1
|
Malla SB, Byrne RM, Lafarge MW, Corry SM, Fisher NC, Tsantoulis PK, Mills ML, Ridgway RA, Lannagan TRM, Najumudeen AK, Gilroy KL, Amirkhah R, Maguire SL, Mulholland EJ, Belnoue-Davis HL, Grassi E, Viviani M, Rogan E, Redmond KL, Sakhnevych S, McCooey AJ, Bull C, Hoey E, Sinevici N, Hall H, Ahmaderaghi B, Domingo E, Blake A, Richman SD, Isella C, Miller C, Bertotti A, Trusolino L, Loughrey MB, Kerr EM, Tejpar S, Maughan TS, Lawler M, Campbell AD, Leedham SJ, Koelzer VH, Sansom OJ, Dunne PD. Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer. Nat Genet 2024; 56:458-472. [PMID: 38351382 PMCID: PMC10937375 DOI: 10.1038/s41588-024-01654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/03/2024] [Indexed: 02/29/2024]
Abstract
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1+ stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are currently under-represented in pre-clinical models and are not identified using existing subtyping classifiers.
Collapse
Affiliation(s)
- Sudhir B Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ryan M Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Maxime W Lafarge
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Shania M Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | | | | | | | | | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sarah L Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Elena Grassi
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Marco Viviani
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Emily Rogan
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Keara L Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Svetlana Sakhnevych
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Courtney Bull
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Hoey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Nicoleta Sinevici
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Holly Hall
- Cancer Research UK Scotland Institute, Glasgow, UK
| | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Andrew Blake
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Claudio Isella
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Crispin Miller
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Andrea Bertotti
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Maurice B Loughrey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Emma M Kerr
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sabine Tejpar
- Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Timothy S Maughan
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Owen J Sansom
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip D Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
- Cancer Research UK Scotland Institute, Glasgow, UK.
| |
Collapse
|
2
|
Flanagan DJ, Amirkhah R, Vincent DF, Gunduz N, Gentaz P, Cammareri P, McCooey AJ, McCorry AMB, Fisher NC, Davis HL, Ridgway RA, Lohuis J, Leach JDG, Jackstadt R, Gilroy K, Mariella E, Nixon C, Clark W, Hedley A, Markert EK, Strathdee D, Bartholin L, Redmond KL, Kerr EM, Longley DB, Ginty F, Cho S, Coleman HG, Loughrey MB, Bardelli A, Maughan TS, Campbell AD, Lawler M, Leedham SJ, Barry ST, Inman GJ, van Rheenen J, Dunne PD, Sansom OJ. Author Correction: Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features. Nat Commun 2023; 14:522. [PMID: 36720858 PMCID: PMC9889781 DOI: 10.1038/s41467-023-36266-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Dustin J Flanagan
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| | - Raheleh Amirkhah
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Nuray Gunduz
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Aoife J McCooey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Amy M B McCorry
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Hayley L Davis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jeroen Lohuis
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joshua D G Leach
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rene Jackstadt
- Cancer Research UK Beatson Institute, Glasgow, UK
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Elisa Mariella
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, UK
- University of Newcastle upon Tyne, Newcastle, UK
| | - Elke K Markert
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Keara L Redmond
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emma M Kerr
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY, USA
| | - Sanghee Cho
- GE Global Research Center, Niskayuna, NY, USA
| | - Helen G Coleman
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Maurice B Loughrey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Mark Lawler
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon J Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon T Barry
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip D Dunne
- Cancer Research UK Beatson Institute, Glasgow, UK
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
3
|
Flanagan DJ, Amirkhah R, Vincent DF, Gunduz N, Gentaz P, Cammareri P, McCooey AJ, McCorry AMB, Fisher NC, Davis HL, Ridgway RA, Lohuis J, Leach JDG, Jackstadt R, Gilroy K, Mariella E, Nixon C, Clark W, Hedley A, Markert EK, Strathdee D, Bartholin L, Redmond KL, Kerr EM, Longley DB, Ginty F, Cho S, Coleman HG, Loughrey MB, Bardelli A, Maughan TS, Campbell AD, Lawler M, Leedham SJ, Barry ST, Inman GJ, van Rheenen J, Dunne PD, Sansom OJ. Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features. Nat Commun 2022; 13:7551. [PMID: 36477656 PMCID: PMC9729215 DOI: 10.1038/s41467-022-35134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
