1
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Kong LR, Gupta K, Wu AJ, Perera D, Ivanyi-Nagy R, Ahmed SM, Tan TZ, Tan SLW, Fuddin A, Sundaramoorthy E, Goh GS, Wong RTX, Costa ASH, Oddy C, Wong H, Patro CPK, Kho YS, Huang XZ, Choo J, Shehata M, Lee SC, Goh BC, Frezza C, Pitt JJ, Venkitaraman AR. A glycolytic metabolite bypasses "two-hit" tumor suppression by BRCA2. Cell 2024; 187:2269-2287.e16. [PMID: 38608703 DOI: 10.1016/j.cell.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 04/14/2024]
Abstract
Knudson's "two-hit" paradigm posits that carcinogenesis requires inactivation of both copies of an autosomal tumor suppressor gene. Here, we report that the glycolytic metabolite methylglyoxal (MGO) transiently bypasses Knudson's paradigm by inactivating the breast cancer suppressor protein BRCA2 to elicit a cancer-associated, mutational single-base substitution (SBS) signature in nonmalignant mammary cells or patient-derived organoids. Germline monoallelic BRCA2 mutations predispose to these changes. An analogous SBS signature, again without biallelic BRCA2 inactivation, accompanies MGO accumulation and DNA damage in Kras-driven, Brca2-mutant murine pancreatic cancers and human breast cancers. MGO triggers BRCA2 proteolysis, temporarily disabling BRCA2's tumor suppressive functions in DNA repair and replication, causing functional haploinsufficiency. Intermittent MGO exposure incites episodic SBS mutations without permanent BRCA2 inactivation. Thus, a metabolic mechanism wherein MGO-induced BRCA2 haploinsufficiency transiently bypasses Knudson's two-hit requirement could link glycolysis activation by oncogenes, metabolic disorders, or dietary challenges to mutational signatures implicated in cancer evolution.
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Affiliation(s)
- Li Ren Kong
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Department of Pharmacology, National University of Singapore, Singapore 117600, Singapore
| | - Komal Gupta
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Andy Jialun Wu
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - David Perera
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | | | - Syed Moiz Ahmed
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Shawn Lu-Wen Tan
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Institute of Molecular and Cell Biology (IMCB), A(∗)STAR, Singapore 138673, Singapore
| | | | | | | | | | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Callum Oddy
- Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Hannan Wong
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - C Pawan K Patro
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Yun Suen Kho
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore
| | - Xiao Zi Huang
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore
| | - Joan Choo
- Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Mona Shehata
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Soo Chin Lee
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; University of Cologne, 50923 Köln, Germany
| | - Jason J Pitt
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; Genome Institute of Singapore, A(∗)STAR, Singapore 138673, Singapore
| | - Ashok R Venkitaraman
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Institute of Molecular and Cell Biology (IMCB), A(∗)STAR, Singapore 138673, Singapore; Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK; Department of Medicine, National University of Singapore, Singapore 119228, Singapore.
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2
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Perera AR, Warrier V, Sundararaman S, Hsiao Y, Ghosh S, Kularatnarajah L, Pitt JJ. Melvin is a conversational voice interface for cancer genomics data. Commun Biol 2024; 7:30. [PMID: 38182884 PMCID: PMC10770357 DOI: 10.1038/s42003-023-05688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024] Open
Abstract
Melvin is a multi-modal Amazon Alexa skill that allows users to quickly explore cancer genomics data from TCGA through simple conversations.
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Affiliation(s)
- Akila R Perera
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Vinay Warrier
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shwetha Sundararaman
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yi Hsiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Soumita Ghosh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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3
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Wu AJ, Perera A, Kularatnarajah L, Korsakova A, Pitt JJ. Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches. Brief Bioinform 2023; 24:bbad331. [PMID: 37742051 PMCID: PMC10518036 DOI: 10.1093/bib/bbad331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/03/2023] [Accepted: 08/27/2023] [Indexed: 09/25/2023] Open
Abstract
Single-base substitution (SBS) mutational signatures have become standard practice in cancer genomics. In lieu of de novo signature extraction, reference signature assignment allows users to estimate the activities of pre-established SBS signatures within individual malignancies. Several tools have been developed for this purpose, each with differing methodologies. However, due to a lack of standardization, there may be inter-tool variability in signature assignment. We deeply characterized three assignment strategies and five SBS signature assignment tools. We observed that assignment strategy choice can significantly influence results and interpretations. Despite varying recommendations by tools, Refit performed best by reducing overfitting and maximizing reconstruction of the original mutational spectra. Even after uniform application of Refit, tools varied remarkably in signature assignments both qualitatively (Jaccard index = 0.38-0.83) and quantitatively (Kendall tau-b = 0.18-0.76). This phenomenon was exacerbated for 'flat' signatures such as the homologous recombination deficiency signature SBS3. An ensemble approach (EnsembleFit), which leverages output from all five tools, increased SBS3 assignment accuracy in BRCA1/2-deficient breast carcinomas. After generating synthetic mutational profiles for thousands of pan-cancer tumors, EnsembleFit reduced signature activity assignment error 15.9-24.7% on average using Catalogue of Somatic Mutations In Cancer and non-standard reference signature sets. We have also released the EnsembleFit web portal (https://www.ensemblefit.pittlabgenomics.com) for users to generate or download ensemble-based SBS signature assignments using any strategy and combination of tools. Overall, we show that signature assignment heterogeneity across tools and strategies is non-negligible and propose a viable, ensemble solution.
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Affiliation(s)
- Andy J Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Medicine, National University of Singapore, Singapore, Singapore
| | - Akila Perera
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | | | - Anna Korsakova
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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4
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Hoppe MM, Jaynes P, Shuangyi F, Peng Y, Sridhar S, Hoang PM, Liu CX, De Mel S, Poon L, Chan EHL, Lee J, Ong CK, Tang T, Lim ST, Nagarajan C, Grigoropoulos NF, Tan SY, Hue SSS, Chang ST, Chuang SS, Li S, Khoury JD, Choi H, Harris C, Bottos A, Gay LJ, Runge HF, Moutsopoulos I, Mohorianu I, Hodson DJ, Farinha P, Mottok A, Scott DW, Pitt JJ, Chen J, Kumar G, Kannan K, Chng WJ, Chee YL, Ng SB, Tripodo C, Jeyasekharan AD. Patterns of Oncogene Coexpression at Single-Cell Resolution Influence Survival in Lymphoma. Cancer Discov 2023; 13:1144-1163. [PMID: 37071673 PMCID: PMC10157367 DOI: 10.1158/2159-8290.cd-22-0998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/29/2022] [Accepted: 02/13/2023] [Indexed: 04/19/2023]
Abstract
Cancers often overexpress multiple clinically relevant oncogenes, but it is not known if combinations of oncogenes in cellular subpopulations within a cancer influence clinical outcomes. Using quantitative multispectral imaging of the prognostically relevant oncogenes MYC, BCL2, and BCL6 in diffuse large B-cell lymphoma (DLBCL), we show that the percentage of cells with a unique combination MYC+BCL2+BCL6- (M+2+6-) consistently predicts survival across four independent cohorts (n = 449), an effect not observed with other combinations including M+2+6+. We show that the M+2+6- percentage can be mathematically derived from quantitative measurements of the individual oncogenes and correlates with survival in IHC (n = 316) and gene expression (n = 2,521) datasets. Comparative bulk/single-cell transcriptomic analyses of DLBCL samples and MYC/BCL2/BCL6-transformed primary B cells identify molecular features, including cyclin D2 and PI3K/AKT as candidate regulators of M+2+6- unfavorable biology. Similar analyses evaluating oncogenic combinations at single-cell resolution in other cancers may facilitate an understanding of cancer evolution and therapy resistance. SIGNIFICANCE Using single-cell-resolved multiplexed imaging, we show that selected subpopulations of cells expressing specific combinations of oncogenes influence clinical outcomes in lymphoma. We describe a probabilistic metric for the estimation of cellular oncogenic coexpression from IHC or bulk transcriptomes, with possible implications for prognostication and therapeutic target discovery in cancer. This article is highlighted in the In This Issue feature, p. 1027.
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Affiliation(s)
- Michal Marek Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Fan Shuangyi
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shruti Sridhar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Phuong Mai Hoang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Clementine Xin Liu
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Sanjay De Mel
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Limei Poon
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Esther Hian Li Chan
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joanne Lee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Choon Kiat Ong
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Tiffany Tang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | | | | | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sheng-Tsung Chang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan
| | - Shaoying Li
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph D. Khoury
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Carl Harris
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | - Laura J. Gay
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | | | | | - Irina Mohorianu
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Daniel J. Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | | | - Anja Mottok
- BC Cancer Research Centre, Vancouver, Canada
| | | | - Jason J. Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Gayatri Kumar
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kasthuri Kannan
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yen Lin Chee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo, Palermo, Italy
- IFOM ETS – The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Anand D. Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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5
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Chan JJ, Zhang B, Chew XH, Salhi A, Kwok ZH, Lim CY, Desi N, Subramaniam N, Siemens A, Kinanti T, Ong S, Sanchez-Mejias A, Ly PT, An O, Sundar R, Fan X, Wang S, Siew BE, Lee KC, Chong CS, Lieske B, Cheong WK, Goh Y, Fam WN, Ooi MG, Koh BTH, Iyer SG, Ling WH, Chen J, Yoong BK, Chanwat R, Bonney GK, Goh BKP, Zhai W, Fullwood MJ, Wang W, Tan KK, Chng WJ, Dan YY, Pitt JJ, Roca X, Guccione E, Vardy LA, Chen L, Gao X, Chow PKH, Yang H, Tay Y. Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis. Nat Cell Biol 2022; 24:928-939. [PMID: 35618746 PMCID: PMC9203280 DOI: 10.1038/s41556-022-00913-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/07/2022] [Indexed: 11/15/2022]
Abstract
Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3′ UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3′ UTR splicing remains poorly understood as splicing studies have traditionally focused on protein-coding alterations. Here we systematically map the pan-cancer landscape of 3′ UTR splicing and present this in SpUR (http://www.cbrc.kaust.edu.sa/spur/home/). 3′ UTR splicing is widespread, upregulated in cancers, correlated with poor prognosis and more prevalent in oncogenes. We show that antisense oligonucleotide-mediated inhibition of 3′ UTR splicing efficiently reduces oncogene expression and impedes tumour progression. Notably, CTNNB1 3′ UTR splicing is the most consistently dysregulated event across cancers. We validate its upregulation in hepatocellular carcinoma and colon adenocarcinoma, and show that the spliced 3′ UTR variant is the predominant contributor to its oncogenic functions. Overall, our study highlights the importance of 3′ UTR splicing in cancer and may launch new avenues for RNA-based anti-cancer therapeutics. Chan et al. report that 3′ UTR splicing is widespread and enhanced across different cancer types and is associated with more advanced tumour progression.
