1
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Frei AL, McGuigan A, Sinha RRAK, Jabbar F, Gneo L, Tomasevic T, Harkin A, Iveson T, Saunders MP, Oien KA, Maka N, Pezzella F, Campo L, Browne M, Glaire M, Kildal W, Danielsen HE, Hay J, Edwards J, Sansom O, Kelly C, Tomlinson I, Kerr R, Kerr D, Domingo E, Church DN, Koelzer VH. Multiplex analysis of intratumoural immune infiltrate and prognosis in patients with stage II-III colorectal cancer from the SCOT and QUASAR 2 trials: a retrospective analysis. Lancet Oncol 2024; 25:198-211. [PMID: 38301689 DOI: 10.1016/s1470-2045(23)00560-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/19/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Tumour-infiltrating CD8+ cytotoxic T cells confer favourable prognosis in colorectal cancer. The added prognostic value of other infiltrating immune cells is unclear and so we sought to investigate their prognostic value in two large clinical trial cohorts. METHODS We used multiplex immunofluorescent staining of tissue microarrays to assess the densities of CD8+, CD20+, FoxP3+, and CD68+ cells in the intraepithelial and intrastromal compartments from tumour samples of patients with stage II-III colorectal cancer from the SCOT trial (ISRCTN59757862), which examined 3 months versus 6 months of adjuvant oxaliplatin-based chemotherapy, and from the QUASAR 2 trial (ISRCTN45133151), which compared adjuvant capecitabine with or without bevacizumab. Both trials included patients aged 18 years or older with an Eastern Cooperative Oncology Group performance status of 0-1. Immune marker predictors were analysed by multiple regression, and the prognostic and predictive values of markers for colorectal cancer recurrence-free interval by Cox regression were assessed using the SCOT cohort for discovery and QUASAR 2 cohort for validation. FINDINGS After exclusion of cases without tissue microarrays and with technical failures, and following quality control, we included 2340 cases from the SCOT trial and 1069 from the QUASAR 2 trial in our analysis. Univariable analysis of associations with recurrence-free interval in cases from the SCOT trial showed a strong prognostic value of intraepithelial CD8 (CD8IE) as a continuous variable (hazard ratio [HR] for 75th vs 25th percentile [75vs25] 0·73 [95% CI 0·68-0·79], p=2·5 × 10-16), and of intrastromal FoxP3 (FoxP3IS; 0·71 [0·64-0·78], p=1·5 × 10-13) but not as strongly in the epithelium (FoxP3IE; 0·89 [0·84-0·96], p=1·5 × 10-4). Associations of other markers with recurrence-free interval were moderate. CD8IE and FoxP3IS retained independent prognostic value in bivariable and multivariable analysis, and, compared with either marker alone, a composite marker including both markers (CD8IE-FoxP3IS) was superior when assessed as a continuous variable (adjusted [a]HR75 vs 25 0·70 [95% CI 0·63-0·78], p=5·1 × 10-11) and when categorised into low, intermediate, and high density groups using previously published cutpoints (aHR for intermediate vs high 1·68 [95% CI 1·29-2·20], p=1·3 × 10-4; low vs high 2·58 [1·91-3·49], p=7·9 × 10-10), with performance similar to the gold-standard Immunoscore. The prognostic value of CD8IE-FoxP3IS was confirmed in cases from the QUASAR 2 trial, both as a continuous variable (aHR75 vs 25 0·84 [95% CI 0·73-0·96], p=0·012) and as a categorical variable for low versus high density (aHR 1·80 [95% CI 1·17-2·75], p=0·0071) but not for intermediate versus high (1·30 [0·89-1·88], p=0·17). INTERPRETATION Combined evaluation of CD8IE and FoxP3IS could help to refine risk stratification in colorectal cancer. Investigation of FoxP3IS cells as an immunotherapy target in colorectal cancer might be merited. FUNDING Medical Research Council, National Institute for Health Research, Cancer Research UK, Swedish Cancer Society, Roche, and Promedica Foundation.
