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Lukacova E, Hanzlikova Z, Podlesnyi P, Sedlackova T, Szemes T, Grendar M, Samec M, Hurtova T, Malicherova B, Leskova K, Budis J, Burjanivova T. Novel liquid biopsy CNV biomarkers in malignant melanoma. Sci Rep 2024; 14:15786. [PMID: 38982214 PMCID: PMC11233564 DOI: 10.1038/s41598-024-65928-y] [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: 03/14/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
Malignant melanoma (MM) is known for its abundance of genetic alterations and a tendency for rapid metastasizing. Identification of novel plasma biomarkers may enhance non-invasive diagnostics and disease monitoring. Initially, we examined copy number variations (CNV) in CDK genes (CDKN2A, CDKN2B, CDK4) using MLPA (gDNA) and ddPCR (ctDNA) analysis. Subsequently, low-coverage whole genome sequencing (lcWGS) was used to identify the most common CNV in plasma samples, followed by ddPCR verification of chosen biomarkers. CNV alterations in CDK genes were identified in 33.3% of FFPE samples (Clark IV, V only). Detection of the same genes in MM plasma showed no significance, neither compared to healthy plasmas nor between pre- versus post-surgery plasma. Sequencing data showed the most common CNV occurring in 6q27, 4p16.1, 10p15.3, 10q22.3, 13q34, 18q23, 20q11.21-q13.12 and 22q13.33. CNV in four chosen genes (KIF25, E2F1, DIP2C and TFG) were verified by ddPCR using 2 models of interpretation. Model 1 was concordant with lcWGS results in 54% of samples, for model 2 it was 46%. Although CDK genes have not been proven to be suitable CNV liquid biopsy biomarkers, lcWGS defined the most frequently affected chromosomal regions by CNV. Among chosen genes, DIP2C demonstrated a potential for further analysis.
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Affiliation(s)
- E Lukacova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | | | - P Podlesnyi
- Instituto de Investigaciones Biomedicas de Barcelona (IIBB), CSIC /Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas (CiberNed), Barcelona, Spain
| | - T Sedlackova
- Geneton Ltd., Bratislava, Slovakia
- Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - T Szemes
- Geneton Ltd., Bratislava, Slovakia
- Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - M Grendar
- Laboratory of Bioinformatics and Biostatistics, Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - M Samec
- Department of Medical Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - T Hurtova
- Department of Dermatovenereology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - B Malicherova
- Department of Clinical Biochemistry, University Hospital in Martin and Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
| | - K Leskova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine and University Hospital in Martin, Comenius University, Martin, Slovakia
| | - J Budis
- Geneton Ltd., Bratislava, Slovakia
- Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - T Burjanivova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.
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Wang X, Wu S, Sun L, Jin P, Zhang J, Liu W, Zhan Z, Wang Z, Liu X, He L. Pan-cancer analysis revealing that PTPN2 is an indicator of risk stratification for acute myeloid leukemia. Sci Rep 2023; 13:18372. [PMID: 37884566 PMCID: PMC10603079 DOI: 10.1038/s41598-023-44892-z] [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: 06/15/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
The non-receptor protein tyrosine phosphatases gene family (PTPNs) is involved in the tumorigenesis and development of many cancers, but the role of PTPNs in acute myeloid leukemia (AML) remains unclear. After a comprehensive evaluation on the expression patterns and immunological effects of PTPNs using a pan-cancer analysis based on RNA sequencing data obtained from The Cancer Genome Atlas, the most valuable gene PTPN2 was discovered. Further investigation of the expression patterns of PTPN2 in different tissues and cells showed a robust correlation with AML. PTPN2 was then systematically correlated with immunological signatures in the AML tumor microenvironment and its differential expression was verified using clinical samples. In addition, a prediction model, being validated and compared with other models, was developed in our research. The systematic analysis of PTPN family reveals that the effect of PTPNs on cancer may be correlated to mediating cell cycle-related pathways. It was then found that PTPN2 was highly expressed in hematologic diseases and bone marrow tissues, and its differential expression in AML patients and normal humans was verified by clinical samples. Based on its correlation with immune infiltrates, immunomodulators, and immune checkpoint, PTPN2 was found to be a reliable biomarker in the immunotherapy cohort and a prognostic predictor of AML. And PTPN2'riskscore can accurately predict the prognosis and response of cancer immunotherapy. These findings revealed the correlation between PTPNs and immunophenotype, which may be related to cell cycle. PTPN2 was differentially expressed between clinical AML patients and normal people. It is a diagnostic biomarker and potentially therapeutic target, providing targeted guidance for clinical treatment.
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Affiliation(s)
- Xuanyu Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Sanyun Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Le Sun
- Department of Urology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Peipei Jin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jianmin Zhang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wen Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhuo Zhan
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zisong Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Xiaoping Liu
- Department of Pathology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
| | - Li He
- Department of Urology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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Zhang X, Peng W, Fan J, Luo R, Liu S, Du W, Luo C, Zheng J, Pan X, Ge H. Regulatory role of Chitinase 3-like 1 gene in papillary thyroid carcinoma proved by integration analyses of single-cell sequencing with cohort and experimental validations. Cancer Cell Int 2023; 23:145. [PMID: 37480002 PMCID: PMC10362555 DOI: 10.1186/s12935-023-02987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is one of the most common thyroid carcinomas. The gross extrathyroidal extension and extensive metastases of PTC lead to high rates of recurrence and poor clinical outcomes. However, the mechanisms underlying PTC development are poorly understood. In this study, using single-cell RNA sequencing, the transcriptome profiles of two PTC patients were addressed, including PTC1 with low malignancy and good prognosis and PTC2 with high malignancy and poor prognosis. We found that epithelial subcluster Epi02 was the most associated with the malignant development of PTC cells, with which the fold change of Chitinase 3-like 1 (CHI3L1) is on the top of the differentially expressed genes between PTC1 and PTC2 (P < 0.001). However CHI3L1 is rarely investigated in PTC as far. We then studied its role in PTC with a series of experiments. Firstly, qRT-PCR analysis of 14 PTC patients showed that the expression of CHI3L1 was positively correlated with malignancy. In addition, overexpression or silencing of CHI3L1 in TPC-1 cells, a PTC cell line, cultured in vitro showed that the proliferation, invasion, and metastasis of the cells were promoted or alleviated by CHI3L1. Further, immunohistochemistry analysis of 110 PTC cases revealed a significant relationship between CHI3L1 protein expression and PTC progression, especially the T (P < 0.001), N (P < 0.001), M stages (P = 0.007) and gross ETE (P < 0.001). Together, our results prove that CHI3L1 is a positive regulator of malignant development of PTC, and it promotes proliferation, invasion, and metastasis of PTC cells. Our study improves understanding of the molecular mechanisms underlying the progression of PTC and provides new insights for the clinical diagnosis and treatment of PTC.
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Affiliation(s)
- Xiaojun Zhang
- Department of Head Neck and Thyroid Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China
| | - Wanwan Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, 510515, Guangzhou, China
| | - Jie Fan
- Department of Head Neck and Thyroid Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China
| | - Ruihua Luo
- Department of Head Neck and Thyroid Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China
| | - Shanting Liu
- Department of Head Neck and Thyroid Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China
| | - Wei Du
- Department of Head Neck and Thyroid Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China
| | - Chaochao Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, 510515, Guangzhou, China
| | - Jiawen Zheng
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, 510515, Guangzhou, China.
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China.
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, 510515, Guangzhou, China.
| | - Hong Ge
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, China.
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Liu Z, Su R, Ahsan A, Liu C, Liao X, Tian D, Su M. Esophageal Squamous Cancer from 4NQO-Induced Mice Model: CNV Alterations. Int J Mol Sci 2022; 23:ijms232214304. [PMID: 36430789 PMCID: PMC9698903 DOI: 10.3390/ijms232214304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Squamous esophageal carcinoma is a common pathological type of esophageal carcinoma around the world. The prognosis of esophageal carcinoma is usually poor and diagnosed at late stages. Recently, research suggested that genomic instability occurred in esophageal cells during the development of esophageal squamous cell carcinoma (ESCC). Identifying prognostic and specific genomic characteristics, especially at the early hyperplasia stage, is critical. Mice were given 4-nitroquinoline 1-oxide (4NQO) with drinking water to induce esophageal cancer. The immortalized human esophageal epithelial cell line (NE2) was also treated with 4NQO. We performed histologic analyses, immunofluorescence, and immunohistochemical staining to detect DNA damage at different time points. Whole-exome sequencing was accomplished on the esophagus tissues at different pathological stages to detect single-nucleotide variants and copy number variation (CNV) in the genome. Our findings indicate that all mice were tumor-forming, and a series of changes from simple hyperplasia (ESSH) to intraepithelial neoplasia (IEN) to esophageal squamous cell carcinoma (ESCC) was seen at different times. The expression of γ-H2AX increased from ESSH to ESCC. In addition, mutations of the Muc4 gene were detected throughout the pathological stages. Furthermore, CNV burden appeared in the esophageal tissues from the beginning of ESSH and accumulated more in cancer with the deepening of the lesions. This study demonstrates that mutations caused by the early appearance of DNA damage may appear in the early stage of malignant tissue before the emergence of atypia. The detection of CNV and mutations of the Muc4 gene may be used as an ultra-early screening indicator for esophageal cancer.
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Affiliation(s)
| | | | | | | | | | | | - Min Su
- Correspondence: ; Fax: +86-0754-88900429
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Liang J, Wang Y, Cai L, Liu J, Yan J, Chen X, Wu X, Chen Q. Comparative Genomic Analysis Reveals Genetic Variations in Multiple Primary Esophageal Squamous Cell Carcinoma of Chinese Population. Front Oncol 2022; 12:868301. [PMID: 35515115 PMCID: PMC9065449 DOI: 10.3389/fonc.2022.868301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common and lethal malignant tumors. The incidence of malignant transformation of esophageal mucosa increases greatly due to long-term exposure to factors such as smoking, drinking, and poor eating habits. Furthermore, multiple primary tumors could occur synchronously or asynchronously in the upper aerodigestive tract, especially in the esophagus, adding difficulty to the treatment of ESCC. Genetic mutations are important during the malignant transformation from normal mucosa to esophageal cancer, but the underlying mechanism has not been fully elucidated. In this study, we used whole-exome sequencing (WES) to profile genetic variations in physiologically normal mucosa (PNM) and ESCC tumors, as well as PNM of non-ESCC subjects. We found significant differences in mutation frequencies of NOTCH1 and NOTCH2, copy number variations (CNVs) at both gene and chromosomal arm levels, and cancer-related HIPPO, WNT, and NRF2 signaling pathways between ESCC tumors and normal mucosa. Our analysis of both primary tumors and paired PNM in bifocal ESCC revealed three different primary tumor evolution modes, and the most common mode exhibited a complete genomic divergence in all the samples from the same patient. Furthermore, the mutation frequency of TP53 was significantly higher in ESCC cases than that in non-ESCC cases. Overall, our results provide important evidence for further elucidating the mechanisms of genetic mutations underlying the cause of ESCC.
