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Kreis J, Aybey B, Geist F, Brors B, Staub E. Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell-intrinsic Stemness or Mesenchymality Characteristics. CANCER RESEARCH COMMUNICATIONS 2024; 4:516-529. [PMID: 38349551 PMCID: PMC10885853 DOI: 10.1158/2767-9764.crc-23-0383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Epithelial-to-mesenchymal transition (EMT) in cancer cells confers migratory abilities, a crucial aspect in the metastasis of tumors that frequently leads to death. In multiple studies, authors proposed gene expression signatures for EMT, stemness, or mesenchymality of tumors based on bulk tumor expression profiling. However, recent studies suggested that noncancerous cells from the microenvironment or macroenvironment heavily influence such signature profiles. Here, we strengthen these findings by investigating 11 published and frequently referenced gene expression signatures that were proposed to describe EMT-related (EMT, mesenchymal, or stemness) characteristics in various cancer types. By analyses of bulk, single-cell, and pseudobulk expression data, we show that the cell type composition of a tumor sample frequently dominates scores of these EMT-related signatures. A comprehensive, integrated analysis of bulk RNA sequencing (RNA-seq) and single-cell RNA-seq data shows that stromal cells, most often fibroblasts, are the main drivers of EMT-related signature scores. We call attention to the risk of false conclusions about tumor properties when interpreting EMT-related signatures, especially in a clinical setting: high patient scores of EMT-related signatures or calls of "stemness subtypes" often result from low cancer cell content in tumor biopsies rather than cancer cell-specific stemness or mesenchymal/EMT characteristics. SIGNIFICANCE Cancer self-renewal and migratory abilities are often characterized via gene module expression profiles, also called EMT or stemness gene expression signatures. Using published clinical tumor samples, cancer cell lines, and single cancer cells, we highlight the dominating influence of noncancer cells in low cancer cell content biopsies on their scores. We caution on their application for low cancer cell content clinical cancer samples with the intent to assign such characteristics or subtypes.
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Affiliation(s)
- Julian Kreis
- The healthcare business of Merck KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Bogac Aybey
- The healthcare business of Merck KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Felix Geist
- The healthcare business of Merck KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
- Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Eike Staub
- The healthcare business of Merck KGaA, Darmstadt, Germany
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Yakubovich E, Cook DP, Rodriguez GM, Vanderhyden BC. Mesenchymal ovarian cancer cells promote CD8 + T cell exhaustion through the LGALS3-LAG3 axis. NPJ Syst Biol Appl 2023; 9:61. [PMID: 38086828 PMCID: PMC10716312 DOI: 10.1038/s41540-023-00322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cancer cells often metastasize by undergoing an epithelial-mesenchymal transition (EMT). Although abundance of CD8+ T-cells in the tumor microenvironment correlates with improved survival, mesenchymal cancer cells acquire greater resistance to antitumor immunity in some cancers. We hypothesized the EMT modulates the immune response to ovarian cancer. Here we show that cancer cells from infiltrated/inflamed tumors possess more mesenchymal cells, than excluded and desert tumors. We also noted high expression of LGALS3 is associated with EMT in vivo, a finding validated with in vitro EMT models. Dissecting the cellular communications among populations in the tumor revealed that mesenchymal cancer cells in infiltrated tumors communicate through LGALS3 to LAG3 receptor expressed by CD8+ T cells. We found CD8+ T cells express high levels of LAG3, a marker of T cell exhaustion. The results indicate that EMT in ovarian cancer cells promotes interactions between cancer cells and T cells through the LGALS3 - LAG3 axis, which could increase T cell exhaustion in infiltrated tumors, dampening antitumor immunity.
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Affiliation(s)
- Edward Yakubovich
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada.
| | - David P Cook
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Galaxia M Rodriguez
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Barbara C Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
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3
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Suzuki T, Conant A, Curow C, Alexander A, Ioffe Y, Unternaehrer JJ. Role of epithelial-mesenchymal transition factor SNAI1 and its targets in ovarian cancer aggressiveness. JOURNAL OF CANCER METASTASIS AND TREATMENT 2023; 9:25. [PMID: 38009093 PMCID: PMC10673625 DOI: 10.20517/2394-4722.2023.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy in the USA. For over twenty years, epithelial-mesenchymal transition (EMT) has been characterized extensively in development and disease. The dysregulation of this process in cancer has been identified as a mechanism by which epithelial tumors become more aggressive, allowing them to survive and invade distant tissues. This occurs in part due to the increased expression of the EMT transcription factor, SNAI1 (Snail). In the case of epithelial ovarian cancer, Snail has been shown to contribute to cancer invasion, stemness, chemoresistance, and metabolic changes. Thus, in this review, we focus on summarizing current findings on the role of EMT (specifically, factors downstream of Snail) in determining ovarian cancer aggressiveness.
