y, Ngang S, Chong DQ, Loh YH, Tan IB, Cheow LF. DARESOME enables concurrent profiling of multiple DNA modifications with restriction enzymes in single cells and cell-free DNA. SCIENCE ADVANCES 2023; 9:eadi0197. [PMID: 37713482 PMCID: PMC10881072 DOI: 10.1126/sciadv.adi0197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the most abundant DNA modifications that have important roles in gene regulation. Detailed studies of these different epigenetic marks aimed at understanding their combined effects and dynamic interconversion are, however, hampered by the inability of current methods to simultaneously measure both modifications, particularly in samples with limited quantities. We present DNA analysis by restriction enzyme for simultaneous detection of multiple epigenomic states (DARESOME), an assay based on modification-sensitive restriction digest and sequential tag ligation that can concurrently perform quantitative profiling of unmodified cytosine, 5mC, and 5hmC in CCGG sites genome-wide. DARESOME reveals the opposing roles of 5mC and 5hmC in gene expression regulation as well as their interconversion during aging in mouse brain. Implementation of DARESOME in single cells demonstrates pronounced 5hmC strand bias that reflects the semiconservative replication of DNA. Last, we showed that DARESOME enables integrative genomic, 5mC, and 5hmC profiling of cell-free DNA that uncovered multiomics cancer signatures in liquid biopsy.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yao Yi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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Şenocak Taşçı E, Yıldız İ, Erdamar S, Özer L. Discrepancy among microsatellite instability detection methodologies in non-colorectal cancer: Report of 3 cases. World J Clin Cases 2023; 11:3105-3113. [PMID: 37215411 PMCID: PMC10198076 DOI: 10.12998/wjcc.v11.i13.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Microsatellite instability (MSI) is a predictive biomarker for cancer immunotherapy. The tumor-agnostic nature of MSI makes it a denominator for immunotherapy in several solid tumors. It can be assessed using next-generation sequencing (NGS), fluorescent multiplex PCR, and immunohistochemistry (IHC).
CASE SUMMARY Here, we report 3 cases with discordant MSI results detected using different methods. A cholangiocellular carcinoma case revealed proficient mismatch repair (MMR) by IHC but high MSI (MSI-H) by liquid NGS. A cervical cancer case revealed deficient MMR by IHC, microsatellite stable by PCR, and MSI-H by NGS. Lastly, an endometrial cancer case revealed proficient MMR by IHC but MSI-H by NGS.
CONCLUSION IHC for MMR status is the first choice due to several advantages. However, in cases of indeterminate IHC results, molecular testing by MSI-PCR is preferred. Recently, NGS-based MSI assays are being widely used to detect MSI-H tumors. All three methods have high accuracy; however, the inconsistencies between them may lead to misdiagnosis.
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Affiliation(s)
- Elif Şenocak Taşçı
- Department of Medical Oncology, Acıbadem MAA University, Istanbul 12345, Turkey
| | - İbrahim Yıldız
- Department of Medical Oncology, Acıbadem MAA University, Istanbul 12345, Turkey
| | - Sibel Erdamar
- Department of Pathology, Acıbadem MAA University, Istanbul 12345, Turkey
| | - Leyla Özer
- Department of Medical Oncology, Acıbadem MAA University, Istanbul 12345, Turkey
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Chattopadhyay A, Teoh ZH, Wu CY, Juang JMJ, Lai LC, Tsai MH, Wu CH, Lu TP, Chuang EY. CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6321046. [PMID: 34259866 PMCID: PMC8278790 DOI: 10.1093/database/baab044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 11/14/2022]
Abstract
Human copy number variations (CNVs) and copy number alterations (CNAs) are DNA segments (>1000 base pairs) of duplications or deletions with respect to the reference genome, potentially causing genomic imbalance leading to diseases such as cancer. CNVs further cause genetic diversity in healthy populations and are predominant drivers of gene/genome evolution. Initiatives have been taken by the research community to establish large-scale databases to comprehensively characterize CNVs in humans. Exome Aggregation Consortium (ExAC) is one such endeavor that catalogs CNVs, of nearly 60 000 healthy individuals across five demographic clusters. Furthermore, large projects such as the Catalogue of Somatic Mutations in Cancer (COSMIC) and the Cancer Cell Line Encyclopedia (CCLE) combine CNA data from cancer-affected individuals and large panels of human cancer cell lines, respectively. However, we lack a structured and comprehensive CNV/CNA resource including both healthy individuals and cancer patients across large populations. CNVIntegrate is the first web-based system that hosts CNV and CNA data from both healthy populations and cancer patients, respectively, and concomitantly provides statistical comparisons between copy number frequencies of multiple ethnic populations. It further includes, for the first time, well-cataloged CNV and CNA data from Taiwanese healthy individuals and Taiwan Breast Cancer data, respectively, along with imported resources from ExAC, COSMIC and CCLE. CNVIntegrate offers a CNV/CNA-data hub for structured information retrieval for clinicians and scientists towards important drug discoveries and precision treatments. Database URL: http://cnvintegrate.cgm.ntu.edu.tw/.
