1
|
Ewing A, Meynert A, Churchman M, Grimes GR, Hollis RL, Herrington CS, Rye T, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Dowson S, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D, McMahon L, Matakidou A, Dougherty B, March R, Barrett JC, McNeish IA, Biankin AV, Roxburgh P, Gourley C, Semple CA. Structural Variants at the BRCA1/2 Loci are a Common Source of Homologous Repair Deficiency in High-grade Serous Ovarian Carcinoma. Clin Cancer Res 2021; 27:3201-3214. [PMID: 33741650 PMCID: PMC7610896 DOI: 10.1158/1078-0432.ccr-20-4068] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/29/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
PURPOSE The abundance and effects of structural variation at BRCA1/2 in tumors are not well understood. In particular, the impact of these events on homologous recombination repair deficiency (HRD) has yet to be demonstrated. EXPERIMENTAL DESIGN Exploiting a large collection of whole-genome sequencing data from high-grade serous ovarian carcinoma (N = 205) together with matched RNA sequencing for the majority of tumors (N = 150), we have comprehensively characterized mutation and expression at BRCA1/2. RESULTS In addition to the known spectrum of short somatic mutations (SSM), we discovered that multi-megabase structural variants (SV) were a frequent, unappreciated source of BRCA1/2 disruption in these tumors, and we found a genome-wide enrichment for large deletions at the BRCA1/2 loci across the cohort. These SVs independently affected a substantial proportion of patients (16%) in addition to those affected by SSMs (24%), conferring HRD and impacting patient survival. We also detail compound deficiencies involving SSMs and SVs at both loci, demonstrating that the strongest risk of HRD emerges from combined SVs at both BRCA1 and BRCA2 in the absence of SSMs. Furthermore, these SVs are abundant and disruptive in other cancer types. CONCLUSIONS These results extend our understanding of the mutational landscape underlying HRD, increase the number of patients predicted to benefit from therapies exploiting HRD, and suggest there is currently untapped potential in SV detection for patient stratification.
Collapse
Affiliation(s)
- Ailith Ewing
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
| | - Alison Meynert
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Graeme R Grimes
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Robert L Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - C Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Edinburgh Pathology, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Tzyvia Rye
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Clare Bartos
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ian Croy
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Michelle Ferguson
- Department of Oncology, Ninewells Hospital, NHS Tayside, Dundee, Scotland, United Kingdom
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, Scotland, United Kingdom
| | - Mairi Lennie
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, Scotland, United Kingdom
| | - Trevor McGoldrick
- Department of Oncology, Aberdeen Royal Infirmary, Aberdeen, Scotland, United Kingdom
- Institute of Education for Medical and Dental Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Neil McPhail
- Department of Oncology, Raigmore Hospital, NHS Highland, Inverness, Scotland, United Kingdom
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom
| | - Suzanne Dowson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Rosalind Glasspool
- Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Melanie Mackean
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh, Scotland, United Kingdom
| | - Fiona Nussey
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh, Scotland, United Kingdom
| | - Brian McDade
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Darren Ennis
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, England, United Kingdom
| | - Lynn McMahon
- Precision Medicine Scotland (PMS-IC), Queen Elizabeth University Hospital, Glasgow, Scotland, United Kingdom
| | - Athena Matakidou
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, England, United Kingdom
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Ruth March
- Precision Medicine, Oncology R&D, AstraZeneca, Cambridge, England, United Kingdom
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Iain A McNeish
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, Scotland, United Kingdom
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, England, United Kingdom
| | - Andrew V Biankin
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom
- South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, New South Wales, Australia
| | - Patricia Roxburgh
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, United Kingdom
- Beatson West of Scotland Cancer Centre and University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Colin A Semple
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| |
Collapse
|
2
|
Li W, Deng X, Chen T. Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy. Front Oncol 2021; 11:644454. [PMID: 33928033 PMCID: PMC8076595 DOI: 10.3389/fonc.2021.644454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/16/2022] Open
Abstract
In the recent decade, gut microbiota has received growing interest due to its role in human health and disease. On the one hand, by utilizing the signaling pathways of the host and interacting with the immune system, the gut microbiota is able to maintain the homeostasis in human body. This important role is mainly modulated by the composition of microbiota, as a normal microbiota composition is responsible for maintaining the homeostasis of human body, while an altered microbiota profile could contribute to several pathogenic conditions and may further lead to oncogenesis and tumor progression. Moreover, recent insights have especially focused on the important role of gut microbiota in current anticancer therapies, including chemotherapy, radiotherapy, immunotherapy and surgery. Research findings have indicated a bidirectional interplay between gut microbiota and these therapeutic methods, in which the implementation of different therapeutic methods could lead to different alterations in gut microbiota, and the presence of gut microbiota could in turn contribute to different therapeutic responses. As a result, manipulating the gut microbiota to reduce the therapy-induced toxicity may provide an adjuvant therapy to achieve a better therapeutic outcome. Given the complex role of gut microbiota in cancer treatment, this review summarizes the interactions between gut microbiota and anticancer therapies, and demonstrates the current strategies for reshaping gut microbiota community, aiming to provide possibilities for finding an alternative approach to lower the damage and improve the efficacy of cancer therapy.
