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Mouillet-Richard S, Cazelles A, Sroussi M, Gallois C, Taieb J, Laurent-Puig P. Clinical Challenges of Consensus Molecular Subtype CMS4 Colon Cancer in the Era of Precision Medicine. Clin Cancer Res 2024; 30:2351-2358. [PMID: 38564259 PMCID: PMC11145159 DOI: 10.1158/1078-0432.ccr-23-3964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Over the past decade, our understanding of the diversity of colorectal cancer has expanded significantly, raising hopes of tailoring treatments more precisely for individual patients. A key achievement in this direction was the establishment of the consensus molecular classification, particularly identifying the challenging consensus molecular subtype (CMS) CMS4 associated with poor prognosis. Because of its aggressive nature, extensive research is dedicated to the CMS4 subgroup. Recent years have unveiled molecular and microenvironmental features at the tissue level specific to CMS4 colorectal cancer. This has paved the way for mechanistic studies and the development of preclinical models. Simultaneously, efforts have been made to easily identify patients with CMS4 colorectal cancer. Reassessing clinical trial results through the CMS classification lens has improved our understanding of the therapeutic challenges linked to this subtype. Exploration of the biology of CMS4 colorectal cancer is yielding potential biomarkers and novel treatment approaches. This overview aims to provide insights into the clinico-biological characteristics of the CMS4 subgroup, the molecular pathways driving this subtype, and available diagnostic options. We also emphasize the therapeutic challenges associated with this subtype, offering potential explanations. Finally, we summarize the current tailored treatments for CMS4 colorectal cancer emerging from fundamental and preclinical studies.
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Affiliation(s)
- Sophie Mouillet-Richard
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Antoine Cazelles
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Marine Sroussi
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Claire Gallois
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Julien Taieb
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Pierre Laurent-Puig
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Department of Biology, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
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Cañellas-Socias A, Sancho E, Batlle E. Mechanisms of metastatic colorectal cancer. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00934-z. [PMID: 38806657 DOI: 10.1038/s41575-024-00934-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Despite extensive research and improvements in understanding colorectal cancer (CRC), its metastatic form continues to pose a substantial challenge, primarily owing to limited therapeutic options and a poor prognosis. This Review addresses the emerging focus on metastatic CRC (mCRC), which has historically been under-studied compared with primary CRC despite its lethality. We delve into two crucial aspects: the molecular and cellular determinants facilitating CRC metastasis and the principles guiding the evolution of metastatic disease. Initially, we examine the genetic alterations integral to CRC metastasis, connecting them to clinically marked characteristics of advanced CRC. Subsequently, we scrutinize the role of cellular heterogeneity and plasticity in metastatic spread and therapy resistance. Finally, we explore how the tumour microenvironment influences metastatic disease, emphasizing the effect of stromal gene programmes and the immune context. The ongoing research in these fields holds immense importance, as its future implications are projected to revolutionize the treatment of patients with mCRC, hopefully offering a promising outlook for their survival.
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Affiliation(s)
- Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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3
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Luo Q, Quan Y, Liu W, Wu Z, Qiu W, Liang W, Yang P, Huang Q, Li G, Wei J, Wang Q, Shen F, Li W, He F, Cao J. Seed and Soil: Consensus Molecular Subgroups (CMS) and Tumor Microenvironment Features Between Primary Lesions and Metastases of Different Organ Sites in Colorectal Cancer. Cancer Manag Res 2024; 16:225-243. [PMID: 38525373 PMCID: PMC10961079 DOI: 10.2147/cmar.s441675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Purpose Consensus molecular subtypes (CMS) are mainly used for biological interpretability and clinical stratification of colorectal cancer (CRC) in primary tumors (PT) but few in metastases. The heterogeneity of CMS distribution in metastases and the concordance of CMS between PT and metastases still lack sufficient study. We used CMS to classify CRC metastases and combine it with histopathological analysis to explore differences between PT and distant metastases. Patients and Methods We obtained gene expression profiles for 942 PT samples from TCGA database (n=376) and GEO database (n=566), as well as 442 metastasis samples from GEO database. Among these, 765 PT samples and 442 metastasis samples were confidently identified with CMS using the "CMS classifier" and enrolled for analysis. Clinicopathological manifestation and CMS classification of CRC metastases were assessed with data from GEO, TCGA, and cBioPortal. Overall, 105 PT-metastasis pairs were extracted from 10 GEO datasets to assess CMS concordance. Tumor microenvironment (TME) features between PT and metastases were analyzed by immune-stromal infiltration with ESTIMATE and xCell algorithms. Finally, TME features were validated with multiplex immunohistochemistry in 27 PT-metastasis pairs we retrospectively collected. Results Up to 64% of CRC metastases exhibited concordant CMS groups with matched PT, and the TME of metastases was similar to that of PT. For most common distant metastases, liver metastases were predominantly CMS2 and lung and peritoneal metastases were mainly CMS4, highlighting "seed" of tumor cells of different CMS groups had a preference for metastasis to "soil" of specific organs. Compared with PT, cancer-associated fibroblasts (CAF) reduced in liver metastases, CD4+T cells and M2-like macrophages increased in lung metastases, and M2-like macrophages and CAF increased in peritoneal metastases. Conclusion Our findings underscore the importance of CMS-guided specific organ monitoring and treatment post-primary tumor surgery for patients. Differences in immune-stromal infiltration among different metastases provide targeted therapeutic opportunities for metastatic CRC.
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Affiliation(s)
- Qingqing Luo
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Yibo Quan
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Wei Liu
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Zixin Wu
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Wenjing Qiu
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Wenlong Liang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Ping Yang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Qing Huang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Guanwei Li
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Jianchang Wei
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Qiang Wang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Fei Shen
- Department of Thyroid Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Wanglin Li
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Feng He
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
| | - Jie Cao
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People’s Republic of China
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Oliveres H, Cascante M, Maurel J. Metabolic interventions to enhance immunotherapy and targeted therapy efficacy in advanced colorectal cancer. Curr Opin Chem Biol 2023; 77:102401. [PMID: 37806262 DOI: 10.1016/j.cbpa.2023.102401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/25/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Current standard-of-care for metastatic colorectal cancer patients includes chemotherapy and anti-angiogenic or anti-epidermal growth factor receptor for microsatellite stable tumors and pembrolizumab for microsatellite instable tumors. However, despite the available therapies, the prognosis remains poor. In recent years, new drugs combined with immune checkpoint inhibitors have been tested in microsatellite stable metastatic colorectal cancer patients, but the benefit was modest. Here, we review the metabolic interactions between the immune microenvironment and cancer cells. More specifically, we highlight potential correlatives of tumor immune and metabolic features with transcriptomic classifications such as the Consensus Molecular Subtype. Finally, we discuss the unmet need of immune-metabolic signatures and the value of a new signature (IMMETCOLS) for guiding new strategies in metastatic colorectal cancer. We conclude that the field is ready to propose customized strategies for modifying metabolism and improving immunotherapy and targeted therapy efficacy.
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Affiliation(s)
- Helena Oliveres
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, Barcelona, Spain
| | - Marta Cascante
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain; Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Universitat de Barcelona, Barcelona, Spain.
| | - Joan Maurel
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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5
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Taraborrelli L, Şenbabaoğlu Y, Wang L, Lim J, Blake K, Kljavin N, Gierke S, Scherl A, Ziai J, McNamara E, Owyong M, Rao S, Calviello AK, Oreper D, Jhunjhunwala S, Argiles G, Bendell J, Kim TW, Ciardiello F, Wongchenko MJ, de Sauvage FJ, de Sousa E Melo F, Yan Y, West NR, Murthy A. Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer. Nat Commun 2023; 14:5945. [PMID: 37741832 PMCID: PMC10517947 DOI: 10.1038/s41467-023-41618-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Microsatellite-stable colorectal cancer (MSS-CRC) is highly refractory to immunotherapy. Understanding tumor-intrinsic determinants of immunotherapy resistance is critical to improve MSS-CRC patient outcomes. Here, we demonstrate that high tumor expression of the core autophagy gene ATG16L1 is associated with poor clinical response to anti-PD-L1 therapy in KRAS-mutant tumors from IMblaze370 (NCT02788279), a large phase III clinical trial of atezolizumab (anti-PD-L1) in advanced metastatic MSS-CRC. Deletion of Atg16l1 in engineered murine colon cancer organoids inhibits tumor growth in primary (colon) and metastatic (liver and lung) niches in syngeneic female hosts, primarily due to increased sensitivity to IFN-γ-mediated immune pressure. ATG16L1 deficiency enhances programmed cell death of colon cancer organoids induced by IFN-γ and TNF, thus increasing their sensitivity to host immunity. In parallel, ATG16L1 deficiency reduces tumor stem-like populations in vivo independently of adaptive immune pressure. This work reveals autophagy as a clinically relevant mechanism of immune evasion and tumor fitness in MSS-CRC and provides a rationale for autophagy inhibition to boost immunotherapy responses in the clinic.
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Affiliation(s)
- Lucia Taraborrelli
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Yasin Şenbabaoğlu
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Lifen Wang
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Junghyun Lim
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Kerrigan Blake
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Noelyn Kljavin
- Department of Molecular Oncology, Genentech Inc., South San Francisco, USA
| | - Sarah Gierke
- Center for Advanced Light Microscopy, Genentech Inc., South San Francisco, USA
- Department of Pathology, Genentech Inc., South San Francisco, USA
| | - Alexis Scherl
- Department of Pathology, Genentech Inc., South San Francisco, USA
| | - James Ziai
- Department of Pathology, Genentech Inc., South San Francisco, USA
| | - Erin McNamara
- Department of In Vivo Pharmacology, Genentech Inc., South San Francisco, USA
| | - Mark Owyong
- Department of In Vivo Pharmacology, Genentech Inc., South San Francisco, USA
| | - Shilpa Rao
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | | | - Daniel Oreper
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Suchit Jhunjhunwala
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Guillem Argiles
- Vall d'Hebrón Institute of Oncology, Vall d'Hebrón University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Johanna Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, TN, USA
| | - Tae Won Kim
- Department of Oncology, Medical Center, University of Ulsan, Seoul, Korea
| | - Fortunato Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | | | | | | | - Yibing Yan
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Nathaniel R West
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA.
| | - Aditya Murthy
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA.
- Gilead Sciences, Foster City, USA.