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Affiliation(s)
- Anja L Frei
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Life Science Zurich Graduate School, PhD Program in Biomedicine, University of Zurich, Zurich, Switzerland
| | - Anthony McGuigan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ritik R A K Sinha
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Faiz Jabbar
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luciana Gneo
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tijana Tomasevic
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrea Harkin
- Cancer Research UK Glasgow Clinical Trials Unit, University of Glasgow, Glasgow, UK
| | | | | | - Karin A Oien
- School of Cancer Sciences, University of Glasgow, Glasgow, UK; Glasgow Tissue Research Facility, University of Glasgow, Queen Elizabeth University Hospital, Glasgow, UK
| | - Noori Maka
- Glasgow Tissue Research Facility, University of Glasgow, Queen Elizabeth University Hospital, Glasgow, UK
| | - Francesco Pezzella
- Nuffield Division of Clinical and Laboratory Sciences, University of Oxford, Oxford, UK
| | - Leticia Campo
- Department of Oncology, University of Oxford, Oxford, UK
| | - Molly Browne
- Department of Oncology, University of Oxford, Oxford, UK
| | - Mark Glaire
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wanja Kildal
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Havard E Danielsen
- Nuffield Division of Clinical and Laboratory Sciences, University of Oxford, Oxford, UK; Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Jennifer Hay
- Glasgow Tissue Research Facility, University of Glasgow, Queen Elizabeth University Hospital, Glasgow, UK
| | - Joanne Edwards
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Owen Sansom
- School of Cancer Sciences, University of Glasgow, Glasgow, UK; Cancer Research UK Beatson Institute of Cancer Research, Glasgow, UK; Cancer Research UK Scotland Centre, Glasgow and Edinburgh, UK
| | - Caroline Kelly
- Cancer Research UK Glasgow Clinical Trials Unit, University of Glasgow, Glasgow, UK
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Nuffield Division of Clinical and Laboratory Sciences, University of Oxford, Oxford, UK
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, UK; Cancer Research UK Scotland Centre, Glasgow and Edinburgh, UK
| | - David N Church
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
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2
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Jiang D, Hveem TS, Glaire M, Church DN, Kerr DJ, Yang L, Danielsen HE. Automated assessment of CD8 + T-lymphocytes and stroma fractions complement conventional staging of colorectal cancer. EBioMedicine 2021; 71:103547. [PMID: 34479131 PMCID: PMC8411014 DOI: 10.1016/j.ebiom.2021.103547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/03/2021] [Revised: 07/18/2021] [Accepted: 08/08/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Tumor development is critically dependent on the supporting stroma consisting of inflammatory cells and fibroblasts. This study intended to improve prognostic prediction for early colorectal cancer (CRC) by combined estimation of T-lymphocyte and stroma fractions with conventional markers. METHODS In total 509 and 1041 stage II/ΙΙΙ CRC from the VICTOR and QUASAR 2 trials were included as a training set and a validation set, respectively. Intratumoral CD8+ T-lymphocytes and stroma were identified and quantified by machine-based learning on digital sections. The primary endpoint was to evaluate the prognostic value of the combined marker for time to recurrence (TTR). FINDINGS For low-risk patients (n = 598; stage Ⅱ, and stage ΙΙΙ pT1-3 pN1 with neither lymphatic (L-) nor vascular (V-) invasion), low stroma fraction (n = 511) identified a good prognostic subgroup with 5-year TTR of 86% (95% CI 83-89), versus the high stroma subgroup TTR of 78% (HR = 1.75, 95% CI 1.05-2.92; P = 0.029). For high-risk patients (n = 394; stage ΙΙΙ pT3 pN1 L+/V+, pT4, or pN2), combined low CD8+ and high stroma fraction identified a poor prognostic subgroup (n = 34) with 5-year TTR of 29% (95% CI 17-50), versus the high CD8+ fraction and low stroma fraction subgroup (n = 138) of 64% (HR = 2.86, 95% CI 1.75-4.69; P < 0.001). INTERPRETATION Quantification of intratumoral CD8+ T-lymphocyte and stroma fractions can be combined with conventional prognostic markers to improve patient stratification.
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Affiliation(s)
- Dan Jiang
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, Chengdu, China; Department of Pathology, West China Hospital, Sichuan University, Chengdu, China; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tarjei S Hveem
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Mark Glaire
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - David J Kerr
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, Chengdu, China; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Li Yang
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, Chengdu, China; Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Håvard E Danielsen
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom; Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway.