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Affiliation(s)
- Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Adil Salhi
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA, USA
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nagavidya Subramaniam
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Angela Siemens
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,The University of British Columbia, Vancouver, British Columbia, Canada
| | - Tyas Kinanti
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shane Ong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Integra Therapeutics S.L., Barcelona, Spain
| | - Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - Xiaonan Fan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok Chung Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Yufen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee Nih Fam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa G Ooi
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan T H Koh
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shridhar Ganpathi Iyer
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Boon-Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | - Glenn Kunnath Bonney
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Brian K P Goh
- Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore
| | - Weiwei Zhai
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wilson Wang
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ernesto Guccione
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Leah A Vardy
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,BioMap, Beijing, China
| | - Pierce K H Chow
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore.,Academic Clinical Programme for Surgery, SingHealth Duke-NUS Academic Medical Centre (AMC), Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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6
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Wai CMM, Chen S, Phyu T, Fan S, Leong SM, Zheng W, Low LCY, Choo SN, Lee CK, Chung TH, Ban KHK, Ghosh S, Lie S, Kato S, Nakamura S, Takahashi E, Ko YH, Khoury JD, Chuang SS, Au-Yeung RKH, Tan SY, Lim ST, Ong CK, Ho YH, Poon LM, De Mel S, Jeyasekharan AD, Chng WJ, Otto F, Quintanilla-Martinez L, Zanardi F, Iannelli F, Tripodo C, Pitt JJ, Ng SB. Immune pathway upregulation and lower genomic instability distinguish EBV-positive nodal T/NK-cell lymphoma from ENKTL and PTCL-NOS. Haematologica 2022; 107:1864-1879. [PMID: 35021606 PMCID: PMC9335103 DOI: 10.3324/haematol.2021.280003] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 11/30/2022] Open
Abstract
Primary Epstein-Barr virus (EBV)-positive nodal T/NK-cell lymphoma (PTCL-EBV) is a poorly understood disease which shows features resembling extranodal NK/T-cell lymphoma (ENKTL) and is currently not recognized as a distinct entity but categorized as a variant of primary T-cell lymphoma not otherwise specified (PTCL-NOS). Herein, we analyzed copy-number aberrations (n=77) with a focus on global measures of genomic instability and homologous recombination deficiency and performed gene expression (n=84) and EBV miRNA expression (n=24) profiling as well as targeted mutational analysis (n=16) to further characterize PTCL-EBV in relation to ENKTL and PTCL-NOS. Multivariate analysis revealed that patients with PTCL-EBV had a significantly worse outcome compared to patients with PTCL-NOS (P=0.002) but not to those with ENKTL. Remarkably, PTCL-EBV exhibited significantly lower genomic instability and homologous recombination deficiency scores compared to ENKTL and PTCL-NOS. Gene set enrichment analysis revealed that many immune-related pathways, interferon α/γ response, and IL6_JAK_STAT3 signaling were significantly upregulated in PTCLEBV and correlated with lower genomic instability scores. We also identified that NFKB-associated genes, BIRC3, NFKB1 (P50) and CD27, and their proteins are upregulated in PTCL-EBV. Most PTCL-EBV demonstrated a type 2 EBV latency pattern and, strikingly, exhibited downregulated expression of most EBV miRNA compared to ENKTL and their target genes were also enriched in immune-related pathways. PTCL-EBV also showed frequent mutations of TET2, PIK3CD and STAT3, and are characterized by microsatellite stability. Overall, poor outcome, low genomic instability, upregulation of immune pathways and downregulation of EBV miRNA are distinctive features of PTCL-EBV. Our data support the concept that PTCL-EBV could be considered as a distinct entity, provide novel insights into the pathogenesis of the disease and offer potential new therapeutic targets for this tumor.
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Affiliation(s)
- Cho Mar Myint Wai
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shangying Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - The Phyu
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wenning Zheng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Louis Ching Yi Low
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shoa-Nian Choo
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chi-Kuen Lee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Kenneth Hon Kim Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Soumita Ghosh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Stefanus Lie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Seiichi Kato
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan; Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Shigeo Nakamura
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Emiko Takahashi
- Department of Pathology, Aichi Medical University Hospital, Nagakute, Japan
| | - Young-Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University, Seoul, Korea
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rex K H Au-Yeung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Pathology, National University Hospital, National University Health System, Singapore
| | - Soon-Thye Lim
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Choon-Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, Singapore, Singapore; Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Yong-Howe Ho
- Department of Pathology, Tan Tock Seng Hospital, Singapore
| | - Li Mei Poon
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore
| | - Sanjay De Mel
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Franziska Otto
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, Tübingen University Hospital, Tübingen, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, Tübingen University Hospital, Tübingen, Germany
| | - Federica Zanardi
- Bioinformatics Unit, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Fabio Iannelli
- Bioinformatics Unit, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo School of Medicine, Palermo, Italy
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Siok-Bian Ng
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pathology, National University Hospital, National University Health System, Singapore.
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7
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Ansari-Pour N, Zheng Y, Yoshimatsu TF, Sanni A, Ajani M, Reynier JB, Tapinos A, Pitt JJ, Dentro S, Woodard A, Rajagopal PS, Fitzgerald D, Gruber AJ, Odetunde A, Popoola A, Falusi AG, Babalola CP, Ogundiran T, Ibrahim N, Barretina J, Van Loo P, Chen M, White KP, Ojengbede O, Obafunwa J, Huo D, Wedge DC, Olopade OI. Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes. Nat Commun 2021; 12:6946. [PMID: 34836952 PMCID: PMC8626467 DOI: 10.1038/s41467-021-27079-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/02/2021] [Indexed: 02/08/2023] Open
Abstract
Black women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast cancers, with RNA-seq in a subset, from women in Nigeria in comparison with The Cancer Genome Atlas (n = 76) reveal a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonal GATA3 mutations with a 10.5-year younger age at diagnosis. We also find non-coding mutations in bona fide drivers (ZNF217 and SYPL1) and a previously unreported INDEL signature strongly associated with African ancestry proportion, underscoring the need to expand inclusion of diverse populations in biomedical research. Finally, we demonstrate that characterizing tumors for homologous recombination deficiency has significant clinical relevance in stratifying patients for potentially life-saving therapies. Breast cancer heterogeneity and tumour evolutionary trajectories remain largely unknown among women of African ancestry. Here, the authors perform whole genome and transcriptome sequencing of Nigerian breast cancer patients and identify unique evolutionary phenomena.
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Affiliation(s)
- Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jean-Baptiste Reynier
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Avraam Tapinos
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Stefan Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Anna Woodard
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Department of Computer Science, The University of Chicago, Chicago, IL, 60637, USA
| | - Padma Sheila Rajagopal
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Andreas J Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.,Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Peace Babalola
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Temidayo Ogundiran
- Department of Surgery, University College Hospital, Ibadan, Oyo, Nigeria
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Jordi Barretina
- Girona Biomedical Research Institute (IDIBGI), Hospital Universitari de Girona Dr Josep Trueta, Girona, Spain
| | | | - Mengjie Chen
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.,Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK. .,Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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8
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Padmanabhan N, Kyon HK, Boot A, Lim K, Srivastava S, Chen S, Wu Z, Lee HO, Mukundan VT, Chan C, Chan YK, Xuewen O, Pitt JJ, Isa ZFA, Xing M, Lee MH, Tan ALK, Ting SHW, Luftig MA, Kappei D, Kruger WD, Bian J, Ho YS, Teh M, Rozen SG, Tan P. Author Correction: Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. Genome Biol 2021; 22:181. [PMID: 34140045 PMCID: PMC8212508 DOI: 10.1186/s13059-021-02405-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Huang Kie Kyon
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kevin Lim
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Hyung-Ok Lee
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yarn Kit Chan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ong Xuewen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zul Fazreen Adam Isa
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Manjie Xing
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ming Hui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Shamaine Ho Wei Ting
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Centre for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, 119228, Singapore
| | - Steve George Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Genome Institute of Singapore, Singapore, 138672, Singapore. .,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169856, Singapore. .,Singapore Gastric Cancer Consortium, Singapore, 119074, Singapore. .,Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
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9
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Padmanabhan N, Kyon HK, Boot A, Lim K, Srivastava S, Chen S, Wu Z, Lee HO, Mukundan VT, Chan C, Chan YK, Xuewen O, Pitt JJ, Isa ZFA, Xing M, Lee MH, Tan ALK, Ting SHW, Luftig MA, Kappei D, Kruger WD, Bian J, Ho YS, Teh M, Rozen SG, Tan P. Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. Genome Biol 2021; 22:167. [PMID: 34074348 PMCID: PMC8170989 DOI: 10.1186/s13059-021-02375-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. Results We identify the cystathionine beta-synthase enzyme (CBS) as a highly recurrent target of epigenetic silencing in CIMP GC. Likewise, we show that CBS epimutations are significantly associated with CIMP in various other cancers, occurring even in premalignant gastroesophageal conditions and longitudinally linked to clinical persistence. Of note, CRISPR deletion of CBS in normal gastric epithelial cells induces widespread DNA methylation changes that overlap with primary GC CIMP patterns. Reflecting its metabolic role as a gatekeeper interlinking the methionine and homocysteine cycles, CBS loss in vitro also causes reductions in the anti-inflammatory gasotransmitter hydrogen sulfide (H2S), with concomitant increase in NF-κB activity. In a murine genetic model of CBS deficiency, preliminary data indicate upregulated immune-mediated transcriptional signatures in the stomach. Conclusions Our results implicate CBS as a bi-faceted modifier of aberrant DNA methylation and inflammation in GC and highlights H2S donors as a potential new therapy for CBS-silenced lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02375-2.
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Affiliation(s)
- Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Huang Kie Kyon
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kevin Lim
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Hyung-Ok Lee
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yarn Kit Chan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ong Xuewen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zul Fazreen Adam Isa
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Manjie Xing
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ming Hui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Shamaine Ho Wei Ting
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Centre for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, 119228, Singapore
| | - Steve George Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Genome Institute of Singapore, Singapore, 138672, Singapore. .,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169856, Singapore. .,Singapore Gastric Cancer Consortium, Singapore, 119074, Singapore. .,Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
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10
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Hoppe MM, Jaynes P, Wardyn JD, Upadhyayula SS, Tan TZ, Lie S, Lim DGZ, Pang BNK, Lim S, P S Yeong J, Karnezis A, Chiu DS, Leung S, Huntsman DG, Sedukhina AS, Sato K, Topp MD, Scott CL, Choi H, Patel NR, Brown R, Kaye SB, Pitt JJ, Tan DSP, Jeyasekharan AD. Quantitative imaging of RAD51 expression as a marker of platinum resistance in ovarian cancer. EMBO Mol Med 2021; 13:e13366. [PMID: 33709473 PMCID: PMC8103098 DOI: 10.15252/emmm.202013366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022] Open
Abstract
Early relapse after platinum chemotherapy in epithelial ovarian cancer (EOC) portends poor survival. A-priori identification of platinum resistance is therefore crucial to improve on standard first-line carboplatin-paclitaxel treatment. The DNA repair pathway homologous recombination (HR) repairs platinum-induced damage, and the HR recombinase RAD51 is overexpressed in cancer. We therefore designed a REMARK-compliant study of pre-treatment RAD51 expression in EOC, using fluorescent quantitative immunohistochemistry (qIHC) to overcome challenges in quantitation of protein expression in situ. In a discovery cohort (n = 284), RAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in univariate and multivariate analyses. The association of RAD51 with relapse/survival was validated in a carboplatin monotherapy SCOTROC4 clinical trial cohort (n = 264) and was predominantly noted in HR-proficient cancers (Myriad HRDscore < 42). Interestingly, overexpression of RAD51 modified expression of immune-regulatory pathways in vitro, while RAD51-High tumours showed exclusion of cytotoxic T cells in situ. Our findings highlight RAD51 expression as a determinant of platinum resistance and suggest possible roles for therapy to overcome immune exclusion in RAD51-High EOC. The qIHC approach is generalizable to other proteins with a continuum instead of discrete/bimodal expression.
