1
|
Gatenbee CD, Baker AM, Prabhakaran S, Swinyard O, Slebos RJC, Mandal G, Mulholland E, Andor N, Marusyk A, Leedham S, Conejo-Garcia JR, Chung CH, Robertson-Tessi M, Graham TA, Anderson ARA. Virtual alignment of pathology image series for multi-gigapixel whole slide images. Nat Commun 2023; 14:4502. [PMID: 37495577 PMCID: PMC10372014 DOI: 10.1038/s41467-023-40218-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register collections of whole slide images (WSI), generating spatially aligned datasets. WSI registration is a two-part problem, the first being the alignment itself and the second the application of transformations to huge multi-gigapixel images. To address both challenges, we developed Virtual Alignment of pathoLogy Image Series (VALIS), software which enables generation of highly multiplexed images by aligning any number of brightfield and/or immunofluorescent WSI, the results of which can be saved in the ome.tiff format. Benchmarking using publicly available datasets indicates VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction. Leveraging existing open-source software tools, VALIS is written in Python, providing a free, fast, scalable, robust, and easy-to-use pipeline for registering multi-gigapixel WSI, facilitating downstream spatial analyses.
Collapse
Affiliation(s)
- Chandler D Gatenbee
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sandhya Prabhakaran
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Ottilie Swinyard
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Robbert J C Slebos
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, CSB 6, Tampa, FL, USA
| | - Gunjan Mandal
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, MRC, Tampa, FL, 336122, USA
| | - Eoghan Mulholland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Noemi Andor
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, USA
| | - Simon Leedham
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Jose R Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, MRC, Tampa, FL, 336122, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, CSB 6, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alexander R A Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| |
Collapse
|
2
|
Fisher NC, Byrne RM, Leslie H, Wood C, Legrini A, Cameron AJ, Ahmaderaghi B, Corry SM, Malla SB, Amirkhah R, McCooey AJ, Rogan E, Redmond KL, Sakhnevych S, Domingo E, Jackson J, Loughrey MB, Leedham S, Maughan T, Lawler M, Sansom OJ, Lamrock F, Koelzer VH, Jamieson NB, Dunne PD. Biological Misinterpretation of Transcriptional Signatures in Tumor Samples Can Unknowingly Undermine Mechanistic Understanding and Faithful Alignment with Preclinical Data. Clin Cancer Res 2022; 28:4056-4069. [PMID: 35792866 PMCID: PMC9475248 DOI: 10.1158/1078-0432.ccr-22-1102] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/08/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Precise mechanism-based gene expression signatures (GES) have been developed in appropriate in vitro and in vivo model systems, to identify important cancer-related signaling processes. However, some GESs originally developed to represent specific disease processes, primarily with an epithelial cell focus, are being applied to heterogeneous tumor samples where the expression of the genes in the signature may no longer be epithelial-specific. Therefore, unknowingly, even small changes in tumor stroma percentage can directly influence GESs, undermining the intended mechanistic signaling. EXPERIMENTAL DESIGN Using colorectal cancer as an exemplar, we deployed numerous orthogonal profiling methodologies, including laser capture microdissection, flow cytometry, bulk and multiregional biopsy clinical samples, single-cell RNA sequencing and finally spatial transcriptomics, to perform a comprehensive assessment of the potential for the most widely used GESs to be influenced, or confounded, by stromal content in tumor tissue. To complement this work, we generated a freely-available resource, ConfoundR; https://confoundr.qub.ac.uk/, that enables users to test the extent of stromal influence on an unlimited number of the genes/signatures simultaneously across colorectal, breast, pancreatic, ovarian and prostate cancer datasets. RESULTS Findings presented here demonstrate the clear potential for misinterpretation of the meaning of GESs, due to widespread stromal influences, which in-turn can undermine faithful alignment between clinical samples and preclinical data/models, particularly cell lines and organoids, or tumor models not fully recapitulating the stromal and immune microenvironment. CONCLUSIONS Efforts to faithfully align preclinical models of disease using phenotypically-designed GESs must ensure that the signatures themselves remain representative of the same biology when applied to clinical samples.
Collapse
Affiliation(s)
- Natalie C. Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Ryan M. Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Holly Leslie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Colin Wood
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Assya Legrini
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J. Cameron
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Shania M. Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Sudhir B. Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Aoife J. McCooey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Emily Rogan
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Keara L. Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Svetlana Sakhnevych
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | | | - James Jackson
- Information Services, Queen's University Belfast, Belfast, United Kingdom
| | - Maurice B. Loughrey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | | | - Tim Maughan
- University of Oxford, Oxford, United Kingdom
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Felicity Lamrock
- School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom
| | - Viktor H. Koelzer
- Department of Pathology and Molecular Pathology, University and University Hospital of Zürich, Zürich, Switzerland
| | - Nigel B. Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Philip D. Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| |
Collapse
|
3
|
Wu CWK, Reid M, Leedham S, Lui RN. The emerging era of personalized medicine in advanced colorectal cancer. J Gastroenterol Hepatol 2022; 37:1411-1425. [PMID: 35815339 DOI: 10.1111/jgh.15937] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/09/2022]
Abstract
Colorectal cancer (CRC) is a genetically heterogeneous disease with its pathogenesis often driven by varying genetic or epigenetic alterations. This has led to a substantial number of patients developing chemoresistance and treatment failure, resulting in a high mortality rate for advanced disease. Deep molecular analysis has allowed for the discovery of key intestinal signaling pathways which impacts colonic epithelial cell fate, and the integral role of the tumor microenvironment on cancer growth and dissemination. Through transitioning pre-clinical knowledge in research into clinical practice, many potential druggable targets within these pathways have been discovered in the hopes of overcoming the roadblocks encountered by conventional therapies. A personalized approach tailoring treatment according to the histopathological and molecular features of individual tumors can hopefully translate to better patient outcomes, and reduce the rate of recurrence in patients with advanced CRC. Herein, the latest understanding on the molecular science behind CRC tumorigenesis, and the potential treatment targets currently at the forefront of research are summarized.
Collapse
Affiliation(s)
- Claudia W K Wu
- Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong, China.,Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
| | - Madeleine Reid
- Translational Gastroenterology Unit, John Radcliffe hospital, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Leedham
- Translational Gastroenterology Unit, John Radcliffe hospital, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rashid N Lui
- Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong, China.,Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China.,Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
4
|
Schenck RO, Jakobsen NA, Turati V, Shibata D, Vyas P, Leedham S, Anderson AR. Abstract A019: Mutation agnostic diagnosis of clonal hematopoiesis of indeterminate potential (CHIP) using fluctuating methylation clocks. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-a019] [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
Clonal hematopoiesis (CH), such as clonal hematopoiesis of indeterminant potential (CHIP), is diagnosed based on somatic genomic alterations in the absence of hematologic malignancy. At present, CHIP is diagnosed using peripheral blood, where putative driver point mutations and small insertions/deletions whose variant allele frequency is greater or equal to two percent. Generally, the prevalence of CH increases as an individual ages and conveys a risk for progression to a malignancy. CH is thought to be driven by the underlying hematopoietic stem cells of an unknown quantity, with estimates in the literature for stem cell numbers differing by orders of magnitude. Previously, we developed a method using fluctuating CpG (fCpG) sites to serve as a fluctuating methylation clock to uncover stem cell dynamics in glandular tissues and orthogonally validated our method using publicly available datasets of human blood from normal cohorts and malignant cohorts. Here we expand on this work by presenting 38 new patients with distinct VAF groups from 1-2% VAF up to greater than 10% VAF for putative drivers with corresponding DNA methylation profiles using the Illumina EPIC array platform. We identify fCpG from our normal and CHIP cohorts to train and validate a machine learning approach that allows us to diagnose CHIP without DNA sequencing. Importantly, our approach allows for the identification of patients who may have CH driven by structural variants such as copy number alterations. We use this method to evaluate two publicly available methylation datasets of reportedly normal patients (n=656 and n=732) showing that evidence of CHIP can be found in 19% and 29% of these datasets, respectively. We then evaluate copy number differences in burden within our CHIP cohort and these newly identified CHIP cohorts. Using a mechanistic model of hematopoietic stem cells containing fCpGs we examine the temporal dynamics of competing founder CHIP drivers and the number of stem cells in the hematopoietic stem cell compartment.