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3
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Workel HH, Lubbers JM, Arnold R, Prins TM, van der Vlies P, de Lange K, Bosse T, van Gool IC, Eggink FA, Wouters MCA, Komdeur FL, van der Slikke EC, Creutzberg CL, Kol A, Plat A, Glaire M, Church DN, Nijman HW, de Bruyn M. A Transcriptionally Distinct CXCL13 +CD103 +CD8 + T-cell Population Is Associated with B-cell Recruitment and Neoantigen Load in Human Cancer. Cancer Immunol Res 2019; 7:784-796. [PMID: 30872264 DOI: 10.1158/2326-6066.cir-18-0517] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/03/2018] [Accepted: 03/06/2019] [Indexed: 11/16/2022]
Abstract
The chemokine CXCL13 mediates recruitment of B cells to tumors and is essential for the formation of tertiary lymphoid structures (TLSs). TLSs are thought to support antitumor immunity and are associated with improved prognosis. However, it remains unknown whether TLSs are formed in response to the general inflammatory character of the tumor microenvironment, or rather, are induced by (neo)antigen-specific adaptive immunity. We here report on the finding that the TGFβ-dependent CD103+CD8+ tumor-infiltrating T-cell (TIL) subpopulation expressed and produced CXCL13. Accordingly, CD8+ T cells from peripheral blood activated in the presence of TGFβ upregulated CD103 and secreted CXCL13. Conversely, inhibition of TGFβ receptor signaling abrogated CXCL13 production. CXCL13+CD103+CD8+ TILs correlated with B-cell recruitment, TLSs, and neoantigen burden in six cohorts of human tumors. Altogether, our findings indicated that TGFβ plays a noncanonical role in coordinating immune responses against human tumors and suggest a potential role for CXCL13+CD103+CD8+ TILs in mediating B-cell recruitment and TLS formation in human tumors.
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Affiliation(s)
- Hagma H Workel
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Joyce M Lubbers
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Thalina M Prins
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Pieter van der Vlies
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Kim de Lange
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Inge C van Gool
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Florine A Eggink
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Maartje C A Wouters
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Fenne L Komdeur
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Elisabeth C van der Slikke
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Carien L Creutzberg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Arjan Kol
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Annechien Plat
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Mark Glaire
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics and Oxford Cancer Centre, University of Oxford, Oxford, United Kingdom
| | - David N Church
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics and Oxford Cancer Centre, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust and John Radcliffe Hospital, Oxford, United Kingdom
| | - Hans W Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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4
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Temko D, Van Gool IC, Rayner E, Glaire M, Makino S, Brown M, Chegwidden L, Palles C, Depreeuw J, Beggs A, Stathopoulou C, Mason J, Baker A, Williams M, Cerundolo V, Rei M, Taylor JC, Schuh A, Ahmed A, Amant F, Lambrechts D, Smit VTHBM, Bosse T, Graham TA, Church DN, Tomlinson I. Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response. J Pathol 2018; 245:283-296. [PMID: 29604063 PMCID: PMC6032922 DOI: 10.1002/path.5081] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [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: 10/23/2017] [Revised: 02/05/2018] [Accepted: 03/20/2018] [Indexed: 01/07/2023]
Abstract
Genomic instability, which is a hallmark of cancer, is generally thought to occur in the middle to late stages of tumourigenesis, following the acquisition of permissive molecular aberrations such as TP53 mutation or whole genome doubling. Tumours with somatic POLE exonuclease domain mutations are notable for their extreme genomic instability (their mutation burden is among the highest in human cancer), distinct mutational signature, lymphocytic infiltrate, and excellent prognosis. To what extent these characteristics are determined by the timing of POLE mutations in oncogenesis is unknown. Here, we have shown that pathogenic POLE mutations are detectable in non-malignant precursors of endometrial and colorectal cancer. Using genome and exome sequencing, we found that multiple driver mutations in POLE-mutant cancers show the characteristic POLE mutational signature, including those in genes conventionally regarded as initiators of tumourigenesis. In POLE-mutant cancers, the proportion of monoclonal predicted neoantigens was similar to that in other cancers, but the absolute number was much greater. We also found that the prominent CD8+ T-cell infiltrate present in POLE-mutant cancers was evident in their precursor lesions. Collectively, these data indicate that somatic POLE mutations are early, quite possibly initiating, events in the endometrial and colorectal cancers in which they occur. The resulting early onset of genomic instability may account for the striking immune response and excellent prognosis of these tumours, as well as their early presentation. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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MESH Headings