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Affiliation(s)
- Tise Suzuki
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Ashlyn Conant
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Casey Curow
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- University of Redlands, Department of Biology, Redlands, CA 92373, USA
| | - Audrey Alexander
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- Division of Natural and Mathematical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA
| | - Yevgeniya Ioffe
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Juli J Unternaehrer
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- Department of Gynecology and Obstetrics, Loma Linda University, Loma Linda, CA 92354, USA
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4
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Proietto M, Crippa M, Damiani C, Pasquale V, Sacco E, Vanoni M, Gilardi M. Tumor heterogeneity: preclinical models, emerging technologies, and future applications. Front Oncol 2023; 13:1164535. [PMID: 37188201 PMCID: PMC10175698 DOI: 10.3389/fonc.2023.1164535] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Heterogeneity describes the differences among cancer cells within and between tumors. It refers to cancer cells describing variations in morphology, transcriptional profiles, metabolism, and metastatic potential. More recently, the field has included the characterization of the tumor immune microenvironment and the depiction of the dynamics underlying the cellular interactions promoting the tumor ecosystem evolution. Heterogeneity has been found in most tumors representing one of the most challenging behaviors in cancer ecosystems. As one of the critical factors impairing the long-term efficacy of solid tumor therapy, heterogeneity leads to tumor resistance, more aggressive metastasizing, and recurrence. We review the role of the main models and the emerging single-cell and spatial genomic technologies in our understanding of tumor heterogeneity, its contribution to lethal cancer outcomes, and the physiological challenges to consider in designing cancer therapies. We highlight how tumor cells dynamically evolve because of the interactions within the tumor immune microenvironment and how to leverage this to unleash immune recognition through immunotherapy. A multidisciplinary approach grounded in novel bioinformatic and computational tools will allow reaching the integrated, multilayered knowledge of tumor heterogeneity required to implement personalized, more efficient therapies urgently required for cancer patients.
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Affiliation(s)
- Marco Proietto
- Next Generation Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Martina Crippa
- Vita-Salute San Raffaele University, Milan, Italy
- Experimental Imaging Center, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, Italy
| | - Chiara Damiani
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
| | - Valentina Pasquale
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
| | - Elena Sacco
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
| | - Marco Vanoni
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
- *Correspondence: Marco Vanoni, ; Mara Gilardi,
| | - Mara Gilardi
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Salk Cancer Center, The Salk Institute for Biological Studies, La Jolla, CA, United States
- *Correspondence: Marco Vanoni, ; Mara Gilardi,
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5
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Corry SM, McCorry AM, Lannagan TR, Leonard NA, Fisher NC, Byrne RM, Tsantoulis P, Cortes-Lavaud X, Amirkhah R, Redmond KL, McCooey AJ, Malla SB, Rogan E, Sakhnevych S, Gillespie MA, White M, Richman SD, Jackstadt RF, Campbell AD, Maguire S, McDade SS, Longley DB, Loughrey MB, Coleman HG, Kerr EM, Tejpar S, Maughan T, Leedham SJ, Small DM, Ryan AE, Sansom OJ, Lawler M, Dunne PD. Activation of innate-adaptive immune machinery by poly(I:C) exposes a therapeutic vulnerability to prevent relapse in stroma-rich colon cancer. Gut 2022; 71:2502-2517. [PMID: 35477539 PMCID: PMC9664095 DOI: 10.1136/gutjnl-2021-326183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/12/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Stroma-rich tumours represent a poor prognostic subtype in stage II/III colon cancer (CC), with high relapse rates and limited response to standard adjuvant chemotherapy. DESIGN To address the lack of efficacious therapeutic options for patients with stroma-rich CC, we stratified our human tumour cohorts according to stromal content, enabling identification of the biology underpinning relapse and potential therapeutic vulnerabilities specifically within stroma-rich tumours that could be exploited clinically. Following human tumour-based discovery and independent clinical validation, we use a series of in vitro and stroma-rich in vivo models to test and validate the therapeutic potential of elevating the biology associated with reduced relapse in human tumours. RESULTS By performing our analyses specifically within the stroma-rich/high-fibroblast (HiFi) subtype of CC, we identify and validate the clinical value of a HiFi-specific prognostic signature (HPS), which stratifies tumours based on STAT1-related signalling (High-HPS v Low-HPS=HR 0.093, CI 0.019 to 0.466). Using in silico, in vitro and in vivo models, we demonstrate that the HPS is associated with antigen processing and presentation within discrete immune lineages in stroma-rich CC, downstream of double-stranded RNA and viral response signalling. Treatment with the TLR3 agonist poly(I:C) elevated the HPS signalling and antigen processing phenotype across in vitro and in vivo models. In an in vivo model of stroma-rich CC, poly(I:C) treatment significantly increased systemic cytotoxic T cell activity (p<0.05) and reduced liver metastases (p<0.0002). CONCLUSION This study reveals new biological insight that offers a novel therapeutic option to reduce relapse rates in patients with the worst prognosis CC.