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6
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Gao H, Ma L, Zou Q, Hu B, Cai K, Sun Y, Lu L, Ren D. Unraveling dynamic interactions between tumor-associated macrophages and consensus molecular subtypes in colorectal cancer: An integrative analysis of single-cell and bulk RNA transcriptome. Heliyon 2023; 9:e19224. [PMID: 37662758 PMCID: PMC10470276 DOI: 10.1016/j.heliyon.2023.e19224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Background Accumulating research substantiated that tumor-associated macrophages (TAMs) have a significant impact on the tumorigenesis, progression, and distant metastasis, representing a novel target for various cancers. However, the underlying dynamic changes and interactions between TAMs and tumor cells remain largely elusive in colorectal cancer (CRC). Methods We depicted the dynamic changes of macrophages using sing-cell RNA-seq data and extracted TAM differentiation-related genes. Next, we utilized the weighted gene co-expression network analysis (WGCNA) to acquire CMS-related modular genes using bulk RNA-seq data. Finally, we utilized univariate Cox and Lasso Cox regression analyses to identify TAM differentiation-related biomarkers and established a novel risk signature model. We employed quantitative real-time polymerase chain reaction (qRT-PCR) on CRC tissue samples and used immunohistochemistry (IHC) data frome the HPA database to validate the mRNA and protein expression of prognostic genes. The interaction of TAMs and each consensus molecular subtype (CMS) subpopulation was analyzed at the cellular level. Results A total of 47,285 cells from single-cell dataset and 1197 CRC patients from bulk dataset were obtained. Among those, 6400 myeloid cells were re-clustered and annotated. RNASE1, F13A1, DAPK1, CLEC10A, RPN2, REG4 and RGS19 were identified as prognostic genes and the risk signature model was established based on the above genes. The qRT-PCR analysis indicated that the expression of RNASE1 and DAPK1 were significantly up-regulated in CRC tumor tissues. The cell-cell communication analysis demonstrated complex interactions between TAMs and CMS malignant cell subpopulations. Conclusion This study presents an in-depth dissection of the dynamic features of TAMs in the tumor microenvironment and provides promising therapeutic targets for CRC.
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Affiliation(s)
- Han Gao
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Linyun Ma
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qi Zou
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bang Hu
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Keyu Cai
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yi Sun
- Kingmed Pathology Center, Guangzhou, China
| | - Li Lu
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Donglin Ren
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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7
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Ruff SM, Shannon AH, Pawlik TM. The Role of Targeted Therapy in the Multi-Disciplinary Approach to Colorectal Liver Metastasis. Cancers (Basel) 2023; 15:3513. [PMID: 37444625 DOI: 10.3390/cancers15133513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related mortality in the United States. Among newly diagnosed patients with CRC, 20% will present with metastatic disease and another 25% will develop metastases. The surgical resection of the primary tumor and metastatic disease sites confers the best chance at long-term survival. Unfortunately, many patients will recur after resection or present with unresectable disease. As such, metastatic CRC is commonly treated with a combination of surgery, systemic therapy, and/or liver-directed therapies. Despite best efforts, 5-year survival for unresectable metastatic CRC is only about 20%. CRC is a heterogeneous disease and the underlying genetic differences inform behavior, treatment strategy, and prognosis. Given the limitations of cytotoxic chemotherapy and the growing role of molecular profiling, research has focused on identifying and developing targeted therapies. We herein review how genetic profiling informs prognosis, crucial cell-signaling pathways that play a role in CRC carcinogenesis, and currently approved targeted therapies for metastatic CRC.
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Affiliation(s)
- Samantha M Ruff
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Alexander H Shannon
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Timothy M Pawlik
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA
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Zaharia C, Veen T, Lea D, Kanani A, Alexeeva M, Søreide K. Histopathological Growth Pattern in Colorectal Liver Metastasis and The Tumor Immune Microenvironment. Cancers (Basel) 2022; 15:cancers15010181. [PMID: 36612177 PMCID: PMC9818232 DOI: 10.3390/cancers15010181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Almost half of all patients with colorectal cancer present with or eventually develop metastasis, most frequently in the liver. Understanding the histopathological growth patterns and tumor immune microenvironment of colorectal liver metastases may help determine treatment strategies and assess prognosis. A literature search was conducted to gather information on cancer biology, histopathological growth patterns, and the tumor immune microenvironment in colorectal liver metastases, including their mechanisms and their impact on clinical outcomes. A first consensus on histopathological growth patterns emerged in 2017, identifying five growth patterns. Later studies found benefits from a two-tier system, desmoplastic and non-desmoplastic, incorporated into the updated 2022 consensus. Furthermore, the tumor immune microenvironment shows additional characteristic features with relevance to cancer biology. This includes density of T-cells (CD8+), expression of claudin-2, presence of vessel co-option versus angiogenesis, as well as several other factors. The relation between histopathological growth patterns and the tumor immune microenvironment delineates distinct subtypes of cancer biology. The distinct subtypes are found to correlate with risk of metastasis or relapse, and hence to clinical outcome and long-term survival in each patient. In order to optimize personalized and precision therapy for patients with colorectal liver metastases, further investigation into the mechanisms of cancer biology and their translational aspects to novel treatment targets is warranted.
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Affiliation(s)
- Claudia Zaharia
- Department of Pathology, Stavanger University Hospital, N-4068 Stavanger, Norway
- Gastrointestinal Translational Research Group, Laboratory for Molecular Medicine, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Torhild Veen
- Gastrointestinal Translational Research Group, Laboratory for Molecular Medicine, Stavanger University Hospital, N-4068 Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Dordi Lea
- Department of Pathology, Stavanger University Hospital, N-4068 Stavanger, Norway
- Gastrointestinal Translational Research Group, Laboratory for Molecular Medicine, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Arezo Kanani
- Gastrointestinal Translational Research Group, Laboratory for Molecular Medicine, Stavanger University Hospital, N-4068 Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Marina Alexeeva
- Gastrointestinal Translational Research Group, Laboratory for Molecular Medicine, Stavanger University Hospital, N-4068 Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Group, Laboratory for Molecular Medicine, Stavanger University Hospital, N-4068 Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, N-4068 Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, N-7804 Bergen, Norway
- Correspondence:
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9
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Brunac AC, Fourquet J, Perot G, Jaffrelot M, Meilleroux J, Danjoux M, Filleron T, Nicolaï V, Guimbaud R, Icher S, Farés N, Selves J, Chibon F. CINSARC signature outperforms gold-standard TNM staging and consensus molecular subtypes for clinical outcome in stage II-III colorectal carcinoma. Mod Pathol 2022; 35:2002-2010. [PMID: 36202996 DOI: 10.1038/s41379-022-01166-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]
Abstract
The outcome of stage II-III colorectal cancer (CRC) is highly variable and therapeutic choice is currently based on TNM staging with a few additional biomarkers. However, studies show that some stage III patients have a better prognosis than some stage II patients. A promising consensus molecular (CMS) classification with prognostic relevance has been developed, but it is not used in daily practice. Our team developed CINSARC, a 67-gene expression prognostic signature, whose prognostic value has been demonstrated in many cancer types. It is applicable to formalin-fixed, paraffin-embedded (FFPE) blocks using NanoString® technology. We investigated whether it could predict outcome in stage II-III CRC. We established the CINSARC classification on the TCGA retrospective cohort comprising 297 stage II-III CRC patients using RNA sequencing and on a second independent cohort comprising 169 cases using NanoString® technology. We compared its recurrence-free and overall survival prognostic value with TNM staging and CMS classification. In the TCGA cohort, we showed that CINSARC significantly splits the population of stage II-III CRC into two groups with different progression-free interval (P = 1.68 × 10-2; HR = 1.87 [1.11-3.16]) and overall survival (P = 3.73 × 10-3; HR = 2.45 [1.31-4.59]) and is a strong prognostic factor in multivariate analysis, outperforming TNM staging and CMS classification. We validated these results in the second cohort by applying CINSARC on FFPE samples with Nanostring® technology. CINSARC is a ready-to-use tool with a robust independent prognostic value in stage II-III CRC.
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Affiliation(s)
- Anne-Cécile Brunac
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Joanna Fourquet
- Oncogenesis of Sarcomas, INSERM UMR1037, Cancer Research Centre of Toulouse, Toulouse, France
| | - Gaëlle Perot
- Oncogenesis of Sarcomas, INSERM UMR1037, Cancer Research Centre of Toulouse, Toulouse, France
| | - Marion Jaffrelot
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Julie Meilleroux
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Marie Danjoux
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Thomas Filleron
- Department of Biostatistics, Institut Claudius-Regaud, Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
| | - Vincent Nicolaï
- Department of Medical Oncology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Rosine Guimbaud
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Samira Icher
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Nadim Farés
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Janick Selves
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Frédéric Chibon
- Oncogenesis of Sarcomas, INSERM UMR1037, Cancer Research Centre of Toulouse, Toulouse, France.
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10
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Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development. Commun Biol 2022; 5:937. [PMID: 36085309 PMCID: PMC9463147 DOI: 10.1038/s42003-022-03884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractColorectal cancer (CRC) is a highly diverse disease, where different genomic instability pathways shape genetic clonal diversity and tumor microenvironment. Although intra-tumor heterogeneity has been characterized in primary tumors, its origin and consequences in CRC outcome is not fully understood. Therefore, we assessed intra- and inter-tumor heterogeneity of a prospective cohort of 136 CRC samples. We demonstrate that CRC diversity is forged by asynchronous forms of molecular alterations, where mutational and chromosomal instability collectively boost CRC genetic and microenvironment intra-tumor heterogeneity. We were able to depict predictor signatures of cancer-related genes that can foresee heterogeneity levels across the different tumor consensus molecular subtypes (CMS) and primary tumor location. Finally, we show that high genetic and microenvironment heterogeneity are associated with lower metastatic potential, whereas late-emerging copy number variations favor metastasis development and polyclonal seeding. This study provides an exhaustive portrait of the interplay between genetic and microenvironment intra-tumor heterogeneity across CMS subtypes, depicting molecular events with predictive value of CRC progression and metastasis development.