- Adenocarcinoma/enzymology
- Adenocarcinoma/genetics
- Adenocarcinoma/immunology
- Adenocarcinoma/pathology
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Colorectal Neoplasms/enzymology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/immunology
- Colorectal Neoplasms/pathology
- DNA Polymerase II/genetics
- DNA Polymerase II/metabolism
- Databases, Genetic
- Endometrial Neoplasms/enzymology
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/immunology
- Endometrial Neoplasms/pathology
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Male
- Middle Aged
- Mutation
- Neoplasm Grading
- Neoplasm Staging
- Phenotype
- Poly-ADP-Ribose Binding Proteins/genetics
- Poly-ADP-Ribose Binding Proteins/metabolism
- Tumor Microenvironment
- Whole Genome Sequencing
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Affiliation(s)
- Daniel Temko
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Maths and Physics in the Life Sciences and Experimental Biology (CoMPLEX)University College LondonLondonUK
- Department of Computer ScienceUniversity College LondonLondonUK
| | - Inge C Van Gool
- Department of PathologyLeiden University Medical CentreLeidenThe Netherlands
| | - Emily Rayner
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Mark Glaire
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Seiko Makino
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Matthew Brown
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Laura Chegwidden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Claire Palles
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Jeroen Depreeuw
- KU Leuven (University of Leuven), University Hospitals Leuven, Department of Obstetrics and GynaecologyDivision of Gynaecological OncologyLeuvenBelgium
- KU Leuven, Department of Human GeneticsLaboratory for Translational GeneticsLeuvenBelgium
- VIB Centre for Cancer BiologyLaboratory for Translational GeneticsLeuvenBelgium
| | - Andrew Beggs
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | | | - John Mason
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ann‐Marie Baker
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Marc Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Margarida Rei
- MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Jenny C Taylor
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Anna Schuh
- Department of OncologyUniversity of OxfordOxfordUK
| | - Ahmed Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Nuffield Department of Obstetrics & GynaecologyUniversity of OxfordOxfordUK
| | - Frédéric Amant
- Centre for Gynaecological Oncology AmsterdamNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Diether Lambrechts
- KU Leuven, Department of Human GeneticsLaboratory for Translational GeneticsLeuvenBelgium
- VIB Centre for Cancer BiologyLaboratory for Translational GeneticsLeuvenBelgium
| | - Vincent THBM Smit
- Department of PathologyLeiden University Medical CentreLeidenThe Netherlands
| | - Tjalling Bosse
- Department of PathologyLeiden University Medical CentreLeidenThe Netherlands
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - David N Church
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ian Tomlinson
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
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5
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Glaire M, Domingo E, Nicholson G, Novelli M, Lawson K, Oukrif D, Kidal W, Danielsen HE, Kerr R, Kerr DJ, Tomlinson I, Church DN. Tumour-infiltrating CD8 + lymphocytes as a prognostic marker in colorectal cancer: A retrospective, pooled analysis of the QUASAR2 and VICTOR trials. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mark Glaire
- University of Oxford, Oxford, United Kingdom
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - George Nicholson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Marco Novelli
- Department of Histopathology, UCL, London, United Kingdom
| | - Kay Lawson
- Department of Histopathology, UCL, London, United Kingdom
| | - Dahmane Oukrif
- Department of Histopathology, UCL, London, United Kingdom
| | - Wanja Kidal
- Institute for Cancer Genetics and Informatics, Oslo, Norway
| | - Havard Emil Danielsen
- Oslo University Hospital, Institute for Cancer Genetics and Informatics, Oslo, Norway
| | - Rachel Kerr
- University of Oxford, Oxford, United Kingdom
| | | | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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6
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Watt E, Gemmell MR, Berry S, Glaire M, Farquharson F, Louis P, Murray GI, El-Omar E, Hold GL. Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome 2016; 4:61. [PMID: 27884202 PMCID: PMC5123352 DOI: 10.1186/s40168-016-0207-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/07/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy. RESULTS Next-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types. CONCLUSIONS We propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.