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Affiliation(s)
- Shania M Corry
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Amy Mb McCorry
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Niamh A Leonard
- Lambe Institute for Translational Research, College of Medicine Nursing and Health Sciences, National University of Ireland, Galway, Ireland
- Discipline of Pharmacology & Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
| | - Natalie C Fisher
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ryan M Byrne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Raheleh Amirkhah
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Keara L Redmond
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sudhir B Malla
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Rogan
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Svetlana Sakhnevych
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Michael A Gillespie
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark White
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Rene-Filip Jackstadt
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) and Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew D Campbell
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
| | - Sarah Maguire
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Maurice B Loughrey
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - Helen G Coleman
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sabine Tejpar
- Digestive Oncology Unit, University Ospital Gasthuisberg, Leuven, Belgium
| | | | - Simon J Leedham
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
| | - Donna M Small
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aideen E Ryan
- Lambe Institute for Translational Research, College of Medicine Nursing and Health Sciences, National University of Ireland, Galway, Ireland
- Discipline of Pharmacology & Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
| | - Owen J Sansom
- Cancer Research UK, Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Philip D Dunne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
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6
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Fisher NC, Byrne RM, Leslie H, Wood C, Legrini A, Cameron AJ, Ahmaderaghi B, Corry SM, Malla SB, Amirkhah R, McCooey AJ, Rogan E, Redmond KL, Sakhnevych S, Domingo E, Jackson J, Loughrey MB, Leedham S, Maughan T, Lawler M, Sansom OJ, Lamrock F, Koelzer VH, Jamieson NB, Dunne PD. Biological Misinterpretation of Transcriptional Signatures in Tumor Samples Can Unknowingly Undermine Mechanistic Understanding and Faithful Alignment with Preclinical Data. Clin Cancer Res 2022; 28:4056-4069. [PMID: 35792866 PMCID: PMC9475248 DOI: 10.1158/1078-0432.ccr-22-1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/08/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Precise mechanism-based gene expression signatures (GES) have been developed in appropriate in vitro and in vivo model systems, to identify important cancer-related signaling processes. However, some GESs originally developed to represent specific disease processes, primarily with an epithelial cell focus, are being applied to heterogeneous tumor samples where the expression of the genes in the signature may no longer be epithelial-specific. Therefore, unknowingly, even small changes in tumor stroma percentage can directly influence GESs, undermining the intended mechanistic signaling. EXPERIMENTAL DESIGN Using colorectal cancer as an exemplar, we deployed numerous orthogonal profiling methodologies, including laser capture microdissection, flow cytometry, bulk and multiregional biopsy clinical samples, single-cell RNA sequencing and finally spatial transcriptomics, to perform a comprehensive assessment of the potential for the most widely used GESs to be influenced, or confounded, by stromal content in tumor tissue. To complement this work, we generated a freely-available resource, ConfoundR; https://confoundr.qub.ac.uk/, that enables users to test the extent of stromal influence on an unlimited number of the genes/signatures simultaneously across colorectal, breast, pancreatic, ovarian and prostate cancer datasets. RESULTS Findings presented here demonstrate the clear potential for misinterpretation of the meaning of GESs, due to widespread stromal influences, which in-turn can undermine faithful alignment between clinical samples and preclinical data/models, particularly cell lines and organoids, or tumor models not fully recapitulating the stromal and immune microenvironment. CONCLUSIONS Efforts to faithfully align preclinical models of disease using phenotypically-designed GESs must ensure that the signatures themselves remain representative of the same biology when applied to clinical samples.
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Affiliation(s)
- Natalie C. Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Ryan M. Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Holly Leslie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Colin Wood
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Assya Legrini
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J. Cameron
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Shania M. Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Sudhir B. Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Aoife J. McCooey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Emily Rogan
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Keara L. Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Svetlana Sakhnevych
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | | | - James Jackson
- Information Services, Queen's University Belfast, Belfast, United Kingdom
| | - Maurice B. Loughrey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | | | - Tim Maughan
- University of Oxford, Oxford, United Kingdom
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Felicity Lamrock
- School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom
| | - Viktor H. Koelzer
- Department of Pathology and Molecular Pathology, University and University Hospital of Zürich, Zürich, Switzerland
| | - Nigel B. Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Philip D. Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
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7
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Salvucci M, Crawford N, Stott K, Bullman S, Longley DB, Prehn JHM. Patients with mesenchymal tumours and high Fusobacteriales prevalence have worse prognosis in colorectal cancer (CRC). Gut 2022; 71:1600-1612. [PMID: 34497144 PMCID: PMC9279747 DOI: 10.1136/gutjnl-2021-325193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Transcriptomic-based subtyping, consensus molecular subtyping (CMS) and colorectal cancer intrinsic subtyping (CRIS) identify a patient subpopulation with mesenchymal traits (CMS4/CRIS-B) and poorer outcome. Here, we investigated the relationship between prevalence of Fusobacterium nucleatum (Fn) and Fusobacteriales, CMS/CRIS subtyping, cell type composition, immune infiltrates and host contexture to refine patient stratification and to identify druggable context-specific vulnerabilities. DESIGN We coupled cell culture experiments with characterisation of Fn/Fusobacteriales prevalence and host biology/microenviroment in tumours from two independent colorectal cancer patient cohorts (Taxonomy: n=140, colon and rectal cases of The Cancer Genome Atlas (TCGA-COAD-READ) cohort: n=605). RESULTS In vitro, Fn infection induced inflammation via nuclear factor kappa-light-chain-enhancer of activated B cells/tumour necrosis factor alpha in HCT116 and HT29 cancer cell lines. In patients, high Fn/Fusobacteriales were found in CMS1, microsatellite unstable () tumours, with infiltration of M1 macrophages, reduced M2 macrophages, and high interleukin (IL)-6/IL-8/IL-1β signalling. Analysis of the Taxonomy cohort suggested that Fn was prognostic for CMS4/CRIS-B patients, despite having lower Fn load than CMS1 patients. In the TCGA-COAD-READ cohort, we likewise identified a differential association between Fusobacteriales relative abundance and outcome when stratifying patients in mesenchymal (either CMS4 and/or CRIS-B) versus non-mesenchymal (neither CMS4 nor CRIS-B). Patients with mesenchymal tumours and high Fusobacteriales had approximately twofold higher risk of worse outcome. These associations were null in non-mesenchymal patients. Modelling the three-way association between Fusobacteriales prevalence, molecular subtyping and host contexture with logistic models with an interaction term disentangled the pathogen-host signalling relationship and identified aberrations (including NOTCH, CSF1-3 and IL-6/IL-8) as candidate targets. CONCLUSION This study identifies CMS4/CRIS-B patients with high Fn/Fusobacteriales prevalence as a high-risk subpopulation that may benefit from therapeutics targeting mesenchymal biology.