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Affiliation(s)
- Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Zi Han Teoh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Yun Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 10008, Taiwan.,College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Physiology, National Taiwan University, Taipei 10051, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Chia-Hsin Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Master Program for Biomedical Engineering, China Medical University, Taichung 40402, Taiwan
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Wijesiriwardhana P, Wetthasinghe K, Dissanayake VHW. Copy Number Variants Captured by the Array Comparative Genomic Hybridization in a Cohort of Patients Affected with Hereditary Colorectal Cancer in Sri Lanka: The First CNV Analysis Study of the Hereditary Colorectal Cancer in the Sri Lankan Population. Asian Pac J Cancer Prev 2021; 22:1957-1966. [PMID: 34181357 PMCID: PMC8418865 DOI: 10.31557/apjcp.2021.22.6.1957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Hereditary non-polyposis colorectal cancer (HNPCC), is an autosomal dominant disorder characterized by the development of multiple cancer types. Molecular diagnosis of HNPCC requires the precise identification of pathogenic germline variants in DNA mismatch repair (MMR) genes. Next Generation Sequencing (NGS) is now the gold standard test in practice, to identify these variants. However, large genomic rearrangements (LGR) in cancer predisposing genes (CPGs) are missed by NGS. This may lead to underestimation of the frequency of the variants, misleading the genetic diagnosis and delaying intervention in high risk individuals. Hence this study was aimed at identifying the presence of large genomic alterations that could explain the missing heritable risk of colon cancer in affected patients with family history strongly suggestive of hereditary colorectal cancer in Sri Lanka. METHODS A cohort of six patients affected with hereditary colorectal cancer who tested negative for pathogenic variants in next generation sequencing studies was investigated using Sure Print G3 Human CGH 4x180K microarray platform. Agilent Genomic-Workbench-v7.0.4.0 software was used to identify the Copy Number Variants (CNV). Four healthy individuals (>55years) were used as controls. Annotations of the CNV regions which were observed were done using the database of Genomic Variants. RESULTS We identified 150 CNVs including regions of both genomic gains and losses in the patient cohort. There was no difference in the average number or the average genomic burden of CNVs identified in the patients versus the controls. CNVs were residing on the positions of 1q21.2, 2q37.3, 2p11.2-p11.1, 5q13.2, 6p12.3, 7q31.33, 7p14.1, 14q32.33, 15q11.1-11.2, 16p11.2, 22q11.22, 22q13.1 that were assessed by the array platform used in the study. CNVs in any of the well-known common CPG s or CNVs that reside on or in close proximity to genes corresponding to MMR pathway were not identified. We found several distinct pathways that have previously been identified as having a direct association with the progression of HNPCC. CONCLUSION This study shows that CNVs are likely contributors to the colorectal cancer predisposition in a small but significant proportion of patients affected with hereditary colorectal cancer in this cohort. Further studies have to perform to get a better understanding on the contribution of CNVs to the cancer predisposition in this cohort of patients in the Sri Lankan population.
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Affiliation(s)
- Prabhavi Wijesiriwardhana
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Ruhuna, Sri Lanka.
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Sri Lanka.
| | - Kalum Wetthasinghe
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Sri Lanka.