Collapse
Affiliation(s)
- Wenyu Li
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Queen Mary School, Nanchang University, Nanchang, China
| | - Xiaorong Deng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tingtao Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, The First Affiliated Hospital, Nanchang University, Nanchang, China
| |
Collapse
|
3
|
Peng Y, Yuan C, Tao X, Zhao Y, Yao X, Zhuge L, Huang J, Zheng Q, Zhang Y, Hong H, Chen H, Sun Y. Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma. Transl Lung Cancer Res 2020; 9:670-681. [PMID: 32676329 PMCID: PMC7354123 DOI: 10.21037/tlcr-19-401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Intratumoral heterogeneity is a crucial factor to the outcome of patients and resistance to therapies, in which structural variants play an indispensable but undiscovered role. Methods We performed an integrated analysis of optical mapping and whole-genome sequencing on a primary tumor (PT) and matched metastases including lymph node metastasis (LNM) and tumor thrombus in the pulmonary vein (TPV). Single nucleotide variants, indels and structural variants were analyzed to reveal intratumoral genetic heterogeneity among tumor cells in different sites. Results Our results demonstrated there were less nonsynonymous somatic variants shared with PT in LNM than in TPV, while there were more structural variants shared with PT in LNM than in TPV. More private variants and its affected genes associated with tumorigenesis and progression were identified in TPV than in LNM. It should be noticed that optical mapping detected an average of 77.1% (74.5-78.5%) large structural variants (>5,000 bp) not detected by whole-genome sequencing and identified several structural variants private to metastases. Conclusions Our study does demonstrate structural variants, especially large structural variants play a crucial role in intratumoral genetic heterogeneity and optical mapping could make up for the deficiency of whole-genome sequencing to identify structural variants.
Collapse
Affiliation(s)
- Yizhou Peng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chongze Yuan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiaoting Tao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xingxin Yao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lingdun Zhuge
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | | | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Hui Hong
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| |
Collapse
|
4
|
McGowan T, Johnson JE, Kumar P, Sajulga R, Mehta S, Jagtap PD, Griffin TJ. Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. Gigascience 2020; 9:giaa025. [PMID: 32236523 PMCID: PMC7102281 DOI: 10.1093/gigascience/giaa025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Proteogenomics integrates genomics, transcriptomics, and mass spectrometry (MS)-based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate 'omic software tools, as well as customized tools to view and interpret results. The flexible Galaxy platform has proven valuable for proteogenomic data analysis. Here, we describe a novel Multi-omics Visualization Platform (MVP) for organizing, visualizing, and exploring proteogenomic results, adding a critically needed tool for data exploration and interpretation. FINDINGS MVP is built as an HTML Galaxy plug-in, primarily based on JavaScript. Via the Galaxy API, MVP uses SQLite databases as input-a custom data type (mzSQLite) containing MS-based peptide identification information, a variant annotation table, and a coding sequence table. Users can interactively filter identified peptides based on sequence and data quality metrics, view annotated peptide MS data, and visualize protein-level information, along with genomic coordinates. Peptides that pass the user-defined thresholds can be sent back to Galaxy via the API for further analysis; processed data and visualizations can also be saved and shared. MVP leverages the Integrated Genomics Viewer JavaScript framework, enabling interactive visualization of peptides and corresponding transcript and genomic coding information within the MVP interface. CONCLUSIONS MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomic results within the Galaxy environment, adding a unique and critically needed tool for empowering exploration and interpretation of results. The platform is extensible, providing a basis for further development of new functionalities for proteogenomic data visualization.
Collapse
Affiliation(s)
- Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
- Bioinformatics and Computational Biology program, University of Minnesota-Rochester, 111 South Broadway, Suite 300, Rochester, MN 55904, USA
| | - Ray Sajulga
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| |
Collapse
|