The pro-tumourigenic role of epithelial TGFβ signalling in colorectal cancer (CRC) is controversial. Here, we identify a cohort of born to be bad early-stage (T1) colorectal tumours, with aggressive features and a propensity to disseminate early, that are characterised by high epithelial cell-intrinsic TGFβ signalling. In the presence of concurrent Apc and Kras mutations, activation of epithelial TGFβ signalling rampantly accelerates tumourigenesis and share transcriptional signatures with those of the born to be bad T1 human tumours and predicts recurrence in stage II CRC. Mechanistically, epithelial TGFβ signalling induces a growth-promoting EGFR-signalling module that synergises with mutant APC and KRAS to drive MAPK signalling that re-sensitise tumour cells to MEK and/or EGFR inhibitors. Together, we identify epithelial TGFβ signalling both as a determinant of early dissemination and a potential therapeutic vulnerability of CRC's with born to be bad traits.
Collapse
Affiliation(s)
- Dustin J Flanagan
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| | - Raheleh Amirkhah
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Nuray Gunduz
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Aoife J McCooey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Amy M B McCorry
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Hayley L Davis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jeroen Lohuis
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joshua D G Leach
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rene Jackstadt
- Cancer Research UK Beatson Institute, Glasgow, UK
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Elisa Mariella
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, UK
- University of Newcastle upon Tyne, Newcastle, UK
| | - Elke K Markert
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Keara L Redmond
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emma M Kerr
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY, USA
| | - Sanghee Cho
- GE Global Research Center, Niskayuna, NY, USA
| | - Helen G Coleman
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Maurice B Loughrey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Mark Lawler
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon J Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon T Barry
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip D Dunne
- Cancer Research UK Beatson Institute, Glasgow, UK
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
4
|
Corry SM, McCorry AM, Lannagan TR, Leonard NA, Fisher NC, Byrne RM, Tsantoulis P, Cortes-Lavaud X, Amirkhah R, Redmond KL, McCooey AJ, Malla SB, Rogan E, Sakhnevych S, Gillespie MA, White M, Richman SD, Jackstadt RF, Campbell AD, Maguire S, McDade SS, Longley DB, Loughrey MB, Coleman HG, Kerr EM, Tejpar S, Maughan T, Leedham SJ, Small DM, Ryan AE, Sansom OJ, Lawler M, Dunne PD. Activation of innate-adaptive immune machinery by poly(I:C) exposes a therapeutic vulnerability to prevent relapse in stroma-rich colon cancer. Gut 2022; 71:2502-2517. [PMID: 35477539 PMCID: PMC9664095 DOI: 10.1136/gutjnl-2021-326183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/12/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Stroma-rich tumours represent a poor prognostic subtype in stage II/III colon cancer (CC), with high relapse rates and limited response to standard adjuvant chemotherapy. DESIGN To address the lack of efficacious therapeutic options for patients with stroma-rich CC, we stratified our human tumour cohorts according to stromal content, enabling identification of the biology underpinning relapse and potential therapeutic vulnerabilities specifically within stroma-rich tumours that could be exploited clinically. Following human tumour-based discovery and independent clinical validation, we use a series of in vitro and stroma-rich in vivo models to test and validate the therapeutic potential of elevating the biology associated with reduced relapse in human tumours. RESULTS By performing our analyses specifically within the stroma-rich/high-fibroblast (HiFi) subtype of CC, we identify and validate the clinical value of a HiFi-specific prognostic signature (HPS), which stratifies tumours based on STAT1-related signalling (High-HPS v Low-HPS=HR 0.093, CI 0.019 to 0.466). Using in silico, in vitro and in vivo models, we demonstrate that the HPS is associated with antigen processing and presentation within discrete immune lineages in stroma-rich CC, downstream of double-stranded RNA and viral response signalling. Treatment with the TLR3 agonist poly(I:C) elevated the HPS signalling and antigen processing phenotype across in vitro and in vivo models. In an in vivo model of stroma-rich CC, poly(I:C) treatment significantly increased systemic cytotoxic T cell activity (p<0.05) and reduced liver metastases (p<0.0002). CONCLUSION This study reveals new biological insight that offers a novel therapeutic option to reduce relapse rates in patients with the worst prognosis CC.