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Lee CT, Chow NH, Chen YL, Ho CL, Yeh YM, Lin SC, Lin PC, Lin BW, Chu CA, Tsai HW, Lee JC. Clinicopathological features of mismatch repair protein expression patterns in colorectal cancer. Pathol Res Pract 2020; 217:153288. [PMID: 33276219 DOI: 10.1016/j.prp.2020.153288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 01/10/2023]
Abstract
Microsatellite instability (MSI) is reflective of a deficient mismatch repair (dMMR) system, which is mostly associated with the methylation of mismatch repair (MMR) genes and BRAF mutations in sporadic colorectal cancers (CRCs). We performed a retrospective study to analyze the clinicopathological features of dMMR CRCs and their association with the BRAF V600E mutation. The incidence of dMMR CRCs in our cohort was 7.4 % (118/1603). Immunohistochemistry (IHC) revealed four common dMMR IHC patterns in 116 dMMR CRCs from 110 patients. dMMR type 1 (MLH1-/PMS2-) CRCs were the most frequent pattern, usually showing typical proximal location and MSI histology. The BRAF V600E mutation was almost exclusively observed in dMMR type 1 (32 of 72) and dMMR type 2 (PMS- only, 7 of 18) CRCs (p = 0.001). Patients with dMMR type 3 (MSH2-/MSH6-) CRCs were usually diagnosed at younger ages (p < 0.001) and had the strongest family history of Lynch syndrome-associated tumors (p = 0.002). dMMR type 3 CRCs frequently presented at advanced stages (p = 0.005) with perineural invasion (p = 0.021). We also found a significant positive association of dMMR type 1 and type 3 with advanced stages of CRC, whereas dMMR types 2 and 4 (MSH6- only) were usually diagnosed at early stages of CRC (p < 0.001). In conclusion, BRAF V600E mutations almost exclusively occurred in dMMR type 1 and 2 CRCs. Patterns of MMR protein expression display distinct associations with tumor staging and age at diagnosis.
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Affiliation(s)
- Chung-Ta Lee
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Dou-Liou Branch, Yunlin, Taiwan.
| | - Nan-Haw Chow
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Lin Chen
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Liang Ho
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Min Yeh
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shao-Chieh Lin
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Peng-Chan Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bo-Wen Lin
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-An Chu
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Wen Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jenq-Chang Lee
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Bui VMH, Mettling C, Jou J, Sun HS. Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma. BMC Med Genomics 2020; 13:149. [PMID: 33087131 PMCID: PMC7579792 DOI: 10.1186/s12920-020-00776-z] [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] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Colorectal carcinoma (CRC) is the third most common cancer in the world and also the third leading cause of cancer-related mortality in Taiwan. CRC tumorigenesis is a multistep process, starting from mutations causing loss of function of tumor suppressor genes, canonically demonstrated in adenomatous polyposis coli pathogenesis. Although many genes or chromosomal alterations have been shown to be involved in this process, there are still unrecognized molecular events within CRC tumorigenesis. Elucidating these mechanisms may help improve the management and treatment. METHODS In this study, we aimed to identify copy number alteration of the smallest chromosomal regions that is significantly associated with sporadic CRC tumorigenesis using high-resolution array-based Comparative Genomic Hybridization (aCGH) and quantitative Polymerase chain reaction (qPCR). In addition, microsatellite instability assay and sequencing-based mutation assay were performed to illustrate the initiation event of CRC tumorigenesis. RESULTS A total of 571 CRC patients were recruited and 377 paired CRC tissues from sporadic CRC cases were used to define the smallest regions with chromosome copy number changes. In addition, 198 colorectal polyps from 160 patients were also used to study the role of 20q13.33 gain in CRC tumorigenesis. We found that gain in 20q13.33 is the main chromosomal abnormalities in this patient population and counts 50.9 and 62.8% in CRC and colon polyps, respectively. Furthermore, APC and KRAS gene mutations were profiled simultaneously and co-analyzed with microsatellite instability and 20q13.33 gain in CRC patients. Our study showed that the frequency of 20q13.33 copy number gain was highest among all reported CRC mutations. CONCLUSION As APC or KRAS mutations are currently identified as the most important targets for CRC therapy, this study proposes that 20q13.33 copy number gain and the associated chromosomal genes function as promising biomarkers for both early stage detection and targeted therapy of sporadic CRCs in the future.