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Affiliation(s)
- Manuela Salvucci
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Nyree Crawford
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Katie Stott
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Susan Bullman
- Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Jochen H M Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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8
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Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, Wang J, Chen Z, Joughin BA, Li W, McKinley ET, Liu Q, Roland JT, Washington MK, Coffey RJ, Lauffenburger DA, Lau KS. Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer. Front Oncol 2022; 12:878920. [PMID: 35600339 PMCID: PMC9114773 DOI: 10.3389/fonc.2022.878920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1CreERT2/+;Apc2lox14/+) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.
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Affiliation(s)
- Paige N Vega
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Avlant Nilsson
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Manu P Kumar
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Hiroaki Niitsu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Alan J Simmons
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James Ro
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jiawei Wang
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Zhengyi Chen
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Brian A Joughin
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wei Li
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Eliot T McKinley
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert J Coffey
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Douglas A Lauffenburger
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ken S Lau
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
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9
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Jain AP, Sambath J, Sathe G, George IA, Pandey A, Thompson EW, Kumar P. Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. J Transl Med 2022; 20:84. [PMID: 35148768 PMCID: PMC8832824 DOI: 10.1186/s12967-021-03227-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/30/2021] [Indexed: 12/31/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a dynamic and complex cellular process that is known to be hijacked by cancer cells to facilitate invasion, metastasis and therapeutic resistance. Several quantitative measures to assess the interplay between EMT and cancer progression are available, based on large scale genome and transcriptome data. However, these large scale multi-omics studies have repeatedly illustrated a lack of correlation in mRNA and protein abundances that may be influenced by diverse post-translational regulation. Hence, it is imperative to understand how changes in the EMT proteome are associated with the process of oncogenic transformation. To this effect, we developed a parallel reaction monitoring-based targeted proteomics method for quantifying abundances of EMT-associated proteins across cancer cell lines. Our study revealed that quantitative measurement of EMT proteome which enabled a more accurate assessment than transcriptomics data and revealed specific discrepancies against a backdrop of generally strong concordance between proteomic and transcriptomic data. We further demonstrated that changes in our EMT proteome panel might play a role in tumor transformation across cancer types. In future, this EMT panel assay has the potential to be used for clinical samples to guide treatment choices and to congregate functional information for the development and advancing novel therapeutics.
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Affiliation(s)
- Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
| | - Janani Sambath
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Erik W Thompson
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia. .,School-Biomedical Sciences, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India. .,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India. .,Somaiya Institute of Research and Consultancy (SIRAC), Somaiya Vidyavihar University (SVU), Vidyavihar, Mumbai, 400077, Maharashtra, India.
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10
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Li S, Liu Q, Zhou H, Lu H, Wang X. Subtyping of sarcomas based on pathway enrichment scores in bulk and single cell transcriptomes. J Transl Med 2022; 20:48. [PMID: 35093080 PMCID: PMC8800234 DOI: 10.1186/s12967-022-03248-3] [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: 11/27/2021] [Accepted: 01/12/2022] [Indexed: 11/28/2022] Open
Abstract
Background Sarcomas are highly heterogeneous in molecular, pathologic, and clinical features. However, a classification of sarcomas by integrating different types of pathways remains mostly unexplored. Methods We performed hierarchical clustering analysis of sarcomas based on the enrichment scores of 14 pathways involved in immune, stromal, DNA damage repair (DDR), and oncogenic signatures in three bulk tumor transcriptome datasets. Results Consistently in the three datasets, sarcomas were classified into three subtypes: Immune Class (Imm-C), Stromal Class (Str-C), and DDR Class (DDR-C). Imm-C had the strongest anti-tumor immune signatures and the lowest intratumor heterogeneity (ITH); Str-C showed the strongest stromal signatures, the highest genomic stability and global methylation levels, and the lowest proliferation potential; DDR-C had the highest DDR activity, expression of the cell cycle pathway, tumor purity, stemness scores, proliferation potential, and ITH, the most frequent TP53 mutations, and the worst survival. We further validated the stability and reliability of our classification method by analyzing a single cell RNA-Seq (scRNA-seq) dataset. Based on the expression levels of five genes in the pathways of T cell receptor signaling, cell cycle, mismatch repair, focal adhesion, and calcium signaling, we built a linear risk scoring model (ICMScore) for sarcomas. We demonstrated that ICMScore was an adverse prognostic factor for sarcomas and many other cancers. Conclusions Our classification method provides novel insights into tumor biology and clinical implications for sarcomas. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03248-3.