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11
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Peters NA, Constantinides A, Ubink I, van Kuik J, Bloemendal HJ, van Dodewaard JM, Brink MA, Schwartz TP, Lolkema MP, Lacle MM, Moons LM, Geesing J, van Grevenstein WM, Roodhart JML, Koopman M, Elias SG, Borel Rinkes IH, Kranenburg O. Consensus molecular subtype 4 (CMS4)-targeted therapy in primary colon cancer: A proof-of-concept study. Front Oncol 2022; 12:969855. [PMID: 36147916 PMCID: PMC9486194 DOI: 10.3389/fonc.2022.969855] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMesenchymal Consensus Molecular Subtype 4 (CMS4) colon cancer is associated with poor prognosis and therapy resistance. In this proof-of-concept study, we assessed whether a rationally chosen drug could mitigate the distinguishing molecular features of primary CMS4 colon cancer.MethodsIn the ImPACCT trial, informed consent was obtained for molecular subtyping at initial diagnosis of colon cancer using a validated RT-qPCR CMS4-test on three biopsies per tumor (Phase-1, n=69 patients), and for neoadjuvant CMS4-targeting therapy with imatinib (Phase-2, n=5). Pre- and post-treatment tumor biopsies were analyzed by RNA-sequencing and immunohistochemistry. Imatinib-induced gene expression changes were associated with molecular subtypes and survival in an independent cohort of 3232 primary colon cancer.ResultsThe CMS4-test classified 52/172 biopsies as CMS4 (30%). Five patients consented to imatinib treatment prior to surgery, yielding 15 pre- and 15 post-treatment samples for molecular analysis. Imatinib treatment caused significant suppression of mesenchymal genes and upregulation of genes encoding epithelial junctions. The gene expression changes induced by imatinib were associated with improved survival and a shift from CMS4 to CMS2.ConclusionImatinib may have value as a CMS-switching drug in primary colon cancer and induces a gene expression program that is associated with improved survival.
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Affiliation(s)
- Niek A. Peters
- Lab Translational Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Alexander Constantinides
- Lab Translational Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Inge Ubink
- Lab Translational Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Joyce van Kuik
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Haiko J. Bloemendal
- Department of Internal Medicine, Meander Medical Center, Amersfoort, Netherlands
- Department of Internal Medicine/Oncology, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | | | - Menno A. Brink
- Department of Gastroenterology, Meander Medical Center, Amersfoort, Netherlands
| | - Thijs P. Schwartz
- Department of Gastroenterology, Meander Medical Center, Amersfoort, Netherlands
| | | | - Miangela M. Lacle
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Leon M. Moons
- Department of Gastroenterology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Joost Geesing
- Department of Gastroenterology, Diakonessenhuis, Utrecht, Netherlands
| | - Wilhelmina M.U. van Grevenstein
- Department of Surgical Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jeanine M. L. Roodhart
- Lab Translational Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Sjoerd G. Elias
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Inne H.M. Borel Rinkes
- Lab Translational Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Surgical Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Inne H.M. Borel Rinkes, ; Onno Kranenburg,
| | - Onno Kranenburg
- Lab Translational Oncology, Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Inne H.M. Borel Rinkes, ; Onno Kranenburg,
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12
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Martelli V, Pastorino A, Sobrero AF. Prognostic and predictive molecular biomarkers in advanced colorectal cancer. Pharmacol Ther 2022; 236:108239. [PMID: 35780916 DOI: 10.1016/j.pharmthera.2022.108239] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
The revolution of precision medicine has produced unprecedented seismic shifts in the treatment paradigm of advanced cancers. Among the major killers, colorectal cancer (CRC) is far behind the others. In fact, the great successes obtained in breast, NSCLC, melanoma, and genitourinary tract tumors have been observed only in fewer than 5 % metastatic colorectal cancer (mCRC): those with the mismatch repair deficiency (dMMR), a well-known predictive factor for to the outstanding efficacy of checkpoint inhibitors (CPI). The treatment of the remaining vast majority mCRC patients is still based upon only two molecular determinants: the RAS and BRAF mutational status. New promising biomarkers include HER2, tumor mutational burden (TMB) for its possible implications on CPI efficacy, and the extremely rare NTRK fusions. The Consensus Molecular Subtypes classification (CMS) is a good example of the efforts to combine different molecular features of this disease, although its relevance in clinical practice is still under investigation. In this Review, we focus on all these prognostic and predictive biomarkers, analyzing data from the most important clinical trials of the last years. We also try to rank them according to their prognostic and predictive power.
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Affiliation(s)
- Valentino Martelli
- Medical Oncology Unit 1, Ospedale Policlinico San Martino - IRCCS, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Alessandro Pastorino
- Medical Oncology Unit 1, Ospedale Policlinico San Martino - IRCCS, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Alberto F Sobrero
- Medical Oncology Unit 1, Ospedale Policlinico San Martino - IRCCS, Largo Rosanna Benzi 10, 16132 Genoa, Italy.
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13
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Emons G, Auslander N, Jo P, Kitz J, Azizian A, Hu Y, Hess CF, Roedel C, Sax U, Salinas G, Stroebel P, Kramer F, Beissbarth T, Grade M, Ghadimi M, Ruppin E, Ried T, Gaedcke J. Gene-expression profiles of pretreatment biopsies predict complete response of rectal cancer patients to preoperative chemoradiotherapy. Br J Cancer 2022; 127:766-775. [PMID: 35597871 PMCID: PMC9381580 DOI: 10.1038/s41416-022-01842-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/19/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Preoperative (neoadjuvant) chemoradiotherapy (CRT) and total mesorectal excision is the standard treatment for rectal cancer patients (UICC stage II/III). Up to one-third of patients treated with CRT achieve a pathological complete response (pCR). These patients could be spared from surgery and its associated morbidity and mortality, and assigned to a “watch and wait” strategy. However, reliably identifying pCR based on clinical or imaging parameters remains challenging. Experimental design We generated gene-expression profiles of 175 patients with locally advanced rectal cancer enrolled in the CAO/ARO/AIO-94 and -04 trials. One hundred and sixty-one samples were used for building, training and validating a predictor of pCR using a machine learning algorithm. The performance of the classifier was validated in three independent cohorts, comprising 76 patients from (i) the CAO/ARO/AIO-94 and -04 trials (n = 14), (ii) a publicly available dataset (n = 38) and (iii) in 24 prospectively collected samples from the TransValid A trial. Results A 21-transcript signature yielded the best classification of pCR in 161 patients (Sensitivity: 0.31; AUC: 0.81), when not allowing misclassification of non-complete-responders (False-positive rate = 0). The classifier remained robust when applied to three independent datasets (n = 76). Conclusion The classifier can identify >1/3 of rectal cancer patients with a pCR while never classifying patients with an incomplete response as having pCR. Importantly, we could validate this finding in three independent datasets, including a prospectively collected cohort. Therefore, this classifier could help select rectal cancer patients for a “watch and wait” strategy. Translational relevance Forgoing surgery with its associated side effects could be an option for rectal cancer patients if the prediction of a pathological complete response (pCR) after preoperative chemoradiotherapy would be possible. Based on gene-expression profiles of 161 patients a classifier was developed and validated in three independent datasets (n = 76), identifying over 1/3 of patients with pCR, while never misclassifying a non-complete-responder. Therefore, the classifier can identify patients suited for “watch and wait”.
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Affiliation(s)
- Georg Emons
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Noam Auslander
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, USA
| | - Peter Jo
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Julia Kitz
- Department of Pathology, University Medical Center, Göttingen, Germany
| | - Azadeh Azizian
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Yue Hu
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clemens F Hess
- Department of Radiotherapy and Radio-oncology, University Medical Center, Göttingen, Germany
| | - Claus Roedel
- Department of Radiation Oncology, University Hospital Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Ulrich Sax
- Department of Medical Informatics, University Medical Center, Göttingen, Germany
| | - Gabriela Salinas
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Philipp Stroebel
- Department of Pathology, University Medical Center, Göttingen, Germany
| | - Frank Kramer
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - Tim Beissbarth
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Ried
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany.
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14
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Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG, Govekar HR, Kam AE, Reiser J, Turaga K, Radovich M, Zang Y, Qiu Y, Liu Y, Fishel ML, Turk A, Gupta V, Al-Sabti R, Subramanian J, Kuzel TM, Sadanandam A, Waldron L, Hussain A, Saleem M, El-Rayes B, Salahudeen AA, Masood A. Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biol 2022; 23:113. [PMID: 35538548 PMCID: PMC9092724 DOI: 10.1186/s13059-022-02677-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/21/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironments is required to elucidate mechanisms of tumor and stroma cell contributions to pathogenesis which may advance subtype-specific therapeutic development. We interrogate racially diverse human CRC samples and analyze multiple independent external cohorts for a total of 487,829 single cells enabling high-resolution depiction of the cellular diversity and heterogeneity within the tumor and microenvironmental cells. RESULTS Tumor cells recapitulate individual CMS subgroups yet exhibit significant intratumoral CMS heterogeneity. Both CMS1 microsatellite instability (MSI-H) CRCs and microsatellite stable (MSS) CRC demonstrate similar pathway activations at the tumor epithelial level. However, CD8+ cytotoxic T cell phenotype infiltration in MSI-H CRCs may explain why these tumors respond to immune checkpoint inhibitors. Cellular transcriptomic profiles in CRC exist in a tumor immune stromal continuum in contrast to discrete subtypes proposed by studies utilizing bulk transcriptomics. We note a dichotomy in tumor microenvironments across CMS subgroups exists by which patients with high cancer-associated fibroblasts (CAFs) and C1Q+TAM content exhibit poor outcomes, providing a higher level of personalization and precision than would distinct subtypes. Additionally, we discover CAF subtypes known to be associated with immunotherapy resistance. CONCLUSIONS Distinct CAFs and C1Q+ TAMs are sufficient to explain CMS predictive ability and a simpler signature based on these cellular phenotypes could stratify CRC patient prognosis with greater precision. Therapeutically targeting specific CAF subtypes and C1Q + TAMs may promote immunotherapy responses in CRC patients.
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Affiliation(s)
- Ateeq M Khaliq
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cihat Erdogan
- Isparta University of Applied Sciences, Isparta, Turkey
| | - Zeyneb Kurt
- Northumbria University, Newcastle Upon Tyne, UK
| | | | | | - Tim Rand
- Tempus Labs, Inc., Chicago, IL, USA
| | | | | | | | - Sam G Pappas
- Rush University Medical Center, Chicago, IL, USA
| | | | - Audrey E Kam
- Rush University Medical Center, Chicago, IL, USA
| | | | | | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yong Zang
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yingjie Qiu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Anita Turk
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vineet Gupta
- Rush University Medical Center, Chicago, IL, USA
| | - Ram Al-Sabti
- Rush University Medical Center, Chicago, IL, USA
| | | | | | | | - Levi Waldron
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Arif Hussain
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Bassel El-Rayes
- University of Alabama, O'Neil Comprehensive Cancer Institute, Birmingham, AL, USA
| | | | - Ashiq Masood
- Indiana University School of Medicine, Indianapolis, IN, USA.