Citation Format: Ryan O. Schenck, Niels Asger Jakobsen, Virginia Turati, Darryl Shibata, Paresh Vyas, Simon Leedham, Alexander R.A. Anderson. Mutation agnostic diagnosis of clonal hematopoiesis of indeterminate potential (CHIP) using fluctuating methylation clocks [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A019.
Collapse
Affiliation(s)
| | | | | | | | - Paresh Vyas
- University of Oxford, Oxford, United Kingdom,
| | | | | |
Collapse
|
5
|
Schenck RO, Brosula G, West J, Leedham S, Shibata D, Anderson AR. Gattaca: Base-Pair Resolution Mutation Tracking for Somatic Evolution Studies using Agent-based Models. Mol Biol Evol 2022; 39:msac058. [PMID: 35298641 PMCID: PMC9034688 DOI: 10.1093/molbev/msac058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 11/12/2022] Open
Abstract
Research over the past two decades has made substantial inroads into our understanding of somatic mutations. Recently, these studies have focused on understanding their presence in homeostatic tissue. In parallel, agent-based mechanistic models have emerged as an important tool for understanding somatic mutation in tissue; yet no common methodology currently exists to provide base-pair resolution data for these models. Here, we present Gattaca as the first method for introducing and tracking somatic mutations at the base-pair resolution within agent-based models that typically lack nuclei. With nuclei that incorporate human reference genomes, mutational context, and sequence coverage/error information, Gattaca is able to realistically evolve sequence data, facilitating comparisons between in silico cell tissue modeling with experimental human somatic mutation data. This user-friendly method, incorporated into each in silico cell, allows us to fully capture somatic mutation spectra and evolution.
Collapse
Affiliation(s)
- Ryan O. Schenck
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX37BN, United Kingdom
| | - Gabriel Brosula
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jeffrey West
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Simon Leedham
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Darryl Shibata
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Alexander R.A. Anderson
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| |
Collapse
|
6
|
Gatenbee CD, Baker AM, Schenck RO, Strobl M, West J, Neves MP, Hasan SY, Lakatos E, Martinez P, Cross WCH, Jansen M, Rodriguez-Justo M, Whelan CJ, Sottoriva A, Leedham S, Robertson-Tessi M, Graham TA, Anderson ARA. Immunosuppressive niche engineering at the onset of human colorectal cancer. Nat Commun 2022; 13:1798. [PMID: 35379804 PMCID: PMC8979971 DOI: 10.1038/s41467-022-29027-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 08/10/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune "cold" ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC.
Collapse
Affiliation(s)
- Chandler D Gatenbee
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ryan O Schenck
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Maximilian Strobl
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Jeffrey West
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Margarida P Neves
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sara Yakub Hasan
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- Lyon Cancer Institute, Lyon, France
| | - William C H Cross
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Marnix Jansen
- Department of Pathology, University College London Hospital, London, UK
| | | | - Christopher J Whelan
- Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL, 60607, USA
| | - Andrea Sottoriva
- Center for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Simon Leedham
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Mark Robertson-Tessi
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| |
Collapse
|
7
|
Ahmaderaghi B, Amirkhah R, Jackson J, Lannagan TRM, Gilroy K, Malla SB, Redmond KL, Quinn G, McDade SS, ACRCelerate Consortium, Maughan T, Leedham S, Campbell ASD, Sansom OJ, Lawler M, Dunne PD. Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data. Dis Model Mech 2022; 15:dmm049257. [PMID: 35112706 PMCID: PMC8990914 DOI: 10.1242/dmm.049257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Generation of transcriptional data has dramatically increased in the past decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by 'wet-lab' users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource (MouSR). This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive 'point-and-click' interface, which includes a suite of molecular characterisation options including quality control, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA sequencing. The MouSR online tool provides a unique freely available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Baharak Ahmaderaghi
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - James Jackson
- Information Services, Queen's University Belfast, Belfast BT7 1NN, UK
| | | | - Kathryn Gilroy
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Sudhir B. Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Keara L. Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Gerard Quinn
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Simon S. McDade
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | | | - Tim Maughan
- Oxford Institute of Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Simon Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow OX3 7DQ, UK
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Philip D. Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| |
Collapse
|
8
|
Heino S, Fang S, Lähde M, Högström J, Nassiri S, Campbell A, Flanagan D, Raven A, Hodder M, Nasreddin N, Xue HH, Delorenzi M, Leedham S, Petrova TV, Sansom O, Alitalo K. Lef1 restricts ectopic crypt formation and tumor cell growth in intestinal adenomas. Sci Adv 2021; 7:eabj0512. [PMID: 34788095 PMCID: PMC8598008 DOI: 10.1126/sciadv.abj0512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Somatic mutations in APC or CTNNB1 genes lead to aberrant Wnt signaling and colorectal cancer (CRC) initiation and progression via-catenin–T cell factor/lymphoid enhancer binding factor TCF/LEF transcription factors. We found that Lef1 was expressed exclusively in Apc-mutant, Wnt ligand–independent tumors, but not in ligand-dependent, serrated tumors. To analyze Lef1 function in tumor development, we conditionally deleted Lef1 in intestinal stem cells of Apcfl/fl mice or broadly from the entire intestinal epithelium of Apcfl/fl or ApcMin/+ mice. Loss of Lef1 markedly increased tumor initiation and tumor cell proliferation, reduced the expression of several Wnt antagonists, and increased Myc proto-oncogene expression and formation of ectopic crypts in Apc-mutant adenomas. Our results uncover a previously unknown negative feedback mechanism in CRC, in which ectopic Lef1 expression suppresses intestinal tumorigenesis by restricting adenoma cell dedifferentiation to a crypt-progenitor phenotype and by reducing the formation of cancer stem cell niches.