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Affiliation(s)
- Jinxiao Liang
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yinjie Wang
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Lei Cai
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Jinshi Liu
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Junrong Yan
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xin Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xiaoying Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qixun Chen
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
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6
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Qu C, Ma T, Yan X, Li X, Li Y. Overexpressed PAQR4 predicts poor overall survival and construction of a prognostic nomogram based on PAQR family for hepatocellular carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:3069-3090. [PMID: 35240821 DOI: 10.3934/mbe.2022142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE We aimed to explore the expression and clinical prognostic significance of PAQR4 in hepatocellular carcinoma (HCC). METHODS We obtained the gene expression matrix and clinical data of HCC from the cancer genome atlas (TCGA) and international cancer genome consortium (ICGC) databases. The prognostic value of PAQR4 in HCC was evaluated using the Kaplan-Meier and Cox regression analyses. PAQR4-related pathways were explored by gene set enrichment analysis (GSEA). A clinical nomogram prognostic model based on the PAQR family was constructed using Cox proportional hazards models. RESULTS We found that PAQR4 is overexpressed in HCC from multiple databases; additionally, quantitative real-time polymerase chain reaction (qRT-PCR) validated the upregulation of PAQR4 in HCC. PAQR4 expression was related to age, grade, alpha fetoprotein (AFP), T classification and clinical stage of HCC patients. High PAQR4 expression was associated with poor overall survival and was an independent prognostic factor for HCC patients through Kaplan-Meier analysis and Cox regression analysis, respectively. In addition, GSEA identified that the high PAQR4 expression phenotype was involved in the cell cycle, Notch signaling pathway, mTOR signaling pathway, etc. Finally, three PAQR family genes (PAQR4, PAQR8 and PAQR9) were associated with the prognosis of patients with HCC. A clinical nomogram prediction model was verified in TCGA training and ICGC validation sets, and it exerted dramatic predictive efficiency in this study. CONCLUSIONS PAQR4 may be regarded as a promising prognostic biomarker and therapeutic target for HCC.
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Affiliation(s)
- Caihao Qu
- Lanzhou University Second Hospital, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Tengda Ma
- Lanzhou University Second Hospital, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Xin Yan
- Lanzhou University Second Hospital, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Xiaomei Li
- Lanzhou University Second Hospital, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Yumin Li
- Lanzhou University Second Hospital, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
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7
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Comprehensive germline-genomic and clinical profiling in 160 unselected children and adolescents with cancer. Eur J Hum Genet 2021; 29:1301-1311. [PMID: 33840814 PMCID: PMC8385053 DOI: 10.1038/s41431-021-00878-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/05/2021] [Accepted: 03/25/2021] [Indexed: 02/02/2023] Open
Abstract
In childhood cancer, the frequency of cancer-associated germline variants and their inheritance patterns are not thoroughly investigated. Moreover, the identification of children carrying a genetic predisposition by clinical means remains challenging. In this single-center study, we performed trio whole-exome sequencing and comprehensive clinical evaluation of a prospectively enrolled cohort of 160 children with cancer and their parents. We identified in 11/160 patients a pathogenic germline variant predisposing to cancer and a further eleven patients carried a prioritized VUS with a strong association to the cancerogenesis of the patient. Through clinical screening, 51 patients (31.3%) were identified as suspicious for an underlying cancer predisposition syndrome (CPS), but only in ten of those patients a pathogenic variant could be identified. In contrast, one patient with a classical CPS and ten patients with prioritized VUS were classified as unremarkable in the clinical work-up. Taken together, a monogenetic causative variant was detected in 13.8% of our patients using WES. Nevertheless, the still unclarified clinical suspicious cases emphasize the need to consider other genetic mechanisms including new target genes, structural variants, or polygenic interactions not previously associated with cancer predisposition.
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8
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Liu G, Zhang J. A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 12:699510. [PMID: 34262604 PMCID: PMC8273656 DOI: 10.3389/fgene.2021.699510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The next-generation sequencing technology offers a wealth of data resources for the detection of copy number variations (CNVs) at a high resolution. However, it is still challenging to correctly detect CNVs of different lengths. It is necessary to develop new CNV detection tools to meet this demand. In this work, we propose a new CNV detection method, called CBCNV, for the detection of CNVs of different lengths from whole genome sequencing data. CBCNV uses a clustering algorithm to divide the read depth segment profile, and assigns an abnormal score to each read depth segment. Based on the abnormal score profile, Tukey's fences method is adopted in CBCNV to forecast CNVs. The performance of the proposed method is evaluated on simulated data sets, and is compared with those of several existing methods. The experimental results prove that the performance of CBCNV is better than those of several existing methods. The proposed method is further tested and verified on real data sets, and the experimental results are found to be consistent with the simulation results. Therefore, the proposed method can be expected to become a routine tool in the analysis of CNVs from tumor-normal matched samples.
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Affiliation(s)
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi’an, China
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9
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lncRNA GAU1 Induces GALNT8 Overexpression and Potentiates Colorectal Cancer Progression. Gastroenterol Res Pract 2021; 2021:5960821. [PMID: 34239555 PMCID: PMC8233076 DOI: 10.1155/2021/5960821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 06/04/2021] [Indexed: 12/17/2022] Open
Abstract
lncRNA is a key epigenetic regulator in biological processes. In the human cancer transcriptome library MiTranscriptome, we identified GAU1 as the top upregulated lncRNA in colorectal cancer (CRC) by sample set enrichment analysis (overexpression ranking percentile = 99.75%, P < 10-50), which is coexpressed with the potential oncogene GALNT8 (Spearman rho = 0.67, P = 2.44 × 10-23, TCGA dataset n = 184). Experimental data revealed that GAU1 regulates the expression of GALNT8. The overexpression of either GAU1 or GALNT8 significantly promotes the cell cycle and proliferation of CRC cell lines and correlates with poor prognosis in patients with CRC (P = 3.04 × 10-2), while silencing of GAU1 or GALNT8 suppressed the cancer cell proliferation and induced the CRC cell line resistance to oxaliplatin in vitro treatment. Our results suggested that the previously less studied GAU1 and GALNT8 may play as CRC prognosis markers and potential targets for chemotherapy treatment.
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10
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Chen S, Lu L, Xian J, Shi C, Chen J, Rao B, Qiu F, Lu J, Yang L. Prognostic Value of Germline Copy Number Variants and Environmental Exposures in Non-small Cell Lung Cancer. Front Genet 2021; 12:681857. [PMID: 34178039 PMCID: PMC8226327 DOI: 10.3389/fgene.2021.681857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Germline copy number variant (gCNV) has been studied as a genetic determinant for prognosis of several types of cancer, but little is known about how it affects non-small cell lung cancer (NSCLC) prognosis. We aimed to develop a prognostic nomogram for NSCLC based on gCNVs. Promising gCNVs that are associated with overall survival (OS) of NSCLC were sorted by analyzing the TCGA data and were validated in a small Chinese population. Then the successfully verified gCNVs were determined in a training cohort (n = 570) to develop a prognostic nomogram, and in a validation cohort (n = 465) to validate the nomogram. Thirty-five OS-related gCNVs were sorted and were reduced to 15 predictors by the Lasso regression analysis. Of them, only CNVR395.1 and CNVR2239.1 were confirmed to be associated with OS of NSCLC in the Chinese population. High polygenic risk score (PRS), which was calculated by the hazard effects of CNVR395.1 and CNVR2239.1, exerted a significantly higher death rate in the training cohort (HR = 1.41, 95%CI: 1.16–1.74) and validation cohort (HR = 1.42, 95%CI: 1.13–1.77) than low PRS. The nomogram incorporating PRS and surrounding factors, achieved admissible concordance indexes of 0.678 (95%CI: 0.664–0.693) and 0.686 (95%CI: 0.670–0.702) in predicting OS in the training and validation cohorts, respectively, and had well-fitted calibration curves. Moreover, an interaction between PRS and asbestos exposure was observed on affecting OS (Pinteraction = 0.042). Our analysis developed a nomogram that achieved an admissible prediction of NSCLC survival, which would be beneficial to the personalized intervention of NSCLC.
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Affiliation(s)
- Shizhen Chen
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Liming Lu
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Jianfeng Xian
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Changhong Shi
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Jinbin Chen
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Boqi Rao
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Fuman Qiu
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Jiachun Lu
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China.,The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lei Yang
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
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11
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Hu H, Xu H, Lu F, Zhang J, Xu L, Xu S, Jiang H, Zeng Q, Chen E, He Z. Exploring the Effect of Differentially Expressed Long Non-coding RNAs Driven by Copy Number Variation on Competing Endogenous RNA Network by Mining Lung Adenocarcinoma Data. Front Cell Dev Biol 2021; 8:627436. [PMID: 33585468 PMCID: PMC7876300 DOI: 10.3389/fcell.2020.627436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the first cause of cancer death, and gene copy number variation (CNV) is a vital cause of lung cancer progression. Prognosis prediction of patients followed by medication guidance by detecting CNV of lung cancer is emerging as a promising precise treatment in the future. In this paper, the differences in CNV and gene expression between cancer tissue and normal tissue of lung adenocarcinoma (LUAD) from The Cancer Genome Atlas Lung Adenocarcinoma data set were firstly analyzed, and greater differences were observed. Furthermore, CNV-driven differentially expressed long non-coding RNAs (lncRNAs) were screened out, and then, a competing endogenous RNA (ceRNA) regulatory network related to the gene CNV was established, which involved 9 lncRNAs, seven microRNAs, and 178 downstream messenger RNAs (mRNAs). Pathway enrichment analyses sequentially performed revealed that the downstream mRNAs were mainly enriched in biological pathways related to cell division, DNA repair, and so on, indicating that these mRNAs mainly affected the replication and growth of tumor cells. Besides, the relationship between lncRNAs and drug effects was explored based on previous studies, and it was found that LINC00511 and LINC00942 in the CNV-associated ceRNA network could be used to determine tumor response to drug treatment. As examined, the drugs affected by these two lncRNAs mainly targeted metabolism, target of rapamycin signaling pathway, phosphatidylinositol-3-kinase signaling pathway, epidermal growth factor receptor signaling pathway, and cell cycle. In summary, the present research was devoted to analyzing CNV, lncRNA, mRNA, and microRNA of lung cancer, and nine lncRNAs that could affect the CNV-associated ceRNA network we constructed were identified, two of which are promising in determining tumor response to drug treatment.