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Affiliation(s)
- Michal M Hoppe
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Patrick Jaynes
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Joanna D Wardyn
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | | | - Tuan Zea Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Stefanus Lie
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Diana G Z Lim
- Department of PathologyNational University HospitalSingapore
| | - Brendan N K Pang
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of PathologyNational University HospitalSingapore
| | - Sherlly Lim
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Joe P S Yeong
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Anthony Karnezis
- British Columbia Cancer AgencyVancouverBCCanada
- Present address:
Pathology and Lab medicineUC Davis Medical CentreSacramentoCAUSA
| | | | | | | | - Anna S Sedukhina
- Department of PharmacogenomicsSt. Marianna UniversityKawasakiJapan
| | - Ko Sato
- Department of PharmacogenomicsSt. Marianna UniversityKawasakiJapan
| | - Monique D Topp
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia
| | - Hyungwon Choi
- Saw Swee Hock School of Public HealthNational University of SingaporeSingapore
| | | | - Robert Brown
- Division of CancerImperial College LondonLondonUK
| | - Stan B Kaye
- Department of Haematology‐OncologyNational University HospitalSingapore
| | - Jason J Pitt
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - David S P Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of Haematology‐OncologyNational University HospitalSingapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of Haematology‐OncologyNational University HospitalSingapore
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11
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Woodard AE, Yoshimatsu TF, Pitt JJ, Zheng Y, Olopade OI. Abstract 5468: Gene fusions in breast cancer in Nigerian women. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: As a chromosomal rearrangement event, gene fusion plays a critical role in the pathogenesis of cancer by creating potentially oncogenic chimeric proteins. However, gene fusions have been understudied in breast cancer patients of African ancestry, who are often diagnosed at a younger age and with more aggressive molecular features of cancer than patients of other races/ethnicities.
Methods: Ninety-six women diagnosed with invasive breast cancer were recruited from Ibadan, Nigeria with mean age at diagnosis of 51.6 ± 12.4 years. Primary tumors were collected, of which 62 (64.6%) were hormone receptor negative (HR-) by immunohistochemistry, and 31 (32.3%) were basal-like subtype by PAM50 classification. Paired-end reads from RNA-seq on these tumors were used for gene fusion detection by three programs, STAR-Fusion, STAR-SEQR, and Arriba. To increase specificity, we applied an ensembling method by selecting fusions identified by at least two of the three callers. Multiple filters were applied to fusion candidates to remove likely false positives, including fusions containing genes of mitochondrial origin, fusions consisting of pairs of paralogues or orthologs, fusions involving HLA genes, and fusions found in several databases of non-cancer tissues. To investigate potentially druggable fusion transcripts, we compared our call set with the OncoKB precision oncology knowledge base.
Results: STAR-Fusion, STAR-SEQR, and Arriba identified 682, 4529, and 3056 unique fusion transcripts, respectively. Following application of the ensembling method and filtering to select final fusions, 709 unique fusions were identified. Comparison with 13 databases and published papers identified 62 of these fusions as previously reported. The mean fusion burden per sample was 7.7 ± 7.4. The fusion burden per sample was significantly smaller for tumors classified as Luminal A subtypes by PAM50 classification than Luminal B, Basal, and HER2 subtypes (P < 0.03) as well as normal like (P < 0.01). Fusion burden was highest in HER2 tumors (NS), consistent with previous reports. The number of fusion transcripts per sample did not differ significantly according to the patient's age. Ninety-six percent of fusion transcripts were only identified in a single sample, including the ETV6-NTRK3 fusion, previously reported in secretory breast carcinoma, and BCR-ABL1, both of which are targeted by a drug identified in OncoKB. The most commonly observed fusion, EDDM13–ZNF71, appeared in 4.2% (4/96) of samples.
Conclusion: The vast majority of breast cancer samples from Nigerian women demonstrate unique fusion transcripts in expressed RNA. Fusion burden per sample was related to PAM50 classification. Future work will incorporate functional studies of the recurrent gene fusion events identified in our cohort. We will additionally focus on validation and refinement of our approach to detecting gene fusions in this understudied population, in order to better identify patients who can benefit from new therapies.
Citation Format: Anna Elizabeth Woodard, Toshio F. Yoshimatsu, WABCS Working Group, Jason J. Pitt, Yonglan Zheng, Olufunmilayo I. Olopade. Gene fusions in breast cancer in Nigerian women [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5468.
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Affiliation(s)
| | | | - Jason J. Pitt
- 2National University of Singapore, Singapore, Singapore
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12
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Ansari-Pour N, Pitt JJ, Dentro S, Fitzgerald D, Zheng Y, Yoshimatsu TF, Rajagopal P, Gruber A, Sanni A, Oluwasola O, Ajani M, Odetunde A, Popoola A, Falusi A, Ogundiran T, Obafunwa J, Ojengbede O, Ibrahim N, White KP, Huo D, Loo PV, Wedge DC, Olopade O. Abstract LB-300: The life history of breast cancer in Nigerian women: Evidence for ethnic differences in tumor evolution based on whole-genome sequencing. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer is a heterogeneous disease and the incidence to mortality ratio is highest for women of African ancestry. Paucity of data from non-European ancestry groups limits our understanding of the underlying etiological differences or alternative routes to progression that may explain differential outcomes. To examine the contribution of genomic differences, we performed high-depth whole-genome sequencing on 100 breast tumors (90X) and their paired normal samples (30X) from indigenous African women with breast cancer in Southwest Nigeria and performed comparative analysis with 84 TCGA whole genome sequences of breast tumor/normal pairs (46 White, 30 African American and 8 samples representing other ethnicities). High confidence somatic single nucleotide variants (SNVs) were obtained by using MuTect and Strelka. To analyse intra-tumoral heterogeneity (ITH), Battenberg and DPClust were used to call copy number aberrations (CNA) and cluster somatic SNVs based on cancer cell fraction (CCF) respectively. We find that in the HR-/HER2+ subtype, clonal losses of chromosome 14q are highly enriched in Nigerians (41%) but absent in the Whites even though the proportion of this subtype was comparable between the two groups (42% and 33% respectively). This is an interesting observation since not only 14q loss is known to be an event associated with breast cancer aggressiveness, but HR-/HER2+ has also been reported to be enriched within the relatively younger Nigerian patients with breast cancer. This may in part explain inter-ethnic disparity in survival. Also, somatic SNV clustering analysis showed that Nigerian cancers have a higher level of ITH than Whites, which may explain the pronounced aggressiveness of breast cancer in women of African ancestry. In contrast, early drivers (e.g. TP53 and PIK3CA) and whole genome duplication rates were mostly similar between the groups. Our observations suggest differences in the underlying evolutionary trajectories of breast cancer across ethnic backgrounds. These data underscore the need for larger and more in-depth studies of diverse cancer genomes and, if validated, may translate into clinical intervention opportunities tailored to women of African ancestry and accelerate progress in precision cancer care.
Note: This abstract was not presented at the meeting.
Citation Format: Naser Ansari-Pour, Jason J. Pitt, Stefan Dentro, Dominic Fitzgerald, Yonglan Zheng, Toshio F. Yoshimatsu, Padma Rajagopal, Andreas Gruber, Ayodele Sanni, Olayiwola Oluwasola, Mustapha Ajani, Abayomi Odetunde, Abiodun Popoola, Adeyinka Falusi, Temidayo Ogundiran, John Obafunwa, Oladosu Ojengbede, Nasiru Ibrahim, Kevin P. White, Dezheng Huo, Peter Van Loo, David C. Wedge, Olufunmilayo Olopade. The life history of breast cancer in Nigerian women: Evidence for ethnic differences in tumor evolution based on whole-genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-300.
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Affiliation(s)
| | - Jason J. Pitt
- 2National University of Singapore, Singapore, Singapore
| | - Stefan Dentro
- 3European Bioinformatics Institute, Hinxton, United Kingdom
| | | | | | | | | | | | - Ayodele Sanni
- 5Lagos State University Teaching Hospital, Lagos, Nigeria
| | | | | | | | | | | | | | - John Obafunwa
- 5Lagos State University Teaching Hospital, Lagos, Nigeria
| | | | - Nasiru Ibrahim
- 5Lagos State University Teaching Hospital, Lagos, Nigeria
| | | | | | - Peter Van Loo
- 8The Francis Crick Institute, London, United Kingdom
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13
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Wang S, Pitt JJ, Zheng Y, Yoshimatsu TF, Gao G, Sanni A, Oluwasola O, Ajani M, Fitzgerald D, Odetunde A, Khramtsova G, Hurley I, Popoola A, Falusi A, Ogundiran T, Obafunwa J, Ojengbede O, Ibrahim N, Barretina J, White KP, Huo D, Olopade OI. Germline variants and somatic mutation signatures of breast cancer across populations of African and European ancestry in the US and Nigeria. Int J Cancer 2019; 145:3321-3333. [PMID: 31173346 PMCID: PMC6851589 DOI: 10.1002/ijc.32498] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 04/10/2019] [Accepted: 05/02/2019] [Indexed: 11/09/2022]
Abstract
Somatic mutation signatures may represent footprints of genetic and environmental exposures that cause different cancer. Few studies have comprehensively examined their association with germline variants, and none in an indigenous African population. SomaticSignatures was employed to extract mutation signatures based on whole-genome or whole-exome sequencing data from female patients with breast cancer (TCGA, training set, n = 1,011; Nigerian samples, validation set, n = 170), and to estimate contributions of signatures in each sample. Association between somatic signatures and common single nucleotide polymorphisms (SNPs) or rare deleterious variants were examined using linear regression. Nine stable signatures were inferred, and four signatures (APOBEC C>T, APOBEC C>G, aging and homologous recombination deficiency) were highly similar to known COSMIC signatures and explained the majority (60-85%) of signature contributions. There were significant heritable components associated with APOBEC C>T signature (h2 = 0.575, p = 0.010) and the combined APOBEC signatures (h2 = 0.432, p = 0.042). In TCGA dataset, seven common SNPs within or near GNB5 were significantly associated with an increased proportion (beta = 0.33, 95% CI = 0.21-0.45) of APOBEC signature contribution at genome-wide significance, while rare germline mutations in MTCL1 was also significantly associated with a higher contribution of this signature (p = 6.1 × 10-6 ). This is the first study to identify associations between germline variants and mutational patterns in breast cancer across diverse populations and geography. The findings provide evidence to substantiate causal links between germline genetic risk variants and carcinogenesis.
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Affiliation(s)
- Shengfeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China.,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL
| | - Ayodele Sanni
- Department of Pathology & Forensic Medicine, Lagos State University Teaching Hospital, Lagos, Nigeria
| | | | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Nigeria
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Ian Hurley
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Lagos, Nigeria
| | - Adeyinka Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - John Obafunwa
- Department of Pathology & Forensic Medicine, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Oladosu Ojengbede
- Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Nasiru Ibrahim
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Jordi Barretina
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | | | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
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14
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Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Benz CC, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas. JAMA Oncol 2019; 3:1654-1662. [PMID: 28472234 DOI: 10.1001/jamaoncol.2017.0595] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Importance African Americans have the highest breast cancer mortality rate. Although racial difference in the distribution of intrinsic subtypes of breast cancer is known, it is unclear if there are other inherent genomic differences that contribute to the survival disparities. Objectives To investigate racial differences in breast cancer molecular features and survival and to estimate the heritability of breast cancer subtypes. Design, Setting, and Participants Among a convenience cohort of patients with invasive breast cancer, breast tumor and matched normal tissue sample data (as of September 18, 2015) were obtained from The Cancer Genome Atlas. Main Outcomes and Measures Breast cancer–free interval, tumor molecular features, and genetic variants. Results Participants were 930 patients with breast cancer, including 154 black patients of African ancestry (mean [SD] age at diagnosis, 55.66 [13.01] years; 98.1% [n = 151] female) and 776 white patients of European ancestry (mean [SD] age at diagnosis, 59.51 [13.11] years; 99.0% [n = 768] female). Compared with white patients, black patients had a worse breast cancer-free interval (hazard ratio, HR=1.67; 95% CI, 1.02-2.74; P = .043). They had a higher likelihood of basal-like (odds ratio, 3.80; 95% CI, 2.46-5.87; P < .001) and human epidermal growth factor receptor 2 (ERBB2 [formerly HER2])–enriched (odds ratio, 2.22; 95% CI, 1.10-4.47; P = .027) breast cancer subtypes, with the Luminal A subtype as the reference. Blacks had more TP53 mutations and fewer PIK3CA mutations than whites. While most molecular differences were eliminated after adjusting for intrinsic subtype, the study found 16 DNA methylation probes, 4 DNA copy number segments, 1 protein, and 142 genes that were differentially expressed, with the gene-based signature having an excellent capacity for distinguishing breast tumors from black vs white patients (cross-validation C index, 0.878). Using germline genotypes, the heritability of breast cancer subtypes (basal vs nonbasal) was estimated to be 0.436 (P = 1.5 × 10−14). The estrogen receptor–positive polygenic risk score built from 89 known susceptibility variants was higher in blacks than in whites (difference, 0.24; P = 2.3 × 10−5), while the estrogen receptor–negative polygenic risk score was much higher in blacks than in whites (difference, 0.48; P = 2.8 × 10−11). Conclusions and Relevance On the molecular level, after adjusting for intrinsic subtype frequency differences, this study found a modest number of genomic differences but a significant clinical survival outcome difference between blacks and whites in The Cancer Genome Atlas data set. Moreover, more than 40% of breast cancer subtype frequency differences could be explained by genetic variants. These data could form the basis for the development of molecular targeted therapies to improve clinical outcomes for the specific subtypes of breast cancers that disproportionately affect black women. Findings also indicate that personalized risk assessment and optimal treatment could reduce deaths from aggressive breast cancers for black women.