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15
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Strating E, Wassenaar E, Verhagen M, Rauwerdink P, van Schelven S, de Hingh I, Rinkes IB, Boerma D, Witkamp A, Lacle M, Fodde R, Volckmann R, Koster J, Stedingk K, Giesel F, de Roos R, Poot A, Bol G, Lam M, Elias S, Kranenburg O. Fibroblast activation protein identifies Consensus Molecular Subtype 4 in colorectal cancer and allows its detection by 68Ga-FAPI-PET imaging. Br J Cancer 2022; 127:145-155. [PMID: 35296803 PMCID: PMC9276750 DOI: 10.1038/s41416-022-01748-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
Background In colorectal cancer (CRC), the consensus molecular subtype 4 (CMS4) is associated with therapy resistance and poor prognosis. Clinical diagnosis of CMS4 is hampered by locoregional and temporal variables influencing CMS classification. Diagnostic tools that comprehensively detect CMS4 are therefore urgently needed. Methods To identify targets for molecular CMS4 imaging, RNA sequencing data of 3232 primary CRC patients were explored. Heterogeneity of marker expression in relation to CMS4 status was assessed by analysing 3–5 tumour regions and 91.103 single-tumour cells (7 and 29 tumours, respectively). Candidate marker expression was validated in CMS4 peritoneal metastases (PM; n = 59). Molecular imaging was performed using the 68Ga-DOTA-FAPI-46 PET tracer. Results Fibroblast activation protein (FAP) mRNA identified CMS4 with very high sensitivity and specificity (AUROC > 0.91), and was associated with significantly shorter relapse-free survival (P = 0.0038). Heterogeneous expression of FAP among and within tumour lesions correlated with CMS4 heterogeneity (AUROC = 1.00). FAP expression was homogeneously high in PM, a near-homogeneous CMS4 entity. FAPI-PET identified focal and diffuse PM that were missed using conventional imaging. Extra-peritoneal metastases displayed extensive heterogeneity of tracer uptake. Conclusion FAP expression identifies CMS4 CRC. FAPI-PET may have value in the comprehensive detection of CMS4 tumours in CRC. This is especially relevant in patients with PM, for whom effective imaging tools are currently lacking. ![]()
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Affiliation(s)
- Esther Strating
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emma Wassenaar
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Surgery, St. Antonius Hospital, Nieuwegein, The Netherlands
| | | | - Paulien Rauwerdink
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Surgery, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Susanne van Schelven
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ignace de Hingh
- Department of Surgery, Catharina Hospital, Eindhoven, The Netherlands
| | - Inne Borel Rinkes
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Djamila Boerma
- Department of Surgery, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Arjen Witkamp
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Miangela Lacle
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Riccardo Fodde
- Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Kris Stedingk
- Department of Oncogenomics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Frederik Giesel
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany.,Department of Nuclear Medicine, Medical Faculty, Heinrich-Heine-University, University Hospital Dusseldorf, Dusseldorf, Germany
| | - Remmert de Roos
- Department of Radiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alex Poot
- Department of Radiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Guus Bol
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marnix Lam
- Department of Radiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Sjoerd Elias
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Onno Kranenburg
- Department of Surgical Oncology, Lab Translational Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands. .,Utrecht Platform for Organoid Technology, Utrecht University, Utrecht, The Netherlands.
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16
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Ignatova EO, Kozlov E, Ivanov M, Mileyko V, Menshikova S, Sun H, Fedyanin M, Tryakin A, Stilidi I. Clinical significance of molecular subtypes of gastrointestinal tract adenocarcinoma. World J Gastrointest Oncol 2022; 14:628-645. [PMID: 35321271 PMCID: PMC8919013 DOI: 10.4251/wjgo.v14.i3.628] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/04/2021] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Adenocarcinomas of the gastrointestinal tract (esophagus, stomach, and colon) represent a heterogeneous group of diseases with distinct etiology, clinical features, treatment approaches, and prognosis. Studies are ongoing to isolate molecular genetic subtypes, perform complete biological characterization of the tumor, determine prognostic groups, and find predictive markers to the effectiveness of therapy. Separate molecular genetic classifications were created for esophageal adenocarcinoma [The Cancer Genome Atlas (TCGA)], stomach cancer (TCGA, Asian Cancer Research Group), and colon cancer (Colorectal Cancer Subtyping Consortium). In 2018, isolation of TCGA molecular genetic subtypes for adenocarcinomas of the gastrointestinal tract (esophagus, stomach, and colon) highlighted the need for further studies and clinical validation of subtyping of gastrointestinal adenocarcinomas. However, this approach has limitations. The aim of our work was to critically analyze integration of molecular genetic subtyping of gastrointestinal adenocarcinomas in clinical practice.
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Affiliation(s)
- Ekaterina Olegovna Ignatova
- Department of Second Chemotherapy, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Moscow, Russia
- Department of Oncogenetics, Research Centre for Medical Genetics Research Centre for Medical Genetics, Moscow 115522, Moscow, Russia
| | | | - Maxim Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow 141700, Moscow, Russia
| | | | - Sofia Menshikova
- Department of Anticancer Drug Treatment, AO K31 City, Moscow 121552, Moscow, Russia
| | - Henian Sun
- Pirogov Russian National Research Medical University (Pirogov Medical University), Moscow 117997, Moscow, Russia
| | - Mikhail Fedyanin
- Department of Second Chemotherapy, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Moscow, Russia
| | - Alexey Tryakin
- Department of Second Chemotherapy, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Moscow, Russia
| | - Ivan Stilidi
- Department of Second Chemotherapy, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow 115478, Moscow, Russia
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17
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Guix I, Liu Q, Pujana MA, Ha P, Piulats J, Linares I, Guedea F, Mao JH, Lazar A, Chapman J, Yom SS, Ashworth A, Barcellos-Hoff MH. Validation of anti-correlated TGFβ signaling and alternative end-joining DNA repair signatures that predict response to genotoxic cancer therapy. Clin Cancer Res 2022; 28:1372-1382. [PMID: 35022323 DOI: 10.1158/1078-0432.ccr-21-2846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/13/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Loss of transforming growth factor β (TGFβ) signaling increases error-prone alternative end-joining (alt-EJ) DNA repair. We previously translated this mechanistic relationship as TGFβ and alt-EJ gene expression signatures, which are anti-correlated across cancer types. A score, βAlt, representing anti-correlation predicts patient outcome in response to genotoxic therapy. Here we sought to verify this biology in live specimens and additional datasets. EXPERIMENTAL DESIGN Human head and neck squamous cell (HNSC) carcinoma explants were treated in vitro to test whether the signatures report TGFβ signaling, indicated by SMAD2 phosphorylation, and unrepaired DNA damage, indicated by persistent 53BP1 foci after irradiation or olaparib. A custom NanoString assay was implemented to analyze the signatures' expression in explants. Each signature gene was then weighted by its association with functional responses to define a modified score, βAltw, that was retested for association with response to genotoxic therapies in independent datasets. RESULTS Most genes in each signature were positively correlated with the expected biological response in tumor explants. Anticorrelation of TGFβ and alt-EJ signatures measured by Nanostring was confirmed in explants. βAltw was significantly (P<0.001) better than βAlt in predicting overall survival in response to genotoxic therapy in TCGA pancancer patients and in independent HNSC and ovarian cancer patient datasets. CONCLUSION Association of the TGFβ and alt-EJ signatures with their biological response validates TGFβ competency as a key mediator of DNA repair that can be readily assayed by gene expression. The predictive value of βAltw supports its development to assist in clinical decision-making.
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Affiliation(s)
- Ines Guix
- Department of Radiation Oncology, University of California, San Francicsco
| | - Qi Liu
- Shenzhen Bay Laboratory, Institute for Biomedical Engineering
| | | | - Patrick Ha
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco
| | - Josep Piulats
- Medical Oncology, Institut Català d'Oncologia-IDIBELL
| | | | | | - Jian-Hua Mao
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, University of California, Berkely
| | - Ann Lazar
- Biostatistics, University of California, San Francisco
| | - Jocelyn Chapman
- Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco
| | - Sue S Yom
- Radiation Oncology, University of California, San Francisco
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Centre
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18
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Brown KM, Xue A, Smith RC, Samra JS, Gill AJ, Hugh TJ. Cancer-associated stroma reveals prognostic biomarkers and novel insights into the tumour microenvironment of colorectal cancer and colorectal liver metastases. Cancer Med 2021; 11:492-506. [PMID: 34874125 PMCID: PMC8729056 DOI: 10.1002/cam4.4452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/26/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022] Open
Abstract
Background and Aims Cancer‐associated stroma (CAS) is emerging as a key determinant of metastasis in colorectal cancer (CRC); however, little is known about CAS in colorectal liver metastases (CRLM). This study aimed to validate the prognostic significance of stromal protein biomarkers in primary CRC and CRLM. Secondly, this study aimed to describe the transcriptome of the CAS of CRLM and identify novel targetable pathways of metastasis. Methods A case–control study design from a prospectively maintained database was adopted. The prognostic value of epithelial and stromal CALD1, IGFBP7, POSTN, FAP, TGF‐β and pSMAD2 expression was assessed by immunohistochemistry (IHC) in multivariate models. Pathway enrichment and sparse partial least square‐discriminant analysis (sPLS‐DA) were performed on a nested cohort after isolating epithelial tumour and CAS by laser capture microdissection. Results 110 CRCs with 124 paired CRLMs, and 110 matched non‐metastatic control CRCs were included. Median follow‐up was 62 and 45 months for primary and CRLM groups, respectively. Stromal FAP and POSTN were independent predictors for the development of CRLM. After CRLM resection, stromal IGFBP7 and POSTN were predictors of poorer survival. sPLS‐DA on the nested cohort identified a number of novel targetable stromal genes and pathways that defined poor prognosis CRC and the CAS of CRLM. Conclusions This study is the first to describe key differences in stromal gene expression between paired primary CRC and CRLM as well as identifying several targetable biomarkers and transcriptomic pathways whose relevance specifically in the CAS of CRC and CRLM have not been previously described.