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Affiliation(s)
- Huihui Hu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hangdi Xu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Fen Lu
- Operation Room, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jisong Zhang
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Li Xu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Shan Xu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hanliang Jiang
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Qingxin Zeng
- Department of Thoracic Surgery, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Enguo Chen
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Zhengfu He
- Department of Thoracic Surgery, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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12
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Chen C, Pan Y, Bai L, Chen H, Duan Z, Si Q, Zhu R, Chuang TH, Luo Y. MicroRNA-3613-3p functions as a tumor suppressor and represents a novel therapeutic target in breast cancer. Breast Cancer Res 2021; 23:12. [PMID: 33494814 PMCID: PMC7836180 DOI: 10.1186/s13058-021-01389-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/11/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND MicroRNAs have been reported to participate in tumorigenesis, treatment resistance, and tumor metastasis. Novel microRNAs need to be identified and investigated to guide the clinical prognosis or therapy for breast cancer. METHOD The copy number variations (CNVs) of MIR3613 from Cancer Genome Atlas (TCGA) or Cancer Cell Line Encyclopedia (CCLE) were analyzed, and its correlation with breast cancer subtypes or prognosis was investigated. The expression level of miR-3613-3p in tumor tissues or serum of breast cancer patients was detected using in situ hybridization and qPCR. Gain-of-function studies were performed to determine the regulatory role of miR-3613-3p on proliferation, apoptosis, and tumor sphere formation of human breast cancer cells MDA-MB-231 or MCF-7. The effects of miR-3613-3p on tumor growth or metastasis in an immunocompromised mouse model of MDA-MB-231-luciferase were explored by intratumor injection of miR-3613-3p analogue. The target genes, interactive lncRNAs, and related signaling pathways of miR-3613-3p were identified by bioinformatic prediction and 3'-UTR assays. RESULTS We found that MIR3613 was frequently deleted in breast cancer genome and its deletion was correlated with the molecular typing, and an unfavorable prognosis in estrogen receptor-positive patients. MiR-3613-3p level was also dramatically lower in tumor tissues or serum of breast cancer patients. Gain-of-function studies revealed that miR-3613-3p could suppress proliferation and sphere formation and promote apoptosis in vitro and impeded tumor growth and metastasis in vivo. Additionally, miR-3613-3p might regulate cell cycle by targeting SMS, PAFAH1B2, or PDK3 to restrain tumor progression. CONCLUSION Our findings indicate a suppressive role of miR-3613-3p in breast cancer progression, which may provide an innovative marker or treatment for breast cancer patients.
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Affiliation(s)
- Chong Chen
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yundi Pan
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Lipeng Bai
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Department of Clinical Laboratory, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Huilin Chen
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhaojun Duan
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Qin Si
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Ruizhe Zhu
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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13
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Heo Y, Heo J, Han SS, Kim WJ, Cheong HS, Hong Y. Difference of copy number variation in blood of patients with lung cancer. Int J Biol Markers 2020; 36:3-9. [PMID: 33307925 DOI: 10.1177/1724600820980739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths worldwide. Copy number variation (CNV) in several genetic regions correlate with cancer susceptibility. Hence, this study evaluated the association between CNV and non-small cell lung cancer (NSCLC) in the peripheral blood. METHODS Blood samples of 150 patients with NSCLC and 150 normal controls were obtained from a bioresource center (Seoul, Korea). Through an epigenome-wide analysis using the MethylationEPIC BeadChip method, we extracted CNVs by using an SVS8 software-supplied multivariate method. We compared CNV frequencies between the NSCLC and controls, and then performed stratification analyses according to smoking status. RESULTS We acquired 979 CNVs, with 582 and 967 copy-number gains and losses, respectively. We identified five nominally significant associations (ACOT1, NAA60, GSDMD, HLA-DPA1, and SLC35B3 genes). Among the current smokers, the NSCLC group had more CNV losses and gains at the GSDMD gene in chromosome 8 (P=0.02) and at the ACOT1 gene in chromosome 14 (P=0.03) than the control group. It also had more CNV losses at the NAA60 gene in chromosome 16 (P=0.03) among non-smokers. In the NSCLC group, current smokers had more CNV gains and losses at the ACOT1 gene in chromosome 14 (P=0.003) and at HLA-DPA1 gene in chromosome 6 (P=0.02), respectively, than non-smokers. CONCLUSION Five nominally significant associations were found between the NSCLC and CNVs. CNVs are associated with the mechanism of lung cancer development. However, the role of CNVs in lung cancer development needs further investigation.
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Affiliation(s)
- Yeonjeong Heo
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Jeongwon Heo
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Seon-Sook Han
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Yoonki Hong
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
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14
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Schubert SA, Morreau H, de Miranda NFCC, van Wezel T. The missing heritability of familial colorectal cancer. Mutagenesis 2020; 35:221-231. [PMID: 31605533 PMCID: PMC7352099 DOI: 10.1093/mutage/gez027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pinpointing heritability factors is fundamental for the prevention and early detection of cancer. Up to one-quarter of colorectal cancers (CRCs) occur in the context of familial aggregation of this disease, suggesting a strong genetic component. Currently, only less than half of the heritability of CRC can be attributed to hereditary syndromes or common risk loci. Part of the missing heritability of this disease may be explained by the inheritance of elusive high-risk variants, polygenic inheritance, somatic mosaicism, as well as shared environmental factors, among others. A great deal of the missing heritability in CRC is expected to be addressed in the coming years with the increased application of cutting-edge next-generation sequencing technologies, routine multigene panel testing and tumour-focussed germline predisposition screening approaches. On the other hand, it will be important to define the contribution of environmental factors to familial aggregation of CRC incidence. This review provides an overview of the known genetic causes of familial CRC and aims at providing clues that explain the missing heritability of this disease.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
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15
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Molecular karyotyping and gene expression analysis in childhood cancer patients. J Mol Med (Berl) 2020; 98:1107-1123. [PMID: 32577795 PMCID: PMC7769790 DOI: 10.1007/s00109-020-01937-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/20/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Abstract The genetic etiology of sporadic childhood cancer cases remains unclear. We recruited a cohort of 20 patients who survived a childhood malignancy and then developed a second primary cancer (2N), and 20 carefully matched patients who survived a childhood cancer without developing a second malignancy (1N). Twenty matched cancer-free (0N) and additional 1000 (0N) GHS participants served as controls. Aiming to identify new candidate loci for cancer predisposition, we compared the genome-wide DNA copy number variations (CNV) with the RNA-expression data obtained after in vitro irradiation of primary fibroblasts. In 2N patients, we detected a total of 142 genes affected by CNV. A total of 53 genes of these were not altered in controls. Six genes (POLR3F, SEC23B, ZNF133, C16orf45, RRN3, and NTAN1) that we found to be overexpressed after irradiation were also duplicated in the genome of the 2N patients. For the 1N collective, 185 genes were affected by CNV and 38 of these genes were not altered in controls. Five genes (ZCWPW2, SYNCRIP, DHX30, DHRS4L2, and THSD1) were located in duplicated genomic regions and exhibited altered RNA expression after irradiation. One gene (ABCC6) was partially duplicated in one 1N and one 2N patient. Analysis of methylation levels of THSD1 and GSTT2 genes which were detected in duplicated regions and are frequently aberrantly methylated in cancer showed no changes in patient’s fibroblasts. In summary, we describe rare and radiation-sensitive genes affected by CNV in childhood sporadic cancer cases, which may have an impact on cancer development. Key messages • Rare CNV’s may have an impact on cancer development in sporadic, non-familial, non-syndromic childhood cancer cases. • In our cohort, each patient displayed a unique pattern of cancer-related gene CNVs, and only few cases shared similar CNV. • Genes that are transcriptionally regulated after radiation can be located in CNVs in cancer patients and controls. • THSD1 and GSTT2 methylation is not altered by CNV. Electronic supplementary material The online version of this article (10.1007/s00109-020-01937-4) contains supplementary material, which is available to authorized users.
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16
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Zhang N, Chen S, Jiang G, Wu Y, Shao J, Liu W, Wang X, Na R, Xu J. The study on copy number alteration of clear cell renal cancer in Chinese population. J Cancer 2020; 11:16-24. [PMID: 31892969 PMCID: PMC6930398 DOI: 10.7150/jca.33316] [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: 01/19/2019] [Accepted: 08/16/2019] [Indexed: 01/24/2023] Open
Abstract
Objectives: Copy number alteration (CNA) is one of the important genetic variations. Although there are many studies on renal cancer CNA, few studies are based on the Chinese population. In our study, our objective is to acquire the whole-genome CNA landscape in Chinese population and explore the tumor risk-associated functional genes in the CNA regions, by detecting whole-genome in the clear cell renal cancer (ccRCC) tissues. Methods: We enrolled 35 formalin fixed paraffin embedded samples, which were processed by Oncoscan assay, and then acquired the data of whole-genome CNA. Then genes annotation and enrichment analyzing were processed. Furthermore, the gene burden and the affected bp (base pair) per Mbp (million bp) regions in whole-genome were analyzed by comparison of different T stage affected by CNA. Results: We acquired the whole-genome CNA landscape by Oncoscan detection, and found out the high-frequency CNA regions which were not reported in previous studies, for example, 11P11, 22q11.23, 20q11.3 (PDRG1), and Xp22.33 so on. During the analyzing of genes annotation and enrichment, we found out some ccRCC functional genes in the CNA regions which might play a role in the biological process, for example, the copy number loss of DNA repair genes (TTC5、PARP2, etc.) and tumor suppressor genes (TADA3, VHL, BAP1, ERC2-IT1, etc.), the copy number gain of oncogenes (ABL2, MET, HUWE1, etc.) and Notch signal pathway genes (MDK, etc.). Besides, gene fusion (GSTTP and GSTTP2) was noticed at 22q11.23 which copy number loss occurred, and the frequency is 46%. And between the different T stage patients affected by CNA, the T2+T3 group carried more high-frequency CNA regions (P-value was 0.012). Conclusions: In this study, the whole-genome ccRCC CNA landscape in Chinese population was acquired, a few functional genes and fusion genes were found out. However, a larger scale of samples is still needed to validate our results.