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Affiliation(s)
- Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois,Center for Clinical Cancer Genetics, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania
| | - Suhn K Rhie
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Jason J Pitt
- Committee of Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Katherine A Hoadley
- Department of Genetics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill
| | - Melissa Troester
- Department of Epidemiology, The University of North Carolina at Chapel Hill
| | - Yuanbin Ru
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania
| | - Tara Lichtenberg
- The Research Institute, Nationwide Children’s Hospital, Columbus, Ohio
| | - Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania
| | - Carl S Shelley
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison
| | | | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan
| | - Craig D Shriver
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center/Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Charles M Perou
- Department of Genetics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics, Department of Medicine, The University of Chicago, Chicago, Illinois,Committee of Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, Illinois
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15
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Cheng J, Demeulemeester J, Wedge DC, Vollan HKM, Pitt JJ, Russnes HG, Pandey BP, Nilsen G, Nord S, Bignell GR, White KP, Børresen-Dale AL, Campbell PJ, Kristensen VN, Stratton MR, Lingjærde OC, Moreau Y, Van Loo P. Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun 2019; 10:525. [PMID: 30692535 PMCID: PMC6349916 DOI: 10.1038/s41467-019-08512-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Jiqiu Cheng
- Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.,Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Jonas Demeulemeester
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK.,Department of Human Genetics, University of Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - David C Wedge
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK.,Big Data Institute, University of Oxford, Old Road, OX3 7LF, Oxford, UK
| | - Hans Kristian M Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway.,The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, 900 East 57th Street, 60637, Chicago, IL, USA.,Committee on Genetics, Genomics, and Systems Biology, University of Chicago, 920 East 58th Street, 60637, Chicago, IL, USA
| | - Hege G Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway.,Department of Pathology, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Bina P Pandey
- Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium
| | - Gro Nilsen
- Department of Informatics and Centre for Cancer Biomedicine, University of Oslo, N-0424, Oslo, Norway
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Graham R Bignell
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, 900 East 57th Street, 60637, Chicago, IL, USA.,Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, 60637, Chicago, IL, USA.,Department of Human Genetics, University of Chicago, 920 East 58th Street, 60637, Chicago, IL, USA.,Tempus Labs, Inc, Chicago, IL, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | | | - Ole Christian Lingjærde
- Department of Informatics and Centre for Cancer Biomedicine, University of Oslo, N-0424, Oslo, Norway
| | - Yves Moreau
- Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK. .,Department of Human Genetics, University of Leuven, Herestraat 49, B-3000, Leuven, Belgium.
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16
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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Author Correction: Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2019; 10:288. [PMID: 30643118 PMCID: PMC6331546 DOI: 10.1038/s41467-018-07886-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained an error in the author affiliations. The affiliation of Kevin P. White with Tempus Labs, Inc. Chicago, IL, USA was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA. .,Tempus Labs, Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), 17007, Girona 17007, Spain.
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17
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Cheng J, Demeulemeester J, Wedge DC, Vollan HKM, Pitt JJ, Russnes HG, Pandey BP, Nilsen G, Nord S, Bignell GR, White KP, Børresen-Dale AL, Campbell PJ, Kristensen VN, Stratton MR, Lingjærde OC, Moreau Y, Van Loo P. Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun 2018; 9:5397. [PMID: 30559362 PMCID: PMC6297227 DOI: 10.1038/s41467-018-07842-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Jiqiu Cheng
- Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.,Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Jonas Demeulemeester
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - David C Wedge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Big Data Institute, University of Oxford, Old Road, Oxford, OX3 7LF, UK
| | - Hans Kristian M Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL, 60637, USA.,Committee on Genetics, Genomics, and Systems Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Hege G Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway.,Department of Pathology, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Bina P Pandey
- Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium
| | - Gro Nilsen
- Department of Informatics and Centre for Cancer Biomedicine, University of Oslo, N-0424, Oslo, Norway
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Graham R Bignell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL, 60637, USA.,Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA.,Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA.,Tempus Labs, Inc., Chicago, IL, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, N-0310, Oslo, Norway
| | | | - Ole Christian Lingjærde
- Department of Informatics and Centre for Cancer Biomedicine, University of Oslo, N-0424, Oslo, Norway
| | - Yves Moreau
- Department of Electrical Engineering (ESAT) and iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. .,Department of Human Genetics, University of Leuven, Herestraat 49, B-3000, Leuven, Belgium.
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18
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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2018; 9:4181. [PMID: 30327465 PMCID: PMC6191428 DOI: 10.1038/s41467-018-06616-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the molecular features of breast cancers using 194 patients from Nigeria and 1037 patients from The Cancer Genome Atlas (TCGA). Relative to Black and White cohorts in TCGA, Nigerian HR + /HER2 - tumors are characterized by increased homologous recombination deficiency signature, pervasive TP53 mutations, and greater structural variation-indicating aggressive biology. GATA3 mutations are also more frequent in Nigerians regardless of subtype. Higher proportions of APOBEC-mediated substitutions strongly associate with PIK3CA and CDH1 mutations, which are underrepresented in Nigerians and Blacks. PLK2, KDM6A, and B2M are also identified as previously unreported significantly mutated genes in breast cancer. This dataset provides novel insights into potential molecular mechanisms underlying outcome disparities and lay a foundation for deployment of precision therapeutics in underserved populations.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven, 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Tempus Labs Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), Girona, 17007, Spain.
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19
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Abstract
In this issue of Cancer Cell, Yuan et al. compared the somatic alterations harbored by tumors from European and African ancestry individuals. They determined that the latter group has a propensity for aberrations that are consistent with genomic instability, potentially lending insight to the genomic basis of cancer health disparities.
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Affiliation(s)
- Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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20
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Wang S, Pitt JJ, Zheng Y, Yoshimatsu TF, Gao G, Riester M, Sanni A, Oluwasola O, Fitzgerald D, Ogundiran T, Babalola C, Popoola A, Falusi A, Winckler W, Obafunwa J, Ojengbede O, Ibrahim N, Barretina J, White KP, Huo D, Olopade OI. Abstract 287: Germline variants and somatic mutation signatures in breast cancer across populations of African and European ancestry. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Somatic mutation signatures may represent the footprints of genetic and environmental exposures that cause different types of cancer. However, few studies have comprehensively examined the association between germline variants and somatic mutation signatures, and none in African ancestry populations. Methods: Study samples consist of 1,011 breast cancer patients from The Cancer Genome Atlas (TCGA; 168 Black, 737 White, and 106 other ancestries, discovery set) and 170 Nigerian women with breast cancer (validation set). SomaticSignatures was employed to extract mutation signatures from whole-genome or whole-exome sequenicng data, and to estimate contributions of signatures on each sample. SNPtest and SKAT-O were used to conduct association tests for the association between somatic signatures and common single nucleotide polymorphisms (SNPs) or rare deleterious variants. SNP array-based heritability was calculated by GCTA. Results: Nine stable signatures were inferred in total. Four of them – APOBEC C>T, APOBEC C>G, aging, and homologous recombination deficiency (HRD) – were highly similar to known COSMIC signatures. These together explained the vast majority (60%~85%) of mutation signature contributions regardless of race/ethnicity or tumor subtype. The heritability estimates displayed significantly heritable components for APOBEC C>T signature (h2 = 0.575, P = 0.010) and combined APOBEC signature (h2 = 0.432, P = 0.042). In TCGA dataset, seven common SNPs on/near GNB5 were significantly associated with an increased proportion (beta = 0.33, 95% CI = 0.21~0.45) of APOBEC signature contribution at genome-wide significance, while rare deleterious variants in MTCL1 and HIV-EP1 were also significantly associated with this signature contribution (P =1.9×10-6, 2.2×10-5, respectively). The combined rare deleterious variants in BRCA1 and BRCA2 were significantly correlated with the contribution of HRD signature (P =1.0×10-8, 1.1×10-5, respectively). In the Nigerian cohort, only the associations in HIV-EP1 and BRCA2 were replicated with relatively higher mutation frequencies (N = 9, 8; P = 0.05, 0.01, respectively). In addition, the combined rare deleterious variants in HRD pathway genes was significantly associated with the contribution of HRD signature in both TCGA (P = 2.8×10-5) and Nigerian samples (P = 0.01). After excluding BRCA1/2, this association turned to be nonsignificant. Conclusion: Our study identified associations between germline variants and mutational patterns in breast cancer across different ethnicities, especially in African women for the first time. This finding has important public health implications as it provides evidence to substantiate causal links between germline genetic variants and carcinogenesis process. Further replications in larger and diverse populations are needed.
Citation Format: Shengfeng Wang, Jason J. Pitt, Yonglan Zheng, Toshio F. Yoshimatsu, Guimin Gao, Markus Riester, Ayodele Sanni, Olayiwola Oluwasola, Dominic Fitzgerald, Temidayo Ogundiran, Chinedum Babalola, Abiodun Popoola, Adeyinka Falusi, Wendy Winckler, John Obafunwa, Oladosu Ojengbede, Nasiru Ibrahim, WABCS Working Group, Jordi Barretina, Kevin P. White, Dezheng Huo, Olufunmilayo I. Olopade. Germline variants and somatic mutation signatures in breast cancer across populations of African and European ancestry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 287.
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21
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Olopade OI, Pitt JJ, Riester M, Odetunde A, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Wang S, Fitzgerald DJ, Grundstad J, Tuteja J, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Chen L, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, White KP, Ibrahim N, Oluwasola O, Barretina J. Abstract PD8-05: Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-pd8-05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Objectives: Paucity of data on populations of African Ancestry in clinical trials continues to limit our ability to design and implement innovative solutions to narrow the breast cancer survival gap amongst Africans, African Americans, and European Americans. We have developed a cross-continent research infrastructure to examine the spectrum of genomic alterations in breast tumors from West Africa and subsequently, to compare them to tumors from African American women and women of European Ancestry in The Cancer Genome Atlas (TCGA) database.