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11
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Stromal scoring in advanced colon and rectal cancer: Stroma-rich tumors and their association with aggressive phenotypes. ARCHIVE OF ONCOLOGY 2022. [DOI: 10.2298/aoo210403003s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: Our aim was to explore relevance of the proportion between neoplastic cell component and tumor-associated stroma in order to assess its association with confirmed aggressive phenotypes of right/left colon and rectum cancers in a large series of patients. Methods: The quantification of stroma component was performed in patients diagnosed with colorectal adenocarcinoma who underwent surgical resection. The analyzed variables were age, gender, anatomical/pathological features, and tumor-stroma proportion. Tumor-stroma proportion was estimated based on slides used in routine pathology for determination of T status and was described as low, with a stromal percentage ?50% or high, with a stromal percentage >50%. The tumor-stroma proportion was estimated by two observers, and the inter-observer agreement was assessed. Results: The sample included 390 colorectal adenocarcinoma patients. Stroma-rich tumors were observed in 53.3% of cases. Well-differentiated tumors had the lowest stromal proportions (p = 0.028). Stroma-poor tumors showed less depth of invasion (p<0.001). High stromal content was observed in association with tumor budding, perineural, angiolymphatic, and lymph node involvement, and distant metastasis (p?0.001). Colorectal adenocarcinoma without lymph node or distant metastasis involvement had lower stromal proportion, while metastatic ones exhibited high stromal content (p <0.001). The inter-rater reliability (concordance) between the estimations of pathologists for tumor-stroma proportions was high (?=0.746). Conclusion: The tumorstroma proportion in colorectal adenocarcinoma was associated with adverse prognostic factors, reflecting the stage of the disease. Stroma-rich tumors showed a significant correlation with advancement of the disease and its aggressiveness. Due to its availability tumor-stroma proportion evaluation has high application potential and can complement current staging system for colorectal adenocarcinoma.
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12
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Pezeshkian Z, Nobili S, Peyravian N, Shojaee B, Nazari H, Soleimani H, Asadzadeh-Aghdaei H, Ashrafian Bonab M, Nazemalhosseini-Mojarad E, Mini E. Insights into the Role of Matrix Metalloproteinases in Precancerous Conditions and in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13246226. [PMID: 34944846 PMCID: PMC8699154 DOI: 10.3390/cancers13246226] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is one of the most common cancer worldwide. CRC is derived from polyps and many factors, such as Matrix Metalloproteinases (MMPs) can gain the progression of colorectal carcinogenesis. Many investigations have indicated the role of MMPs in CRC development while there is not enough knowledge about the function of MMPs in precancerous conditions. This review summarizes the current information about the role of MMPs in polyps and CRC progression. Abstract Colorectal cancer (CRC) is the third and second cancer for incidence and mortality worldwide, respectively, and is becoming prevalent in developing countries. Most CRCs derive from polyps, especially adenomatous polyps, which can gradually transform into CRC. The family of Matrix Metalloproteinases (MMPs) plays a critical role in the initiation and progression of CRC. Prominent MMPs, including MMP-1, MMP-2, MMP-7, MMP-8, MMP-9, MMP-12, MMP-13, MMP-14, and MMP-21, have been detected in CRC patients, and the expression of most of them correlates with a poor prognosis. Moreover, many studies have explored the inhibition of MMPs and targeted therapy for CRC, but there is not enough information about the role of MMPs in polyp malignancy. In this review, we discuss the role of MMPs in colorectal cancer and its pathogenesis
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Affiliation(s)
- Zahra Pezeshkian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19835-178, Iran; (Z.P.); (N.P.); (B.S.); (H.A.-A.)
| | - Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Noshad Peyravian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19835-178, Iran; (Z.P.); (N.P.); (B.S.); (H.A.-A.)
| | - Bahador Shojaee
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19835-178, Iran; (Z.P.); (N.P.); (B.S.); (H.A.-A.)
| | - Haniye Nazari
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Science, Islamic Azad University, Tehran 19395-1495, Iran;
| | - Hiva Soleimani
- Department of General Biology, Faculty of Fundamental Science, Islamic Azad University of Shahr-E-Qods, Tehran 37515-374, Iran;
| | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19835-178, Iran; (Z.P.); (N.P.); (B.S.); (H.A.-A.)
| | - Maziar Ashrafian Bonab
- School of Medicine, University of Sunderland, City Campus, Chester Road, Sunderland SR1 3SD, UK;
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19835-178, Iran
- Correspondence: (E.N.-M.); (E.M.)
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
- DENOTHE Excellence Center, University of Florence, 50139 Florence, Italy
- Correspondence: (E.N.-M.); (E.M.)