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Affiliation(s)
- Vo-Minh-Hoang Bui
- Institute of Basic Medicine, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Histology, Embryology and Pathology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Clément Mettling
- Institut de Génétique Humaine, Unité Propre de Recherche 1142 du Centre National de la Recherche Scientifique, 34396, Montpellier Cedex 5, France
| | - Jonathan Jou
- College of Medicine, University of Illinois, Champaign, IL, 61820, USA
| | - H Sunny Sun
- Institute of Basic Medicine, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan. .,Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan.
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Xiao F, Luo X, Hao N, Niu YS, Xiao X, Cai G, Amos CI, Zhang H. An accurate and powerful method for copy number variation detection. Bioinformatics 2020; 35:2891-2898. [PMID: 30649252 DOI: 10.1093/bioinformatics/bty1041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/28/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Integration of multiple genetic sources for copy number variation detection (CNV) is a powerful approach to improve the identification of variants associated with complex traits. Although it has been shown that the widely used change point based methods can increase statistical power to identify variants, it remains challenging to effectively detect CNVs with weak signals due to the noisy nature of genotyping intensity data. We previously developed modSaRa, a normal mean-based model on a screening and ranking algorithm for copy number variation identification which presented desirable sensitivity with high computational efficiency. To boost statistical power for the identification of variants, here we present a novel improvement that integrates the relative allelic intensity with external information from empirical statistics with modeling, which we called modSaRa2. RESULTS Simulation studies illustrated that modSaRa2 markedly improved both sensitivity and specificity over existing methods for analyzing array-based data. The improvement in weak CNV signal detection is the most substantial, while it also simultaneously improves stability when CNV size varies. The application of the new method to a whole genome melanoma dataset identified novel candidate melanoma risk associated deletions on chromosome bands 1p22.2 and duplications on 6p22, 6q25 and 19p13 regions, which may facilitate the understanding of the possible roles of germline copy number variants in the etiology of melanoma. AVAILABILITY AND IMPLEMENTATION http://c2s2.yale.edu/software/modSaRa2 or https://github.com/FeifeiXiaoUSC/modSaRa2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Feifei Xiao
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | - Xizhi Luo
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | - Ning Hao
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - Yue S Niu
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - Xiangjun Xiao
- Department of Quantitative Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, University of South Carolina, Columbia, SC, USA
| | - Christopher I Amos
- Department of Quantitative Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Heping Zhang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
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Korphaisarn K, Pongpaibul A, Roothumnong E, Pongsuktavorn K, Thamlikitkul L, Anekpuritanang T, Poungvarin N, Thongnoppakhun W, Pithukpakorn M. High Frequency of KRAS Codon 146 and FBXW7 Mutations in Thai Patients with Stage II-III Colon Cancer. Asian Pac J Cancer Prev 2019; 20:2319-2326. [PMID: 31450901 PMCID: PMC6852819 DOI: 10.31557/apjcp.2019.20.8.2319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Indexed: 12/24/2022] Open
Abstract
Background: KRAS, NRAS, and BRAF gene mutations are the most clinically relevant and frequently reported in
colorectal cancer (CRC). Although data on these genes are frequently reported in several counties, data specific to these
genes among Thai population are scarce. The aim of this study was to investigate and identify molecular alterations
associated with colon cancer in Thai population, and to determine the impact of these genetic aberrations on clinical
outcome. Methods: DNA from 108 archived formalin-fixed, paraffin-embedded (FFPE) tissue samples that histologically
confirmed adenocarcinoma of stage II-III colon cancer between 2010 and 2012 at Siriraj Hospital (Bangkok, Thailand)
were extracted. Gene mutational analysis was performed by next-generation sequencing (NGS) using an Oncomine
Solid Tumor DNA kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Results: A total of 22 somatic gene
mutations were detected. The mutation frequency observed in KRAS, NRAS, BRAF, PIK3CA, and FBXW7 mutations
was 47.2%, 1.9%, 1.9%, 12%, and 14.8%, respectively. KRAS mutation codon 12, 13, 59, 61, 117, and 146 mutations
were identified in 29.6%, 8.3%, 1.8%, 0.9%, 0.0%, and 8.3%, respectively. KRAS Exon 4 had better DFS compared
with Exon 2 and 3. Conclusions: This study is the first to comprehensively report hotspot mutations using NGS in Thai
colon cancer patients. The most commonly identified gene mutation frequencies among Thai patients (KRAS, NRAS,
BRAF, TP53, and PIK3CA) were similar to the gene mutation frequencies reported in Western population, except for
subgroup of KRAS codon 146 and FBXW7 mutations that had a slightly higher frequency.