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Affiliation(s)
- Kai M Brown
- Cancer Surgery and Metabolism Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, New South Wales, Australia.,Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Aiqun Xue
- Cancer Surgery and Metabolism Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ross C Smith
- Cancer Surgery and Metabolism Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jaswinder S Samra
- Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, New South Wales, Australia.,Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Anthony J Gill
- Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Cancer Diagnosis and Pathology Group, University of Sydney, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Thomas J Hugh
- Cancer Surgery and Metabolism Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, New South Wales, Australia.,Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
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Ros J, Baraibar I, Martini G, Salvà F, Saoudi N, Cuadra-Urteaga JL, Dienstmann R, Tabernero J, Élez E. The Evolving Role of Consensus Molecular Subtypes: a Step Beyond Inpatient Selection for Treatment of Colorectal Cancer. Curr Treat Options Oncol 2021; 22:113. [PMID: 34741675 DOI: 10.1007/s11864-021-00913-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2021] [Indexed: 12/24/2022]
Abstract
OPINION STATEMENT The heterogenous nature of colorectal cancer (CRC) renders it a major clinical challenge. Increasing genomic understanding of CRC has improved our knowledge of this heterogeneity and the main cancer drivers, with significant improvements in clinical outcomes. Comprehensive molecular characterization has allowed clinicians a more precise range of treatment options based on biomarker selection. Furthermore, this deep molecular understanding likely extends therapeutic options to a larger number of patients. The biological associations of consensus molecular subtypes (CMS) with clinical outcomes in localized CRC have been validated in retrospective clinical trials. The prognostic role of CMS has also been confirmed in the metastatic setting, with CMS2 having the best prognosis, whereas CMS1 tumors are associated with a higher risk of progression and death after chemotherapy. Similarly, according to mesenchymal features and immunosuppressive molecules, CMS1 responds to immunotherapy, whereas CMS4 has a poorer prognosis, suggesting that a CMS1 signature could identify patients who may benefit from immune checkpoint inhibitors regardless of microsatellite instability (MSI) status. The main goal of these comprehensive analyses is to switch from "one marker-one drug" to "multi-marker drug combinations" allowing oncologists to give "the right drug to the right patient." Despite the revealing data from transcriptomic analyses, the high rate of intra-tumoral heterogeneity across the different CMS subgroups limits its incorporation as a predictive biomarker. In clinical practice, when feasible, comprehensive genomic tests should be performed to identify potentially targetable alterations, particularly in RAS/BRAF wild-type, MSI, and right-sided tumors. Furthermore, CMS has not only been associated with clinical outcomes and specific tumor and patient phenotypes but also with specific microbiome patterns. Future steps will include the integration of clinical features, genomics, transcriptomics, and microbiota to select the most accurate biomarkers to identify optimal treatments, improving individual clinical outcomes. In summary, CMS is context specific, identifies a level of heterogeneity beyond standard genomic biomarkers, and offers a means of maximizing personalized therapy.
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Affiliation(s)
- Javier Ros
- Medical Oncology, Vall d'Hebron University Hospital and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain. .,Department of Precision Medicine, Medical Oncology, Università Degli Studi Della Campania Luigi Vanvitelli, Naples, Campania, Italy.
| | - Iosune Baraibar
- Medical Oncology, Vall d'Hebron University Hospital and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Giulia Martini
- Department of Precision Medicine, Medical Oncology, Università Degli Studi Della Campania Luigi Vanvitelli, Naples, Campania, Italy
| | - Francesc Salvà
- Medical Oncology, Vall d'Hebron University Hospital and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Nadia Saoudi
- Medical Oncology, Vall d'Hebron University Hospital and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Rodrigo Dienstmann
- Oncology Data Science (ODysSey) Group, Vall D'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall D'Hebron, Vall D'Hebron Barcelona Hospital Campus (Spain), Barcelona, Spain
| | - Josep Tabernero
- Medical Oncology, Vall d'Hebron University Hospital and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,IOB, Barcelona, Spain.,UVic-UCC, Vic, Spain
| | - Elena Élez
- Medical Oncology, Vall d'Hebron University Hospital and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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20
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APC and TP53 Mutations Predict Cetuximab Sensitivity across Consensus Molecular Subtypes. Cancers (Basel) 2021; 13:cancers13215394. [PMID: 34771559 PMCID: PMC8582550 DOI: 10.3390/cancers13215394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/03/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is a major cause of cancer deaths. Cetuximab is an FDA-approved, underutilized therapeutic targeting the epidermal growth factor receptor (EGFR) in metastatic CRC. To date, despite selection of patients with wild-type RAS, it is still difficult to identify patients who may benefit from EGFR inhibitor (e.g., cetuximab) therapy. Our aim is to molecularly classify CRC patients to better identify subpopulations sensitive to EGFR targeted therapy. APC and TP53 are two major tumor suppressor genes in CRC whose mutations contribute to tumor initiation and progression and may identify cetuximab-sensitive tumors. Recently, it has been suggested that the consensus molecular subtype (CMS) classification may be used to help identify cetuximab-sensitive patients. Here, we report an analysis of multiple CRC tumor/PDX/cell line datasets using combined APC and TP53 mutations to refine the CMS classification to better predict responses to cetuximab to improve patient outcomes. Abstract Recently, it was suggested that consensus molecular subtyping (CMS) may aide in predicting response to EGFR inhibitor (cetuximab) therapies. We recently identified that APC and TP53 as two tumor suppressor genes, when mutated, may enhance cetuximab sensitivity and may represent easily measured biomarkers in tumors or blood. Our study aimed to use APC and TP53 mutations (AP) to refine the CMS classification to better predict responses to cetuximab. In total, 433 CRC tumors were classified into CMS1-4 subtypes. The cetuximab sensitivity (CTX-S) signature scores of AP vs. non-AP tumors were determined across each of the CMS classes. Tumors harboring combined AP mutations were predominantly enriched in the CMS2 class, and to a lesser degree, in the CMS4 class. On the other hand, AP mutated CRCs had significantly higher CTX-S scores compared to non-AP CRCs across all CMS classes. Similar results were also obtained in independent TCGA tumor collections (n = 531) and in PDMR PDX/PDO/PDC models (n = 477). In addition, the in vitro cetuximab growth inhibition was preferentially associated with the CMS2 cell lines harboring A/P genotypes. In conclusion, the AP mutation signature represents a convenient biomarker that refines the CMS classification to identify CRC subpopulations predicted to be sensitive to EGFR targeted therapies.
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21
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Stahler A, Heinemann V, Schuster V, Heinrich K, Kurreck A, Gießen-Jung C, Fischer von Weikersthal L, Kaiser F, Decker T, Held S, Graeven U, Schwaner I, Denzlinger C, Schenk M, Neumann J, Kirchner T, Jung A, Kumbrink J, Stintzing S, Modest DP. Consensus molecular subtypes in metastatic colorectal cancer treated with sequential versus combined fluoropyrimidine, bevacizumab and irinotecan (XELAVIRI trial). Eur J Cancer 2021; 157:71-80. [PMID: 34507244 DOI: 10.1016/j.ejca.2021.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND The XELAVIRI trial compared sequential (fluoropyrimidine and bevacizumab; irinotecan (Iri) at progression) versus initial combination therapy (fluoropyrimidine, bevacizumab, Iri) of treatment-naïve metastatic colorectal cancer (mCRC). In the confirmatory analysis, the primary end-point (non-inferiority of sequential therapy regarding time to failure of strategy, TFS) was not met. Nevertheless, significant differences regarding treatment efficacy were observed according to RAS status. Here, we evaluate the consensus molecular subtypes (CMS) as additional biomarkers for sequential versus combination therapy. MATERIAL AND METHODS Gene expression was measured using NanoString after mRNA extraction from formalin-fixed paraffin-embedded tumour specimens. CMS were predicted using multinomial regression and correlated with updated data for TFS, overall (OS) and progression-free survival. RESULTS CMS were predicted in 337 of 421 (80.0%) patients (CMS1: 18.4%; CMS2: 51.6%; CMS3: 2.7%; CMS4: 27.3%). CMS2 together with RAS/BRAF wild-type status was identified as potential predictive marker of benefit from initial combination therapy for OS (HR 0.56, 95% CI 0.33-0.96, p = 0.036) and progression-free survival (HR 0.28, 95% CI 0.29-0.79, p = 0.004) and also trending in TFS (HR 0.63, 90% CI 0.41-0.95, p = 0.066). In patients with RAS-mutated mCRC, CMS1 was associated with longer OS after initial combination therapy (HR 0.43, 95% CI 0.20-0.95, p = 0.038). Interaction testing (two-sided) of CMS and RAS/BRAF status in favour of the combination treatment strategy was significant for OS (p = 0.012) CONCLUSIONS: In patients with RAS/BRAF wild-type mCRC, CMS2 may serve as an additional biomarker of benefit from the initial combination therapy, including Iri. TRIAL REGISTRATION Trial registration ID (clinicaltrials.gov) NCT01249638.
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Affiliation(s)
- Arndt Stahler
- Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Tumour Immunology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Volker Heinemann
- Department of Medicine III, University Hospital, LMU, Munich, Germany; LMU Munich, German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Veronika Schuster
- Department of Medicine III, University Hospital, LMU, Munich, Germany
| | - Kathrin Heinrich
- Department of Medicine III, University Hospital, LMU, Munich, Germany
| | - Annika Kurreck
- Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Tumour Immunology, Charitéplatz 1, 10117, Berlin, Germany
| | | | | | | | | | | | - Ullrich Graeven
- Department of Hematology, Oncology and Gastroenterology, Kliniken Maria Hilf GmbH, Mönchengladbach, Germany
| | - Ingo Schwaner
- Onkologische Schwerpunktpraxis Kurfürstendamm, Berlin, Germany
| | | | - Michael Schenk
- Krankenhaus Barmherzige Brüder Regensburg, Regensburg, Germany
| | - Jens Neumann
- Institute of Pathology, University of Munich, Germany
| | - Thomas Kirchner
- LMU Munich, German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, University of Munich, Germany
| | - Andreas Jung
- LMU Munich, German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, University of Munich, Germany
| | - Jörg Kumbrink
- LMU Munich, German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, University of Munich, Germany
| | - Sebastian Stintzing
- Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Tumour Immunology, Charitéplatz 1, 10117, Berlin, Germany; Charité - Universitätsmedizin, German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik P Modest
- Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Tumour Immunology, Charitéplatz 1, 10117, Berlin, Germany; Charité - Universitätsmedizin, German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
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22
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Moosavi SH, Eide PW, Eilertsen IA, Brunsell TH, Berg KCG, Røsok BI, Brudvik KW, Bjørnbeth BA, Guren MG, Nesbakken A, Lothe RA, Sveen A. De novo transcriptomic subtyping of colorectal cancer liver metastases in the context of tumor heterogeneity. Genome Med 2021; 13:143. [PMID: 34470666 PMCID: PMC8411513 DOI: 10.1186/s13073-021-00956-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 08/17/2021] [Indexed: 12/17/2022] Open
Abstract
Background Gene expression-based subtyping has the potential to form a new paradigm for stratified treatment of colorectal cancer. However, current frameworks are based on the transcriptomic profiles of primary tumors, and metastatic heterogeneity is a challenge. Here we aimed to develop a de novo metastasis-oriented framework. Methods In total, 829 transcriptomic profiles from patients with colorectal cancer were analyzed, including primary tumors, liver metastases, and non-malignant liver samples. High-resolution microarray gene expression profiling was performed of 283 liver metastases from 171 patients treated by hepatic resection, including multiregional and/or multi-metastatic samples from each of 47 patients. A single randomly selected liver metastasis sample from each patient was used for unsupervised subtype discovery by nonnegative matrix factorization, and a random forest prediction model was trained to classify multi-metastatic samples, as well as liver metastases from two independent series of 308 additional patients. Results Initial comparisons with non-malignant liver samples and primary colorectal tumors showed a highly variable degree of influence from the liver microenvironment in metastases, which contributed to inter-metastatic transcriptomic heterogeneity, but did not define subtype distinctions. The de novo liver metastasis subtype (LMS) framework recapitulated the main distinction between epithelial-like and mesenchymal-like tumors, with a strong immune and stromal component only in the latter. We also identified biologically distinct epithelial-like subtypes originating from different progenitor cell types. LMS1 metastases had several transcriptomic features of cancer aggressiveness, including secretory progenitor cell origin, oncogenic addictions, and microsatellite instability in a microsatellite stable background, as well as frequent RAS/TP53 co-mutations. The poor-prognostic association of LMS1 metastases was independent of mutation status, clinicopathological variables, and current subtyping frameworks (consensus molecular subtypes and colorectal cancer intrinsic subtypes). LMS1 was also the least heterogeneous subtype in comparisons of multiple metastases per patient, and tumor heterogeneity did not confound the prognostic value of LMS1. Conclusions We report the first large study of multi-metastatic gene expression profiling of colorectal cancer. The new metastasis-oriented subtyping framework showed potential for clinically relevant transcriptomic classification in the context of metastatic heterogeneity, and an LMS1 mini-classifier was constructed to facilitate prognostic stratification and further clinical testing. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00956-1.