Methods: Consecutive women with breast cancer presenting for treatment at the University College Hospital, Ibadan and at Lagos State University Teaching Hospital, Lagos, Nigeria gave informed consent and were recruited to the West African Breast Cancer Study (WABCS) between 2013-2016. Tumor-normal pairs were subjected to exome and/or high-depth (90x) genome sequencing. High confidence somatic mutations (substitutions, insertions/deletions and structural variants) were obtained by using multiple variant callers. Furthermore, 1,089 exomic and 80 genomic breast tumor-normal pairs from TCGA were harmonized with WABCS samples, resulting in a cohort of 147 West Africans (147 exome; 40 genome), 154 African Americans (154 exome; 31 genome), and 776 Caucasians (776 exome; 43 genome).
Results: Across the exomes, genes commonly altered in breast cancer in TCGA are also altered in women of African ancestry, but the mutational spectrum is quite different, demonstrating overrepresentation of tumors with aggressive phenotypes. Overall, TP53 (65%), ERBB2 (27%), and GATA3 (17%) showed statistically significant higher alteration frequencies in West Africans and African Americans. In contrast, PIK3CA (24%) was less frequently mutated. Of note, GATA3 mutation was statistically significantly more frequent in Nigerians (39%) and African Americans (16.7%) compared to Caucasians (10.5%), in ER-positive cancers. Analysis on Structural Variants (SV), on the other hand, has shown that the genome-wide SV counts among three populations are comparable in ER-negative cancers, while Nigerians have significantly more SV counts compared to African Americans (P=0.0013) or European Americans (P=2.9x10-5) in ER-positive cancers. Similarly, genome-wide substitution patterns in ER+ and ER- cancers varied widely by race/ethnicity. In ER- cases, West Africans carried the highest proportion of canonical APOBEC-associated substitutions, particularly C>T transitions. Conversely, European Americans with ER+ disease showed a higher proportion of C>T than both West Africans (Welch t-test P = 0.044) and African Americans (Welch t-test P = 0.011). Mutation signature analyses highlighted multiple APOBEC signatures, with notable contribution differences across ancestry and ER status. A signature likely corresponding to DNA damage repair correlated with the proportion of genetic ancestry, being most prevalent in European Americans and least common in Nigerians, particularly in ER-negative cancers, with African Americans showing a degree of this signature's contribution in between the two populations (linear model adjusted for age, P=1.0x10-10).
Conclusions: Overall, our data suggests mutation spectra differences in across race/ethnicity and geography. Identification of molecular characteristics such as higher rates of HER2 enriched tumors and higher rates of GATA3 mutations in ER positive tumors are beginning to reveal the genomic basis of race-associated phenotypes and outcomes in breast cancer. Population differences in frequency and spectrum of mutations should now inform the design of innovative clinical trials that improve health equity and accelerate Precision Oncology care in diverse populations.
Citation Format: Olopade OI, Pitt JJ, Riester M, Odetunde A, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Wang S, Fitzgerald DJ, Grundstad J, Tuteja J, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Chen L, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, White KP, Ibrahim N, Oluwasola O, Barretina J. Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD8-05.
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Affiliation(s)
- OI Olopade
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - JJ Pitt
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - M Riester
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - A Odetunde
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - T Yoshimatsu
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - E Labrot
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - A Ademola
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - A Sanni
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - B Okedere
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - S Mahan
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - I Nwosu
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - R Leary
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - M Ajani
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - RS Johnson
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - E Sveen
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Y Zheng
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - S Wang
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - DJ Fitzgerald
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - J Grundstad
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - J Tuteja
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - W Clayton
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - G Khramtsova
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - M Oludara
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - F Omodele
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - O Benson
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - A Adeoye
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - O Morhason-Bello
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - T Ogundiran
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - C Babalola
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - A Popoola
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - M Morrissey
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - L Chen
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - D Huo
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - A Falusi
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - W Winckler
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - J Obafunwa
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - D Papoutsakis
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - O Ojengbede
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - KP White
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - N Ibrahim
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - O Oluwasola
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - J Barretina
- Center for Global Health, The University of Chicago, Chicago, IL; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL; Novartis Institutes for BioMedical Research, Cambridge, MA; Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria; University of Ibadan, Ibadan, Oyo, Nigeria; Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria; Oncology Unit, Lagos State University, Ikeja, Lagos, Nigeria; The University of Chicago, Chicago, IL, Nigeria; Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
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Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Abstract P1-05-11: Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in the cancer genome atlas. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-05-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: African American breast cancer patients have worse survival rates than European American patients. Although racial differences in the distribution of breast cancer intrinsic subtype are known, it is unclear if there are other inherent genomic differences contributing to this racial outcome disparity.
Methods: We defined patient race based on genomic ancestry and compared multiple molecular features of breast cancer between 154 black and 776 white patients in The Cancer Genome Atlas (TCGA). We examined the contribution of these molecular features to survival outcomes using Cox proportional hazards models. We also estimated the heritability of breast cancer subtypes using a mixed effect model.
Results: Compared to whites, black patients had higher odds of basal-like (odds ratio=3.80, p<0.001) and HER2-enriched (odds ratio=2.22, p=0.027) breast cancers in reference to luminal A subtype. Beyond differences in relative frequency of intrinsic subtypes, black and white patients had distinct gene expression, protein expression, and somatic mutation landscapes. However, the majority of these molecular differences were eliminated after adjusting for subtype; in the subtype-adjusted models, we found 142 genes, 16 methylation probes, 4 copy number segments, 1 protein, and no somatic mutation were differentially expressed or present between black and white patients. Using the top 40 differentially expressed genes, we built a race-enriched gene signature, which had excellent capacity of distinguishing breast tumors from black versus white patients (c-index=0.852 in the validation dataset). We also estimated the heritability of breast cancer subtype (basal vs. non-basal) to be 0.436 (p=1.5x10-14) and showed that two genetic variants (rs1078806 in FGFR2, rs34084277 in BABAM1) were associated with intrinsic subtype and can partially explain racial differences in subtype frequencies.
Conclusion: On the molecular level, once intrinsic subtype frequency differences are accounted for, there are few genomic or proteomic differences observed between blacks and whites. More than 40% of breast cancer subtype frequency differences may be due to genetic ancestry. These results suggest that future studies are warranted to investigate genetic and non-genetic factors that contribute to the development and progression of breast cancer subtypes in order to reduce racial disparity.
Citation Format: Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in the cancer genome atlas [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-11.
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Affiliation(s)
- D Huo
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - H Hu
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - SK Rhie
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - ER Gamazon
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - AD Cherniack
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - J Liu
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - TF Yoshimatsu
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - JJ Pitt
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - KA Hoadley
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - M Troester
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - Y Ru
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - T Lichtenberg
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - LA Sturtz
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - CS Shelley
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - GB Mills
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - PW Laird
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - CD Shriver
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - CM Perou
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - OI Olopade
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
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Pitt JJ, Yoshimatsu TF, Zheng Y, Grundstad J, Tuteja J, Wang J, Odetunde A, Khramtsova G, Clayton W, Ademola A, Ogundiran TO, Adeniji-Sofoluwe AT, Obajimi M, Adeoye A, Babalola C, Ojengbede OA, Olopade CO, Olayiwola OA, Chen L, Huo D, White KP, Olopade OI. Abstract 4494: Whole genome sequencing reveals different patterns of mutational mechanisms in breast tumors between women of African and European descent. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Across race/ethnicities, breast cancer incidence and mortality rates markedly differ. Numerous studies have demonstrated that individuals of African ancestry acquire aggressive, early-onset breast cancers more frequently than other populations for reasons that remain unexplained. The sources of these disparities are complex, and a comprehensive characterization of mutation landscapes amongst indigenous Africans, African Americans (AA), and Caucasian breast tumors has not been performed.
We generated high-depth whole genome sequencing on 31 Nigerian breast cancers (90x) along with matched blood (30x). Breast cancer whole genomes (tumor-normal pairs) from The Cancer Genome Atlas were harmonized with our samples, resulting in a cohort of 31 Nigerians (17 estrogen receptor negative, ER-), 31 AA (22 ER-), and 43 Caucasians (19 ER-). High confidence somatic mutations (substitutions and insertions/deletions) were obtained by using multiple variant callers. Regardless of race, ER- tumors carried similar numbers of mutations than their estrogen receptor positive (ER+) counterparts (Welch t-test p = 0.57 - 0.82). TP53 (64%) was the most frequently mutated gene in ER- disease, while canonical PIK3CA activating mutations were prevalent in ER+ cases (33.3%). Additionally, tumor suppressor genes RB1, NF1, and PTEN were disrupted via structural rearrangements in ∼6 to 15% of samples. Rearrangements in the H3K27 methylation regulator EZH1 were identified in six Caucasians but only one individual with African _ancest. Notably, within coding regions, no striking mutation rate differences amongst races were identified. However, global substitution patterns in ER+ and ER- cancers varied widely by race/ethnicity. In ER- cases, Nigerians carried the highest proportion of canonical APOBEC-associated substitutions, particularly C>T transitions. Conversely, Caucasians with ER+ disease showed a higher proportion of C>T than both Nigerians (Welch t-test p = 0.044) and AA (Welch t-test p = 0.011). Kataegis, or clustered mutations, was most prevalent in Nigerian samples, regardless of ER status. Evidence for kataegis was often corroborated by structural variant breakpoints and aberrant copy number states at the hypermutated locus. Mutation signature analyses highlighted multiple APOBEC signatures, with moderate contribution differences across race and ER status.
Overall, our data suggests potential mutation spectra differences in Caucasian, African American and indigenous African breast tumors. Identification of these molecular characteristics by ancestry and geography may help understand race-associated phenotypes and exposures that drive outcomes in breast cancer.
Citation Format: Jason J. Pitt, Toshio F. Yoshimatsu, Yonglan Zheng, Jason Grundstad, Jigyasa Tuteja, Jiebiao Wang, Abayomi Odetunde, Galina Khramtsova, Wendy Clayton, Adeyinka Ademola, Temidayo O. Ogundiran, Adenike T. Adeniji-Sofoluwe, Millicent Obajimi, Adewunmi Adeoye, Chinedum Babalola, Oladosu A. Ojengbede, Christopher O. Olopade, Oluwasola A. Olayiwola, Lin Chen, Dezheng Huo, Kevin P. White, Olufunmilayo I. Olopade. Whole genome sequencing reveals different patterns of mutational mechanisms in breast tumors between women of African and European descent. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4494.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lin Chen
- 1University of Chicago, Chicago, IL
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Ou O, Huppi K, Chakka S, Gehlhaus K, Dubois W, Patel J, Chen J, Mackiewicz M, Jones TL, Pitt JJ, Martin SE, Goldsmith P, Simmons JK, Mock BA, Caplen NJ. Loss-of-function RNAi screens in breast cancer cells identify AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 as sensitizing targets of rapamycin activity. Cancer Lett 2014; 354:336-47. [PMID: 25193464 PMCID: PMC4240001 DOI: 10.1016/j.canlet.2014.08.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 02/05/2023]
Abstract
The use of molecularly targeted drugs as single agents has shown limited utility in many tumor types, largely due to the complex and redundant nature of oncogenic signaling networks. Targeting of the PI3K/AKT/mTOR pathway through inhibition of mTOR in combination with aromatase inhibitors has seen success in particular sub-types of breast cancer and there is a need to identify additional synergistic combinations to maximize the clinical potential of mTOR inhibitors. We have used loss-of-function RNAi screens of the mTOR inhibitor rapamycin to identify sensitizers of mTOR inhibition. RNAi screens conducted in combination with rapamycin in multiple breast cancer cell lines identified six genes, AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 that when silenced, each enhanced the sensitivity of multiple breast cancer lines to rapamycin. Using selective pharmacological agents we confirmed that inhibition of AURKB or PLK1 synergizes with rapamycin. Compound-associated gene expression data suggested histone deacetylation (HDAC) inhibition as a strategy for reducing the expression of several of the rapamycin-sensitizing genes, and we tested and validated this using the HDAC inhibitor entinostat in vitro and in vivo. Our findings indicate new approaches for enhancing the efficacy of rapamycin including the use of combining its application with HDAC inhibition.