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Affiliation(s)
- Ning Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siteng Chen
- Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guangliang Jiang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yishuo Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jialiang Shao
- Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wennuan Liu
- Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201, USA
| | - Xiang Wang
- Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201, USA
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17
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Zhang S, Pan X, Zeng T, Guo W, Gan Z, Zhang YH, Chen L, Zhang Y, Huang T, Cai YD. Copy Number Variation Pattern for Discriminating MACROD2 States of Colorectal Cancer Subtypes. Front Bioeng Biotechnol 2019; 7:407. [PMID: 31921812 PMCID: PMC6930883 DOI: 10.3389/fbioe.2019.00407] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Copy number variation (CNV) is a common structural variation pattern of DNA, and it features a higher mutation rate than single-nucleotide polymorphisms (SNPs) and affects a larger fragment of genomes. CNV is related with the genesis of complex diseases and can thus be used as a strategy to identify novel cancer-predisposing markers or mechanisms. In particular, the frequent deletions of mono-ADP-ribosylhydrolase 2 (MACROD2) locus in human colorectal cancer (CRC) alters DNA repair and the sensitivity to DNA damage and results in chromosomal instability. The relationship between CNV and cancer has not been explained. In this study, on the basis of the genome variation profiling by the SNP array from 651 CRC primary tumors, we computationally analyzed the CNV data to select crucial SNP sites with the most relevance to three different states of MACROD2 (heterozygous deletion, homozygous deletion, and normal state), suggesting that these CNVs may play functional roles in CRC tumorigenesis. Our study can shed new insights into the genesis of cancer based on CNV, providing reference for clinical diagnosis, and treatment prognosis of CRC.
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Affiliation(s)
- ShiQi Zhang
- School of Life Sciences, Shanghai University, Shanghai, China.,Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - XiaoYong Pan
- Key Laboratory of System Control and Information Processing, Institute of Image Processing and Pattern Recognition, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Guo
- Institute of Health Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Zijun Gan
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China.,Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai, China
| | - YunHua Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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18
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Liu Y, Liu J, Wang Y. Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs. Bioinformatics 2019; 35:4955-4961. [PMID: 31125057 DOI: 10.1093/bioinformatics/btz429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Whole-genome sequencing (WGS) of tumor-normal sample pairs is a powerful approach for comprehensively characterizing germline copy number variations (CNVs) and somatic copy number alterations (SCNAs) in cancer research and clinical practice. Existing computational approaches for detecting copy number events cannot detect germline CNVs and SCNAs simultaneously, and yield low accuracy for SCNAs. RESULTS In this study, we developed TumorCNV, a novel approach for jointly detecting germline CNVs and SCNAs from WGS data of the matched tumor-normal sample pair. We compared TumorCNV with existing copy number event detection approaches using the simulated data and real data for the COLO-829 melanoma cell line. The experimental results showed that TumorCNV achieved superior performance than existing approaches. AVAILABILITY AND IMPLEMENTATION The software TumorCNV is implemented using a combination of Java and R, and it is freely available from the website at https://github.com/yongzhuang/TumorCNV. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yongzhuang Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jian Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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19
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Du Y, Lin J, Zhang R, Yang W, Quan H, Zang L, Han Y, Li B, Sun H, Wu J. Ubiquitin specific peptidase 5 promotes ovarian cancer cell proliferation through deubiquitinating HDAC2. Aging (Albany NY) 2019; 11:9778-9793. [PMID: 31727867 PMCID: PMC6874447 DOI: 10.18632/aging.102425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/28/2019] [Indexed: 12/14/2022]
Abstract
Globally, epithelial ovarian cancer (EOC) is the most common gynecological malignancy with poor prognosis. The expression and oncogenic roles of ubiquitin specific peptidase 5 (USP5) have been reported in several cancers except EOC. In the current study, USP5 amplification was highly prevalent in patients with EOC and associated with higher mRNA expression of USP5. USP5 amplification and overexpression was positively correlated with poor prognosis of patients of ovarian serous carcinomas. Disruption of USP5 profoundly repressed cell proliferation by inducing cell cycle G0/G1 phase arrest in ovarian cancer cells. Additionally, USP5 knockdown inhibited xenograft growth in nude mice. Knockdown of USP5 decreased histone deacetylase 2 (HDAC2) expression and increased p27 (an important cell cycle inhibitor) expression in vitro and in vivo. The promoting effects of USP5 overexpression on cell proliferation and cell cycle transition, as well as the inhibitory effects of USP5 overexpression on p27 expression were mediated by HDAC2. Moreover, USP5 interacted with HDAC2, and disruption of USP5 enhanced the ubiquitination of HDAC2. HDAC2 protein was positively correlated USP5 protein, and negatively correlated with p27 protein in ovarian serous carcinomas tissues. Collectively, our data suggest the oncogenic function of USP5 and the potential regulatory mechanisms in ovarian carcinogenesis.
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Affiliation(s)
- Yanhua Du
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, P. R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, P. R. China
| | - Jun Lin
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P. R. China
| | - Rulin Zhang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, P. R. China
| | - Wanli Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
| | - Heng Quan
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, P. R. China
| | - Lijuan Zang
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P. R. China
| | - Yaqin Han
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P. R. China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
| | - Hong Sun
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, P. R. China
| | - Jun Wu
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, P. R. China
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20
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Dai X, Zhang X, Lu P. Toward a holistic view of multiscale breast cancer molecular biomarkers. Biomark Med 2019; 13:1509-1533. [PMID: 31668082 DOI: 10.2217/bmm-2019-0143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Powered by rapid technology developments, biomarkers become increasingly diverse, including those detected at genomic, transcriptomic, proteomic, metabolomic and cellular levels. While diverse sets of biomarkers have been utilized in breast cancer predisposition, diagnosis, prognosis, treatment and management, recent additions derived from lincRNA, circular RNA, circulating DNA together with its methylated and hydroxymethylated forms and immune signatures are likely to further transform clinical practice. Here, we take breast cancer as an example of heterogeneous diseases that require many informed decisions from treatment to care to review the huge variety of biomarkers. By assessing the advantages and limitations of modern biomarkers in diverse use scenarios, this article outlines the prospects and challenges of releasing complimentary advantages by augmentation of multiscale molecular biomarkers.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Xuanhao Zhang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Peihua Lu
- Wuxi People's Hospital, Nan Chang Qu, Wuxi, Jiangsu, PR China
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21
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Wang Y, Liyanarachchi S, Miller KE, Nieminen TT, Comiskey DF, Li W, Brock P, Symer DE, Akagi K, DeLap KE, He H, Koboldt DC, de la Chapelle A. Identification of Rare Variants Predisposing to Thyroid Cancer. Thyroid 2019; 29:946-955. [PMID: 30957677 PMCID: PMC6648188 DOI: 10.1089/thy.2018.0736] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Familial non-medullary thyroid cancer (NMTC) accounts for a relatively small proportion of thyroid cancer cases, but it displays strong genetic predisposition. So far, only a few NMTC susceptible genes and low-penetrance variants contributing to NMTC have been described. This study aimed to identify rare germline variants that may predispose individuals to NMTC by sequencing a cohort of 17 NMTC families. Methods: Whole-genome sequencing and genome-wide linkage analysis were performed in 17 NMTC families. MendelScan and BasePlayer were applied to screen germline variants followed by customized filtering. The remaining candidate variants were subsequently validated by Sanger sequencing. A panel of 277 known cancer predisposition genes was also screened in these families. Results: A total of 41 rare coding candidate variants in 40 genes identified by whole-genome sequencing are reported, including 24 missense, five frameshift, five splice change, and seven nonsense variants. Sanger sequencing confirmed all 41 rare variants and proved their co-segregation with NMTC in the extended pedigrees. In silico functional analysis of the candidate genes using Ingenuity Pathway Analysis showed that cancer was the top category of "Diseases and Disorders." Additionally, a targeted search displayed six variants in known cancer predisposition genes, including one frameshift variant and five missense variants. Conclusions: The data identify rare germline variants that may play important roles in NMTC predisposition. It is proposed that in future research including functional characterization, these variants and genes be considered primary candidates for thyroid cancer predisposition.
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Affiliation(s)
- Yanqiang Wang
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Sandya Liyanarachchi
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Katherine E. Miller
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Taina T. Nieminen
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Daniel F. Comiskey
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Wei Li
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Pamela Brock
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - David E. Symer
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keiko Akagi
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Katherine E. DeLap
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Huiling He
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Daniel C. Koboldt
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Albert de la Chapelle
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Address correspondence to: Albert de la Chapelle, MD, PhD, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, 804 Biomedical Research Tower, 460 W. 12th Avenue, Columbus, OH 43210
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22
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Bi H, Liu Y, Tian T, Xia T, Pu R, Zhang Y, Hu F, Zhao Y. A Propensity Score-adjusted Analysis of the Effects of Ubiquitin E3 Ligase Copy Number Variation in Peripheral Blood Leukocytes on Colorectal Cancer Risk. J Cancer 2019; 10:3291-3302. [PMID: 31289601 PMCID: PMC6603381 DOI: 10.7150/jca.29872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/07/2019] [Indexed: 12/29/2022] Open
Abstract
Background: The ubiquitin ligases E3 (E3s) plays a key role in the specific protein degradation in many carcinogenic biological processes. Colorectal cancer (CRC) development may be affected by the copy number variation (CNV) of E3s. Prior studies may have underestimated the impact of potential confounding factors' effects on the association between gene CNV and CRC risk, and CRC risk predictive model integrating gene CNV patterns is lacking. Our research sought to assess the genes CNVs of MDM2, SKP2, FBXW7, β-TRCP, and NEDD4-1 and CRC risk by using propensity score (PS) adjustment and developing models that integrate CNV patterns for CRC risk predictions. Methods: This study comprising 1036 participants used traditional regression and different PS techniques to adjust the confounding factors to evaluate the relationships between five gene CNVs and CRC risk, and to establish a CRC risk predictive model. The AUC was applied to evaluate the effect of the model. The categorical net reclassification improvement (NRI) and the integrated discrimination improvement (IDI) were analyzed to evaluate the discriminatory accuracy improvement among the models. Results: Compared to variable adjustment, the odds ratios (ORs) tended to be conservative and accurate with narrow confidence intervals (CIs) after PS adjustment. After PS adjustment, MDM2 amplification was related to increased CRC risk (Amp-pattern: OR = 8.684, 95% CI: 1.213-62.155, P = 0.031), whereas SKP2 deletion and the (del+amp) genotype were associated with reduced CRC risk (Del-pattern: OR = 0.323, 95% CI: 0.106-0.979, P = 0.046; Var-pattern: OR = 0.339, 95% CI: 0.135-0.854, P = 0.024). The predictive model integrating the gene CNV pattern could correctly reclassify 1.7% of the subjects. Conclusions: MDM2 amplification and SKP2 CNVs are associated with increased and decreased CRC risk, respectively; abnormal CNV-integrated model is more precise for predicting CRC risk. Further studies are needed to verify these encouraging outcomes.