Collapse
Affiliation(s)
- Shania M Corry
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Amy Mb McCorry
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Niamh A Leonard
- Lambe Institute for Translational Research, College of Medicine Nursing and Health Sciences, National University of Ireland, Galway, Ireland
- Discipline of Pharmacology & Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
| | - Natalie C Fisher
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ryan M Byrne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Raheleh Amirkhah
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Keara L Redmond
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sudhir B Malla
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Rogan
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Svetlana Sakhnevych
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Michael A Gillespie
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark White
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Rene-Filip Jackstadt
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) and Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew D Campbell
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
| | - Sarah Maguire
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Maurice B Loughrey
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - Helen G Coleman
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sabine Tejpar
- Digestive Oncology Unit, University Ospital Gasthuisberg, Leuven, Belgium
| | | | - Simon J Leedham
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
| | - Donna M Small
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aideen E Ryan
- Lambe Institute for Translational Research, College of Medicine Nursing and Health Sciences, National University of Ireland, Galway, Ireland
- Discipline of Pharmacology & Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
| | - Owen J Sansom
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Philip D Dunne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| |
Collapse
|
5
|
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
|
6
|
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
|
7
|
Sirinukunwattana K, Domingo E, Richman SD, Redmond KL, Blake A, Verrill C, Leedham SJ, Chatzipli A, Hardy C, Whalley CM, Wu CH, Beggs AD, McDermott U, Dunne PD, Meade A, Walker SM, Murray GI, Samuel L, Seymour M, Tomlinson I, Quirke P, Maughan T, Rittscher J, Koelzer VH. Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using deep learning. Gut 2021; 70:544-554. [PMID: 32690604 PMCID: PMC7873419 DOI: 10.1136/gutjnl-2019-319866] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/19/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Complex phenotypes captured on histological slides represent the biological processes at play in individual cancers, but the link to underlying molecular classification has not been clarified or systematised. In colorectal cancer (CRC), histological grading is a poor predictor of disease progression, and consensus molecular subtypes (CMSs) cannot be distinguished without gene expression profiling. We hypothesise that image analysis is a cost-effective tool to associate complex features of tissue organisation with molecular and outcome data and to resolve unclassifiable or heterogeneous cases. In this study, we present an image-based approach to predict CRC CMS from standard H&E sections using deep learning. DESIGN Training and evaluation of a neural network were performed using a total of n=1206 tissue sections with comprehensive multi-omic data from three independent datasets (training on FOCUS trial, n=278 patients; test on rectal cancer biopsies, GRAMPIAN cohort, n=144 patients; and The Cancer Genome Atlas (TCGA), n=430 patients). Ground truth CMS calls were ascertained by matching random forest and single sample predictions from CMS classifier. RESULTS Image-based CMS (imCMS) accurately classified slides in unseen datasets from TCGA (n=431 slides, AUC)=0.84) and rectal cancer biopsies (n=265 slides, AUC=0.85). imCMS spatially resolved intratumoural heterogeneity and provided secondary calls correlating with bioinformatic prediction from molecular data. imCMS classified samples previously unclassifiable by RNA expression profiling, reproduced the expected correlations with genomic and epigenetic alterations and showed similar prognostic associations as transcriptomic CMS. CONCLUSION This study shows that a prediction of RNA expression classifiers can be made from H&E images, opening the door to simple, cheap and reliable biological stratification within routine workflows.