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Affiliation(s)
- Krittiya Korphaisarn
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand. ,Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ananya Pongpaibul
- Department of Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ekkapong Roothumnong
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Khontawan Pongsuktavorn
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Lucksamon Thamlikitkul
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Tauangtham Anekpuritanang
- Department of Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanna Thongnoppakhun
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
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10
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Berardinelli GN, Scapulatempo-Neto C, Durães R, Antônio de Oliveira M, Guimarães D, Reis RM. Advantage of HSP110 (T17) marker inclusion for microsatellite instability (MSI) detection in colorectal cancer patients. Oncotarget 2018; 9:28691-28701. [PMID: 29983889 PMCID: PMC6033349 DOI: 10.18632/oncotarget.25611] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/04/2018] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer death worldwide. Microsatellite instability (MSI) is a genetic pathway leading to CRC, associated with particular clinicopathological features, and recently a major biomarker of immunotherapy response. There is little information the frequency MSI among Brazilian CRC patients, and it is still debatable the ideal methodology for MSI screening in countries with limited resources. We proposed to evaluate MSI by molecular and immunohistochemistry (IHC) methods, to compare both methodologies and also to assess the inclusion of a novel microsatellite marker, HSP110 (T17). The molecular MSI evaluation was performed using a PCR-multiplex panel in a total of 1013 CRC patients. Mismatch repair (MMR) proteins (MLH1, MSH2, MSH6 and PMS2) expression were evaluated by IHC. HSP110 (T17) marker was analyzed by fragment analysis. Molecularly, 89.5% of cases were MSI-negative and 10.5% were MSI-positive. The IHC showed that 88.9% of cases exhibited MMR-proficient status, 10.2% were MMR-deficient and 0.9% was inconclusive. Genotyping of the HSP110 (T17) in 106 MSI-positive and 215 MSI-negative cases showed its alteration only among the MSI-positive cases. We observed agreement (0.956, Kappa Test) between both molecular and IHC methodologies, with only eight discordant results, and in this subset of cases the HSP110 (T17) corroborate the molecular findings. This study suggests the use of molecular assays over IHC for MSI analysis and proposes the inclusion HSP110 (T17) marker as a complementary analysis in discordant cases.
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Affiliation(s)
| | | | - Ronílson Durães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Oncology, Barretos Cancer Hospital, Jales, São Paulo, Brazil
| | | | - Denise Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health sciences Research Institute, University of Minho, Gualtar Campus, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Gualtar Campus, Braga, Portugal
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11
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Natsume S, Yamaguchi T, Takao M, Iijima T, Wakaume R, Takahashi K, Matsumoto H, Nakano D, Horiguchi SI, Koizumi K, Miyaki M. Clinicopathological and molecular differences between right-sided and left-sided colorectal cancer in Japanese patients. Jpn J Clin Oncol 2018; 48:609-618. [DOI: 10.1093/jjco/hyy069] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 04/29/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Soichiro Natsume
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Tatsuro Yamaguchi
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Misato Takao
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Takeru Iijima
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Rika Wakaume
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Keiichi Takahashi
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Hiroshi Matsumoto
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Daisuke Nakano
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Shin-ichiro Horiguchi
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Koichi Koizumi
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
| | - Michiko Miyaki
- Tokyo Metropolitan Cancer and Infectious diseases Center Komagome Hospital, Tokyo, Japan
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12
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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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13
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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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14
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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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15
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Wang H, Liang L, Fang JY, Xu J. Somatic gene copy number alterations in colorectal cancer: new quest for cancer drivers and biomarkers. Oncogene 2015; 35:2011-9. [PMID: 26257062 DOI: 10.1038/onc.2015.304] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/07/2015] [Accepted: 07/12/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) results from the accumulation of genetic alterations, and somatic copy number alterations (CNAs) are crucial for the development of CRC. Genome-wide survey of CNAs provides opportunities for identifying cancer driver genes in an unbiased manner. The detection of aberrant CNAs may provide novel markers for the early diagnosis and personalized treatment of CRC. A major challenge in array-based profiling of CNAs is to distinguish the alterations that play causative roles from the random alterations that accumulate during colorectal carcinogenesis. In this view, we systematically discuss the frequent CNAs in CRC, focusing on functional genes that have potential diagnostic, prognostic and therapeutic significance.