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Affiliation(s)
- Haoran Bi
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Tian Tian
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Tingting Xia
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Rui Pu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Yiwei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Fulan Hu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
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23
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Cheng Y, Dai JY, Wang X, Kooperberg C. Identifying disease-associated copy number variations by a doubly penalized regression model. Biometrics 2018; 74:1341-1350. [PMID: 29894562 PMCID: PMC6663092 DOI: 10.1111/biom.12920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 11/27/2022]
Abstract
Copy number variation (CNV) of DNA plays an important role in the development of many diseases. However, due to the irregularity and sparsity of the CNVs, studying the association between CNVs and a disease outcome or a trait can be challenging. Up to now, not many methods have been proposed in the literature for this problem. Most of the current researchers reply on an ad hoc two-stage procedure by first identifying CNVs in each individual genome and then performing an association test using these identified CNVs. This potentially leads to information loss and as a result a lower power to identify disease associated CNVs. In this article, we describe a new method that combines the two steps into a single coherent model to identify the common CNV across patients that are associated with certain diseases. We use a double penalty model to capture CNVs' association with both the intensities and the disease trait. We validate its performance in simulated datasets and a data example on platinum resistance and CNV in ovarian cancer genome.
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Affiliation(s)
- Yichen Cheng
- Institute for Insight, Georgia State University, Atlanta, Georgia, USA
| | - James Y. Dai
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Xiaoyu Wang
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
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24
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Hehir-Kwa JY, Tops BBJ, Kemmeren P. The clinical implementation of copy number detection in the age of next-generation sequencing. Expert Rev Mol Diagn 2018; 18:907-915. [PMID: 30221560 DOI: 10.1080/14737159.2018.1523723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts. Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual's genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants. Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.
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Affiliation(s)
- Jayne Y Hehir-Kwa
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Bastiaan B J Tops
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Patrick Kemmeren
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
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25
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Wang H, Chau MHK, Cao Y, Kwok KY, Choy KW. Chromosome copy number variants in fetuses with syndromic malformations. Birth Defects Res 2018; 109:725-733. [PMID: 28568742 DOI: 10.1002/bdr2.1054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosome copy number variants (CNVs; gains and losses of DNA sequences >1 kb) are wide-spread throughout the genome of healthy individuals. Laboratory studies show that a subset of CNVs are pathogenic, and not only can be responsible for the pathogenesis of major birth defects and cancer, but are also associated with neurodevelopmental disorders at birth. The characteristics of the pathogenic microdeletions and microduplications are important for both clinical implications and genetic counselling regarding test selection for prenatal screening and diagnosis. Unfortunately, our knowledge of the phenotypic effects of most CNV is still minimal, leading to the classification of many CNVs as "genomic imbalances of unknown clinical significance". Microdeletions and microduplications can occur in all pregnancies and the spectrum of pathogenic CNVs in fetuses with syndromic malformations is not well studied. This review summarizes our current understanding of CNVs, the common detection methods, and the characteristics of pathogenic CNVs identified in fetuses with syndromic malformations. Birth Defects Research 109:725-733, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Huilin Wang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shenzhen, China
| | - Ka Yin Kwok
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shenzhen, China
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26
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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27
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Fan J, Sun W, Lin M, Yu K, Wang J, Duan D, Zheng B, Yang Z, Wang Q. Genetic association study identifies a functional CNV in the WWOX gene contributes to the risk of intracranial aneurysms. Oncotarget 2017; 7:16104-11. [PMID: 26910372 PMCID: PMC4941300 DOI: 10.18632/oncotarget.7546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/31/2016] [Indexed: 01/19/2023] Open
Abstract
Intracranial aneurysms (IAs) accounts for 85% of hemorrhagic stroke. Genetic factors have been known to play an important role in the development of IAs. A functional CNV (CNV-67048) of human WW domain-containing oxidoreductase (WWOX), which has been identified as a tumor suppressor gene in multiple cancers, was identified to be associated with gliomas risk previously. Here, we hypothesized that the CNV-67048 could also affect susceptibility of IAs. Based on a two-stage, case− control study with a total of 976 patients of IAs and 1,200 matched healthy controls, we found the effect size for per copy deletion was 1.35 (95% CI = 1.16–1.57; Ptrend = 1.18 × 10−4). Compared with the individuals having no deletion, significantly higher risk of IAs was detected for both subjects carrying 1 copy deletion (OR = 1.24, 95% CI = 1.02–1.52) and subjects carrying 2 copy deletion (OR = 1.77, 95% CI = 1.24–2.53). Real-time PCR was used to confirm the abnormal expression of WWOX in tissues of IA patients and influence of genotypes of CNV-67048. The expression level of WWOX in IA tissues was significantly lower than that in corresponding normal tissues (P = 0.004), and the deletion genotypes of CNV-67048 have lower WWOX mRNA levels in both tumor tissues and border tissues (P < 0.01). Our data suggests that the deletion genotypes of CNV-67048 in WWOX predispose their carriers to IAs, which might be a genetic biomarker to predict risk of IAs in Chinese.
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Affiliation(s)
- Jin Fan
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Wen Sun
- Department of Neurology, Jinling Hospital of Nanjing University, Nanjing, China
| | - Min Lin
- Department of Neurology, Fuzhou General Hospital of Nanjing Command, PLA and Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Ke Yu
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Jian Wang
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Dan Duan
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Bo Zheng
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Zhenghui Yang
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Qingsong Wang
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
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28
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Kumaran M, Cass CE, Graham K, Mackey JR, Hubaux R, Lam W, Yasui Y, Damaraju S. Germline copy number variations are associated with breast cancer risk and prognosis. Sci Rep 2017; 7:14621. [PMID: 29116104 PMCID: PMC5677082 DOI: 10.1038/s41598-017-14799-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array. Principal component analysis for population stratification revealed 84 outliers leaving 366 cases and 320 controls of Caucasian ancestry for association analysis; CNVs with frequency > 10% and overlapping with protein coding genes were considered for breast cancer risk and prognostic relevance. Coding genes within the CNVs identified were interrogated for gene- dosage effects by correlating copy number status with gene expression profiles in breast tumor tissue. We identified 200 CNVs associated with breast cancer (q-value < 0.05). Of these, 21 CNV regions (overlapping with 22 genes) also showed association with prognosis. We validated representative CNVs overlapping with APOBEC3B and GSTM1 genes using the TaqMan assay. Germline CNVs conferred dosage effects on gene expression in breast tissue. The candidate CNVs identified in this study warrant independent replication.
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Affiliation(s)
- Mahalakshmi Kumaran
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Carol E Cass
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Roland Hubaux
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Wan Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada. .,Cross Cancer Institute, Alberta Health Services, Edmonton, AB, Canada.
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29
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El Naqa I, Kerns SL, Coates J, Luo Y, Speers C, West CML, Rosenstein BS, Ten Haken RK. Radiogenomics and radiotherapy response modeling. Phys Med Biol 2017; 62:R179-R206. [PMID: 28657906 PMCID: PMC5557376 DOI: 10.1088/1361-6560/aa7c55] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Advances in patient-specific information and biotechnology have contributed to a new era of computational medicine. Radiogenomics has emerged as a new field that investigates the role of genetics in treatment response to radiation therapy. Radiation oncology is currently attempting to embrace these recent advances and add to its rich history by maintaining its prominent role as a quantitative leader in oncologic response modeling. Here, we provide an overview of radiogenomics starting with genotyping, data aggregation, and application of different modeling approaches based on modifying traditional radiobiological methods or application of advanced machine learning techniques. We highlight the current status and potential for this new field to reshape the landscape of outcome modeling in radiotherapy and drive future advances in computational oncology.
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Affiliation(s)
- Issam El Naqa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States of America
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30
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Walker LC, Pearson JF, Wiggins GAR, Giles GG, Hopper JL, Southey MC. Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry. Breast Cancer Res 2017; 19:30. [PMID: 28302160 PMCID: PMC5356248 DOI: 10.1186/s13058-017-0825-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/03/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Women with breast cancer who have multiple affected relatives are more likely to have inherited genetic risk factors for the disease. All the currently known genetic risk factors for breast cancer account for less than half of the average familial risk. Furthermore, the genetic factor(s) underlying an increased cancer risk for many women from multiple-case families remain unknown. Rare genomic duplications and deletions, known as copy number variants (CNVs), cover more than 10% of a human genome, are often not assessed in studies of genetic predisposition, and could account for some of the so-called "missing heritability". METHODS We carried out a hypothesis-generating case-control study of breast cancer diagnosed before age 40 years (200 cases, 293 controls) using population-based cases from the Australian Breast Cancer Family Study. Genome-wide scanning for CNVs was performed using the Human610-Quad BeadChip and fine-mapping was conducted using PennCNV. RESULTS We identified deletions overlapping two known cancer susceptibility genes, (BRCA1 and BLM), and a duplication overlapping SMARCB1, associated with risk. The number of deletions across the genome was 1.5-fold higher for cases than controls (P = 10-16), and 2-fold higher when only rare deletions overlapping genes (frequency <1%) were assessed (P = 5 × 10-4). Association tests of CNVs, followed by experimental validation of CNV calls, found deletions overlapping the OR4C11 and OR4P4 genes were associated with breast cancer (P = 0.02 and P = 0.03, respectively). CONCLUSION These results suggest rare CNVs might have a role in breast cancer susceptibility, at least for disease at a young age.
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Affiliation(s)
- Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - George A R Wiggins
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia.
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
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31
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Villacis RAR, Basso TR, Canto LM, Nóbrega AF, Achatz MI, Rogatto SR. Germline large genomic alterations on 7q in patients with multiple primary cancers. Sci Rep 2017; 7:41677. [PMID: 28139749 PMCID: PMC5282589 DOI: 10.1038/srep41677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/29/2016] [Indexed: 11/11/2022] Open
Abstract
Patients with multiple primary cancers (MPCs) are suspected to have a hereditary cancer syndrome. However, only a small proportion may be explained by mutations in high-penetrance genes. We investigate two unrelated MPC patients that met Hereditary Breast and Ovaria Cancer criteria, both presenting triple negative breast tumors and no mutations in BRCA1, BRCA2 and TP53 genes. Germline rearrangements on chromosome 7q, involving over 40 Mb of the same region, were found in both patients: one with mosaic loss (80% of cells) and the other with cnLOH (copy-neutral loss of heterozygosity) secondary to maternal allele duplication. Five children tested had no alterations on 7q. The patients shared 330 genes in common on 7q22.1-q34, including several tumor suppressor genes (TSGs) previously related to breast cancer risk and imprinted genes. The analysis of the triple negative BC from one patient revealed a mosaic gain of 7q translated for over-expressed cancer-related genes. The involvement of TSGs and imprinted genes, mapped on 7q, has the potential of being associated to MPC risk, as well as cancer progression. To our knowledge, this is the first description of patients with MPCs that harbor constitutive large alterations on 7q.