Collapse
Affiliation(s)
- Korsuk Sirinukunwattana
- Institute of Biomedical Engineering (IBME), Department of Engineering Science, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, UK
| | - Susan D Richman
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK
| | - Keara L Redmond
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Andrew Blake
- Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Simon J Leedham
- Gastrointestinal Stem-cell Biology Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | | | - Celina M Whalley
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - Andrew D Beggs
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | | | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Angela Meade
- MRC Clinical Trials Unit at University College London, London, UK
| | | | - Graeme I Murray
- Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Leslie Samuel
- Department of Clinical Oncology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Matthew Seymour
- Department of Oncology, Leeds Institute of Cancer and Pathology, Leeds, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Edinburgh Cancer Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Phil Quirke
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK
| | - Timothy Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Jens Rittscher
- Institute of Biomedical Engineering (IBME), Department of Engineering Science, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Viktor H Koelzer
- Department of Oncology, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Pathology and Molecular Pathology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
8
|
Malla SB, Fisher DJ, Domingo E, Blake A, Hassanieh S, Redmond KL, Richman SD, Youdell M, Walker SM, Logan GE, Chatzipli A, Amirkhah R, Humphries MP, Craig SG, McDermott U, Seymour MT, Morton DG, Quirke P, West NP, Salto-Tellez M, Kennedy RD, Johnston PG, Tomlinson I, Koelzer VH, Campo L, Kaplan RS, Longley DB, Lawler M, Maughan TS, Brown LC, Dunne PD. In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer. Clin Cancer Res 2021; 27:288-300. [PMID: 33028592 PMCID: PMC7614625 DOI: 10.1158/1078-0432.ccr-20-3237] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE The DNA damage immune response (DDIR) assay was developed in breast cancer based on biology associated with deficiencies in homologous recombination and Fanconi anemia pathways. A positive DDIR call identifies patients likely to respond to platinum-based chemotherapies in breast and esophageal cancers. In colorectal cancer, there is currently no biomarker to predict response to oxaliplatin. We tested the ability of the DDIR assay to predict response to oxaliplatin-based chemotherapy in colorectal cancer and characterized the biology in DDIR-positive colorectal cancer. EXPERIMENTAL DESIGN Samples and clinical data were assessed according to DDIR status from patients who received either 5-fluorouracil (5-FU) or 5FUFA (bolus and infusion 5-FU with folinic acid) plus oxaliplatin (FOLFOX) within the FOCUS trial (n = 361, stage IV), or neoadjuvant FOLFOX in the FOxTROT trial (n = 97, stage II/III). Whole transcriptome, mutation, and IHC data of these samples were used to interrogate the biology of DDIR in colorectal cancer. RESULTS Contrary to our hypothesis, DDIR-negative patients displayed a trend toward improved outcome for oxaliplatin-based chemotherapy compared with DDIR-positive patients. DDIR positivity was associated with microsatellite instability (MSI) and colorectal molecular subtype 1. Refinement of the DDIR signature, based on overlapping IFN-related chemokine signaling associated with DDIR positivity across colorectal cancer and breast cancer cohorts, further confirmed that the DDIR assay did not have predictive value for oxaliplatin-based chemotherapy in colorectal cancer. CONCLUSIONS DDIR positivity does not predict improved response following oxaliplatin treatment in colorectal cancer. However, data presented here suggest the potential of the DDIR assay in identifying immune-rich tumors that may benefit from immune checkpoint blockade, beyond current use of MSI status.