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Affiliation(s)
- Euan Watt
- Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Matthew R. Gemmell
- Centre for Genome Enabled Biology and Medicine, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Susan Berry
- Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Mark Glaire
- Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Freda Farquharson
- Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Petra Louis
- Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Graeme I. Murray
- Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Emad El-Omar
- Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
- St George and Sutherland Clinical School, University of New South Wales, St George Hospital, Short Street, Kogarah, Sydney, NSW 2217 Australia
| | - Georgina L. Hold
- Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD UK
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7
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Domingo E, Freeman-Mills L, Rayner E, Glaire M, Briggs S, Vermeulen L, Fessler E, Medema JP, Boot A, Morreau H, van Wezel T, Liefers GJ, Lothe RA, Danielsen SA, Sveen A, Nesbakken A, Zlobec I, Lugli A, Koelzer VH, Berger MD, Castellví-Bel S, Muñoz J, de Bruyn M, Nijman HW, Novelli M, Lawson K, Oukrif D, Frangou E, Dutton P, Tejpar S, Delorenzi M, Kerr R, Kerr D, Tomlinson I, Church DN. Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study. Lancet Gastroenterol Hepatol 2016; 1:207-216. [PMID: 28404093 DOI: 10.1016/s2468-1253(16)30014-0] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Precision cancer medicine depends on defining distinct tumour subgroups using biomarkers that may occur at very modest frequencies. One such subgroup comprises patients with exceptionally mutated (ultramutated) cancers caused by mutations that impair DNA polymerase epsilon (POLE) proofreading. METHODS We examined the association of POLE proofreading domain mutation with clinicopathological variables and immune response in colorectal cancers from clinical trials (VICTOR, QUASAR2, and PETACC-3) and colorectal cancer cohorts (Leiden University Medical Centre 1 and 2, Oslo 1 and 2, Bern, AMC-AJCC-II, and Epicolon-1). We subsequently investigated its association with prognosis in stage II/III colorectal cancer by Cox regression of pooled individual patient data from more than 4500 cases from these studies. FINDINGS Pathogenic somatic POLE mutations were detected in 66 (1·0%) of 6517 colorectal cancers, and were mutually exclusive with mismatch repair deficiency (MMR-D) in the 6277 cases for whom both markers were determined (none of 66 vs 833 [13·4%] of 6211; p<0·0001). Compared with cases with wild-type POLE, cases with POLE mutations were younger at diagnosis (median 54·5 years vs 67·2 years; p<0·0001), were more frequently male (50 [75·8%] of 66 vs 3577 [55·5%] of 6445; p=0·0010), more frequently had right-sided tumour location (44 [68·8%] of 64 vs 2463 [39·8%] of 6193; p<0·0001), and were diagnosed at an earlier disease stage (p=0·006, χ2 test for trend). Compared with mismatch repair proficient (MMR-P) POLE wild-type tumours, POLE-mutant colorectal cancers displayed increased CD8+ lymphocyte infiltration and expression of cytotoxic T-cell markers and effector cytokines, similar in extent to that observed in immunogenic MMR-D cancers. Both POLE mutation and MMR-D were associated with significantly reduced risk of recurrence compared with MMR-P colorectal cancers in multivariable analysis (HR 0·34 [95% CI 0·11-0·76]; p=0·0060 and 0·72 [0·60-0·87]; p=0·00035), although the difference between the groups was not significant. INTERPRETATION POLE proofreading domain mutations identify a subset of immunogenic colorectal cancers with excellent prognosis. This association underscores the importance of rare biomarkers in precision cancer medicine, but also raises important questions about how to identify and implement them in practice. FUNDING Cancer Research UK, Academy of Medical Sciences, Health Foundation, EU, ERC, NIHR, Wellcome Trust, Dutch Cancer Society, Dutch Digestive Foundation.
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Affiliation(s)
- Enric Domingo
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
| | - Luke Freeman-Mills
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Emily Rayner
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Mark Glaire
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK
| | - Sarah Briggs
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Louis Vermeulen
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Evelyn Fessler
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Jan Paul Medema
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden, Netherlands
| | | | | | | | - Ragnhild A Lothe
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Stine A Danielsen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Gastrointestinal Surgery, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Institute of Pathology, University of Bern, Bern, Switzerland
| | - Martin D Berger
- Department of Medical Oncology, University Hospital of Bern, Bern, Switzerland
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hans W Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Kay Lawson
- Department of Histopathology, UCL, London, UK
| | | | - Eleni Frangou
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Peter Dutton
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sabine Tejpar
- Department of Molecular Digestive Oncology, University of Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute Bioinformatics, Lausanne, Switzerland
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK
| | - David Kerr
- Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David N Church
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK.