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Affiliation(s)
- H Wang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - L Liang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J-Y Fang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J Xu
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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16
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Kadowaki S, Kakuta M, Takahashi S, Takahashi A, Arai Y, Nishimura Y, Yatsuoka T, Ooki A, Yamaguchi K, Matsuo K, Muro K, Akagi K. Prognostic value of KRAS and BRAF mutations in curatively resected colorectal cancer. World J Gastroenterol 2015; 21:1275-1283. [PMID: 25632202 PMCID: PMC4306173 DOI: 10.3748/wjg.v21.i4.1275] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/09/2014] [Accepted: 10/15/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the prognostic role of KRAS and BRAF mutations after adjustment for microsatellite instability (MSI) status in Japanese colorectal cancer (CRC) population.
METHODS: We assessed KRAS and BRAF mutations and MSI status in 813 Japanese patients with curatively resected, stage I-III CRC and examined associations of these mutations with disease-free survival (DFS) and overall survival (OS) using uni- and multivariate Cox proportional hazards models.
RESULTS: KRAS and BRAF mutations were detected in 312 (38%) of 812 and 40 (5%) of 811 tumors, respectively. KRAS mutations occurred more frequently in females than in males (P = 0.02), while the presence of BRAF mutations was significantly associated with the female gender (P = 0.006), proximal tumor location (P < 0.001), mucinous or poorly differentiated histology (P < 0.001), and MSI-high tumors (P < 0.001). After adjusting for relevant variables, including MSI status, KRAS mutations were associated with poorer DFS (HR = 1.35; 95%CI: 1.03-1.75) and OS (HR = 1.46; 95%CI: 1.09-1.97). BRAF mutations were poor prognostic factors for DFS (HR = 2.20; 95%CI: 1.19-4.06) and OS (HR = 2.30; 95%CI: 1.15-4.71). Neither the BRAF by MSI interaction test nor the KRAS by MSI interaction test yielded statistically significant results for DFS and OS.
CONCLUSION: KRAS and BRAF mutations are associated with inferior survival, independent of MSI status, in Japanese patients with curatively resected CRC.
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17
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Shivakumar BM, Rotti H, Vasudevan TG, Balakrishnan A, Chakrabarty S, Bhat G, Rao L, Pai CG, Satyamoorthy K. Copy number variations are progressively associated with the pathogenesis of colorectal cancer in ulcerative colitis. World J Gastroenterol 2015; 21:616-622. [PMID: 25605985 PMCID: PMC4296023 DOI: 10.3748/wjg.v21.i2.616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/10/2014] [Accepted: 07/22/2014] [Indexed: 02/07/2023] Open
Abstract
AIM: To evaluate the association of known copy number variations (CNVs) in ulcerative colitis (UC) progressing to colorectal cancer.
METHODS: Microsatellite instability analysis using the National Cancer Institute’s panel of markers, and CNV association studies using Agilent 2 × 105 k arrays were done in tissue samples from four patient groups with UC: those at low risk (LR) or high risk of developing colorectal cancer, those with premalignant dysplastic lesions, and those with colitis-associated colorectal cancer (CAC). DNA from tissue samples of these groups were independently hybridized on arrays and analyzed. The data obtained were further subjected to downstream bioinformatics enrichment analysis to examine the correlation with CAC progression.