Collapse
Affiliation(s)
- Sudhir B Malla
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - David J Fisher
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Enric Domingo
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Andrew Blake
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Sylvana Hassanieh
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Keara L Redmond
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Susan D Richman
- Pathology and data analytics, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Michael Youdell
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | | | - Gemma E Logan
- Almac Diagnostic Services, Craigavon, United Kingdom
| | - Aikaterina Chatzipli
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Raheleh Amirkhah
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Matthew P Humphries
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Stephanie G Craig
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
- AstraZeneca, United Kingdom
| | | | - Dion G Morton
- University of Birmingham, Birmingham, United Kingdom
| | - Philip Quirke
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Nicholas P West
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Manuel Salto-Tellez
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Richard D Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Patrick G Johnston
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | | | | | - Letitia Campo
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Richard S Kaplan
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Timothy S Maughan
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom.
| | - Louise C Brown
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | | |
Collapse
|
9
|
Dutton LR, Hoare OP, McCorry AMB, Redmond KL, Adam NE, Canamara S, Bingham V, Mullan PB, Lawler M, Dunne PD, Brazil DP. Fibroblast-derived Gremlin1 localises to epithelial cells at the base of the intestinal crypt. Oncotarget 2019; 10:4630-4639. [PMID: 31384391 PMCID: PMC6659803 DOI: 10.18632/oncotarget.27050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/19/2019] [Indexed: 01/15/2023] Open
Abstract
Gremlin1 (GREM1) is a secreted glycoprotein member of the differential screening-selected gene in aberrant neuroblastoma (DAN) family of bone morphogenetic protein (BMP) antagonists, which binds to BMPs preventing their receptor engagement. Previous studies have identified that stage II colorectal cancer (CRC) patients with high levels of GREM1 gene expression in their tumour tissue have a poorer prognosis. Using a series of in silico and in situ methodologies, we demonstrate that GREM1 gene expression is significantly higher (p < 0.0001) in CRC consensus molecular subtype 4 (CMS4), compared to the other CMS subtypes and correlates (p < 0.0001) with levels of cancer-associated fibroblasts (CAFs) within the CRC tumour microenvironment (TME). Our optimised immunohistochemistry protocol identified endogenous GREM1 protein expression in both the muscularis mucosa and adjacent colonic crypt bases in mouse intestine, in contrast to RNA expression which was shown to localise specifically to the muscularis mucosa, as determined by in situ hybridisation. Importantly, we demonstrate that cells with high levels of GREM1 expression display low levels of phospho-Smad1/5, consistent with reduced BMP signalling. Taken together, these data highlight a novel paracrine signalling circuit, which involves uptake of mature GREM1 protein by colonic crypt cells following secretion from neighbouring fibroblasts in the TME.
Collapse
Affiliation(s)
- Louise R Dutton
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,These authors contributed equally to this work
| | - Owen P Hoare
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,These authors contributed equally to this work
| | - Amy M B McCorry
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,These authors contributed equally to this work
| | - Keara L Redmond
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Noor Eisa Adam
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, United Arab Emirates
| | - Shannon Canamara
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Indonesia International Institute for Life-Sciences, University of East Jakarta, Jakarta Timur, Indonesia
| | - Victoria Bingham
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Paul B Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,Co-senior authors
| | - Derek P Brazil
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Co-senior authors
| |
Collapse
|
10
|
Abstract
The recent discovery of oncogenic drivers and subsequent development of novel targeted strategies has significantly added to the therapeutic armamentarium of anti-cancer therapies. Targeting BCR-ABL in chronic myeloid leukemia (CML) or HER2 in breast cancer has led to practice-changing clinical benefits, while promising therapeutic responses have been achieved by precision medicine approaches in EGFR mutant lung cancer, colorectal cancer and BRAF mutant melanoma. However, although initial therapeutic responses to targeted therapies can be substantial, many patients will develop disease progression within 6-12 months. An increasing application of powerful omics-based approaches and improving preclinical models have enabled the rapid identification of secondary resistance mechanisms. Herein, we discuss how this knowledge has translated into rational, novel treatment strategies for relapsed patients in genomically selected cancer populations.