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8
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Worthley DL, Churchill M, Compton JT, Tailor Y, Rao M, Si Y, Levin D, Schwartz MG, Uygur A, Hayakawa Y, Gross S, Renz BW, Setlik W, Martinez AN, Chen X, Nizami S, Lee HG, Kang HP, Caldwell JM, Asfaha S, Westphalen CB, Graham T, Jin G, Nagar K, Wang H, Kheirbek MA, Kolhe A, Carpenter J, Glaire M, Nair A, Renders S, Manieri N, Muthupalani S, Fox JG, Reichert M, Giraud AS, Schwabe RF, Pradere JP, Walton K, Prakash A, Gumucio D, Rustgi AK, Stappenbeck TS, Friedman RA, Gershon MD, Sims P, Grikscheit T, Lee FY, Karsenty G, Mukherjee S, Wang TC. Gremlin 1 identifies a skeletal stem cell with bone, cartilage, and reticular stromal potential. Cell 2015; 160:269-84. [PMID: 25594183 DOI: 10.1016/j.cell.2014.11.042] [Citation(s) in RCA: 470] [Impact Index Per Article: 52.2] [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: 05/27/2014] [Revised: 09/09/2014] [Accepted: 11/12/2014] [Indexed: 12/14/2022]
Abstract
The stem cells that maintain and repair the postnatal skeleton remain undefined. One model suggests that perisinusoidal mesenchymal stem cells (MSCs) give rise to osteoblasts, chondrocytes, marrow stromal cells, and adipocytes, although the existence of these cells has not been proven through fate-mapping experiments. We demonstrate here that expression of the bone morphogenetic protein (BMP) antagonist gremlin 1 defines a population of osteochondroreticular (OCR) stem cells in the bone marrow. OCR stem cells self-renew and generate osteoblasts, chondrocytes, and reticular marrow stromal cells, but not adipocytes. OCR stem cells are concentrated within the metaphysis of long bones not in the perisinusoidal space and are needed for bone development, bone remodeling, and fracture repair. Grem1 expression also identifies intestinal reticular stem cells (iRSCs) that are cells of origin for the periepithelial intestinal mesenchymal sheath. Grem1 expression identifies distinct connective tissue stem cells in both the bone (OCR stem cells) and the intestine (iRSCs).
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Affiliation(s)
- Daniel L Worthley
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA; Department of Medicine, University of Adelaide, SA, 5005, Australia; Cancer theme, South Australian Health and Medical Research Institute, SA, 5001, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Vic., 3052, Australia
| | - Michael Churchill
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Jocelyn T Compton
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Yagnesh Tailor
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Meenakshi Rao
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Yiling Si
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Daniel Levin
- Children's Hospital Los Angeles, Saban Research Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90027, USA
| | | | - Aysu Uygur
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Yoku Hayakawa
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Stefanie Gross
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Bernhard W Renz
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Wanda Setlik
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Ashley N Martinez
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiaowei Chen
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Saqib Nizami
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Heon Goo Lee
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - H Paco Kang
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Jon-Michael Caldwell
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Samuel Asfaha
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - C Benedikt Westphalen
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA; Department of Internal Medicine III, University Hospital Munich, Ludwig-Maximilians-University Munich - Campus Groβhadern, Munich 81377, Germany
| | - Trevor Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Guangchun Jin
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Karan Nagar
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Hongshan Wang
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Mazen A Kheirbek
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
| | - Alka Kolhe
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Jared Carpenter
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Mark Glaire
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Abhinav Nair
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Simon Renders
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Nicholas Manieri
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Sureshkumar Muthupalani
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maximilian Reichert
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Andrew S Giraud
- Murdoch Children's Research Institute, Royal Children's Hospital, Vic., 3052, Australia
| | - Robert F Schwabe
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA
| | - Jean-Phillipe Pradere
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA; Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paul Sabatier, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC)- UMR1048, Toulouse 31432, France
| | - Katherine Walton
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ajay Prakash
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah Gumucio
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Richard A Friedman
- Herbert Irving Comprehensive Cancer Center Biomedical Informatics Shared Resource and Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Michael D Gershon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Peter Sims
- Department of Systems Biology, Columbia University, NY, 10032, USA
| | - Tracy Grikscheit
- Children's Hospital Los Angeles, Saban Research Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90027, USA
| | - Francis Y Lee
- Department of Orthopedic Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Gerard Karsenty
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Siddhartha Mukherjee
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA.
| | - Timothy C Wang
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY 10032, USA.
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