Collapse
Affiliation(s)
- Sarika Heino
- Translational Cancer Medicine Program (CAN-PRO), iCAN Digital Precision Cancer Medicine Flagship and Wihuri Research Institute, Faculty of Medicine, HiLIFE-Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
| | - Shentong Fang
- Translational Cancer Medicine Program (CAN-PRO), iCAN Digital Precision Cancer Medicine Flagship and Wihuri Research Institute, Faculty of Medicine, HiLIFE-Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
| | - Marianne Lähde
- Translational Cancer Medicine Program (CAN-PRO), iCAN Digital Precision Cancer Medicine Flagship and Wihuri Research Institute, Faculty of Medicine, HiLIFE-Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
| | - Jenny Högström
- Translational Cancer Medicine Program (CAN-PRO), iCAN Digital Precision Cancer Medicine Flagship and Wihuri Research Institute, Faculty of Medicine, HiLIFE-Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
| | - Sina Nassiri
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andrew Campbell
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, Garscube Estate, Glasgow G61 1QH, UK
| | - Dustin Flanagan
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, Garscube Estate, Glasgow G61 1QH, UK
| | - Alexander Raven
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, Garscube Estate, Glasgow G61 1QH, UK
| | - Michael Hodder
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, Garscube Estate, Glasgow G61 1QH, UK
| | - Nadia Nasreddin
- Intestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA
| | - Mauro Delorenzi
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Oncology, University of Lausanne and CHUV, Epalinges, Switzerland
- Ludwig Institute for Cancer Research Lausanne, Epalinges, Switzerland
| | - Simon Leedham
- Intestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tatiana V. Petrova
- Department of Oncology, University of Lausanne and CHUV, Epalinges, Switzerland
- Ludwig Institute for Cancer Research Lausanne, Epalinges, Switzerland
| | - Owen Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, Garscube Estate, Glasgow G61 1QH, UK
| | - Kari Alitalo
- Translational Cancer Medicine Program (CAN-PRO), iCAN Digital Precision Cancer Medicine Flagship and Wihuri Research Institute, Faculty of Medicine, HiLIFE-Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
9
|
McCorry AM, Leonard NA, Jackstadt R, Flanagan DJ, Sansom OJ, Maughan T, Leedham S, Kerr EM, Ryan AE, Lawler M, Dunne PD. Abstract 3867: STAT1-related antigen processing and presentation dictates prognosis in the fibroblast-rich subtype of stage II/III colon cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: Molecular subtyping of colon cancer (CC) has repeatedly identified a poor-prognostic group of patients, characterized by high levels of stroma (particularly fibroblast) in the tumor microenvironment. To date, the benefit of standard 5FU-based adjuvant chemotherapy in these high-fibroblast (HiFi) patients has been unclear. Given TGF-β signaling is associated with HiFi tumors, a number of recent clinical trials have focussed on targeting TGF-β in these patients. While these efforts are ongoing, we set out to identify novel therapeutically-relevant biological signaling within HiFi tumors.
Methods: Untreated stage II (n=215) and stage II/III (n=258) tumors were assigned a fibroblast score, using single-sample gene set enrichment analysis, enabling stratification into HiFi and LoFi groups based on their histology and transcriptome. Supervised stratification, based on relapse-free survival, within the HiFi group allowed for in silico discovery, interrogation and independent validation of the HiFi-specific biology underpinning relapse. Upstream regulators of these processes were identified as potential therapeutic targets, and assessed in an in vitro co-culture model, to confirm mechanistic signaling, and an in vivo HiFi model, to confirm efficacy.
Results: We confirmed the poor prognosis of the HiFi group (p = 0.008), followed by discovery and independent validation of the prognostic value of STAT1-related signaling in stratifying HiFi tumors based on disease relapse (HR 0.2 (0.1-0.5) and 0.09 (0.02-0.47)). This signaling was significantly associated with activation of antigen processing and presentation in specific immune lineages (p < 0.001). In line with the upstream regulator analysis, treatment with poly I:C (a TLR3 agonist) increased STAT1-related signaling and antigen processing in an in vitro macrophage-stromal co-culture system.
Conclusions: We have found that increased levels of STAT1-related signaling, resulting in antigen processing and presentation in specific subclasses of immune cells, is associated with reduced risk of recurrence in the otherwise poor-prognostic HiFi subtype of CC. Using in silico and in vitro methods, we demonstrate that poly I:C is a potential therapeutic option for patients with stromal-rich tumors. Results from ongoing in vivo validation in a HiFi mouse model will provide preclinical evidence of the utility of poly I:C in this setting and support a phase II clinical trial.
Citation Format: Amy M. McCorry, Niamh A. Leonard, Rene Jackstadt, Dustin J. Flanagan, Owen J. Sansom, Tim Maughan, Simon Leedham, Emma M. Kerr, Aideen E. Ryan, Mark Lawler, Philip D. Dunne, ACRCelerate and S:CORT consortia. STAT1-related antigen processing and presentation dictates prognosis in the fibroblast-rich subtype of stage II/III colon cancer [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 3867.
Collapse
Affiliation(s)
| | | | - Rene Jackstadt
- 3Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | | | - Owen J. Sansom
- 3Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Tim Maughan
- 4University of Oxford, Oxford, United Kingdom
| | | | - Emma M. Kerr
- 1Queen's University Belfast, Belfast, United Kingdom
| | | | - Mark Lawler
- 1Queen's University Belfast, Belfast, United Kingdom
| | | | | |
Collapse
|
10
|
Thomas R, Trapani D, Goodyer-Sait L, Tomkova M, Fernandez-Rozadilla C, Sahnane N, Woolley C, Davis H, Chegwidden L, Kriaucionis S, Maughan T, Leedham S, Palles C, Furlan D, Tomlinson I, Lewis A. The polymorphic variant rs1800734 influences methylation acquisition and allele-specific TFAP4 binding in the MLH1 promoter leading to differential mRNA expression. Sci Rep 2019; 9:13463. [PMID: 31530880 PMCID: PMC6748923 DOI: 10.1038/s41598-019-49952-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 11/09/2018] [Accepted: 08/29/2019] [Indexed: 12/14/2022] Open
Abstract
Expression of the mismatch repair gene MutL homolog 1 (MLH1) is silenced in a clinically important subgroup of sporadic colorectal cancers. These cancers exhibit hypermutability with microsatellite instability (MSI) and differ from microsatellite-stable (MSS) colorectal cancers in both prognosis and response to therapies. Loss of MLH1 is usually due to epigenetic silencing with associated promoter methylation; coding somatic mutations rarely occur. Here we use the presence of a colorectal cancer (CRC) risk variant (rs1800734) within the MLH1 promoter to investigate the poorly understood mechanisms of MLH1 promoter methylation and loss of expression. We confirm the association of rs1800734 with MSI+ but not MSS cancer risk in our own data and by meta-analysis. Using sensitive allele-specific detection methods, we demonstrate that MLH1 is the target gene for rs1800734 mediated cancer risk. In normal colon tissue, small allele-specific differences exist only in MLH1 promoter methylation, but not gene expression. In contrast, allele-specific differences in both MLH1 methylation and expression are present in MSI+ cancers. We show that MLH1 transcriptional repression is dependent on DNA methylation and can be reversed by a methylation inhibitor. The rs1800734 allele influences the rate of methylation loss and amount of re-expression. The transcription factor TFAP4 binds to the rs1800734 region but with much weaker binding to the risk than the protective allele. TFAP4 binding is absent on both alleles when promoter methylation is present. Thus we propose that TFAP4 binding shields the protective rs1800734 allele of the MLH1 promoter from BRAF induced DNA methylation more effectively than the risk allele.