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Affiliation(s)
- R. A. R. Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília - UnB, Brasília, DF, Brazil
| | - T. R. Basso
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - L. M. Canto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - A. F. Nóbrega
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - M. I. Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - S. R. Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Clinical Genetics, Vejle Hospital, DK and University of Southern Denmark, Denmark
- Department of Urology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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32
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Shi J, Zhou W, Zhu B, Hyland PL, Bennett H, Xiao Y, Zhang X, Burke LS, Song L, Hsu CH, Yan C, Chen Q, Meerzaman D, Dagnall CL, Burdette L, Hicks B, Freedman ND, Chanock SJ, Yeager M, Tucker MA, Goldstein AM, Yang XR. Rare Germline Copy Number Variations and Disease Susceptibility in Familial Melanoma. J Invest Dermatol 2016; 136:2436-2443. [PMID: 27476724 PMCID: PMC5123914 DOI: 10.1016/j.jid.2016.07.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 06/02/2016] [Accepted: 07/05/2016] [Indexed: 01/12/2023]
Abstract
Mounting evidence suggests that copy number variations (CNVs) can contribute to cancer susceptibility. The main goal of this study was to evaluate the role of germline CNVs in melanoma predisposition in high-risk melanoma families. We used genome-wide tiling comparative genomic hybridization and single nucleotide polymorphism arrays to characterize CNVs in 335 individuals (240 melanoma cases) from American melanoma-prone families (22 with germline CDKN2A or CDK4 mutations). We found that the global burden of overall CNVs (or deletions or duplications separately) was not significantly associated with case-control or CDKN2A/CDK4 mutation status after accounting for the familial dependence. However, we identified several rare CNVs that either involved known melanoma genes (e.g., PARP1, CDKN2A) or cosegregated with melanoma (duplication on 10q23.23, 3p12.2 and deletions on 8q424.3, 2q22.1) in families without mutations in known melanoma high-risk genes. Some of these CNVs were correlated with expression changes in disrupted genes based on RNASeq data from a subset of melanoma cases included in the CNV study. These results suggest that rare cosegregating CNVs may influence melanoma susceptibility in some melanoma-prone families and genes found in our study warrant further evaluation in future genetic analyses of melanoma.
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Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Hunter Bennett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Xijun Zhang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Laura S Burke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA; Statistics Collaborative, Inc., Washington, DC, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Chih Hao Hsu
- Computational Genomics Research Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Chunhua Yan
- Computational Genomics Research Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Qingrong Chen
- Computational Genomics Research Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Daoud Meerzaman
- Computational Genomics Research Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Laurie Burdette
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA.
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Xi R, Lee S, Xia Y, Kim TM, Park PJ. Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants. Nucleic Acids Res 2016; 44:6274-86. [PMID: 27260798 PMCID: PMC5772337 DOI: 10.1093/nar/gkw491] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/22/2016] [Indexed: 12/16/2022] Open
Abstract
Whole-genome sequencing data allow detection of copy number variation (CNV) at high resolution. However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors. Here, we develop an algorithm called BIC-seq2 that combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline CNVs accurately. Analysis of simulation data showed that this method outperforms existing methods. We apply this algorithm to low coverage whole-genome sequencing data from peripheral blood of nearly a thousand patients across eleven cancer types in The Cancer Genome Atlas (TCGA) to identify cancer-predisposing CNV regions. We confirm known regions and discover new ones including those covering KMT2C, GOLPH3, ERBB2 and PLAG1. Analysis of colorectal cancer genomes in particular reveals novel recurrent CNVs including deletions at two chromatin-remodeling genes RERE and NPM2. This method will be useful to many researchers interested in profiling CNVs from whole-genome sequencing data.
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Affiliation(s)
- Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Semin Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuchao Xia
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Tae-Min Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, 137-701 Seoul, Korea
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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Shivakumar BM, Chakrabarty S, Rotti H, Seenappa V, Rao L, Geetha V, Tantry BV, Kini H, Dharamsi R, Pai CG, Satyamoorthy K. Comparative analysis of copy number variations in ulcerative colitis associated and sporadic colorectal neoplasia. BMC Cancer 2016; 16:271. [PMID: 27080994 PMCID: PMC4831153 DOI: 10.1186/s12885-016-2303-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
Background The incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection. Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the copy number variations (CNVs) and the associated genes which could be potential markers for the detection of neoplasia in both ulcerative colitis-associated neoplasia (UC-CRN) and sporadic colorectal neoplasia (S-CRN). Methods We employed array comparative genome hybridization (aCGH) to identify CNVs in tissue samples of UC nonprogressor, progressor and sporadic CRC. Select genes within these CNV regions as a panel of markers were validated using quantitative real time PCR (qRT-PCR) method along with the microsatellite instability (MSI) in an independent cohort of samples. Immunohistochemistry (IHC) analysis was also performed. Results Integrated analysis showed 10 overlapping CNV regions between UC-Progressor and S-CRN, with the 8q and 12p regions showing greater overlap. The qRT-PCR based panel of MYC, MYCN, CCND1, CCND2, EGFR and FNDC3A was successful in detecting neoplasia with an overall accuracy of 54 % in S-CRN compared to that of 29 % in UC neoplastic samples. IHC study showed that p53 and CCND1 were significantly overexpressed with an increasing frequency from pre-neoplastic to neoplastic stages. EGFR and AMACR were expressed only in the neoplastic conditions. Conclusion CNVs that are common and unique to both UC-associated and sporadic colorectal neoplasm could be the key players driving carcinogenesis. Comparative analysis of CNVs provides testable driver aberrations but needs further evaluation in larger cohorts of samples. These markers may help in developing more effective neoplasia-detection strategies during screening and surveillance programs. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2303-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B M Shivakumar
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Manipal, India.,School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | | | - Harish Rotti
- School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Venu Seenappa
- School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Lakshmi Rao
- Department of Pathology, Kasturba Medical College, Manipal University, Manipal, India
| | - Vasudevan Geetha
- Department of Pathology, Kasturba Medical College, Manipal University, Manipal, India
| | - B V Tantry
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Hema Kini
- Department of Pathology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Rajesh Dharamsi
- Dharamsi Hospital, Chandni Chowk, Sangli, Maharashtra, India
| | - C Ganesh Pai
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Manipal, India
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Villacis RAR, Abreu FB, Miranda PM, Domingues MAC, Carraro DM, Santos EMM, Andrade VP, Rossi BM, Achatz MI, Rogatto SR. ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients. Tumour Biol 2016; 37:3145-53. [PMID: 26427657 DOI: 10.1007/s13277-015-4145-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/23/2015] [Indexed: 01/22/2023] Open
Abstract
Despite one third of breast (BC) and colorectal cancer (CRC) cases having a hereditary component, only a small proportion can be explained by germline mutations. The aim of this study was to identify potential genomic alterations related to cancer predisposition. Copy number variations (CNVs) were interrogated in 113 unrelated cases fulfilling the criteria for hereditary BC/CRC and presenting non-pathogenic mutations in BRCA1, BRCA2, MLH1, MSH2, TP53, and CHEK2 genes. An identical germline deep intronic deletion of ROBO1 was identified in three index patients using two microarray platforms (Agilent 4x180K and Affymetrix CytoScan HD). The ROBO1 deletion was confirmed by quantitative PCR (qPCR). Six relatives were also evaluated by CytoScan HD Array. Genomic analysis confirmed a co-segregation of the ROBO1 deletion with the occurrence of cancer in two families. Direct sequencing revealed no pathogenic ROBO1 point mutations. Transcriptomic analysis (HTA 2.0, Affymetrix) in two breast carcinomas from a single patient revealed ROBO1 down-expression with no splicing events near the intronic deletion. Deeper in silico analysis showed several enhancer regions and a histone methylation mark in the deleted region. The ROBO1 deletion in a putative transcriptional regulatory region, its down-expression in tumor samples, and the results of the co-segregation analysis revealing the presence of the alteration in affected individuals suggest a pathogenic effect of the ROBO1 in cancer predisposition.
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Affiliation(s)
- Rolando A R Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Francine B Abreu
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Priscila M Miranda
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Maria A C Domingues
- Department of Pathology, Faculty of Medicine, University of São Paulo State (UNESP), Botucatu, SP, Brazil
| | - Dirce M Carraro
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | | | - Victor P Andrade
- Department of Pathology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Maria I Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Silvia R Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil.
- Department of Urology, Faculty of Medicine, University of São Paulo State (UNESP), CEP: 18618-970, Botucatu, SP, Brazil.
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36
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Laitinen VH, Akinrinade O, Rantapero T, Tammela TLJ, Wahlfors T, Schleutker J. Germline copy number variation analysis in Finnish families with hereditary prostate cancer. Prostate 2016; 76:316-24. [PMID: 26552734 DOI: 10.1002/pros.23123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/21/2015] [Indexed: 11/09/2022]
Abstract
BACKGROUND The inherited factors that predispose individuals to prostate cancer (PrCa) remain largely unknown. The aim of this study was to identify germline copy number variants (CNVs) in Finnish individuals that could contribute to an increased PrCa risk. METHODS Genome-wide CNV screening was performed by analyzing single nucleotide polymorphisms from 105 PrCa patients and 37 unaffected relatives, representing 31 Finnish hereditary PrCa (HPC) families. The CNVs that aggregated in affected individuals and overlapped with genes implicated in cancer were validated using quantitative PCR in 189 index patients from Finnish HPC families and in 476 controls. RESULTS An intronic deletion (14.7 kb) in the EPHA3 gene coding for class A ephrin receptor was observed in 11.6% of PrCa patients and in 6.1% of controls. The deletion associated with an increased PrCa risk (P = 0.018, OR = 2.06, 95%CI = 1.18-3.61). Although incomplete segregation with affection status was observed, the results show that the deletion was overrepresented in PrCa patients (56.1%) when compared to unaffected male relatives (31.2%). Interestingly, PrCa-specific mortality was higher among EPHA3 deletion carriers (24.3%) than among patients with a normal EPHA3 copy number (3.4%). CONCLUSIONS This study is the first investigation of the contribution of germline CNVs to HPC susceptibility in Finland. A novel association between the EPHA3 deletion and PrCa risk was observed and, if confirmed, screening for this variant may aid in risk stratification among HPC patients.