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Affiliation(s)
- Oliver Ou
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Konrad Huppi
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sirisha Chakka
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kristen Gehlhaus
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy Dubois
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jyoti Patel
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinqiu Chen
- Office of Science and Technology Partnerships, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Mackiewicz
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tamara L Jones
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason J Pitt
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott E Martin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Paul Goldsmith
- Office of Science and Technology Partnerships, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John K Simmons
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Bethesda, MD 20892, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natasha J Caplen
- Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA.
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Garimella SV, Gehlhaus K, Dine JL, Pitt JJ, Grandin M, Chakka S, Nau MM, Caplen NJ, Lipkowitz S. Identification of novel molecular regulators of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in breast cancer cells by RNAi screening. Breast Cancer Res 2014; 16:R41. [PMID: 24745479 PMCID: PMC4053258 DOI: 10.1186/bcr3645] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/02/2014] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) binds to its receptors, TRAIL-receptor 1 (TRAIL-R1) and TRAIL-receptor 2 (TRAIL-R2), leading to apoptosis by activation of caspase-8 and the downstream executioner caspases, caspase-3 and caspase-7 (caspase-3/7). Triple-negative breast cancer (TNBC) cell lines with a mesenchymal phenotype are sensitive to TRAIL, whereas other breast cancer cell lines are resistant. The underlying mechanisms that control TRAIL sensitivity in breast cancer cells are not well understood. Here, we performed small interfering RNA (siRNA) screens to identify molecular regulators of the TRAIL pathway in breast cancer cells. METHODS We conducted siRNA screens of the human kinome (691 genes), phosphatome (320 genes), and about 300 additional genes in the mesenchymal TNBC cell line MB231. Forty-eight hours after transfection of siRNA, parallel screens measuring caspase-8 activity, caspase-3/7 activity, or cell viability were conducted in the absence or presence of TRAIL for each siRNA, relative to a negative control siRNA (siNeg). A subset of genes was screened in cell lines representing epithelial TNBC (MB468), HER2-amplified breast cancer (SKBR3), and estrogen receptor-positive breast cancer (T47D). Selected putative negative regulators of the TRAIL pathway were studied by using small-molecule inhibitors. RESULTS The primary screens in MB231 identified 150 genes, including 83 kinases, 4 phosphatases, and 63 nonkinases, as potential negative regulators of TRAIL. The identified genes are involved in many critical cell processes, including apoptosis, growth factor-receptor signaling, cell-cycle regulation, transcriptional regulation, and DNA repair. Gene-network analysis identified four genes (PDPK1, IKBKB, SRC, and BCL2L1) that formed key nodes within the interaction network of negative regulators. A secondary screen of a subset of the genes identified in additional cell lines representing different breast cancer subtypes and sensitivities to TRAIL validated and extended these findings. Further, we confirmed that small-molecule inhibition of SRC or BCL2L1, in combination with TRAIL, sensitizes breast cancer cells to TRAIL-induced apoptosis, including cell lines resistant to TRAIL-induced cytotoxicity. CONCLUSIONS These data identify novel molecular regulators of TRAIL-induced apoptosis in breast cancer cells and suggest strategies for the enhanced application of TRAIL as a therapy for breast cancer.
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Huppi K, Ou OL, Pitt JJ, Wahlberg B, Jones TL, Neppalli V, Janz S, Caplen NJ. Abstract 1834: Noncoding RNAs of the 8q24 locus: Consequences of the over-expression or suppression of miR-1204 and PVT1 in developing B cells. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immortalized models of the mouse B lymphocyte lineage have proven to be valuable resources for a wide variety of B cell neoplasms and for the study of normal B cell differentiation. Whether these models have been engineered in mice (in vivo) or in cell culture (in vitro), there are distinct advantages and disadvantages to both. Homogeneity and ease of accessibility can be considered a benefit of working with cultured cells, whereas the contribution from accessory or stromal cells can be an important element not readily available in the in vitro model system. We originally used immortalized Burkitt's Lymphoma (BL) cells to discover a cluster of microRNAs, miR-1204∼1208, that map within the noncoding PVT1 locus in the region of human 8q24 region down-stream of MYC. The BL cell lines allowed us to isolate a large amount of RNA from a homogeneous resource that enhanced discovery of low-level transcripts. Using probes for mouse miR-1204∼1208 to examine expression in a panel of mouse cell lines representing different stages of B cell development, we were able to show that expression of miR-1204∼1208 appeared to arise at the small B cell stage and that these higher levels of expression continued through to the mature plasma cell. This suggested that the pre-B cell or naïve small B cell stages may be most illuminating in assigning targets and function to miR-1204∼1208 or PVT1.
To determine if over-expression of one of these miRNAs, miR-1204, influences the latency and/or type of B cell malignancy we used two mouse transgenic (TG) models of B cell malignancy, H2-Ld-hu-IL6 and iMyc, lentiviral expression of miR-1204 reduced the latency of tumor development in both models and in the case of iMyc-TG, there was also a shift in tumor type from late stage plasmacytoma to the earlier stage of large B cell lymphoma. However, further interpretation of these results was confounded by heterogeneity of lentiviral integration and expression among tumors. Thus, we turned to several human and mouse in vitro models of B cell development, representing pro-B, pre-B, small B, mature B and plasma cell stages to address the effects of modulating the expression of miR-1204 and its host noncoding transcript, PVT1. Over-expression of miR-1204 has been achieved through the use of lentiviruses or synthetic mimics and suppressed expression has been achieved through application of synthetic inhibitors. We also over-expressed PVT1 using a lentiviral vector and suppressed PVT1 expression through the use of siRNA corresponding to various exons of PVT1. Resultant changes in growth and morphology of these cell lines hint that microarray expression analyses will reveal functional targets of miR-1204 in normal and malignant lymphoid development. It will also be of interest to examine whether over-expression or inhibition of miR-1204 plays an additional role in maturation of the normal B cell.
Citation Format: Konrad Huppi, Oliver L. Ou, Jason J. Pitt, Brady Wahlberg, Tamara L. Jones, Vishala Neppalli, Siegfried Janz, Natasha J. Caplen. Noncoding RNAs of the 8q24 locus: Consequences of the over-expression or suppression of miR-1204 and PVT1 in developing B cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1834. doi:10.1158/1538-7445.AM2013-1834
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Camps J, Pitt JJ, Emons G, Hummon AB, Case CM, Grade M, Jones TL, Nguyen QT, Ghadimi BM, Beissbarth T, Difilippantonio MJ, Caplen NJ, Ried T. Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer. Cancer Res 2013; 73:2003-13. [PMID: 23319804 DOI: 10.1158/0008-5472.can-12-3159] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromosomal copy number alterations (aneuploidy) define the genomic landscape of most cancer cells, but identification of the oncogenic drivers behind these imbalances remains an unfinished task. In this study, we conducted a systematic analysis of colorectal carcinomas that integrated genomic copy number changes and gene expression profiles. This analysis revealed 44 highly overexpressed genes mapping to localized amplicons on chromosome 13, gains of which occur often in colorectal cancers (CRC). RNA interference (RNAi)-mediated silencing identified eight candidates whose loss-of-function reduced cell viability 20% or more in CRC cell lines. The functional space of the genes NUPL1, LNX2, POLR1D, POMP, SLC7A1, DIS3, KLF5, and GPR180 was established by global expression profiling after RNAi exposure. One candidate, LNX2, not previously known as an oncogene, was involved in regulating NOTCH signaling. Silencing LNX2 reduced NOTCH levels but also downregulated the transcription factor TCF7L2 and markedly reduced WNT signaling. LNX2 overexpression and chromosome 13 amplification therefore constitutively activates the WNT pathway, offering evidence of an aberrant NOTCH-WNT axis in CRC.
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Affiliation(s)
- Jordi Camps
- Cancer Genomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20893, USA.
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Abstract
Understanding the functional effects of the wide-range of aberrant genetic characteristics associated with the human chromosome 8q24 region in cancer remains daunting due to the complexity of the locus. The most logical target for study remains the MYC proto-oncogene, a prominent resident of 8q24 that was first identified more than a quarter of a century ago. However, many of the amplifications, translocation breakpoints, and viral integration sites associated with 8q24 are often found throughout regions surrounding large expanses of the MYC locus that include other transcripts. In addition, chr.8q24 is host to a number of single nucleotide polymorphisms associated with cancer risk. Yet, the lack of a direct correlation between cancer risk alleles and MYC expression has also raised the possibility that MYC is not always the target of these genetic associations. The 8q24 region has been described as a "gene desert" because of the paucity of functionally annotated genes located within this region. Here we review the evidence for the role of other loci within the 8q24 region, most of which are non-coding transcripts, either in concert with MYC or independent of MYC, as possible candidate gene targets in malignancy.
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Affiliation(s)
- Konrad Huppi
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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Huppi K, Ou OL, Pitt JJ, Wahlberg B, Jones TL, Rodriguez-Canales J, Erickson HS, Emmert-Buck M, Caplen NJ. Abstract 199: Noncoding RNAs of the 8q24 locus. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The 8q24 locus has been found to be involved in many types of cancers as a consequence of somatic changes associated with chromosome instability including amplification, translocation or deletion or frequent viral integration (HPV). A number of SNPs in Genome Wide Association (GWA) studies have also implicated the 8q24 locus as a region of susceptibility for many types of cancer. The most likely 8q24 candidate target may be the MYC proto-oncogene that is a well characterized transcription factor. However, the assumed correlation between MYC expression and disease is lacking suggesting a connection between 8q24 involvement and disease is much more complicated than simply targeting MYC. While other transcription units also reside within the 8q24 locus (PRNCR1, POU5F1P1, PVT1 and the miRNA cluster miR-1204∼1208), they are remarkable in that no coding potential has been readily associated with any of these genes. Thus, the region has been referred to as the “8q24 Gene Desert”. With the renewed realization that many noncoding RNAs do have a functional role, the location of the miR-1204∼1208 cluster of miRNAs within the PVT1 lincRNA transcriptional unit actually suggests an “Oasis of transcription” that could be the additional or alternative target to MYC. We have now compared expression of transcripts of the miR-1204∼1208 cluster with MYC and PVT1 in multiple cancer cell lines and we have found them to be uniformly up-regulated in expression, particularly in those cell lines with amplified or translocated 8q24. These results confirm a pilot study of microdissected primary prostate tumors that also show correlated high expression in MYC, miR-1204∼1208 and PVT1. To further analyze the functional role of the 8q24 transcripts, we have now introduced mimics or inhibitors of each miRNA and siRNAs corresponding to MYC and PVT1 into prostate or colon cell lines (with and without amplified 8q24). In amplified prostate cell lines, mimics of miR-1204, miR-1206 and miR-1208 appear to be as effective as MYC or PVT1 siRNAs in arresting cell growth and inducing apoptosis. This result is not seen in normal prostate cells. Predictably, inhibitors of the miR-1204, miR-1206 and miR-1208 seem to have no effect or seem to enhance cellular proliferation. In colon cell lines with amplified 8q24, miR-1204, miR-1206, miR-1207 and miR-1208 mimics all appear to be as effective in arresting growth as silencing MYC or PVT1. What is particularly striking is that down-regulation or silencing of PVT1 produces the same effect as over-expression (mimic) of the embedded cluster of miRNAs suggesting opposing actions of miRNAs and host transcript. Experiments to determine whether synergy or promoter competition of the PVT1/miR-1204∼1208 cluster is specifically active in amplified 8q24 will be presented. Nevertheless, we can already assign viable functional roles to transcripts besides MYC that could represent alternative molecular targets within the 8q24 locus for cancer susceptibility.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 199. doi:1538-7445.AM2012-199
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Hummon AB, Pitt JJ, Camps J, Emons G, Skube SB, Huppi K, Jones TL, Beissbarth T, Kramer F, Grade M, Difilippantonio MJ, Ried T, Caplen NJ. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells. Mol Cancer 2012; 11:1. [PMID: 22216762 PMCID: PMC3281783 DOI: 10.1186/1476-4598-11-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 01/04/2012] [Indexed: 11/11/2022] Open
Abstract
Background Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway. Conclusions We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.