RESULTS: Microarray analysis highlighted a progressive increase in the total number of CNVs [LR (n = 178) vs CAC (n = 958), 5.3-fold], gains and losses [LR (n = 37 and 141) vs CAC (n = 495 and 463), 13.4- and 3.3-fold, respectively], size [LR (964.2 kb) vs CAC (10540 kb), 10.9-fold] and the number of genes in such regions [LR (n = 119) vs CAC (n = 455), 3.8-fold]. Chromosome-wise analysis of CNVs also showed an increase in the number of CNVs across each chromosome. There were 38 genes common to all four groups in the study; 13 of these were common to cancer genes from the Genetic Disease Association dataset. The gene set enrichment analysis and ontology analysis highlighted many cancer-associated genes. All the samples in the different groups were microsatellite stable.
CONCLUSION: Increasing numbers of CNVs are associated with the progression of UC to CAC, and warrant further detailed exploration.
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18
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Lin PC, Lin JK, Lin CH, Lin HH, Yang SH, Jiang JK, Chen WS, Chou CC, Tsai SF, Chang SC. Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array. Ann Surg Oncol 2014; 22 Suppl 3:S1419-27. [PMID: 25472652 DOI: 10.1245/s10434-014-4277-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND DNA methylation is a potential tumor marker for several cancers, including colorectal cancer (CRC), because of its heritable and stable characteristics. METHODS Using a high-resolution, genome-wide approach, we epigenotyped >450,000 CpG sites in tumor and adjacent non-tumor tissues from 23 microsatellite instability (MSI)/microsatellite stability (MSS) CRC cases. Using matrix-assisted laser desorption ionization-time of flight mass spectrometry, the methylation status of five frequently hypermethylated genes were confirmed in 75 independent CRC series and 353 CRC patients with available plasma. RESULTS Compared with non-tumor tissues, 13 MSI tumors had 34,836 (7 %) aberrant methylation sites, 87 % of which were hypermethylated. In contrast, only 9,806 (2 %) differentially methylated sites were identified in ten MSS cases (62 % hypermethylated). In both MSI and MSS, 228 promoter-associated CpG islands were hypermethylated, with AGBL4, ZNF625, MDFI, TWIST1, and FLI1 being most frequently hypermethylated. In an independent set of 35 MSI and 40 MSS cases, the methylation status of these five genes significantly differed between tumor and adjacent non-tumor tissues. Of 353 CRC patients, 230 (65.2 %), 232 (65.7 %), and 247 (70.0 %) had AGBL4, FLI1, and TWIST1 promoter hypermethylation in circulating cell-free DNA, respectively. In patients without metastasis, the sensitivity of any two or three hypermethylation markers was 52.8-57.8 and 27.9-38.9 %, respectively. The sensitivity of any two or three markers was significantly high in patients with stage IV disease (73.0 and 55.6 %, respectively). The prognostic value of these epimarkers was inconclusive. CONCLUSION DNA methylation patterns differed in CRC subtypes. The identified hypermethylation markers in CRC patients may have good sensitivity in different CRC stages.
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Affiliation(s)
- Pei-Ching Lin
- Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan
| | - Jen-Kou Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsing Lin
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Hung-Hsin Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jeng-Kai Jiang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Shone Chen
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Chi Chou
- Department of Life Sciences and Genome Research Center and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Feng Tsai
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan. .,Department of Life Sciences and Genome Research Center and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan. .,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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19
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Eldai H, Periyasamy S, Al Qarni S, Al Rodayyan M, Muhammed Mustafa S, Deeb A, Al Sheikh E, Afzal Khan M, Johani M, Yousef Z, Aziz MA. Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner. PLoS One 2013; 8:e76251. [PMID: 24204606 PMCID: PMC3813709 DOI: 10.1371/journal.pone.0076251] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 08/22/2013] [Indexed: 12/13/2022] Open
Abstract
Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway and target prediction analysis of CNA affected genes and microRNAs, respectively indicates TGF-β signaling pathway to be involved in causing CRC. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.