Collapse
Affiliation(s)
- Keara L Redmond
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Anastasia Papafili
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom.
| |
Collapse
|
11
|
Dunne PD, Dasgupta S, Blayney JK, McArt DG, Redmond KL, Weir JA, Bradley CA, Sasazuki T, Shirasawa S, Wang T, Srivastava S, Ong CW, Arthur K, Salto-Tellez M, Wilson RH, Johnston PG, Van Schaeybroeck S. EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer. Clin Cancer Res 2015; 22:230-242. [PMID: 26283684 DOI: 10.1158/1078-0432.ccr-15-0603] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/30/2015] [Indexed: 12/20/2022]
Abstract
PURPOSE EphA2, a member of the Eph receptor tyrosine kinases family, is an important regulator of tumor initiation, neovascularization, and metastasis in a wide range of epithelial and mesenchymal cancers; however, its role in colorectal cancer recurrence and progression is unclear. EXPERIMENTAL DESIGN EphA2 expression was determined by immunohistochemistry in stage II/III colorectal tumors (N = 338), and findings correlated with clinical outcome. The correlation between EphA2 expression and stem cell markers CD44 and Lgr5 was examined. The role of EphA2 in migration/invasion was assessed using a panel of KRAS wild-type (WT) and mutant (MT) parental and invasive colorectal cancer cell line models. RESULTS Colorectal tumors displayed significantly higher expression levels of EphA2 compared with matched normal tissue, which positively correlated with high CD44 and Lgr5 expression levels. Moreover, high EphA2 mRNA and protein expression were found to be associated with poor overall survival in stage II/III colorectal cancer tissues, in both univariate and multivariate analyses. Preclinically, we found that EphA2 was highly expressed in KRASMT colorectal cancer cells and that EphA2 levels are regulated by the KRAS-driven MAPK and RalGDS-RalA pathways. Moreover, EphA2 levels were elevated in several invasive daughter cell lines, and downregulation of EphA2 using RNAi or recombinant EFNA1 suppressed migration and invasion of KRASMT colorectal cancer cells. CONCLUSIONS These data show that EpHA2 is a poor prognostic marker in stage II/III colorectal cancer, which may be due to its ability to promote cell migration and invasion, providing support for the further investigation of EphA2 as a novel prognostic biomarker and therapeutic target.
Collapse
Affiliation(s)
- Philip D Dunne
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Sonali Dasgupta
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Jaine K Blayney
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Darragh G McArt
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Keara L Redmond
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Jessica-Anne Weir
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Conor A Bradley
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Takehiko Sasazuki
- Institute for Advanced Study, Kyushu University, Fukuoka 812-8582, Higashi-ku, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-Ku, Fukuoka 814-0180, Japan
| | - Tingting Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Supriya Srivastava
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Chee Wee Ong
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Ken Arthur
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Richard H Wilson
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Patrick G Johnston
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| |
Collapse
|
12
|
Van Schaeybroeck S, Kalimutho M, Dunne PD, Carson R, Allen W, Jithesh PV, Redmond KL, Sasazuki T, Shirasawa S, Blayney J, Michieli P, Fenning C, Lenz HJ, Lawler M, Longley DB, Johnston PG. ADAM17-dependent c-MET-STAT3 signaling mediates resistance to MEK inhibitors in KRAS mutant colorectal cancer. Cell Rep 2014; 7:1940-55. [PMID: 24931611 DOI: 10.1016/j.celrep.2014.05.032] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [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: 08/24/2012] [Revised: 03/01/2014] [Accepted: 05/12/2014] [Indexed: 12/28/2022] Open
Abstract
There are currently no approved targeted therapies for advanced KRAS mutant (KRASMT) colorectal cancer (CRC). Using a unique systems biology approach, we identified JAK1/2-dependent activation of STAT3 as the key mediator of resistance to MEK inhibitors in KRASMT CRC in vitro and in vivo. Further analyses identified acute increases in c-MET activity following treatment with MEK inhibitors in KRASMT CRC models, which was demonstrated to promote JAK1/2-STAT3-mediated resistance. Furthermore, activation of c-MET following MEK inhibition was found to be due to inhibition of the ERK-dependent metalloprotease ADAM17, which normally inhibits c-MET signaling by promoting shedding of its endogenous antagonist, soluble "decoy" MET. Most importantly, pharmacological blockade of this resistance pathway with either c-MET or JAK1/2 inhibitors synergistically increased MEK-inhibitor-induced apoptosis and growth inhibition in vitro and in vivo in KRASMT models, providing clear rationales for the clinical assessment of these combinations in KRASMT CRC patients.