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Affiliation(s)
- Amanda B Hummon
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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Camps J, Hummon AH, Emons G, Kramer F, Pitt JJ, Grade M, Nguyen QT, Ghadimi BM, Difilippantonio MJ, Beissbarth T, Caplen NJ, Ried T. Abstract 247: A functional genomics and a systems biology approach identify POMP as a potential therapeutic target for colorectal cancer. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal cancer (CRC) is one of the most frequent malignancies in many parts of the world and a leading cause of cancer deaths in both men and women. The identification of rationale therapeutic targets is one possibility to provide personalized medicine to cancer patients. Our approach consisted of identifying overexpressed genes located at sites of recurrent chromosomal amplifications, as these regions are likely to harbor genes required for cancer cell survival. Thirty-one colon cancers and 15 CRC cell lines were analyzed by high-resolution array CGH and microarray gene expression profiling. RNA interference (RNAi)-based analysis identified a subset of genes whose loss-of-function (LOF) reduced the cellular viability of CRC cell lines. Consistent with previous reports, the vast majority of CRC assayed exhibited amplification of the chromosome band 13q12.13-q12.3. Among the genes residing within the 13q12.13-q12.3 amplified region showing an overexpression level of at least two-fold higher in the tumor compared to normal mucosa and whose gene silencing impaired cellular survival, we identified NUPL1, LNX2, POLR1D, CDX2, POMP, and SLC7A1. As little is know of the function of these proteins, we decided to use an unbiased systems biology approach to identify genes, pathways and networks altered following RNAi-mediated LOF of each of these candidate genes. To do this we perturbed the expression of each candidate gene through application of two or more siRNAs corresponding to each gene, followed by whole genome expression profiling to monitor cellular transcriptional responses to gene specific LOF. Concordant gene expression signatures generated using three different RNAi effectors targeting POMP, over a time-course (10, 24, 48, and 72 hours), showed that a decrease in POMP expression of more than 80% at 24 hours initially resulted in only minor downstream changes in gene expression. However, by 48 hours approximately 100 genes exhibited altered expression and by 72 hours nearly 2000 genes. At this last time point a statistically significant enrichment (p<0.05) for the altered expression of genes linked to the gene ontologies of cancer, cell death, and cellular growth was observed. POMP, a proteasome maturation protein, is an essential factor for mammalian proteasome biogenesis. This dynamic loss-of-function approach revealed a regulatory network that controls the transcriptional response of colorectal cancer cells after impairing the function of the proteasome. We are also investigating whether the gene expression profiles observed following silencing of POMP resemble the transcriptomic changes that undergo cells treated with proteasome inhibitors as this may shed further light on the mechanism of action of this new class of anti-cancer drugs particularly in CRC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 247.
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Affiliation(s)
- Jordi Camps
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Amanda H. Hummon
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Georg Emons
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Frank Kramer
- 2Department of General and Visceral Surgery, University Medicine Göttingen, Göttingen, Germany
| | - Jason J. Pitt
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Marian Grade
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Quang T. Nguyen
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - B. Michael Ghadimi
- 2Department of General and Visceral Surgery, University Medicine Göttingen, Göttingen, Germany
| | | | - Tim Beissbarth
- 2Department of General and Visceral Surgery, University Medicine Göttingen, Göttingen, Germany
| | - Natasha J. Caplen
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas Ried
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
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Boneh A, Andresen BS, Gregersen N, Ibrahim M, Tzanakos N, Peters H, Yaplito-Lee J, Pitt JJ. VLCAD deficiency: pitfalls in newborn screening and confirmation of diagnosis by mutation analysis. Mol Genet Metab 2006; 88:166-70. [PMID: 16488171 DOI: 10.1016/j.ymgme.2005.12.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 12/21/2005] [Accepted: 12/21/2005] [Indexed: 11/15/2022]
Abstract
We diagnosed six newborn babies with very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) through newborn screening in three years in Victoria (prevalence rate: 1:31,500). We identified seven known and two new mutations in our patients (2/6 homozygotes; 4/6 compound heterozygotes). Blood samples taken at age 48-72 h were diagnostic whereas repeat samples at an older age were normal in 4/6 babies. Urine analysis was normal in 5/5. We conclude that the timing of blood sampling for newborn screening is important and that it is important to perform mutation analysis to avoid false-negative diagnoses of VLCADD in asymptomatic newborn babies. In view of the emerging genotype-phenotype correlation in this disorder, the information derived from mutational analysis can be helpful in designing the appropriate follow-up and therapeutic regime for these patients.
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Affiliation(s)
- A Boneh
- Metabolic Service and Newborn Screening Laboratory, Genetic Health Services Victoria, Melbourne, Australia.
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33
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Abstract
As well as characteristic increases in C(8) carnitine, dried blood spot samples from 11 newborns with medium-chain acyl-CoA dehydrogenase deficiency detected by tandem mass spectrometry screening using butyl esters showed apparent increases in glutarylcarnitine (m / z 388 signals). In four of the newborns in which it was measured, apparent increases in malonylcarnitine (m / z 360) were also detected. It was shown that the apparent increases were caused by interfering acylcarnitines, putatively identified as hydroxyoctanoylcarnitine and hydroxydecanoylcarnitine, respectively, using alternative derivatives for tandem mass spectrometry. Levels of the two abnormal carnitines correlated with C(8) carnitine levels and normalized with repeat testing in 10 cases. These results indicated that the abnormal carnitines were significantly elevated only during periods of increased fatty acid catabolism, as may occur in the immediate postnatal period.
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Affiliation(s)
- N Napolitano
- Genetic Health Services Victoria, Murdoch Children's Research Institute, Parkville, Vic. 3052, Australia
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34
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Wallis TP, Pitt JJ, Gorman JJ. Identification of disulfide-linked peptides by isotope profiles produced by peptic digestion of proteins in 50% (18)O water. Protein Sci 2001; 10:2251-71. [PMID: 11604532 PMCID: PMC2374058 DOI: 10.1110/ps.15401] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Determination of the disulfide-bond arrangement of a protein by characterization of disulfide-linked peptides in proteolytic digests may be complicated by resistance of the protein to specific proteases, disulfide interchange, and/or production of extremely complex mixtures by less specific proteolysis. In this study, mass spectrometry has been used to show that incorporation of (18)O into peptides during peptic digestion of disulfide-linked proteins in 50% (18)O water resulted in isotope patterns and increases in average masses that facilitated identification and characterization of disulfide-linked peptides even in complex mixtures, without the need for reference digests in 100% (16)O water. This is exemplified by analysis of peptic digests of model proteins lysozyme and ribonuclease A (RNaseA) by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry (MS). Distinct isotope profiles were evident when two peptide chains were linked by disulfide bonds, provided one of the chains did not contain the C terminus of the protein. This latter class of peptide, and single-chain peptides containing an intrachain disulfide bond, could be identified and characterized by mass shifts produced by reduction. Reduction also served to confirm other assignments. Isotope profiling of peptic digests showed that disulfide-linked peptides were often enriched in the high molecular weight fractions produced by size exclusion chromatography (SEC) of the digests. Applicability of these procedures to analysis of a more complex disulfide-bond arrangement was shown with the hemagglutinin/neuraminidase of Newcastle disease virus.
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Affiliation(s)
- T P Wallis
- Biomolecular Research Institute, Parkville VIC 3052, Australia
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35
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Abstract
Medium chain acyl-coenzyme A dehydrogenase (MCAD) deficiency classically presents as hypoketotic hypoglycemia. Under-production of ketones has been presumed to be the cause of hypoketosis, but this has never been proven. Stable isotope dilution studies of ketone kinetics were performed on three well children with homozygous 985G MCAD deficiency using 1,3-13C2 sodium acetoacetate and 1,2,3,4-13C4 sodium 3-hydroxybutyrate to ascertain the rates of ketone production, interconversion, and use. All children were fasted for 9 to 11.5 hours before the beginning of the study period. Euglycemia was maintained in all cases. Ketone kinetics were calculated using a two-accessible pool model and showed normal ketone production in all three children compared with published control data from children fasted for a similar length of time. There is no evidence for underproduction or overuse of ketones in these MCAD-deficient children, at least when they are well. We propose that another factor, such as fever, may be required to reduce ketone production and result in the biochemical phenotype recognized in unwell children.
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Affiliation(s)
- J M Fletcher
- Murdoch Institute and Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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36
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Pitt JJ, Da Silva E, Gorman JJ. Determination of the disulfide bond arrangement of Newcastle disease virus hemagglutinin neuraminidase. Correlation with a beta-sheet propeller structural fold predicted for paramyxoviridae attachment proteins. J Biol Chem 2000; 275:6469-78. [PMID: 10692451 DOI: 10.1074/jbc.275.9.6469] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disulfide bonds stabilize the structure and functions of the hemagglutinin neuraminidase attachment glycoprotein (HN) of Newcastle disease virus. Until this study, the disulfide linkages of this HN and structurally similar attachment proteins of other members of the paramyxoviridae family were undefined. To define these linkages, disulfide-linked peptides were produced by peptic digestion of purified HN ectodomains of the Queensland strain of Newcastle disease virus, isolated by reverse phase high performance liquid chromatography, and analyzed by mass spectrometry. Analysis of peptides containing a single disulfide bond revealed Cys(531)-Cys(542) and Cys(172)-Cys(196) linkages and that HN ectodomains dimerize via Cys(123). Another peptide, with a chain containing Cys(186) linked to a chain containing Cys(238), Cys(247), and Cys(251), was cleaved at Met(249) with cyanogen bromide. Subsequent tandem mass spectrometry established Cys(186)-Cys(247) and Cys(238)-Cys(251) linkages. A glycopeptide with a chain containing Cys(344) linked to a chain containing Cys(455), Cys(461), and Cys(465) was treated sequentially with peptide-N-glycosidase F and trypsin. Further treatment of this peptide by one round of manual Edman degradation or tandem mass spectrometry established Cys(344)-Cys(461) and Cys(455)-Cys(465) linkages. These data, establishing the disulfide linkages of all thirteen cysteines of this protein, are consistent with published predictions that the paramyxoviridae HN forms a beta-propeller structural fold.
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Affiliation(s)
- J J Pitt
- Biomolecular Research Institute, Parkville, Victoria 3052, Australia
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37
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Fletcher JM, Pitt JJ. Pitfalls in the use of 2-octynoic acid as an in vivo model of medium-chain acyl-coenzyme A dehydrogenase deficiency: ketone turnover and metabolite studies in the rat. Metabolism 1999; 48:685-8. [PMID: 10381140 DOI: 10.1016/s0026-0495(99)90165-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
2-Octynoic acid was administered by intraperitoneal injection to fasted Sprague-Dawley rats in an attempt to simulate medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency. The resultant urine organic acid profile showed a mild dicarboxylic aciduria but lacked the glycine conjugates characteristic of MCAD deficiency. Further studies with infused 13C(4)-3-hydroxybutyrate and 13C(2)-acetoacetate demonstrated reduced ketone production in treated rats compared with control animals. Although plasma ketone body concentrations were low in treated rats, plasma free fatty acids were also low, thereby providing diminished substrate for ketone production. This is the reverse of the finding in children with MCAD deficiency, who have low levels of plasma ketones despite elevated free fatty acids. These animal studies were therefore not helpful in improving our understanding of ketone body kinetics in children with MCAD deficiency.