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Affiliation(s)
- Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. box 1171 Blindern, NO-0318, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. box 1171 Blindern, NO-0318, Oslo, Norway
| | - Tuva H Brunsell
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway
| | - Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway
| | - Bård I Røsok
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. box 4950, NO-0424, Oslo, Norway
| | - Kristoffer W Brudvik
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. box 4950, NO-0424, Oslo, Norway
| | - Bjørn A Bjørnbeth
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. box 4950, NO-0424, Oslo, Norway
| | - Marianne G Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Department of Oncology, Oslo University Hospital, P.O. box 4953, NO-0424, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. box 1171 Blindern, NO-0318, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. box 4950, NO-0424, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. box 1171 Blindern, NO-0318, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. box 4953 Nydalen, NO-0424, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, P.O. Box 4953 Nydalen, NO-0424, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. box 1171 Blindern, NO-0318, Oslo, Norway.
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23
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Eide PW, Moosavi SH, Eilertsen IA, Brunsell TH, Langerud J, Berg KCG, Røsok BI, Bjørnbeth BA, Nesbakken A, Lothe RA, Sveen A. Metastatic heterogeneity of the consensus molecular subtypes of colorectal cancer. NPJ Genom Med 2021; 6:59. [PMID: 34262039 PMCID: PMC8280229 DOI: 10.1038/s41525-021-00223-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023] Open
Abstract
Gene expression-based subtypes of colorectal cancer have clinical relevance, but the representativeness of primary tumors and the consensus molecular subtypes (CMS) for metastatic cancers is not well known. We investigated the metastatic heterogeneity of CMS. The best approach to subtype translation was delineated by comparisons of transcriptomic profiles from 317 primary tumors and 295 liver metastases, including multi-metastatic samples from 45 patients and 14 primary-metastasis sets. Associations were validated in an external data set (n = 618). Projection of metastases onto principal components of primary tumors showed that metastases were depleted of CMS1-immune/CMS3-metabolic signals, enriched for CMS4-mesenchymal/stromal signals, and heavily influenced by the microenvironment. The tailored CMS classifier (available in an updated version of the R package CMScaller) therefore implemented an approach to regress out the liver tissue background. The majority of classified metastases were either CMS2 or CMS4. Nonetheless, subtype switching and inter-metastatic CMS heterogeneity were frequent and increased with sampling intensity. Poor-prognostic value of CMS1/3 metastases was consistent in the context of intra-patient tumor heterogeneity.
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Affiliation(s)
- Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tuva H Brunsell
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bård I Røsok
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Bjørn A Bjørnbeth
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway. .,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
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24
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Marisa L, Blum Y, Taieb J, Ayadi M, Pilati C, Le Malicot K, Lepage C, Salazar R, Aust D, Duval A, Blons H, Taly V, Gentien D, Rapinat A, Selves J, Mouillet-Richard S, Boige V, Emile JF, de Reyniès A, Laurent-Puig P. Intratumor CMS Heterogeneity Impacts Patient Prognosis in Localized Colon Cancer. Clin Cancer Res 2021; 27:4768-4780. [PMID: 34168047 PMCID: PMC8974433 DOI: 10.1158/1078-0432.ccr-21-0529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE The consensus molecular subtypes (CMS) represent a significant advance in the understanding of intertumor heterogeneity in colon cancer. Intratumor heterogeneity (ITH) is the new frontier for refining prognostication and understanding treatment resistance. This study aims at deciphering the transcriptomic ITH of colon cancer and understanding its potential prognostic implications. EXPERIMENTAL DESIGN We deconvoluted the transcriptomic profiles of 1,779 tumors from the PETACC8 trial and 155 colon cancer cell lines as weighted sums of the four CMSs, using the Weighted In Silico Pathology (WISP) algorithm. We assigned to each tumor and cell line a combination of up to three CMS subtypes with a threshold above 20%. RESULTS Over 55% of tumors corresponded to mixtures of at least two CMSs, demonstrating pervasive ITH in colon cancer. Of note, ITH was associated with shorter disease-free survival (DFS) and overall survival, [HR, 1.34; 95% confidence interval (CI; 1.12-1.59), 1.40, 95% CI (1.14-1.71), respectively]. Moreover, we uncovered specific combinations of CMS associated with dismal prognosis. In multivariate analysis, ITH represents the third parameter explaining DFS variance, after T and N stages. At a cellular level, combined WISP and single-cell transcriptomic analysis revealed that most colon cancer cell lines are a mixture of cells falling into different CMSs, indicating that ITH may correspond to distinct functional statuses of colon cancer cells. CONCLUSIONS This study shows that CMS-based transcriptomic ITH is frequent in colon cancer and impacts its prognosis. CMS-based transcriptomic ITH may correspond to distinct functional statuses of colon cancer cells, suggesting plasticity between CMS-related cell populations. Transcriptomic ITH deserves further assessment in the context of personalized medicine.
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Affiliation(s)
- Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Julien Taieb
- Institut du cancer Paris CARPEM, AP-HP, European Georges Pompidou Hospital, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Camilla Pilati
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Karine Le Malicot
- Fédération Francophone de Cancérologie Digestive, INSERM, Université de Bourgogne et Franche Comté, Dijon, France
| | - Côme Lepage
- Fédération Francophone de Cancérologie Digestive, INSERM, Université de Bourgogne et Franche Comté, Dijon, France.,Hepatogastroenterology and Digestive Oncology department, CHU Dijon, Dijon, France
| | - Ramon Salazar
- Catalan Institute of Oncology (IDIBELL), Universitat de Barcelona, CIBERONC, Spanish Gastrointestinal Tumors TTD Group, Barcelona, Spain
| | - Daniela Aust
- Institute for Pathology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Alex Duval
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Equipe Instabilité des Microsatellites et Cancer, équipe labellisé par la Ligue Nationale contre le Cancer, Paris, France
| | - Hélène Blons
- Institut du cancer Paris CARPEM, AP-HP, European Georges Pompidou Hospital, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Valérie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - David Gentien
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Audrey Rapinat
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Janick Selves
- Centre de Recherche en Cancérologie de Toulouse, INSERM, Université Toulouse III, Department of Pathology, CHU Toulouse, Toulouse, France
| | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Valérie Boige
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France.,Department of Cancer Medicine, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean-François Emile
- Department of Pathology, AP-HP, Hôpital Ambroise Paré, Boulogne-Billancourt, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.,Corresponding Authors: Pierre Laurent-Puig, UMR-S1138, Université Paris Descartes, 15 rue de l'Ecole de Médecine, Paris 75006, France. Phone: 336-0843-7691; E-mail: ; and Aurélien de Reyniès,
| | - Pierre Laurent-Puig
- Institut du cancer Paris CARPEM, AP-HP, European Georges Pompidou Hospital, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France.,Corresponding Authors: Pierre Laurent-Puig, UMR-S1138, Université Paris Descartes, 15 rue de l'Ecole de Médecine, Paris 75006, France. Phone: 336-0843-7691; E-mail: ; and Aurélien de Reyniès,
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25
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Ten Hoorn S, de Back TR, Sommeijer DW, Vermeulen L. Clinical Value of Consensus Molecular Subtypes in Colorectal Cancer: A Systematic Review and Meta-Analysis. J Natl Cancer Inst 2021; 114:503-516. [PMID: 34077519 PMCID: PMC9002278 DOI: 10.1093/jnci/djab106] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/23/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background The consensus molecular subtypes (CMSs) of colorectal cancer (CRC) capture tumor heterogeneity at the gene-expression level. Currently, a restricted number of molecular features are used to guide treatment for CRC. We summarize the evidence on the clinical value of the CMSs. Methods We systematically identified studies in Medline and Embase that evaluated the prognostic and predictive value of CMSs in CRC patients. A random-effect meta-analysis was performed on prognostic data. Predictive data were summarized. Results In local disease, CMS4 tumors were associated with worse overall survival (OS) compared with CMS1 (hazard ratio [HR] = 3.28, 95% confidence interval = 1.27 to 8.47) and CMS2 cancers (HR = 2.60, 95% confidence interval = 1.93 to 3.50). In metastatic disease, CMS1 consistently had worse survival than CMS2-4 (OS HR range = 0.33-0.55; progression-free survival HR range = 0.53-0.89). Adjuvant chemotherapy in stage II and III CRC was most beneficial for OS in CMS2 and CMS3 (HR range = 0.16-0.45) and not effective in CMS4 tumors. In metastatic CMS4 cancers, an irinotecan-based regimen improved outcome compared with oxaliplatin (HR range = 0.31-0.72). The addition of bevacizumab seemed beneficial in CMS1, and anti-epidermal growth factor receptor therapy improved outcome for KRAS wild-type CMS2 patients. Conclusions The CMS classification holds clear potential for clinical use in predicting both prognosis and response to systemic therapy, which seems to be independent of the classifier used. Prospective studies are warranted to support implementation of the CMS taxonomy in clinical practice.