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Affiliation(s)
- Hisham Eldai
- Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Sathish Periyasamy
- Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Saeed Al Qarni
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Maha Al Rodayyan
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | | | - Ahmad Deeb
- Research Office, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Ebthehal Al Sheikh
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | | | - Mishal Johani
- Endoscopy, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Zeyad Yousef
- Surgery, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammad Azhar Aziz
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- * E-mail:
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Li G, Jin T, Liang H, Tu Y, Zhang W, Gong L, Su Q, Gao G. Skewed X-chromosome inactivation in patients with esophageal carcinoma. Diagn Pathol 2013; 8:55. [PMID: 23556484 PMCID: PMC3640911 DOI: 10.1186/1746-1596-8-55] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 04/01/2013] [Indexed: 11/15/2022] Open
Abstract
Abstract Skewed X-chromosome inactivation (SXCI) was found in some apparently healthy females mainly from Western countries. It has been linked to development of ovarian, breast and pulmonary carcinomas. The present study aimed to observe the SXCI frequencies in apparently healthy Chinese females and patients with esophageal carcinoma. DNA was extracted from the peripheral blood cells from 401 Chinese females without a detectable tumor and 143 female patients with esophageal carcinoma. Exon 1 of androgen receptor (AR) gene was amplified, and the products of different CAG alleles were resolved on denaturing polyacrylamide gels and visualized after silver staining. The corrected ratios (CR) of the products before and after HpaII digestion were calculated. As to the healthy females, when CR ≥ 3 was used as a criterion, SXCI was found in two (4.3%) of the 46 neonates, 13 (7.8%) of the 166 younger adults (16–50 years) and 37 (25.7%) of the 144 elderly females (51–96 years), with the frequency higher in the elderly subjects than in the two former groups (P < 0.05). When a more stringent criterion (CR ≥ 10) was used, SXCI was found in one (2.2%), two (1.2%) and 16 (11.1%) of the subjects in the three age groups, respectively, itsfrequency being higher in the elderly than in the younger age groups (P < 0.05). Occurrence of SXCI was detected in both the patients and controls at similar frequencies. However, the phenomenon, as defined as CR ≥ 3, was more frequent in the patients aging <40 years (35.7%) compared to the corresponding reference group (7.6%, P = 0.006). When CR ≥ 10 was adopted, the frequencies were 7.1% and 1.2%, respectively. Their difference did not attain statistical significance (P = 0. 217). SXCI also occurs in apparently healthy Chinese females, and is associated with age. It may be considered as a predisposing factor for the early development of esophageal carcinoma. Virtual slides The virtual slide(s) for this article can be found here http://www.diagnosticpathology.diagnomx.eu/vs/1542364337927656
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Affiliation(s)
- Gang Li
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, China
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Yam YY, Hoh BP, Othman NH, Hassan S, Yahya MM, Zakaria Z, Ankathil R. Somatic copy-neutral loss of heterozygosity and copy number abnormalities in Malaysian sporadic colorectal carcinoma patients. GENETICS AND MOLECULAR RESEARCH 2013; 12:319-27. [PMID: 23420356 DOI: 10.4238/2013.february.7.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Colorectal cancer is one of the most common cancers in many countries, including Malaysia. The accumulation of genomic alterations is an important feature of colorectal carcinogenesis. A better understanding of the molecular events underlying the stages of colorectal carcinogenesis might be helpful in the detection and management of the disease. We used a commercially available single-nucleotide polymorphism genotyping array to detect both copy number abnormalities (CNAs) and copy-neutral loss of heterozygosity (LOH) in sporadic colorectal carcinomas. Matched tumor and normal tissues of 13 colorectal carcinomas (Dukes' stages A-D) were analyzed using a 250K single nucleotide polymorphism array. An additional assay was performed to determine the microsatellite instability status by using the National Cancer Institute-recommended BAT-26 panel. In general, copy number gain (92.3%) was most common, followed by copy number loss (53.8%) and copy-neutral LOH (46.2%). Frequent CNAs of gains and losses were observed on chromosomes 7p, 8, 13q, 17p, 18q, and 20q, and copy-neutral LOH was observed on chromosomes 2, 6, 12, 13q, 14q, 17, 20p, 19q, and 22q. Even though genomic alterations are associated with colorectal cancer progression, our results showed that DNA CNAs and copy-neutral LOH do not reflect disease progression in at least 50% tumors. Copy-neutral LOH was observed in both early and advanced tumors, which favors the involvement of these genomic alterations in the early stages of tumor development.
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Affiliation(s)
- Y Y Yam
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
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