Collapse
Affiliation(s)
- Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Murugan Kalimutho
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Robbie Carson
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Wendy Allen
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Puthen V Jithesh
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Keara L Redmond
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Takehiko Sasazuki
- Institute for Advanced Study, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-Ku, Fukuoka 814-0180, Japan
| | - Jaine Blayney
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Paolo Michieli
- Laboratory of Experimental Therapy, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino 10060, Italy; Department of Oncology, University of Torino Medical School, Candiolo, Torino 10060, Italy
| | - Cathy Fenning
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Heinz-Josef Lenz
- Division of Medical Oncology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Daniel B Longley
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Patrick G Johnston
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK.
| |
Collapse
|
13
|
Majkut J, Sgobba M, Holohan C, Crawford N, Logan AE, Kerr E, Higgins CA, Redmond KL, Riley JS, Stasik I, Fennell DA, Van Schaeybroeck S, Haider S, Johnston PG, Haigh D, Longley DB. Differential affinity of FLIP and procaspase 8 for FADD's DED binding surfaces regulates DISC assembly. Nat Commun 2014; 5:3350. [PMID: 24577104 PMCID: PMC3942653 DOI: 10.1038/ncomms4350] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [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: 12/23/2013] [Accepted: 01/30/2014] [Indexed: 01/05/2023] Open
Abstract
Death receptor activation triggers recruitment of FADD, which via its death effector domain (DED) engages the DEDs of procaspase 8 and its inhibitor FLIP to form death-inducing signalling complexes (DISCs). The DEDs of FADD, FLIP and procaspase 8 interact with one another using two binding surfaces defined by α1/α4 and α2/α5 helices, respectively. Here we report that FLIP has preferential affinity for the α1/α4 surface of FADD, whereas procaspase 8 has preferential affinity for FADD's α2/α5 surface. These relative affinities contribute to FLIP being recruited to the DISC at comparable levels to procaspase 8 despite lower cellular expression. Additional studies, including assessment of DISC stoichiometry and functional assays, suggest that following death receptor recruitment, the FADD DED preferentially engages FLIP using its α1/α4 surface and procaspase 8 using its α2/α5 surface; these tripartite intermediates then interact via the α1/α4 surface of FLIP DED1 and the α2/α5 surface of procaspase 8 DED2.
Collapse
Affiliation(s)
- J Majkut
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - M Sgobba
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
- Now at Department of Bioengineering and Therapeutic Sciences, University of California
| | - C Holohan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - N Crawford
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - A E Logan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - E Kerr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - C A Higgins
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - K L Redmond
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - J S Riley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - I Stasik
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - D A Fennell
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
- Now at Cancer Studies and Molecular Medicine, University of Leicester, UK
| | - S Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - S Haider
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
- Now at School of Pharmacy, University College London
| | - P G Johnston
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - D Haigh
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - D B Longley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| |
Collapse
|