Collapse
Affiliation(s)
- Rachael Thomas
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Davide Trapani
- Anatomic Pathology Unit, Department of Medicine and Surgery and Research Center of Hereditary and Familial Tumors, University of Insubria, Varese, 21100, Italy
| | - Lily Goodyer-Sait
- Institute of Structural and Molecular Biology, Department of, Biological Sciences, Birkbeck, London, UK
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ceres Fernandez-Rozadilla
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, IDIS, Santiago de Compostela, Spain
| | - Nora Sahnane
- Anatomic Pathology Unit, Department of Medicine and Surgery and Research Center of Hereditary and Familial Tumors, University of Insubria, Varese, 21100, Italy
| | - Connor Woolley
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Hayley Davis
- Intestinal Stem Cell Biology Group, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Timothy Maughan
- Oxford Institute of Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Simon Leedham
- Intestinal Stem Cell Biology Group, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Daniela Furlan
- Anatomic Pathology Unit, Department of Medicine and Surgery and Research Center of Hereditary and Familial Tumors, University of Insubria, Varese, 21100, Italy
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Annabelle Lewis
- Cancer Gene Regulation Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Division of Biosciences, Department of Life Sciences, Brunel University London, Old Road Campus Research Building, Roosevelt Drive, Uxbridge, UB8 3PN, UK.
| |
Collapse
|
11
|
Law PJ, Timofeeva M, Fernandez-Rozadilla C, Broderick P, Studd J, Fernandez-Tajes J, Farrington S, Svinti V, Palles C, Orlando G, Sud A, Holroyd A, Penegar S, Theodoratou E, Vaughan-Shaw P, Campbell H, Zgaga L, Hayward C, Campbell A, Harris S, Deary IJ, Starr J, Gatcombe L, Pinna M, Briggs S, Martin L, Jaeger E, Sharma-Oates A, East J, Leedham S, Arnold R, Johnstone E, Wang H, Kerr D, Kerr R, Maughan T, Kaplan R, Al-Tassan N, Palin K, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J, Kaasinen E, Sarin AP, Eriksson JG, Rissanen H, Knekt P, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Buchanan DD, Win AK, Hopper J, Jenkins ME, Lindor NM, Newcomb PA, Gallinger S, Duggan D, Casey G, Hoffmann P, Nöthen MM, Jöckel KH, Easton DF, Pharoah PDP, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai Z, Muir K, Pashayan N, Harkin A, Allan K, McQueen J, Paul J, Iveson T, Saunders M, Butterbach K, Chang-Claude J, Hoffmeister M, Brenner H, Kirac I, Matošević P, Hofer P, Brezina S, Gsur A, Cheadle JP, Aaltonen LA, Tomlinson I, Houlston RS, Dunlop MG. Association analyses identify 31 new risk loci for colorectal cancer susceptibility. Nat Commun 2019; 10:2154. [PMID: 31089142 PMCID: PMC6517433 DOI: 10.1038/s41467-019-09775-w] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [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: 10/31/2018] [Accepted: 03/29/2019] [Indexed: 02/02/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide, and has a strong heritable basis. We report a genome-wide association analysis of 34,627 CRC cases and 71,379 controls of European ancestry that identifies SNPs at 31 new CRC risk loci. We also identify eight independent risk SNPs at the new and previously reported European CRC loci, and a further nine CRC SNPs at loci previously only identified in Asian populations. We use in situ promoter capture Hi-C (CHi-C), gene expression, and in silico annotation methods to identify likely target genes of CRC SNPs. Whilst these new SNP associations implicate target genes that are enriched for known CRC pathways such as Wnt and BMP, they also highlight novel pathways with no prior links to colorectal tumourigenesis. These findings provide further insight into CRC susceptibility and enhance the prospects of applying genetic risk scores to personalised screening and prevention.
Collapse
Affiliation(s)
- Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ceres Fernandez-Rozadilla
- Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación de Santiago, Santiago de Compostela, 15706, Spain
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - James Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Juan Fernandez-Tajes
- Wellcome Centre for Human Genetics, McCarthy Group, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Steven Penegar
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Evropi Theodoratou
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Peter Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Harry Campbell
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Lina Zgaga
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin, University of Dublin, Dublin, D02 PN40, Ireland
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah Harris
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - John Starr
- Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Medical Genetics Section, Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Laura Gatcombe
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Maria Pinna
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Sarah Briggs
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Lynn Martin
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Emma Jaeger
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Archana Sharma-Oates
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - James East
- Translational Gastroenterology Unit, Nuffield Department. of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Simon Leedham
- Wellcome Centre for Human Genetics, McCarthy Group, Roosevelt Drive, Oxford, OX3 7BN, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Roland Arnold
- Cancer Bioinfomatics Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Elaine Johnstone
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - Haitao Wang
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - Tim Maughan
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7LE, UK
| | - Richard Kaplan
- Medical Research Council Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Nada Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Ulrika A Hänninen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Eevi Kaasinen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, 00250, Helsinki, Finland
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, 00014, Finland
| | - Harri Rissanen
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Paul Knekt
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland, and Faculty of Social Sciences, University of Tampere, Tampere, 33014, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, 33014, Finland
| | - Pekka Jousilahti
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
- Department of Public Health, University of Helsinki, Helsinki, 00014, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Anna Lepistö
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, 40620, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, Jyväskylä, 40620, Finland
- Department of Health Sciences, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne, Centre for Cancer Research, Parkville, Victoria, 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Aung-Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mark E Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Polly A Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Steven Gallinger
- Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - David Duggan
- Translational Genomics Research Institute (TGen), An Affiliate of City of Hope, Phoenix, AZ, 85004, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Virginia, VA, 22903, USA
| | - Per Hoffmann
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, 4031, Switzerland
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, 53127, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, 45147, Germany
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Andrea Harkin
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Karen Allan
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - John McQueen
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Timothy Iveson
- University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Mark Saunders
- The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, 20251, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, 69120, Germany
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumours, Sestre milosrdnice University Hospital Centre, Zagreb, 10000, Croatia
| | - Petar Matošević
- Department of Surgery, University Hospital Center Zagreb, 10000, Zagreb, Croatia
| | - Philipp Hofer
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Stefanie Brezina
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Andrea Gsur
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Jeremy P Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum and Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| |
Collapse
|
12
|
Lannagan TRM, Lee YK, Wang T, Roper J, Bettington ML, Fennell L, Vrbanac L, Jonavicius L, Somashekar R, Gieniec K, Yang M, Ng JQ, Suzuki N, Ichinose M, Wright JA, Kobayashi H, Putoczki TL, Hayakawa Y, Leedham S, Abud HE, Yilmaz ÖH, Marker J, Klebe S, Wirapati P, Mukherjee S, Tejpar S, Leggett BA, Whitehall VLJ, Worthley DL, Woods SL. Genetic editing of colonic organoids provides a molecularly distinct and orthotopic preclinical model of serrated carcinogenesis. Gut 2019; 68:684-692. [PMID: 29666172 PMCID: PMC6192855 DOI: 10.1136/gutjnl-2017-315920] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/14/2018] [Accepted: 03/27/2018] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Serrated colorectal cancer (CRC) accounts for approximately 25% of cases and includes tumours that are among the most treatment resistant and with worst outcomes. This CRC subtype is associated with activating mutations in the mitogen-activated kinase pathway gene, BRAF, and epigenetic modifications termed the CpG Island Methylator Phenotype, leading to epigenetic silencing of key tumour suppressor genes. It is still not clear which (epi-)genetic changes are most important in neoplastic progression and we begin to address this knowledge gap herein. DESIGN We use organoid culture combined with CRISPR/Cas9 genome engineering to sequentially introduce genetic alterations associated with serrated CRC and which regulate the stem cell niche, senescence and DNA mismatch repair. RESULTS Targeted biallelic gene alterations were verified by DNA sequencing. Organoid growth in the absence of niche factors was assessed, as well as analysis of downstream molecular pathway activity. Orthotopic engraftment of complex organoid lines, but not BrafV600E alone, quickly generated adenocarcinoma in vivo with serrated features consistent with human disease. Loss of the essential DNA mismatch repair enzyme, Mlh1, led to microsatellite instability. Sphingolipid metabolism genes are differentially regulated in both our mouse models of serrated CRC and human CRC, with key members of this pathway having prognostic significance in the human setting. CONCLUSION We generate rapid, complex models of serrated CRC to determine the contribution of specific genetic alterations to carcinogenesis. Analysis of our models alongside patient data has led to the identification of a potential susceptibility for this tumour type.