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13
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Volovetskiy AB, Malinina PA, Kapitannikova AY, Smetanina SV, Kruglova IA, Maslennikova AV. Isolation of Circulating Tumor Cells from Peripheral Blood Samples of Cancer Patients Using Microfluidic Technology. Sovrem Tekhnologii Med 2021; 12:62-68. [PMID: 34796020 PMCID: PMC8596232 DOI: 10.17691/stm2020.12.6.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Indexed: 11/23/2022] Open
Abstract
The aim of the investigation was to study the potential of an innovative microfluidic technology for the isolation of circulating tumor cells (CTCs) from the peripheral blood samples of cancer patients.
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Affiliation(s)
- A B Volovetskiy
- Researcher, Laboratory of Nanotheranostics, Institute for Molecular Medicine, Biomedical Science and Technology Park; I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Malaya Trubetskaya St., Moscow, 119991, Russia
| | - P A Malinina
- Clinical Resident, Department of Oncology, Radiation Therapy and Radiation Diagnostics; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - A Y Kapitannikova
- Researcher, Laboratory of Nanoteranology, Institute for Molecular Medicine, Biomedical Science and Technology Park; I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Malaya Trubetskaya St., Moscow, 119991, Russia
| | - S V Smetanina
- Head of the Сytological Laboratory; Nizhny Novgorod Regional Oncologic Dispensary, 11/1 Delovaya St., Nizhny Novgorod, 603163, Russia
| | - I A Kruglova
- Physician of Clinical Laboratory Diagnostics; City Hospital No.35, 47 Respublikanskaya St., Nizhny Novgorod, 603089, Russia
| | - A V Maslennikova
- Head of the Department of Oncology, Radiation Therapy and Radiation Diagnostics; Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia; Professor, Department of Biophysics National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
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14
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Loughrey MB, Fisher NC, McCooey AJ, Dunne PD. Comment on "Identification of EMT-related high-risk stage II colorectal cancer and characterisation of metastasis-related genes". Br J Cancer 2021; 124:1175-1176. [PMID: 33311590 PMCID: PMC7961054 DOI: 10.1038/s41416-020-01213-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Affiliation(s)
- Maurice B Loughrey
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Philip D Dunne
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
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15
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AKT3 Expression in Mesenchymal Colorectal Cancer Cells Drives Growth and Is Associated with Epithelial-Mesenchymal Transition. Cancers (Basel) 2021; 13:cancers13040801. [PMID: 33673003 PMCID: PMC7918753 DOI: 10.3390/cancers13040801] [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: 01/08/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Colorectal cancer can be subdivided into four distinct subtypes that are characterised by different clinical features and responses to therapies currently used in the clinic to treat this disease. One of those subtypes, called CMS4, is associated with a worse prognosis and poor response to therapies compared to other subtypes. We therefore set out to explore what proteins are differentially expressed and used in CMS4 to find potential new targets for therapy. We found that protein AKT3 is highly expressed in CMS4, and that active AKT3 inhibits a protein that stalls growth of cancer cells (p27KIP1). We can target AKT3 with inhibitors which leads to strongly reduced growth of cancer cell lines that are categorised as CMS4. Furthermore, our data suggests that high AKT3 expression in tumour cells may be used to identify poor prognosis colorectal cancer patients. Future research should point out if high AKT3 expression can be used to select colorectal cancer patients that have a poor prognosis but that could benefit from AKT3-targeted treatment. Abstract Colorectal cancer (CRC) is a heterogeneous disease that can currently be subdivided into four distinct consensus molecular subtypes (CMS) based on gene expression profiling. The CMS4 subtype is marked by high expression of mesenchymal genes and is associated with a worse overall prognosis compared to other CMSs. Importantly, this subtype responds poorly to the standard therapies currently used to treat CRC. We set out to explore what regulatory signalling networks underlie the CMS4 phenotype of cancer cells, specifically, by analysing which kinases were more highly expressed in this subtype compared to others. We found AKT3 to be expressed in the cancer cell epithelium of CRC specimens, patient derived xenograft (PDX) models and in (primary) cell cultures representing CMS4. Importantly, chemical inhibition or knockout of this gene hampers outgrowth of this subtype, as AKT3 controls expression of the cell cycle regulator p27KIP1. Furthermore, high AKT3 expression was associated with high expression of epithelial-mesenchymal transition (EMT) genes, and this observation could be expanded to cell lines representing other carcinoma types. More importantly, this association allowed for the identification of CRC patients with a high propensity to metastasise and an associated poor prognosis. High AKT3 expression in the tumour epithelial compartment may thus be used as a surrogate marker for EMT and may allow for a selection of CRC patients that could benefit from AKT3-targeted therapy.