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Affiliation(s)
- Virpi H Laitinen
- BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
| | - Oyediran Akinrinade
- BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Children's Hospital, Institute of Clinical Medicine, University of Helsinki and Helsinki University Central Hospital, HUS, Finland
| | - Tommi Rantapero
- BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and School of Health Sciences, University of Tampere, Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
| | - Johanna Schleutker
- BioMediTech, University of Tampere and Fimlab Laboratories, Tampere, Finland
- Medical Biochemistry and Genetics, Institute of Biomedicine, Turku, Finland
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, Turku, Finland
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37
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Roversi G, Picinelli C, Bestetti I, Crippa M, Perotti D, Ciceri S, Saccheri F, Collini P, Poliani PL, Catania S, Peissel B, Pagni F, Russo S, Peterlongo P, Manoukian S, Finelli P. Constitutional de novo deletion of the FBXW7 gene in a patient with focal segmental glomerulosclerosis and multiple primitive tumors. Sci Rep 2015; 5:15454. [PMID: 26482194 PMCID: PMC4612309 DOI: 10.1038/srep15454] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/21/2015] [Indexed: 11/09/2022] Open
Abstract
Multiple primary malignant neoplasms are rare entities in the clinical setting, but represent an important issue in the clinical management of patients since they could be expression of a genetic predisposition to malignancy. A high resolution genome wide array CGH led us to identify the first case of a de novo constitutional deletion confined to the FBXW7 gene, a well known tumor suppressor, in a patient with a syndromic phenotype characterized by focal segmental glomerulosclerosis and multiple primary early/atypical onset tumors, including Hodgkin's lymphoma, Wilms tumor and breast cancer. Other genetic defects may be associated with patient's phenotype. In this light, constitutional mutations at BRCA1, BRCA2, TP53, PALB2 and WT1 genes were excluded by performing sequencing and MLPA analysis; similarly, we ruled out constitutional abnormalities at the imprinted 11p15 region by methylation specific -MLPA assay. Our observations sustain the role of FBXW7 as cancer predisposition gene and expand the spectrum of its possible associated diseases.
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Affiliation(s)
- Gaia Roversi
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, Monza, Italy.,Medical Genetics Lab, San Gerardo Hospital, Monza, Italy
| | - Chiara Picinelli
- Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Ilaria Bestetti
- Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Milena Crippa
- Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Daniela Perotti
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Ciceri
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Paola Collini
- Soft Tissue and Bone Pathology, Histopathology and Pediatric Pathology Unit, Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Pietro L Poliani
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Serena Catania
- Pediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Fabio Pagni
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, Monza, Italy
| | - Silvia Russo
- Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Palma Finelli
- Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
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38
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High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer. PLoS One 2015; 10:e0138141. [PMID: 26375816 PMCID: PMC4574474 DOI: 10.1371/journal.pone.0138141] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023] Open
Abstract
Background Cancer is caused by somatic DNA alterations such as gene point mutations, DNA copy number aberrations (CNA) and structural variants (SVs). Genome-wide analyses of SVs in large sample series with well-documented clinical information are still scarce. Consequently, the impact of SVs on carcinogenesis and patient outcome remains poorly understood. This study aimed to perform a systematic analysis of genes that are affected by CNA-associated chromosomal breaks in colorectal cancer (CRC) and to determine the clinical relevance of recurrent breakpoint genes. Methods Primary CRC samples of patients with metastatic disease from CAIRO and CAIRO2 clinical trials were previously characterized by array-comparative genomic hybridization. These data were now used to determine the prevalence of CNA-associated chromosomal breaks within genes across 352 CRC samples. In addition, mutation status of the commonly affected APC, TP53, KRAS, PIK3CA, FBXW7, SMAD4, BRAF and NRAS genes was determined for 204 CRC samples by targeted massive parallel sequencing. Clinical relevance was assessed upon stratification of patients based on gene mutations and gene breakpoints that were observed in >3% of CRC cases. Results In total, 748 genes were identified that were recurrently affected by chromosomal breaks (FDR <0.1). MACROD2 was affected in 41% of CRC samples and another 169 genes showed breakpoints in >3% of cases, indicating that prevalence of gene breakpoints is comparable to the prevalence of well-known gene point mutations. Patient stratification based on gene breakpoints and point mutations revealed one CRC subtype with very poor prognosis. Conclusions We conclude that CNA-associated chromosomal breaks within genes represent a highly prevalent and clinically relevant subset of SVs in CRC.
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39
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Saliba J, Saint-Martin C, Di Stefano A, Lenglet G, Marty C, Keren B, Pasquier F, Valle VD, Secardin L, Leroy G, Mahfoudhi E, Grosjean S, Droin N, Diop M, Dessen P, Charrier S, Palazzo A, Merlevede J, Meniane JC, Delaunay-Darivon C, Fuseau P, Isnard F, Casadevall N, Solary E, Debili N, Bernard OA, Raslova H, Najman A, Vainchenker W, Bellanné-Chantelot C, Plo I. Germline duplication of ATG2B and GSKIP predisposes to familial myeloid malignancies. Nat Genet 2015; 47:1131-40. [DOI: 10.1038/ng.3380] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/21/2015] [Indexed: 02/07/2023]
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40
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Weren RDA, Venkatachalam R, Cazier JB, Farin HF, Kets CM, de Voer RM, Vreede L, Verwiel ETP, van Asseldonk M, Kamping EJ, Kiemeney LA, Neveling K, Aben KKH, Carvajal-Carmona L, Nagtegaal ID, Schackert HK, Clevers H, van de Wetering M, Tomlinson IP, Ligtenberg MJL, Hoogerbrugge N, Geurts van Kessel A, Kuiper RP. Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development. J Pathol 2015; 236:155-64. [PMID: 25712196 PMCID: PMC6681464 DOI: 10.1002/path.4520] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/09/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022]
Abstract
Heritable genetic variants can significantly affect the lifetime risk of developing cancer, including polyposis and colorectal cancer (CRC). Variants in genes currently known to be associated with a high risk for polyposis or CRC, however, explain only a limited number of hereditary cases. The identification of additional genetic causes is, therefore, crucial to improve CRC prevention, detection and treatment. We have performed genome-wide and targeted DNA copy number profiling and resequencing in early-onset and familial polyposis/CRC patients, and show that deletions affecting the open reading frame of the tumour suppressor gene FOCAD are recurrent and significantly enriched in CRC patients compared with unaffected controls. All patients carrying FOCAD deletions exhibited a personal or family history of polyposis. RNA in situ hybridization revealed FOCAD expression in epithelial cells in the colonic crypt, the site of tumour initiation, as well as in colonic tumours and organoids. Our data suggest that monoallelic germline deletions in the tumour suppressor gene FOCAD underlie moderate genetic predisposition to the development of polyposis and CRC.
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Affiliation(s)
- Robbert D A Weren
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | | | - Henner F Farin
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | - C Marleen Kets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lilian Vreede
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Eugène T P Verwiel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Monique van Asseldonk
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
| | - Luis Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, CA, USA
| | - Iris D Nagtegaal
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Hans Clevers
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | | | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics University of Oxford, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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41
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Moir-Meyer GL, Pearson JF, Lose F, Scott RJ, McEvoy M, Attia J, Holliday EG, Pharoah PD, Dunning AM, Thompson DJ, Easton DF, Spurdle AB, Walker LC. Rare germline copy number deletions of likely functional importance are implicated in endometrial cancer predisposition. Hum Genet 2015; 134:269-78. [PMID: 25381466 DOI: 10.1007/s00439-014-1507-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/29/2014] [Indexed: 01/15/2023]
Abstract
Endometrial cancer is the most common invasive gynaecological cancer in women, and relatively little is known about inherited risk factors for this disease. This is the first genome-wide study to explore the role of common and rare germline copy number variants (CNVs) in predisposition to endometrial cancer. CNVs were called from germline DNA of 1,209 endometrioid endometrial cancer cases and 528 cancer-unaffected female controls. Overall CNV load of deletions or DNA gains did not differ significantly between cases and controls (P > 0.05), but cases presented with an excess of rare germline deletions overlapping likely functional genomic regions including genes (P = 8 × 10(-10)), CpG islands (P = 1 × 10(-7)) and sno/miRNAs regions (P = 3 × 10(-9)). On average, at least one additional gene and two additional CpG islands were disrupted by rare deletions in cases compared to controls. The most pronounced difference was that over 30 sno/miRNAs were disrupted by rare deletions in cases for every single disruption event in controls. A total of 13 DNA repair genes were disrupted by rare deletions in 19/1,209 cases (1.6%) compared to one gene in 1/528 controls (0.2%; P = 0.007), and this increased DNA repair gene loss in cases persisted after excluding five individuals carrying CNVs disrupting mismatch repair genes MLH1, MSH2 and MSH6 (P = 0.03). There were 34 miRNA regions deleted in at least one case but not in controls, the most frequent of which encompassed hsa-mir-661 and hsa-mir-203. Our study implicates rare germline deletions of functional and regulatory regions as possible mechanisms conferring endometrial cancer risk, and has identified specific regulatory elements as candidates for further investigation.
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Affiliation(s)
- Gemma L Moir-Meyer
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand,
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Seiser EL, Innocenti F. Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. Cancer Inform 2015; 13:77-83. [PMID: 25657572 PMCID: PMC4310714 DOI: 10.4137/cin.s16345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 12/24/2022] Open
Abstract
Somatic alterations in DNA copy number have been well studied in numerous malignancies, yet the role of germline DNA copy number variation in cancer is still emerging. Genotyping microarrays generate allele-specific signal intensities to determine genotype, but may also be used to infer DNA copy number using additional computational approaches. Numerous tools have been developed to analyze Illumina genotype microarray data for copy number variant (CNV) discovery, although commonly utilized algorithms freely available to the public employ approaches based upon the use of hidden Markov models (HMMs). QuantiSNP, PennCNV, and GenoCN utilize HMMs with six copy number states but vary in how transition and emission probabilities are calculated. Performance of these CNV detection algorithms has been shown to be variable between both genotyping platforms and data sets, although HMM approaches generally outperform other current methods. Low sensitivity is prevalent with HMM-based algorithms, suggesting the need for continued improvement in CNV detection methodologies.
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Affiliation(s)
- Eric L Seiser
- Center for Pharmacogenomics and Individualized Therapy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Federico Innocenti
- Center for Pharmacogenomics and Individualized Therapy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ; UNC Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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43
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Yauk CL, Aardema MJ, Benthem JV, Bishop JB, Dearfield KL, DeMarini DM, Dubrova YE, Honma M, Lupski JR, Marchetti F, Meistrich ML, Pacchierotti F, Stewart J, Waters MD, Douglas GR. Approaches for identifying germ cell mutagens: Report of the 2013 IWGT workshop on germ cell assays(☆). MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 783:36-54. [PMID: 25953399 DOI: 10.1016/j.mrgentox.2015.01.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 01/06/2023]
Abstract
This workshop reviewed the current science to inform and recommend the best evidence-based approaches on the use of germ cell genotoxicity tests. The workshop questions and key outcomes were as follows. (1) Do genotoxicity and mutagenicity assays in somatic cells predict germ cell effects? Limited data suggest that somatic cell tests detect most germ cell mutagens, but there are strong concerns that dictate caution in drawing conclusions. (2) Should germ cell tests be done, and when? If there is evidence that a chemical or its metabolite(s) will not reach target germ cells or gonadal tissue, it is not necessary to conduct germ cell tests, notwithstanding somatic outcomes. However, it was recommended that negative somatic cell mutagens with clear evidence for gonadal exposure and evidence of toxicity in germ cells could be considered for germ cell mutagenicity testing. For somatic mutagens that are known to reach the gonadal compartments and expose germ cells, the chemical could be assumed to be a germ cell mutagen without further testing. Nevertheless, germ cell mutagenicity testing would be needed for quantitative risk assessment. (3) What new assays should be implemented and how? There is an immediate need for research on the application of whole genome sequencing in heritable mutation analysis in humans and animals, and integration of germ cell assays with somatic cell genotoxicity tests. Focus should be on environmental exposures that can cause de novo mutations, particularly newly recognized types of genomic changes. Mutational events, which may occur by exposure of germ cells during embryonic development, should also be investigated. Finally, where there are indications of germ cell toxicity in repeat dose or reproductive toxicology tests, consideration should be given to leveraging those studies to inform of possible germ cell genotoxicity.