Collapse
Affiliation(s)
- Tamsin RM Lannagan
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Young K Lee
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Tongtong Wang
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Jatin Roper
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
- Division of Gastroenterology, Tufts Medical Center, Boston, MA, United States
| | - Mark L Bettington
- Envoi Specialist Pathologists, Brisbane, QLD Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Lochlan Fennell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Laura Vrbanac
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Lisa Jonavicius
- Department of Anatomical Pathology, Flinders Medical Centre, Bedford Park, SA Australia
| | - Roshini Somashekar
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Krystyna Gieniec
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Miao Yang
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Jia Q Ng
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Nobumi Suzuki
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Mari Ichinose
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Josephine A Wright
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Hiroki Kobayashi
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Tracy L Putoczki
- Department of Medical Biology, University of Melbourne and the Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Yoku Hayakawa
- Dept of Gastroenterology, University of Tokyo, Japan
| | - Simon Leedham
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics University of Oxford, Oxford, & Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, Headington, UK
| | - Helen E Abud
- Cancer Program, Monash Biomedicine Discovery Institute and the Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC Australia
| | - Ömer H. Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA United States
| | | | - Sonja Klebe
- Department of Anatomical Pathology, Flinders Medical Centre, Bedford Park, SA Australia
| | - Pratyaksha Wirapati
- Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland
| | | | - Sabine Tejpar
- Digestive Oncology Unit, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara A Leggett
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
- School of Medicine, University of Queensland, QLD Australia
- Royal Brisbane and Womens Hospital, Brisbane, QLD Australia
| | - Vicki LJ Whitehall
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
- School of Medicine, University of Queensland, QLD Australia
- Pathology Queensland, Brisbane, QLD
| | - Daniel L Worthley
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| | - Susan L Woods
- School of Medicine, University of Adelaide and South Australian Health and Medical Research Institute, Adelaide, SA Australia
| |
Collapse
|
13
|
Dunne P, Loughrey MB, Coleman HG, McBride R, Campbell J, Alderdice M, Redmond KL, McArt DG, Isella C, Leedham S, Maughan T, Lawler M, consortium S. Abstract 5175: Advancing the molecular understanding of stage I colorectal cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5175] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: There are ~1.4 million cases of colorectal cancer (CRC) annually worldwide. Bowel cancer screening (BCS) detects cancers and high-risk adenomas earlier; previously stage I accounted for 12% of CRC, but 42% of screen-detected cancers are now stage I. This study is based on the hypothesis that within the early lesions detected by BCS there are "hopeful monsters"; a term used to describe highly aggressive tumours that are simply being caught earlier while they are still potentially curable. Colorectal tumour evolution models have proposed the “Big Bang” of tumour growth, where a single expansion in adenoma development dictates disease outcome. In line with the “hopeful monsters” theory, this model reason that some tumours are “born-to-be-bad” from the earliest point in CRC tumour evolution.
Aims: This proposal aims to develop a molecular stratifier of lethal vs non-lethal early-invasive disease based on comprehensive molecular pathological profiling, improved biological understanding and multiple tiers of validation to inform the management of CRC disease at the earliest stage. Methods: In contrast to stage II-IV CRC, there are limited stage I molecular studies, reducing opportunities to identify lethal early-disseminating tumours in patients who account for ~50% of screen-detected cancers. This study is undertaking collection and molecular profiling of a cohort of retrospective stage I tissue (n=200), enriched for patients that experienced relapsed, to identify factors associated with early-dissemination.
Results: Pathological characterisation of the stage I cohort indicated that histological factors such as fibroblast content or depth of invasive front are not associated with eventual metastatic relapse. Unsupervised analysis highlighted a detectable shift in transcriptional signalling between recurrent and non-recurrent samples. Further supervised analysis indicates that intrinsic “stem-like” factors may be more prognostic than extrinsic factors in stage I.
Conclusions: In order to find any effective treatment you have to first understand the biology underpinning disease. Given the increasing numbers of early stage patients being diagnosed as a result of BCS, and the paucity of tissue cohorts and focussed molecular studies of stage I CRC, this study aims to increase our understanding of specific factors underpinning prognosis at this early stage.
Citation Format: Philip Dunne, M B. Loughrey, H G. Coleman, R McBride, J Campbell, M Alderdice, K L. Redmond, D G. McArt, C Isella, S Leedham, T Maughan, M Lawler, S:CORT consortium. Advancing the molecular understanding of stage I colorectal cancer [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 5175.
Collapse
Affiliation(s)
| | | | | | - R McBride
- 2Queen's Univ. Belfast, Belfast, United Kingdom
| | - J Campbell
- 2Queen's Univ. Belfast, Belfast, United Kingdom
| | - M Alderdice
- 2Queen's Univ. Belfast, Belfast, United Kingdom
| | | | - D G. McArt
- 2Queen's Univ. Belfast, Belfast, United Kingdom
| | | | - S Leedham
- 4University of Oxford, United Kingdom
| | - T Maughan
- 4University of Oxford, United Kingdom
| | - M Lawler
- 2Queen's Univ. Belfast, Belfast, United Kingdom
| | | |
Collapse
|
14
|
Fernandez-Rozadilla C, Kartsonaki C, Woolley C, McClellan M, Whittington D, Horgan G, Leedham S, Kriaucionis S, East JE, Tomlinson I. Author Correction: Telomere length and genetics are independent colorectal tumour risk factors in an evaluation of biomarkers in normal bowel. Br J Cancer 2018; 118:1683. [PMID: 29780161 PMCID: PMC6008464 DOI: 10.1038/s41416-018-0111-0] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Since the publication of this paper, the authors noticed that James E. East was assigned to the incorrect affiliation. The affiliation information is provided correctly, above.
Collapse
Affiliation(s)
| | - Christiana Kartsonaki
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, Old Road Campus, Oxford, OX3 7DQ, UK
| | - Connor Woolley
- Molecular and Population Genetics Laboratory University of Oxford, Oxford, OX3 7BN, UK
| | - Michael McClellan
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Deb Whittington
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Gareth Horgan
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Simon Leedham
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Gastrointestinal Stem Cell Biology Laboratory, Oxford Centre for Cancer Gene Research, Oxford, UK
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - James E East
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory University of Oxford, Oxford, OX3 7BN, UK. .,Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
15
|
Fernandez-Rozadilla C, Kartsonaki C, Woolley C, McClellan M, Whittington D, Horgan G, Leedham S, Kriaucionis S, East J, Tomlinson I. Telomere length and genetics are independent colorectal tumour risk factors in an evaluation of biomarkers in normal bowel. Br J Cancer 2018; 118:727-732. [PMID: 29438375 PMCID: PMC5846076 DOI: 10.1038/bjc.2017.486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 06/20/2017] [Revised: 12/09/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) screening might be improved by using a measure of prior risk to modulate screening intensity or the faecal immunochemical test threshold. Intermediate molecular biomarkers could aid risk prediction by capturing both known and unknown risk factors. METHODS We sampled normal bowel mucosa from the proximal colon, distal colon and rectum of 317 individuals undergoing colonoscopy. We defined cases as having a personal history of colorectal polyp(s)/cancer, and controls as having no history of colorectal neoplasia. Molecular analyses were performed for: telomere length (TL); global methylation; and the expression of genes in molecular pathways associated with colorectal tumourigenesis. We also calculated a polygenic risk score (PRS) based on CRC susceptibility polymorphisms. RESULTS Bowel TL was significantly longer in cases than controls, but was not associated with blood TL. PRS was significantly and independently higher in cases. Hypermethylation showed a suggestive association with case:control status. No gene or pathway was differentially expressed between cases and controls. Gene expression often varied considerably between bowel locations. CONCLUSIONS PRS and bowel TL (but not blood TL) may be clinically-useful predictors of CRC risk. Sample collection to assess these biomarkers is feasible in clinical practice, especially where population screening uses flexible sigmoidoscopy or colonoscopy.