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16
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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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17
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Abstract
Epithelial–mesenchymal plasticity contributes to many biological processes, including tumor progression. Various epithelial–mesenchymal transition (EMT) responses have been reported and no common, EMT-defining gene expression program has been identified. Here, we have performed a comparative analysis of the EMT response, leveraging highly multiplexed single-cell RNA sequencing (scRNA-seq) to measure expression profiles of 103,999 cells from 960 samples, comprising 12 EMT time course experiments and independent kinase inhibitor screens for each. We demonstrate that the EMT is vastly context specific, with an average of only 22% of response genes being shared between any two conditions, and over half of all response genes were restricted to 1–2 time course experiments. Further, kinase inhibitor screens revealed signaling dependencies and modularity of these responses. These findings suggest that the EMT is not simply a single, linear process, but is highly variable and modular, warranting quantitative frameworks for understanding nuances of the transition. It is unclear if a common EMT expression program exists. Here, the authors perform multiplexed single-cell RNA sequencing across 12 EMT time courses and 16 kinase inhibitor screens, and find that EMT transcriptional responses are context specific and EMT is not a single, linear transition.
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18
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Galmiche A, Saidak Z, Bouaoud J, Mirghani H, Page C, Dakpé S, Clatot F. Genomics and precision surgery for head and neck squamous cell carcinoma. Cancer Lett 2020; 481:45-54. [PMID: 32272147 DOI: 10.1016/j.canlet.2020.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/26/2020] [Accepted: 04/02/2020] [Indexed: 12/24/2022]
Abstract
The identification of the biological determinants that shape the response of tumors to medical therapies offers perspectives for better patient stratification and therapeutic targeting. Here, we discuss how genomics could help to improve the surgical treatment of head and neck squamous cell carcinoma (HNSCC). We examine the potential use of genomic analyses for: i) refining and standardizing the indications for surgery, ii) the choice of surgical procedure, and iii) the follow-up of patients with resected tumors. We highlight the studies that used genomics to explore the contribution of tumor biology to the outcome of surgery. We discuss the important developments that are challenging current surgical practice in HNSCC, such as neoadjuvant immunotherapy and the analysis of circulating DNA. Genomic analyses provide practical tools that could help improve the pathological diagnosis and staging of HNSCC, and increase the appreciation of the importance of tumor biology in the outcome of surgery. Identification of biomarkers will likely contribute to a move toward precision surgery of HNSCC, i.e. the personalization of surgical practice based on tumor biology.
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Affiliation(s)
- Antoine Galmiche
- EA7516 « CHIMERE », Université de Picardie Jules Verne, Amiens, France; Department of Biochemistry, Centre de Biologie Humaine, CHU, Amiens, France.
| | - Zuzana Saidak
- EA7516 « CHIMERE », Université de Picardie Jules Verne, Amiens, France; Department of Molecular Oncobiology, Centre de Biologie Humaine, CHU, Amiens, France
| | - Jebrane Bouaoud
- Department of Maxillofacial Surgery and Stomatology, Pitié Salpétrière Hospital, Pierre et Marie Curie University Paris 6, Sorbonne Paris Cité, Paris, France
| | - Haitham Mirghani
- Department of Otorhinolaryngology and Head and Neck Surgery, Georges Pompidou European Hospital, Paris Descartes University, Paris, France
| | - Cyril Page
- Department of Otorhinolaryngology, CHU, Amiens, France
| | - Stéphanie Dakpé
- EA7516 « CHIMERE », Université de Picardie Jules Verne, Amiens, France; Department of Maxillofacial Surgery, CHU, Amiens, France
| | - Florian Clatot
- Centre Henri Becquerel, Rouen, France; INSERM U1245, IRON Team, Rouen, France
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19
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Jackstadt R, van Hooff SR, Leach JD, Cortes-Lavaud X, Lohuis JO, Ridgway RA, Wouters VM, Roper J, Kendall TJ, Roxburgh CS, Horgan PG, Nixon C, Nourse C, Gunzer M, Clark W, Hedley A, Yilmaz OH, Rashid M, Bailey P, Biankin AV, Campbell AD, Adams DJ, Barry ST, Steele CW, Medema JP, Sansom OJ. Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis. Cancer Cell 2019; 36:319-336.e7. [PMID: 31526760 PMCID: PMC6853173 DOI: 10.1016/j.ccell.2019.08.003] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/31/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022]
Abstract
The metastatic process of colorectal cancer (CRC) is not fully understood and effective therapies are lacking. We show that activation of NOTCH1 signaling in the murine intestinal epithelium leads to highly penetrant metastasis (100% metastasis; with >80% liver metastases) in KrasG12D-driven serrated cancer. Transcriptional profiling reveals that epithelial NOTCH1 signaling creates a tumor microenvironment (TME) reminiscent of poorly prognostic human CRC subtypes (CMS4 and CRIS-B), and drives metastasis through transforming growth factor (TGF) β-dependent neutrophil recruitment. Importantly, inhibition of this recruitment with clinically relevant therapeutic agents blocks metastasis. We propose that NOTCH1 signaling is key to CRC progression and should be exploited clinically.
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Affiliation(s)
| | - Sander R van Hooff
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Joshua D Leach
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | | | | | | | - Valérie M Wouters
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University, Durham, NC, USA
| | - Timothy J Kendall
- Division of Pathology/Centre for Inflammation Research, University of Edinburgh, UK
| | - Campbell S Roxburgh
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Glasgow, UK
| | - Paul G Horgan
- Academic Unit of Surgery, School of Medicine, University of Glasgow, Glasgow, UK
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | | | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Omer H Yilmaz
- Division of Gastroenterology, Tufts Medical Center, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mamunur Rashid
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Peter Bailey
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | - Andrew V Biankin
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | | | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Simon T Barry
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Colin W Steele
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK.