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Affiliation(s)
- J M Fletcher
- Murdoch Institute and Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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38
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Pitt JJ, Hauser S. Transient 5-oxoprolinuria and high anion gap metabolic acidosis: clinical and biochemical findings in eleven subjects. Clin Chem 1998; 44:1497-503. [PMID: 9665429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We describe biochemical and clinical features of 11 subjects (ages, 1.2-84 years, nine females and two males) with transient 5-oxoprolinuria (0.6-23.6 mol/mol of creatinine, reference range <0.07). A variety of conditions preceded the onset of acidosis, and all had taken acetaminophen (paracetamol), although in therapeutic amounts in most subjects. Metabolic acidosis was documented in nine subjects, and all had an increased anion gap and abnormal liver functions. 5-Oxoproline was the major urinary organic acid in five subjects, whereas the rest had more complex profiles comprising 5-oxoproline and other organic acids, such as lactate, 3-hydroxybutyrate, and 4-hydroxyphenyl lactate. The 5-oxoproline was predominantly of the L-configuration. One subject died during an acidotic episode, and the rest recovered with no apparent long-term ill effects. Urinary 5-oxoproline was within the reference range in six subjects that were re-tested after the anion gap normalized. These findings suggest that acetaminophen, in association with other unidentified factors, is involved in the development of this condition through a mechanism of depletion of liver glutathione stores.
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Affiliation(s)
- J J Pitt
- Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Australia.
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39
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Affiliation(s)
- G N Thompson
- Murdoch Institute, Parkville, Victoria, Australia
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40
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Pitt JJ, Gorman JJ. Oligosaccharide characterization and quantitation using 1-phenyl-3-methyl-5-pyrazolone derivatization and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 1997; 248:63-75. [PMID: 9177725 DOI: 10.1006/abio.1997.2080] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatives of monosaccharides, maltooligosaccharides, and oligosaccharides enzymatically released from asparagine-linked sites in ribonuclease B and fetuin have been investigated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Use of the matrix 2,6-dihydroxyacetophenone containing diammonium hydrogen citrate (DHAP/DAHC) resulted in predominance of protonated over sodiated pseudomolecular ions of PMP-derivatized oligosaccharides. By comparison, the matrices alpha-cyano-4-hydroxycinnamic acid and 2,5-dihydroxybenzoic acid resulted in predominantly sodiated pseudomolecular ions. In addition, tendencies for fragmentation of PMP-oligosaccharide derivatives were significantly lower with DHAP/DAHC which enabled meaningful data to be obtained in reflector mode, even for samples with high excipient levels. The relative magnitude of the ion signals for PMP-derivatized maltooligosaccharides and ribonuclease B oligosaccharides correlated well with the oligomer distribution apparent by HPLC. PMP-maltohexose was used as an internal standard to quantitate PMP-oligosaccharides from ribonuclease B and asialofetuin in crude derivatization mixtures. A linear relationship was observed between the ratio of the intensities of pseudomolecualr ions and the amount of glycoprotein derivatized. The limit of detection for the major oligosaccharide of each protein was reached with ca. 3 micrograms of glycoprotein but may be further enhanced by optimization of sample handling. PMP derivatives of sialylated fetuin oligosaccharides were readily detected as protonated pseudomolecular ions by linear mode analyses. By comparison, reflector mode analyses revealed substantially reduced magnitudes of protonated pseudomolecular ions and considerable post-source fragmentation of sialic acid residues. The PMP derivatives of fetuin oligosaccharides were also amenable to exoglycosidase treatment as shown by the mass shifts found upon treatment with sialidase.
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Affiliation(s)
- J J Pitt
- Biomolecular Research Institute, Parkville, Victoria, Australia
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41
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Pitt JJ, Hawkins R, Cleary M, Eggington M, Thorburn DR, Warwick L. Succinic semialdehyde dehydrogenase deficiency: low excretion of metabolites in a neonate. J Inherit Metab Dis 1997; 20:39-42. [PMID: 9061565 DOI: 10.1023/a:1005353305705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A neonate at risk for succinic semialdehyde dehydrogenase deficiency was investigated on day 1. The urine level of 4-hydroxybutyrate was only slightly elevated (23 mumol/mmol of creatinine; controls 1.6-14, n = 18). This value was considerably less than those found for older children with succinic semialdehyde dehydrogenase deficiency and made interpretation of the result uncertain. The diagnosis of succinic semialdehyde dehydrogenase deficiency was confirmed by enzyme assay, and repeat urine testing showed a steady increase in the level of 4-hydroxybutyrate to 359 mumol/mmol at 6 months.
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Affiliation(s)
- J J Pitt
- Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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42
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Abstract
Mutation at the phenylalanine hydroxylase (PAH) locus is a cause of hyperphenylalaninaemia. Genotype-phenotype correlation relative to the predicted PAH activity may differ at the metabolite level and at the IQ level in untreated phenylketonuria. Discordant metabolic phenotypes have been noted in siblings; influences on transport and metabolism of phenylalanine determining homeostasis may account for differing metabolic phenotypes. We report two siblings of different sex and identical genotype at the PAH locus who demonstrate a difference in phenylalanine disposal. A stable isotope infusion of [2H5]phenylalanine was used to measure protein turnover, phenylalanine hydroxylation and excretion of phenylalanine transamination metabolites. The siblings were observed to have identical hydroxylation rates under the experimental conditions of the study while manifesting differences in renal excretion rates of phenylalanine transamination metabolites and protein accretion.
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Affiliation(s)
- E Treacy
- McGill University-Montreal Children's Hospital Research Institute, Canada
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43
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Treacy E, Johnson D, Pitt JJ, Danks DM. Trimethylaminuria, fish odour syndrome: a new method of detection and response to treatment with metronidazole. J Inherit Metab Dis 1995; 18:306-12. [PMID: 7474897 DOI: 10.1007/bf00710420] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trimethylaminuria is an autosomal recessive disorder involving deficient N-oxidation of the dietary-derived amine trimethylamine (TMA). TMA, a volatile tertiary amine, accumulates and is excreted in urine of patients with deficient TMA oxidase activity. Treatment strategies for this condition are limited. We report a new stable-isotope dilution method for rapid sequential analysis of TMA concentrations and the clinical and biochemical response to treatment with metronidazole.
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Affiliation(s)
- E Treacy
- Biochemical Genetics, Montreal Children's Hospital, Quebec, Canada
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44
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Abstract
The urinary excretions of several organic acids were quantitatively studied by gas chromatography/mass spectrometry in subjects with disorders of peroxisome biogenesis (n = 8) and controls (n = 26). The excretion of 3,6-epoxtetradecanedioic acid was significantly elevated in all subjects with disorders of peroxisome biogenesis (1.8-20.8; controls, not detected-0.5, mumol/mmol of creatinine). 3,6-Epoxydodecanedioic acid excretion was usually elevated (1.4-19.8; controls, not detected-4.2) and 3,6-epoxyoctanedioic acid excretion was not elevated not detected-8.8; controls, 0.6-9.5 mumol/mmol of creatinine). It is suggested that measurement of 3,6-epoxydicarboxylic acids may be useful for the diagnosis of these disorders.
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Affiliation(s)
- J J Pitt
- Department of Clinical Biochemistry, Royal Children's Hospital, Melbourne, Australia
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45
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Abstract
The glycine conjugates of isocaproic, 4-methylhexanoic, 7-hydroxyoctanoic and 8-hydroxyoctanoic acids have been identified in the urine of children with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency using gas chromatography-mass spectrometry of the trimethylsilyl derivatives. A quantitative study showed that the glycine conjugates of isocaproic and 4-methylhexanoics acids were excreted during acute episodes and in smaller amounts when subjects were asymptomatic. The glycine conjugates of 7-hydroxyoctanoic and 8-hydroxyoctanoic acids were detectable during acute episodes. None of the conjugates was detected in controls or controls receiving a diet containing medium-chain triglycerides. It is suggested that the glycine conjugates of isocaproic acid and 4-methylhexanoic acid are metabolites of branched-chain fatty acids and that they are specific for MCAD deficiency.
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Affiliation(s)
- J J Pitt
- Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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46
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Affiliation(s)
- J J Pitt
- Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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47
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Affiliation(s)
- J J Pitt
- Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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48
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Abstract
A girl of first cousin parents presented in the 1st year of life with a progressive neurological disease with muscle weakness and hypotonia, accompanied later by dystonia. Investigations, including gas chromatography of urine, showed no abnormality. Autopsy showed marked neuronal loss and gliosis in the putamen and globus pallidus. The activity of glutaryl-CoA dehydrogenase in cultured fibroblasts was normal, but the activity of electron transfer flavoprotein was markedly diminished. Retrospective study of urine by capillary gas chromatography/mass spectrometry showed small amounts of glutaric and other organic acids. This is the first report of striatal degeneration in association with glutaric acidaemia type II. The neuropathological changes were milder than those in glutaric acidaemia type I.
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Affiliation(s)
- C W Chow
- Department of Anatomical Pathology, Royal Children's Hospital, Victoria, Australia
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Yong AB, Pitt JJ, Montalto J, Davies HE, Warne GL, Connelly JF. Diagnosis of 21-hydroxylase deficiency in newborn infants by GC-MS of urinary steroids. Aust Paediatr J 1988; 24:280-5. [PMID: 3265870 DOI: 10.1111/j.1440-1754.1988.tb01363.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In a study using gas chromatography-mass spectrometry (GC-MS) on urine specimens from 16 normal infants and 16 infants with congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (aged 1 day to 4 weeks), the major steroids recognized in all infants were: 16 alpha-hydroxy-dehydroepiandrosterone, 16 beta-hydroxy-dehydroepiandrosterone, 16-oxo-androstenediol, androstenetriol, 15 beta,17 alpha-dihydroxy-pregnenolone and 16 alpha-hydroxy-pregnenolone. Pregnanetriol was detectable in three normal infants (aged 3, 6 and 15 days) but the levels seen in 15 CAH patients were in a higher range. Pregnanetriolone, 5 beta-17-hydroxy-pregnanolone and 15 beta,17 alpha-dihydroxy-pregnanolone were present in the urine of 15 CAH patients, but were not detectable in any of the normal infants. The older the patient, the higher the level was of each of these four steroids. The results indicate that, even on day 1, patients with CAH due to 21-hydroxylase deficiency may be positively identified using GC-MS of urine specimens. This does not preclude the possibility that a minority of patients with CAH, most likely those with mild 21-hydroxylase deficiency, may not exhibit the characteristic GC-MS findings on day 1, as seen in one of the 16 CAH patients.
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Affiliation(s)
- A B Yong
- Department of Clinical Biochemistry, Royal Children's Hospital, Parkville, Victoria, Australia
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50
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Abstract
Persistent excretion of 3-methylglutaconic acid was found in a 6-month-old infant with multiple minor physical malformations and delayed development. During two episodes of intercurrent viral illness, the patient developed severe metabolic acidosis and excreted large amounts of lactate, 3-hydroxybutyrate and acetoacetate. The excretion of 3-methylglutaconic acid did not change during these episodes, nor did it increase following leucine loading. In vitro studies suggest that in this patient, as in the majority of other patients with 3-methylglutaconic aciduria, a primary defect in leucine metabolism is not responsible for the biochemical abnormality.
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Affiliation(s)
- E A Haan
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Vic., Australia
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