Collapse
Affiliation(s)
| | - Christiana Kartsonaki
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, Old Road Campus, Oxford OX3 7DQ, UK
| | - Connor Woolley
- Molecular and Population Genetics Laboratory University of Oxford, Oxford OX3 7BN, UK
| | - Michael McClellan
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Deb Whittington
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Gareth Horgan
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Simon Leedham
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Gastrointestinal Stem Cell Biology Laboratory, Oxford Centre for Cancer Gene Research and
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - James East
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory University of Oxford, Oxford OX3 7BN, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| |
Collapse
|
16
|
Abstract
Barrett's oesophagus surveillance biopsies represent a significant share of the daily workload for a busy histopathology department. Given the emphasis on endoscopic detection and dysplasia grading, it is easy to forget that the benefits of these screening programs remain unproven. The majority of patients are at low risk of progression to oesophageal adenocarcinoma, and periodic surveillance of these patients is burdensome and costly. Here, we investigate the parallels in the development of Barrett's oesophagus and other scenarios of wound healing in the intestine. There is now increased recognition of the full range of glandular phenotypes that can be found in patients' surveillance biopsies, and emerging evidence suggests parallel pathways to oesophageal adenocarcinoma. Greater understanding of the conditions that favour progression to cancer in the distal oesophagus will allow us to focus resources on patients at increased risk.
Collapse
Affiliation(s)
- Sujata Biswas
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michael Quante
- II. Medizinische Klinik, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Simon Leedham
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Marnix Jansen
- UCL Cancer Institute, London, UK. .,University College London Hospital, London, UK.
| |
Collapse
|
17
|
Salaga M, Leedham S. Young GI angle: Effective data presentation. United European Gastroenterol J 2017; 5:601-602. [PMID: 28588892 DOI: 10.1177/2050640617709664] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Maciej Salaga
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Poland (Junior Contributor)
| | - Simon Leedham
- Associate Professor of Gastroenterology Course Co-director, UEG Young Investigators, Meeting Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (Senior Contributor)
| |
Collapse
|
18
|
Hellner K, Miranda F, Fotso Chedom D, Herrero-Gonzalez S, Hayden DM, Tearle R, Artibani M, Carrami EM, Williams R, Gaitskell K, Elorbany S, Xu R, Laios A, Buiga P, Ahmed K, Dhar S, Zhang RY, Campo L, Myers KA, Lozano M, Ruiz-Miró M, Gatius S, Mota A, Moreno-Bueno G, Matias-Guiu X, Benítez J, Witty L, McVean G, Leedham S, Tomlinson I, Drmanac R, Cazier JB, Klein R, Dunne K, Bast RC, Kennedy SH, Hassan B, Lise S, Garcia MJ, Peters BA, Yau C, Sauka-Spengler T, Ahmed AA. Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies. EBioMedicine 2016; 10:137-49. [PMID: 27492892 PMCID: PMC5006641 DOI: 10.1016/j.ebiom.2016.06.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 05/31/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 02/01/2023] Open
Abstract
Current screening methods for ovarian cancer can only detect advanced disease. Earlier detection has proved difficult because the molecular precursors involved in the natural history of the disease are unknown. To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points over three years from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). The functional and clinical significance of the identified mutations was examined using a combination of population-based whole genome sequencing, targeted deep sequencing, multi-center analysis of protein expression, loss of function experiments in an in-vivo reporter assay and mammalian models, and gain of function experiments in primary cultured fallopian tube epithelial (FTE) cells. We identified frequent mutations involving a 40kb distal repressor region for the key stem cell differentiation gene SOX2. In the apparently normal FTE, the region was also mutated. This was associated with a profound increase in SOX2 expression (p<2(-16)), which was not found in patients without cancer (n=108). Importantly, we show that SOX2 overexpression in FTE is nearly ubiquitous in patients with HGSOCs (n=100), and common in BRCA1-BRCA2 mutation carriers (n=71) who underwent prophylactic salpingo-oophorectomy. We propose that the finding of SOX2 overexpression in FTE could be exploited to develop biomarkers for detecting disease at a premalignant stage, which would reduce mortality from this devastating disease.
Collapse
Affiliation(s)
- Karin Hellner
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Fabrizio Miranda
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Donatien Fotso Chedom
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK; Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sandra Herrero-Gonzalez
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Daniel M Hayden
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States
| | - Rick Tearle
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK; University of Oxford, Gene Regulatory Networks in Development and Disease Laboratory, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Eli M Carrami
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ruth Williams
- University of Oxford, Gene Regulatory Networks in Development and Disease Laboratory, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Kezia Gaitskell
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Samar Elorbany
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ruoyan Xu
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Alex Laios
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Petronela Buiga
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Karim Ahmed
- Trinity College, University of Cambridge, Cambridge CB2 1TQ, UK
| | - Sunanda Dhar
- Department of Histopathology, Oxford University Hospitals, Oxford OX3 9DU, UK
| | - Rebecca Yu Zhang
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States
| | - Leticia Campo
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kevin A Myers
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - María Lozano
- Histopathology Core Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María Ruiz-Miró
- Biobank, Institut de Recerca Biomèdica Lleida (IRBLLEIDA), Lleida, Spain
| | - Sónia Gatius
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, Lleida, Spain
| | - Alba Mota
- Department of Biochemistry, Universidad Autonoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain; MD Anderson international Foundation, Madrid, Spain
| | - Gema Moreno-Bueno
- Department of Biochemistry, Universidad Autonoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain; MD Anderson international Foundation, Madrid, Spain
| | - Xavier Matias-Guiu
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, Lleida, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Lorna Witty
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Simon Leedham
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Radoje Drmanac
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States; BGI-Shenzhen, Shenzhen, China
| | - Jean-Baptiste Cazier
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Centre for Computational Biology, University of Birmingham, Edgbaston B15 2TT, UK
| | - Robert Klein
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States
| | - Kevin Dunne
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States
| | - Robert C Bast
- Department of Experimental Therapeutics, M.D. Anderson Cancer Center, University of Texas, USA
| | - Stephen H Kennedy
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Bassim Hassan
- Tumor Growth Control Group, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Stefano Lise
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK
| | - María José Garcia
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Brock A Peters
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA 94043, United States; BGI-Shenzhen, Shenzhen, China
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, NIHR Biomedical Research Centre, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, Gene Regulatory Networks in Development and Disease Laboratory, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Ahmed Ashour Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK.
| |
Collapse
|
19
|
Biswas S, Davis H, Irshad S, Sandberg T, Worthley D, Leedham S. Microenvironmental control of stem cell fate in intestinal homeostasis and disease. J Pathol 2015; 237:135-45. [PMID: 25974319 PMCID: PMC4744721 DOI: 10.1002/path.4563] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [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: 03/22/2015] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 12/27/2022]
Abstract
The conventional model of intestinal epithelial architecture describes a unidirectional tissue organizational hierarchy with stem cells situated at the crypt base and daughter cells proliferating and terminally differentiating as they progress along the vertical (crypt-luminal) axis. In this model, the fate of a cell that has left the niche is determined and its lifespan limited. Evidence is accumulating to suggest that stem cell control and daughter cell fate determination is not solely an intrinsic, cell autonomous property but is heavily influenced by the microenvironment including paracrine, mesenchymal, and endogenous epithelial morphogen gradients. Recent research suggests that in intestinal homeostasis, stem cells transit reversibly between states of variable competence in the niche. Furthermore, selective pressures that disrupt the homeostatic balance, such as intestinal inflammation or morphogen dysregulation, can cause committed progenitor cells and even some differentiated cells to regain stem cell properties. Importantly, it has been recently shown that this disruption of cell fate determination can lead to somatic mutation and neoplastic transformation of cells situated outside the crypt base stem cell niche. This paper reviews the exciting developments in the study of stem cell dynamics in homeostasis, intestinal regeneration, and carcinogenesis, and explores the implications for human disease and cancer therapies.