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20
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Dutton LR, Hoare OP, McCorry AMB, Redmond KL, Adam NE, Canamara S, Bingham V, Mullan PB, Lawler M, Dunne PD, Brazil DP. Fibroblast-derived Gremlin1 localises to epithelial cells at the base of the intestinal crypt. Oncotarget 2019; 10:4630-4639. [PMID: 31384391 PMCID: PMC6659803 DOI: 10.18632/oncotarget.27050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/19/2019] [Indexed: 01/15/2023] Open
Abstract
Gremlin1 (GREM1) is a secreted glycoprotein member of the differential screening-selected gene in aberrant neuroblastoma (DAN) family of bone morphogenetic protein (BMP) antagonists, which binds to BMPs preventing their receptor engagement. Previous studies have identified that stage II colorectal cancer (CRC) patients with high levels of GREM1 gene expression in their tumour tissue have a poorer prognosis. Using a series of in silico and in situ methodologies, we demonstrate that GREM1 gene expression is significantly higher (p < 0.0001) in CRC consensus molecular subtype 4 (CMS4), compared to the other CMS subtypes and correlates (p < 0.0001) with levels of cancer-associated fibroblasts (CAFs) within the CRC tumour microenvironment (TME). Our optimised immunohistochemistry protocol identified endogenous GREM1 protein expression in both the muscularis mucosa and adjacent colonic crypt bases in mouse intestine, in contrast to RNA expression which was shown to localise specifically to the muscularis mucosa, as determined by in situ hybridisation. Importantly, we demonstrate that cells with high levels of GREM1 expression display low levels of phospho-Smad1/5, consistent with reduced BMP signalling. Taken together, these data highlight a novel paracrine signalling circuit, which involves uptake of mature GREM1 protein by colonic crypt cells following secretion from neighbouring fibroblasts in the TME.
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Affiliation(s)
- Louise R Dutton
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,These authors contributed equally to this work
| | - Owen P Hoare
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,These authors contributed equally to this work
| | - Amy M B McCorry
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,These authors contributed equally to this work
| | - Keara L Redmond
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Noor Eisa Adam
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, United Arab Emirates
| | - Shannon Canamara
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Indonesia International Institute for Life-Sciences, University of East Jakarta, Jakarta Timur, Indonesia
| | - Victoria Bingham
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Paul B Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,Co-senior authors
| | - Derek P Brazil
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Co-senior authors
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21
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Libanje F, Raingeaud J, Luan R, Thomas Z, Zajac O, Veiga J, Marisa L, Adam J, Boige V, Malka D, Goéré D, Hall A, Soazec J, Prall F, Gelli M, Dartigues P, Jaulin F. ROCK2 inhibition triggers the collective invasion of colorectal adenocarcinomas. EMBO J 2019; 38:e99299. [PMID: 31304629 PMCID: PMC6627234 DOI: 10.15252/embj.201899299] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/19/2019] [Accepted: 05/10/2019] [Indexed: 12/20/2022] Open
Abstract
The metastatic progression of cancer is a multi-step process initiated by the local invasion of the peritumoral stroma. To identify the mechanisms underlying colorectal carcinoma (CRC) invasion, we collected live human primary cancer specimens at the time of surgery and monitored them ex vivo. This revealed that conventional adenocarcinomas undergo collective invasion while retaining their epithelial glandular architecture with an inward apical pole delineating a luminal cavity. To identify the underlying mechanisms, we used microscopy-based assays on 3D organotypic cultures of Caco-2 cysts as a model system. We performed two siRNA screens targeting Rho-GTPases effectors and guanine nucleotide exchange factors. These screens revealed that ROCK2 inhibition triggers the initial leader/follower polarization of the CRC cell cohorts and induces collective invasion. We further identified FARP2 as the Rac1 GEF necessary for CRC collective invasion. However, FARP2 activation is not sufficient to trigger leader cell formation and the concomitant inhibition of Myosin-II is required to induce invasion downstream of ROCK2 inhibition. Our results contrast with ROCK pro-invasive function in other cancers, stressing that the molecular mechanism of metastatic spread likely depends on tumour types and invasion mode.
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Affiliation(s)
| | | | - Rui Luan
- INSERM U‐981Gustave RoussyVillejuifFrance
| | | | - Olivier Zajac
- INSERM U‐981Gustave RoussyVillejuifFrance
- Present address:
Department of Translational ResearchCurie InstituteParisFrance
| | - Joel Veiga
- Cell Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
- Present address:
Imagine InstituteParisFrance
| | - Laetitia Marisa
- Programme “Cartes d'Identité des Tumeurs”Ligue Nationale Contre le CancerParisFrance
| | - Julien Adam
- Pathology DepartmentGustave RoussyVillejuifFrance
| | | | - David Malka
- Digestive Cancer UnitGustave RoussyVillejuifFrance
| | - Diane Goéré
- Digestive Cancer UnitGustave RoussyVillejuifFrance
| | - Alan Hall
- Cell Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
| | | | - Friedrich Prall
- Institute of PathologyUniversity Medicine of RostockRostockGermany
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