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Affiliation(s)
- Sanne Ten Hoorn
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands
| | - Tim R de Back
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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26
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Lau YC, Schmeier S, Frizelle F, Purcell R. Consensus molecular subtypes of primary colon tumors and their hepatic metastases. Future Sci OA 2021; 7:FSO722. [PMID: 34258029 PMCID: PMC8256330 DOI: 10.2144/fsoa-2021-0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/12/2021] [Indexed: 01/29/2023] Open
Abstract
Aim: This pilot study aimed to evaluate the congruency in consensus molecular subtypes (CMS) of primary colorectal cancer and corresponding hepatic metastasis (HM). Materials & methods: RNA was extracted from both primary colorectal cancer and HM from ten patients, sequenced to establish gene-expression profiles and classified into CMS. Clinical data were collected retrospectively. Results: Of the ten patients recruited, nine had primary tumors that were classifiable: seven were CMS2, one was CMS3 and one was CMS4. Five had incongruent classification in the corresponding HM. Three out of the five patients with incongruent classification had received adjuvant chemotherapy prior to hepatic resection. Conclusion: A change in CMS type between matched primary and metastatic colorectal tumors is common and may be attributable to chemotherapy. Colorectal cancer can be classified into different subtypes and these subtypes can give useful information about the prognosis of disease. Mortality from colorectal cancer often results from tumors spreading to the liver, but little is known about subtypes of the liver metastases. In this preliminary study, we investigated whether colorectal tumors and liver metastases from the same patient had the same subtype profile and whether chemotherapy might cause a change in subtype. This has implications for understanding the effect of chemotherapy on tumors, and whether subtyping metastases gives useful clinical information.
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Affiliation(s)
- Yee Chen Lau
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
| | - Sebastian Schmeier
- School of Natural & Computational Sciences, Massey University, Auckland, New Zealand
| | - Frank Frizelle
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
| | - Rachel Purcell
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
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27
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Barriuso J, Nagaraju RT, Belgamwar S, Chakrabarty B, Burghel GJ, Schlecht H, Foster L, Kilgour E, Wallace AJ, Braun M, Dive C, Evans DG, Bristow RG, Saunders MP, O'Dwyer ST, Aziz O. Early Adaptation of Colorectal Cancer Cells to the Peritoneal Cavity Is Associated with Activation of "Stemness" Programs and Local Inflammation. Clin Cancer Res 2021; 27:1119-1130. [PMID: 33257424 PMCID: PMC7611320 DOI: 10.1158/1078-0432.ccr-20-3320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/20/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE At diagnosis, colorectal cancer presents with synchronous peritoneal metastasis in up to 10% of patients. The peritoneum is poorly characterized with respect to its superspecialized microenvironment. Our aim was to describe the differences between peritoneal metastases and their matched primary tumors excised simultaneously at the time of surgery. Also, we tested the hypothesis of these differences being present in primary colorectal tumors and having prognostic capacity. EXPERIMENTAL DESIGN We report a comprehensive analysis of 30 samples from peritoneal metastasis with their matched colorectal cancer primaries obtained during cytoreductive surgery. We tested and validated the prognostic value of our findings in a pooled series of 660 colorectal cancer primary samples with overall survival (OS) information and 743 samples with disease-free survival (DFS) information from publicly available databases. RESULTS We identified 20 genes dysregulated in peritoneal metastasis that promote an early increasing role of "stemness" in conjunction with tumor-favorable inflammatory changes. When adjusted for age, gender, and stage, the 20-gene peritoneal signature proved to have prognostic value for both OS [adjusted HR for the high-risk group (vs. low-risk) 2.32 (95% confidence interval, CI, 1.69-3.19; P < 0.0001)] and for DFS [adjusted HR 2.08 (95% CI, 1.50-2.91; P < 0.0001)]. CONCLUSIONS Our findings indicated that the activation of "stemness" pathways and adaptation to the peritoneal-specific environment are key to early stages of peritoneal carcinomatosis. The in silico analysis suggested that this 20-gene peritoneal signature may hold prognostic information with potential for development of new precision medicine strategies in this setting.
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Affiliation(s)
- Jorge Barriuso
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom.
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Raghavendar T Nagaraju
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| | - Shreya Belgamwar
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Bipasha Chakrabarty
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Department of Pathology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - George J Burghel
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Helene Schlecht
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Lucy Foster
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Elaine Kilgour
- Cancer Research UK Manchester Institute, Cancer Biomarker Centre, University of Manchester, Manchester, England, United Kingdom
| | - Andrew J Wallace
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Michael Braun
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Caroline Dive
- Cancer Research UK Manchester Institute, Cancer Biomarker Centre, University of Manchester, Manchester, England, United Kingdom
| | - D Gareth Evans
- Department of Genomic Medicine, Division of Evolution and Genomic Science, University of Manchester, England, United Kingdom
| | - Robert G Bristow
- Manchester Cancer Research Centre, CRUK Manchester Institute, University of Manchester, Manchester, England, United Kingdom
| | - Mark P Saunders
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Sarah T O'Dwyer
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| | - Omer Aziz
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom.
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
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28
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Huang X, Liu J, Liu H, Mo X, Meng Y, Zhang L, Deng Y, Zhang Y, Tang W. A Combined Epithelial Mesenchymal Transformation and DNA Repair Gene Panel in Colorectal Cancer With Prognostic and Therapeutic Implication. Front Oncol 2021; 10:595182. [PMID: 33520707 PMCID: PMC7843609 DOI: 10.3389/fonc.2020.595182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/23/2020] [Indexed: 01/13/2023] Open
Abstract
Background Epithelial mesenchymal transformation (EMT) and DNA repair status represent intrinsic features of colorectal cancer (CRC) and are associated with patient prognosis and treatment responsiveness. We sought to develop a combined EMT and DNA repair gene panel with potential application in patient classification and precise treatment. Methods We comprehensively evaluated the EMT and DNA repair patterns of 1,652 CRC patients from four datasets. Unsupervised clustering was used for classification. The clinical features, genetic mutation, tumor mutation load, and chemotherapy as well as immunotherapy sensitivity among different clusters were systematically compared. The least absolute shrinkage and selection operator regression method was used to develop the risk model. Results Three distinct CRC clusters were determined. Clustet1 was characterized by down-regulated DNA repair pathways but active epithelial markers and metabolism pathway and had intermediate prognosis. Clustet2 was characterized by down-regulated both epithelial markers and DNA repair pathways and had poor outcome. Clustet3 presented with activation of DNA repair pathway and epithelial markers had favorable prognosis. Clustet1 might benefit form chemotherapy and Clustet3 had a higher response rate to immunotherapy. An EMT and DNA repair risk model related to prognosis and treatment response was developed. Conclusions This work developed and validated a combined EMT and DNA repair gene panel for CRC classification, which may be an effective tool for survival prediction and treatment guidance in CRC patients.
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Affiliation(s)
- Xiaoliang Huang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China
| | - Jungang Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China.,Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, United States
| | - Haizhou Liu
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xianwei Mo
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China
| | - Yongsheng Meng
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China
| | - Lihua Zhang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China
| | - Yuqing Deng
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, United States
| | - Weizhong Tang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, China
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29
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Lin CC, Liao TT, Yang MH. Immune Adaptation of Colorectal Cancer Stem Cells and Their Interaction With the Tumor Microenvironment. Front Oncol 2020; 10:588542. [PMID: 33312953 PMCID: PMC7708331 DOI: 10.3389/fonc.2020.588542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Metastasis is the primary cause of death in colorectal cancer (CRC) patients. Emerging evidence has shown that CRC stem cells (CRCSCs) play a significant role in metastatic dissemination and tumor recurrence. However, strategies for targeting CRCSCs are limited because CRCSCs are resistant to therapeutic interventions and because the tumor microenvironment (TME) provides a supportive niche. Moreover, growing evidence highlights the critical role of CRCSCs in immune adaptation and modulation of the TME. CRCSCs escape immune surveillance by avoiding recognition by the innate immune system and shaping the TME through exosomes, cytokines, and chemokines to generate an immunosuppressive niche that facilitates cancer progression. In this review, we summarize studies investigating the immunomodulatory properties of CRCSCs and their underlying mechanisms in order to improve the efficacy of treatment strategies against advanced CRC.
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Affiliation(s)
- Chun-Chi Lin
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Colorectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tsai-Tsen Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang-Ming University, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
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30
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Sawayama H, Miyamoto Y, Ogawa K, Yoshida N, Baba H. Investigation of colorectal cancer in accordance with consensus molecular subtype classification. Ann Gastroenterol Surg 2020; 4:528-539. [PMID: 33005848 PMCID: PMC7511559 DOI: 10.1002/ags3.12362] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/06/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
The classification of colorectal cancer (CRC) plays a pivotal role in predicting a patient's prognosis and determining treatment strategies. The consensus molecular subtype (CMS) classification system was constructed by analyzing genetic information from 18 CRC data sets, containing 4151 CRC samples. CRC was classified into four subtypes with distinct molecular and biological characteristics: CMS1 (microsatellite instability immune), CMS2 (canonical), CMS3 (metabolic), and CMS4 (mesenchymal). Since their designation in 2015, these classifications have been applied to basic and translational research of CRC, with the hope that understanding these subsets will influence a clinician's approach to therapeutic treatment and improve clinical outcomes. We reviewed CRC investigations in accordance with CMSs published in the last 5 years to further explore the clinical significance of these subtypes and identify underlying trends that may direct relevant future research. We determined that CMSs linked common features of CRC cell lines and PDX models in various studies. Furthermore, associations between prognosis and clinicopathological findings, including pathological grade and the stage of carcinogenesis, tumor budding, and tumor location, were correlated with CMS classification. Novel prognostic factors were identified, and the relationship between chemotherapeutic drug resistance and CMS has been fortified by our compilation of research; thus, indicating that this review provides advanced insight into clinical questions and treatment strategies for CRC.