Collapse
Affiliation(s)
- Sujata Biswas
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford, UK
| | - Hayley Davis
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Shazia Irshad
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Tessa Sandberg
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Daniel Worthley
- South Australian Health and Medical Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Simon Leedham
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford, UK
| |
Collapse
|
20
|
Huels DJ, Ridgway RA, Radulescu S, Leushacke M, Campbell AD, Biswas S, Leedham S, Serra S, Chetty R, Moreaux G, Parry L, Matthews J, Song F, Hedley A, Kalna G, Ceteci F, Reed KR, Meniel VS, Maguire A, Doyle B, Söderberg O, Barker N, Watson A, Larue L, Clarke AR, Sansom OJ. E-cadherin can limit the transforming properties of activating β-catenin mutations. EMBO J 2015; 34:2321-33. [PMID: 26240067 PMCID: PMC4570519 DOI: 10.15252/embj.201591739] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [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: 04/08/2015] [Revised: 06/23/2015] [Accepted: 07/01/2015] [Indexed: 11/09/2022] Open
Abstract
Wnt pathway deregulation is a common characteristic of many cancers. Only colorectal cancer predominantly harbours mutations in APC, whereas other cancer types (hepatocellular carcinoma, solid pseudopapillary tumours of the pancreas) have activating mutations in β-catenin (CTNNB1). We have compared the dynamics and the potency of β-catenin mutations in vivo. Within the murine small intestine (SI), an activating mutation of β-catenin took much longer to achieve Wnt deregulation and acquire a crypt-progenitor cell (CPC) phenotype than Apc or Gsk3 loss. Within the colon, a single activating mutation of β-catenin was unable to drive Wnt deregulation or induce the CPC phenotype. This ability of β-catenin mutation to differentially transform the SI versus the colon correlated with higher expression of E-cadherin and a higher number of E-cadherin:β-catenin complexes at the membrane. Reduction in E-cadherin synergised with an activating mutation of β-catenin resulting in a rapid CPC phenotype within the SI and colon. Thus, there is a threshold of β-catenin that is required to drive transformation, and E-cadherin can act as a buffer to sequester mutated β-catenin.
Collapse
Affiliation(s)
| | | | | | - Marc Leushacke
- A∗STAR Institute of Medical Biology, Singapore City, Singapore
| | | | - Sujata Biswas
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics University of Oxford, Oxford, UK Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, Headington, UK
| | - Simon Leedham
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics University of Oxford, Oxford, UK Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, Headington, UK
| | - Stefano Serra
- Department of Pathology, University Health Network/Toronto Medical Laboratories, Toronto, Canada
| | - Runjan Chetty
- Department of Pathology, University Health Network/Toronto Medical Laboratories, Toronto, Canada
| | | | - Lee Parry
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
| | - James Matthews
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
| | - Fei Song
- Institute of Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Fatih Ceteci
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Karen R Reed
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
| | - Valerie S Meniel
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
| | - Aoife Maguire
- Department of Histopathology, Trinity College Dublin St James's Hospital, Dublin, Ireland
| | - Brendan Doyle
- Cancer Research UK Beatson Institute, Glasgow, UK Department of Histopathology, Trinity College Dublin St James's Hospital, Dublin, Ireland
| | - Ola Söderberg
- Department of Immunology, Genetics and Pathology Science for Life Laboratory, BMC Uppsala University, Uppsala, Sweden
| | - Nick Barker
- A∗STAR Institute of Medical Biology, Singapore City, Singapore
| | - Alastair Watson
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lionel Larue
- Institut Curie, CNRS UMR3347 INSERM, U1021 Equipe labellisée - Ligue Nationale contre le Cancer, Orsay, France
| | - Alan R Clarke
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
| | | |
Collapse
|
21
|
Lewis A, Freeman-Mills L, de la Calle-Mustienes E, Giráldez-Pérez RM, Davis H, Jaeger E, Becker M, Hubner NC, Nguyen LN, Zeron-Medina J, Bond G, Stunnenberg HG, Carvajal JJ, Gomez-Skarmeta JL, Leedham S, Tomlinson I. A polymorphic enhancer near GREM1 influences bowel cancer risk through differential CDX2 and TCF7L2 binding. Cell Rep 2014; 8:983-90. [PMID: 25131200 PMCID: PMC4471812 DOI: 10.1016/j.celrep.2014.07.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/09/2014] [Accepted: 07/15/2014] [Indexed: 02/04/2023] Open
Abstract
A rare germline duplication upstream of the bone morphogenetic protein antagonist GREM1 causes a Mendelian-dominant predisposition to colorectal cancer (CRC). The underlying disease mechanism is strong, ectopic GREM1 overexpression in the intestinal epithelium. Here, we confirm that a common GREM1 polymorphism, rs16969681, is also associated with CRC susceptibility, conferring ∼20% differential risk in the general population. We hypothesized the underlying cause to be moderate differences in GREM1 expression. We showed that rs16969681 lies in a region of active chromatin with allele- and tissue-specific enhancer activity. The CRC high-risk allele was associated with stronger gene expression, and higher Grem1 mRNA levels increased the intestinal tumor burden in Apc(Min) mice. The intestine-specific transcription factor CDX2 and Wnt effector TCF7L2 bound near rs16969681, with significantly higher affinity for the risk allele, and CDX2 overexpression in CDX2/GREM1-negative cells caused re-expression of GREM1. rs16969681 influences CRC risk through effects on Wnt-driven GREM1 expression in colorectal tumors.