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Affiliation(s)
- Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | | | - Jan van Benthem
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jack B Bishop
- National Institute of Environmental Health Sciences, NC, USA
| | | | | | | | | | - James R Lupski
- Department of Molecular and Human Genetics, and Department of Pediatrics, Baylor College of Medicine, USA
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | | | - Francesca Pacchierotti
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Italy
| | | | | | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
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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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45
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Sapkota Y. Germline DNA variations in breast cancer predisposition and prognosis: a systematic review of the literature. Cytogenet Genome Res 2014; 144:77-91. [PMID: 25401968 DOI: 10.1159/000369045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is the most common cancer and the second leading cause of death in women worldwide. The disease is caused by a combination of genetic, environmental, lifestyle, and reproductive risk factors. Linkage and family-based studies have identified many pathological germline mutations, which account for around 20% of the genetic risk of familial breast cancer. In recent years, single nucleotide polymorphism-based genetic association studies, especially genome-wide association studies (GWASs), have been very successful in uncovering low-penetrance common variants associated with breast cancer risk. These common variants alone may explain up to an additional 30% of the familial risk of breast cancer. With the advent of available genetic resources and growing collaborations among researchers across the globe, the much needed large sample size to capture variants with small effect sizes and low population frequencies is being addressed, and hence many more common variants are expected to be discovered in the coming days. Here, major GWASs conducted for breast cancer predisposition and prognosis until 2013 are summarized. Few studies investigating other forms of genetic variations contributing to breast cancer predisposition and disease outcomes are also discussed. Finally, the potential utility of the GWAS-identified variants in disease risk models and some future perspectives are presented.
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Affiliation(s)
- Yadav Sapkota
- The Neurogenetics Laboratory, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Qld., Australia
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46
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Ordóñez R, Gallo-Oller G, Martínez-Soto S, Legarra S, Pata-Merci N, Guegan J, Danglot G, Bernheim A, Meléndez B, Rey JA, Castresana JS. Genome-wide microarray expression and genomic alterations by array-CGH analysis in neuroblastoma stem-like cells. PLoS One 2014; 9:e113105. [PMID: 25392930 PMCID: PMC4231109 DOI: 10.1371/journal.pone.0113105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC), a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture). Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-β) and contribute to CSC phenotype. We focused on the aberrant activation of TGF-β and Hh signalling pathways, confirming the inhibition of repressors of TGF-β pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells.
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Affiliation(s)
- Raquel Ordóñez
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Gabriel Gallo-Oller
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Soledad Martínez-Soto
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Sheila Legarra
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | | | | | | | | | - Bárbara Meléndez
- Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Toledo, Spain
| | - Juan A. Rey
- IdiPaz Research Unit, La Paz University Hospital, Madrid, Spain
| | - Javier S. Castresana
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
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Waugh MG. Amplification of Chromosome 1q Genes Encoding the Phosphoinositide Signalling Enzymes PI4KB, AKT3, PIP5K1A and PI3KC2B in Breast Cancer. J Cancer 2014; 5:790-6. [PMID: 25368680 PMCID: PMC4216804 DOI: 10.7150/jca.9794] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
Little is known about the possible oncogenic roles of genes encoding for the phosphatidylinositol 4-kinases, a family of enzymes that regulate an early step in phosphoinositide signalling. To address this issue, the mutational status of all four human phosphatidylinositol 4-kinases genes was analyzed across 852 breast cancer samples using the COSMIC data resource. Point mutations in the phosphatidylinositol 4-kinase genes were uncommon and appeared in less than 1% of the patient samples however, 62% of the tumours had increases in gene copy number for PI4KB which encodes the phosphatidylinositol 4-kinase IIIbeta isozyme. Extending this analysis to subsequent enzymes in the phosphoinositide signalling cascades revealed that the only PIP5K1A, PI3KC2B and AKT3 genes exhibited similar patterns of gene copy number variation. By comparison, gene copy number increases for established oncogenes such as EGFR and HER2/Neu were only evident in 20% of the samples. The PI4KB, PIP5K1A, PI3KC2B and AKT3 genes are related in that they all localize to chromosome 1q which is often structurally and numerically abnormal in breast cancer. These results demonstrate that a gene quartet encoding a potential phosphoinositide signalling pathway is amplified in a subset of breast cancers.
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Affiliation(s)
- Mark G Waugh
- Lipid and Membrane Biology Group, Institute for Liver and Digestive Health, UCL, Royal Free Campus, Rowland Hill Street, London, NW3 2PF United Kingdom
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48
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Horpaopan S, Spier I, Zink AM, Altmüller J, Holzapfel S, Laner A, Vogt S, Uhlhaas S, Heilmann S, Stienen D, Pasternack SM, Keppler K, Adam R, Kayser K, Moebus S, Draaken M, Degenhardt F, Engels H, Hofmann A, Nöthen MM, Steinke V, Perez-Bouza A, Herms S, Holinski-Feder E, Fröhlich H, Thiele H, Hoffmann P, Aretz S. Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis. Int J Cancer 2014; 136:E578-89. [PMID: 25219767 DOI: 10.1002/ijc.29215] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022]
Abstract
To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mutation negative patient cohort followed by a targeted next generation sequencing (NGS) approach. Genomic DNA from 221 unrelated German patients was genotyped on high-resolution SNP arrays. Putative CNVs were filtered according to stringent criteria, compared with those of 531 population-based German controls, and validated by qPCR. Candidate genes were prioritized using in silico, expression, and segregation analyses, data mining and enrichment analyses of genes and pathways. In 27% of the 221 unrelated patients, a total of 77 protein coding genes displayed rare, nonrecurrent, germline CNVs. The set included 26 candidates with molecular and cellular functions related to tumorigenesis. Targeted high-throughput sequencing found truncating point mutations in 12% (10/77) of the prioritized genes. No clear evidence was found for autosomal recessive subtypes. Six patients had potentially causative mutations in more than one of the 26 genes. Combined with data from recent studies of early-onset colorectal and breast cancer, recurrent potential loss-of-function alterations were detected in CNTN6, FOCAD (KIAA1797), HSPH1, KIF26B, MCM3AP, YBEY and in three genes from the ARHGAP family. In the canonical Wnt pathway oncogene CTNNB1 (β-catenin), two potential gain-of-function mutations were found. In conclusion, the present study identified a group of rarely affected genes which are likely to predispose to colorectal adenoma formation and confirmed previously published candidates for tumor predisposition as etiologically relevant.
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49
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Combined analysis with copy number variation identifies risk loci in lung cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:469103. [PMID: 25093167 PMCID: PMC4100386 DOI: 10.1155/2014/469103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 12/26/2022]
Abstract
Background. Lung cancer is the most important cause of cancer mortality worldwide, but the underlying mechanisms of this disease are not fully understood. Copy number variations (CNVs) are promising genetic variations to study because of their potential effects on cancer.
Methodology/Principal Findings. Here we conducted a pilot study in which we systematically analyzed the association of CNVs in two lung cancer datasets: the Environment And Genetics in Lung cancer Etiology (EAGLE) and the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial datasets. We used a preestablished association method to test the datasets separately and conducted a combined analysis to test the association accordance between the two datasets. Finally, we identified 167 risk SNP loci and 22 CNVs associated with lung cancer and linked them with recombination hotspots. Functional annotation and biological relevance analyses implied that some of our predicted risk loci were supported by other studies and might be potential candidate loci for lung cancer studies. Conclusions/Significance. Our results further emphasized the importance of copy number variations in cancer and might be a valuable complement to current genome-wide association studies on cancer.
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50
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Haitjema A, Mol BM, Kooi IE, Massink MPG, Jørgensen JAL, Rockx DAP, Rooimans MA, de Winter JP, Meijers-Heijboer H, Joenje H, Dorsman JC. Coregulation of FANCA and BRCA1 in human cells. SPRINGERPLUS 2014; 3:381. [PMID: 25161863 PMCID: PMC4143540 DOI: 10.1186/2193-1801-3-381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/30/2014] [Indexed: 12/23/2022]
Abstract
Fanconi anemia (FA) is a genetically heterogeneous syndrome associated with increased cancer predisposition. The underlying genes govern the FA pathway which functions to protect the genome during the S-phase of the cell cycle. While upregulation of FA genes has been linked to chemotherapy resistance, little is known about their regulation in response to proliferative stimuli. The purpose of this study was to examine how FA genes are regulated, especially in relation to the cell cycle, in order to reveal their possible participation in biochemical networks. Expression of 14 FA genes was monitored in two human cell-cycle models and in two RB1/E2F pathway-associated primary cancers, retinoblastoma and basal breast cancer. In silico studies were performed to further evaluate coregulation and identify connected networks and diseases. Only FANCA was consistently induced over 2-fold; FANCF failed to exhibit any regulatory fluctuations. Two tools exploiting public data sets indicated coregulation of FANCA with BRCA1. Upregulation of FANCA and BRCA1 correlated with upregulation of E2F3. Genes coregulated with both FANCA and BRCA1 were enriched for MeSH-Term id(s) genomic instability, microcephaly, and Bloom syndrome, and enriched for the cellular component centrosome. The regulation of FA genes appears highly divergent. In RB1-linked tumors, upregulation of FA network genes was associated with reduced expression of FANCF. FANCA and BRCA1 may jointly act in a subnetwork - supporting vital function(s) at the subcellular level (centrosome) as well as at the level of embryonic development (mechanisms controlling head circumference).
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Affiliation(s)
- Anneke Haitjema
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Berber M Mol
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Irsan E Kooi
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Maarten PG Massink
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Jens AL Jørgensen
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Davy AP Rockx
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Martin A Rooimans
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Johan P de Winter
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hans Joenje
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
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