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Affiliation(s)
- Hiroshi Sawayama
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Yuji Miyamoto
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Katsuhiro Ogawa
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Naoya Yoshida
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Hideo Baba
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
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31
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Martini G, Dienstmann R, Ros J, Baraibar I, Cuadra-Urteaga JL, Salva F, Ciardiello D, Mulet N, Argiles G, Tabernero J, Elez E. Molecular subtypes and the evolution of treatment management in metastatic colorectal cancer. Ther Adv Med Oncol 2020; 12:1758835920936089. [PMID: 32782486 PMCID: PMC7383645 DOI: 10.1177/1758835920936089] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease representing a therapeutic challenge, which is further complicated by the common occurrence of several molecular alterations that confer resistance to standard chemotherapy and targeted agents. Mechanisms of resistance have been identified at multiple levels in the epidermal growth factor receptor (EGFR) pathway, including mutations in KRAS, NRAS, and BRAF V600E, and in the HER2 and MET receptors. These alterations represent oncogenic drivers that may co-exist in the same tumor with other primary and acquired alterations via a clonal selection process. Other molecular alterations include DNA damage repair mechanisms and rare kinase fusions, potentially offering a rationale for new therapeutic strategies. In recent years, genomic analysis has been expanded by a more complex study of epigenomic, transcriptomic, and microenvironment features. The Consensus Molecular Subtype (CMS) classification describes four CRC subtypes with distinct biological characteristics that show prognostic and potential predictive value in the clinical setting. Here, we review the panorama of actionable targets in CRC, and the developments in more recent molecular tests, such as liquid biopsy analysis, which are increasingly offering clinicians a means of ensuring optimal tailored treatments for patients with metastatic CRC according to their evolving molecular profile and treatment history.
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Affiliation(s)
- Giulia Martini
- Università della Campania L. Vanvitelli, Naples
- Vall d’Hebron Institute of Oncology, P/ Vall D’Hebron 119-121, Barcelona, 08035, Spain
| | | | - Javier Ros
- Vall d’Hebron Hospital, Barcelona, Catalunya, Spain
| | | | | | | | - Davide Ciardiello
- Università della Campania L. Vanvitelli, Naples
- Vall d’Hebron Hospital, Barcelona, Catalunya, Spain
| | - Nuria Mulet
- Vall d’Hebron Hospital, Barcelona, Catalunya, Spain
| | | | | | - Elena Elez
- Vall D’Hebron Institute of Oncology P/Vall D’Hebron 119-121, Barcelona, 08035 Spain
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32
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Buikhuisen JY, Torang A, Medema JP. Exploring and modelling colon cancer inter-tumour heterogeneity: opportunities and challenges. Oncogenesis 2020; 9:66. [PMID: 32647253 PMCID: PMC7347540 DOI: 10.1038/s41389-020-00250-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Colon cancer inter-tumour heterogeneity is installed on multiple levels, ranging from (epi)genetic driver events to signalling pathway rewiring reflected by differential gene expression patterns. Although the existence of heterogeneity in colon cancer has been recognised for a longer period of time, it is sparingly incorporated as a determining factor in current clinical practice. Here we describe how unsupervised gene expression-based classification efforts, amongst which the consensus molecular subtypes (CMS), can stratify patients in biological subgroups associated with distinct disease outcome and responses to therapy. We will discuss what is needed to extend these subtyping efforts to the clinic and we will argue that preclinical models recapitulate CMS subtypes and can be of vital use to increase our understanding of treatment response and resistance and to discover novel targets for therapy.
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Affiliation(s)
- Joyce Y Buikhuisen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Arezo Torang
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands. .,Oncode Institute, Amsterdam, The Netherlands.
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Orjuela S, Menigatti M, Schraml P, Kambakamba P, Robinson MD, Marra G. The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers. BMC Cancer 2020; 20:290. [PMID: 32252665 PMCID: PMC7137338 DOI: 10.1186/s12885-020-06777-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Identifying molecular differences between primary and metastatic colorectal cancers-now possible with the aid of omics technologies-can improve our understanding of the biological mechanisms of cancer progression and facilitate the discovery of novel treatments for late-stage cancer. We compared the DNA methylomes of primary colorectal cancers (CRCs) and CRC metastases to the liver. Laser microdissection was used to obtain epithelial tissue (10 to 25 × 106 μm2) from sections of fresh-frozen samples of primary CRCs (n = 6), CRC liver metastases (n = 12), and normal colon mucosa (n = 3). DNA extracted from tissues was enriched for methylated sequences with a methylCpG binding domain (MBD) polypeptide-based protocol and subjected to deep sequencing. The performance of this protocol was compared with that of targeted enrichment for bisulfite sequencing used in a previous study of ours. RESULTS MBD enrichment captured a total of 322,551 genomic regions (249.5 Mb or ~ 7.8% of the human genome), which included over seven million CpG sites. A few of these regions were differentially methylated at an expected false discovery rate (FDR) of 5% in neoplastic tissues (primaries: 0.67%, i.e., 2155 regions containing 279,441 CpG sites; liver metastases: 1%, i.e., 3223 regions containing 312,723 CpG sites) as compared with normal mucosa samples. Most of the differentially methylated regions (DMRs; 94% in primaries; 70% in metastases) were hypermethylated, and almost 80% of these (1882 of 2396) were present in both lesion types. At 5% FDR, no DMRs were detected in liver metastases vs. primary CRC. However, short regions of low-magnitude hypomethylation were frequent in metastases but rare in primaries. Hypermethylated DMRs were far more abundant in sequences classified as intragenic, gene-regulatory, or CpG shelves-shores-island segments, whereas hypomethylated DMRs were equally represented in extragenic (mainly, open-sea) and intragenic (mainly, gene bodies) sequences of the genome. Compared with targeted enrichment, MBD capture provided a better picture of the extension of CRC-associated DNA hypermethylation but was less powerful for identifying hypomethylation. CONCLUSIONS Our findings demonstrate that the hypermethylation phenotype in CRC liver metastases remains similar to that of the primary tumor, whereas CRC-associated DNA hypomethylation probably undergoes further progression after the cancer cells have migrated to the liver.
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Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University of Zurich, Zürich, Switzerland
| | - Patryk Kambakamba
- Division of Surgical Research, University of Zurich, Zürich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Sveen A, Kopetz S, Lothe RA. Biomarker-guided therapy for colorectal cancer: strength in complexity. Nat Rev Clin Oncol 2020; 17:11-32. [PMID: 31289352 PMCID: PMC7577509 DOI: 10.1038/s41571-019-0241-1] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 12/16/2022]
Abstract
The number of molecularly stratified treatment options available to patients with colorectal cancer (CRC) is increasing, with a parallel rise in the use of biomarkers to guide prognostication and treatment decision-making. The increase in both the number of biomarkers and their use has resulted in a progressively complex situation, evident both from the extensive interactions between biomarkers and from their sometimes complex associations with patient prognosis and treatment benefit. Current and emerging biomarkers also reflect the genomic complexity of CRC, and include a wide range of aberrations such as point mutations, amplifications, fusions and hypermutator phenotypes, in addition to global gene expression subtypes. In this Review, we provide an overview of current and emerging clinically relevant biomarkers and their role in the management of patients with CRC, illustrating the intricacies of biomarker interactions and the growing treatment opportunities created by the availability of comprehensive molecular profiling.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Molecular and Functional Characterization of the Somatic PIWIL1/piRNA Pathway in Colorectal Cancer Cells. Cells 2019; 8:cells8111390. [PMID: 31694219 PMCID: PMC6912267 DOI: 10.3390/cells8111390] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023] Open
Abstract
PIWI-like (PIWIL) proteins and small non-coding piRNAs, involved in genome regulation in germline cells, are found aberrantly expressed in human tumors. Gene expression data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, and the European Genome-Phenome Archive (EGA) indicate that the PIWIL1 gene is ectopically activated in a significant fraction of colorectal cancers (CRCs), where this is accompanied by promoter demethylation, together with germline factors required for piRNA production. Starting from this observation, the PIWIL/piRNA pathway was studied in detail in COLO 205 CRC cells, which express significant levels of this protein, to investigate role and significance of ectopic PIWIL1 expression in human tumors. RNA sequencing and cell and computational biology led to the demonstration that PIWIL1 localizes in a nuage-like structure located in the perinuclear region of the cell and that a significant fraction of the piRNAs expressed in these cells are methylated, and, therefore, present in an active form. This was further supported by RNA immunoprecipitation, which revealed how several piRNAs can be found loaded into PIWIL1 to form complexes also comprising their target mRNAs. The mature transcripts associated with the PIWIL-piRNA complex encode key regulatory proteins involved in the molecular mechanisms sustaining colorectal carcinogenesis, suggesting that the PIWI/piRNA pathway may actively contribute to the establishment and/or maintenance of clinico-pathological features of CRCs.
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Sveen A, Cremolini C, Dienstmann R. Predictive modeling in colorectal cancer: time to move beyond consensus molecular subtypes. Ann Oncol 2019; 30:1682-1685. [PMID: 31868904 DOI: 10.1093/annonc/mdz412] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- A Sveen
- Division for Cancer Medicine, Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - C Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - R Dienstmann
- Oncology Data Science, Vall d'Hebron Institute of Oncology, Barcelona, Spain.
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Eilertsen IA, Moosavi SH, Strømme JM, Nesbakken A, Johannessen B, Lothe RA, Sveen A. Technical differences between sequencing and microarray platforms impact transcriptomic subtyping of colorectal cancer. Cancer Lett 2019; 469:246-255. [PMID: 31678167 DOI: 10.1016/j.canlet.2019.10.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/24/2019] [Accepted: 10/27/2019] [Indexed: 01/12/2023]
Abstract
Gene expression profiling has increasing relevance in the molecular screening of patients with colorectal cancer (CRC). We investigated potential platform-specific effects on transcriptomic subtyping according to established frameworks by comparisons of expression profiles from RNA sequencing and exon-resolution microarrays in 126 primary microsatellite stable CRCs. There was a strong platform correspondence in global gene expression levels, albeit with systematic technical bias likely attributed to few sequencing reads covering short (<2000 nucleotides) and/or lowly expressed genes (<1 FPKM), as well as over-saturation of highly expressed genes on microarrays. Classification concordances according to both the consensus molecular subtypes and CRC intrinsic subtypes (CRIS) were also strong, but with disproportionate subtype distributions between platforms caused by frequent disagreements in adherence to sample classification thresholds. Subtypes defined largely by genes expressed at low levels, including the CRIS-D subtype and the estimated level of tumor-infiltrating cytotoxic lymphocytes, had a weaker correspondence in classification metrics between platforms. In conclusion, even subtle differences between platforms suggest that clinical translation of transcriptomic CRC subtyping frameworks is dependent on assay standardization, and systematic technical biases reinforce the need for careful selection of classifier genes.
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Affiliation(s)
- Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171 Blindern, NO-0318, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171 Blindern, NO-0318, Oslo, Norway
| | - Jonas M Strømme
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. Box 1080, Blindern, NO-0316, Oslo, Norway
| | - Arild Nesbakken
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171 Blindern, NO-0318, Oslo, Norway; Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171 Blindern, NO-0318, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171 Blindern, NO-0318, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171 Blindern, NO-0318, Oslo, Norway.
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