Collapse
Affiliation(s)
- Annabelle Lewis
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Luke Freeman-Mills
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km1, 41013 Sevilla, Spain
| | - Rosa María Giráldez-Pérez
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km1, 41013 Sevilla, Spain
| | - Hayley Davis
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Emma Jaeger
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martin Becker
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD Nijmegen, the Netherlands
| | - Nina C Hubner
- Department of Molecular Biology, Radboud Institute for Molecular Life Science, Geert Grooteplein 26/28, 6525 GA Nijmegen, the Netherlands
| | - Luan N Nguyen
- Department of Molecular Biology, Radboud Institute for Molecular Life Science, Geert Grooteplein 26/28, 6525 GA Nijmegen, the Netherlands
| | - Jorge Zeron-Medina
- Ludwig Institute for Cancer Research, Ltd., Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Gareth Bond
- Ludwig Institute for Cancer Research, Ltd., Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud Institute for Molecular Life Science, Geert Grooteplein 26/28, 6525 GA Nijmegen, the Netherlands
| | - Jaime J Carvajal
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km1, 41013 Sevilla, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km1, 41013 Sevilla, Spain
| | - Simon Leedham
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| |
Collapse
|
22
|
Gill P, Wang LM, Bailey A, East JE, Leedham S, Chetty R. Reporting trends of right-sided hyperplastic and sessile serrated polyps in a large teaching hospital over a 4-year period (2009-2012). J Clin Pathol 2013; 66:655-8. [PMID: 23576460 DOI: 10.1136/jclinpath-2013-201608] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AIM An audit of serrated polyps diagnosed over a 4-year period: 2009 to 2012 was undertaken to ascertain the reporting trends of sessile serrated polyps (SSP). METHODS All right sided hyperplastic polyps (HP) proximal to the splenic flexure and all polyps designated SSP were retrieved from the study period. Three pathologists blinded to the original diagnosis re-examined the slides. Recent American College of Gastroenterology guidelines for the diagnosis of SSP was utilised. RESULTS No cases of SSP were diagnosed in 2009. In 2010, 32 right-sided cases were encountered, 83 confirmed in 2011 and 134 confirmed in 2012. The vast majority of these were right-sided. With regards to right-sided HP that were re-classified as SSP the data is as follows: 20 of 66 in 2009 (30%); 58 of 91 in 2010 (64%); 42 of 106 (40%) in 2011 and 69 of 206 in 2012 (33%). CONCLUSIONS This study has demonstrated an almost exponential increase in the diagnosis of SSP over a 4-year period. In addition, 30 to 64% of right-sided HP were re-classified as SSP over the 4-year period suggesting that greater awareness of the diagnostic criteria for SSP is required. SSP is an important precursor lesion in the serrated pathway of colorectal cancer. Its recognition is important for surveillance and therapeutic strategies.
Collapse
Affiliation(s)
- Pelvender Gill
- Department of Cellular Pathology, Oxford University Hospitals, Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | | | | | | |
Collapse
|
23
|
|
24
|
Leedham S, East JE, Chetty R. Diagnosis of sessile serrated polyps/adenomas: what does this mean for the pathologist, gastroenterologist and patient? J Clin Pathol 2013; 66:265-8. [PMID: 23404799 DOI: 10.1136/jclinpath-2013-201457] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
25
|
Jaeger E, Leedham S, Lewis A, Segditsas S, Becker M, Cuadrado PR, Davis H, Kaur K, Heinimann K, Howarth K, East J, Taylor J, Thomas H, Tomlinson I. Hereditary mixed polyposis syndrome is caused by a 40-kb upstream duplication that leads to increased and ectopic expression of the BMP antagonist GREM1. Nat Genet 2012; 44:699-703. [PMID: 22561515 PMCID: PMC4594751 DOI: 10.1038/ng.2263] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [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: 11/21/2011] [Accepted: 04/06/2012] [Indexed: 12/11/2022]
Abstract
The hereditary mixed polyposis syndrome (HMPS) was first described about 50 years ago in a large Ashkenazi Jewish family from St Mark’s Hospital, London. The family showed apparent autosomal dominant inheritance of multiple types of colorectal polyp, with colorectal carcinoma in a high proportion of individuals. In the last 15 years, we have mapped the HMPS gene to chromosome 15q13.3 and identified an ancestral haplotype common to all the known HMPS families. Here, we have used genetic mapping, copy number analysis, exclusion of mutations by high-throughput sequencing, gene expression analysis and functional assays to show that HMPS is caused by a large duplication spanning the 3′ end of the SCG5 gene and a region upstream of the GREM1 locus. This mutation has no effect on SCG5 expression, but is associated with greatly increased, allele-specific GREM1 expression. Whilst GREM1 is expressed in intestinal sub-epithelial myofibroblasts in controls, HMPS patients predominantly express GREM1 in the epithelium of the large bowel. The HMPS duplication contains predicted transcriptional enhancer elements; we have shown that some of these interact with the GREM1 promoter and are capable of driving gene expression in vitro. Increased GREM1 expression is predicted to lead to reduced bone morphogenetic protein pathway activity, a mechanism that also underlies tumorigenesis in juvenile polyposis of the large bowel. The pathogenic mechanism in HMPS is extremely unusual in Mendelian cancer syndromes and highlights ectopic gene expression as a mechanism of tumorigenesis.
Collapse
Affiliation(s)
- Emma Jaeger
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Simon Leedham
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.,Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Annabelle Lewis
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Stefania Segditsas
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Martin Becker
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Pedro Rodenas Cuadrado
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Hayley Davis
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Kulvinder Kaur
- NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Karl Heinimann
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.,Abt. Medizinische Genetik, Universitaetskinderspital beider Basel, Burgfelderstrasse 101, Haus J CH-4055 Basel, Switzerland
| | - Kimberley Howarth
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | | | - James East
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Jenny Taylor
- NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Huw Thomas
- Family Cancer Clinic, Imperial College School of Medicine, St Mark's Hospital, Watford Road, Harrow A1 3UJ, United Kingdom
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.,NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| |
Collapse
|
26
|
Abstract
Berger and colleagues recently proposed a continuum model of how somatic mutations cause tumors to grow, thus supplementing the established binary models, such as oncogene activation and "two hits" at tumor suppressor loci. In the basic continuum model, decreases or increases in gene function, short of full inactivation or activation, impact linearly on cancer development. An extension, called the fail-safe model, envisaged an optimum level of gene derangement for tumor growth, but proposed that the cell gained protection from tumorigenesis because additional mutations caused excessive derangement. Most of the evidence in support of the continuum model came from Pten mutant mice rather than humans. In this article, we assess the validity and applicability of the continuum and fail-safe models. We suggest that the latter is of limited use: In part, it restates the existing "just right" of optimum intermediate gene derangement in tumorigenesis, and in part it is inherently implausible that a cell should avoid becoming cancerous only when it is some way down the road to that state. In contrast, the basic continuum model is a very useful addition to the other genetic models of tumorigenesis, especially in certain scenarios. Fittingly for a quantitative model, we propose that the continuum model is most likely to apply where multiple, cancer-promoting mutations have relatively small, additive effects, either through the well-established case of additive germline predisposition alleles or in a largely hypothetical situation where cancers may have acquired several somatic "mini-driver" mutations, each with weaker effects than classical tumor suppressors or fully activated oncogenes.
Collapse
Affiliation(s)
- Simon Leedham
- Molecular and Population Genetics Laboratory, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
27
|
|
28
|
Abstract
Gastric acid is believed to be an important etiological factor in the pathogenesis of Barrett's esophagus. Pulsatile acid exposure increases cell proliferation in ex vivo Barrrett's tissue and normalization of esophageal pH reverses this. Proton pump inhibitors (PPIs) are the mainstay of therapy in Barrett's esophagus, and have numerous beneficial effects including symptom control, reduction of inflammation, and promotion of the development of squamous islands. However, PPI therapy causes hypergastrinemia and has not prevented recent increase in the incidences of esophageal cancer. Additionally, evidence presented here by Feagins et al. suggests that acid exposure has a p53-mediated, antiproliferative effect on a nondysplastic Barrett's epithelial cell line, an effect that acid suppression might abrogate. These complex pH, inflammation, and growth factor biological interactions can be most reliably tested in large clinical trials with hard end points like cancer conversion or all causes of mortality. Combining the anti-inflammatory effects of acid suppression with aspirin, a nonsteroidal anti-inflammatory agent, is the subject of the AspECT clinical trial, and this may be the future of chemoprevention in Barrett's.
Collapse
|