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López-Gil JC, García-Silva S, Ruiz-Cañas L, Navarro D, Palencia-Campos A, Giráldez-Trujillo A, Earl J, Dorado J, Gómez-López G, Monfort-Vengut A, Alcalá S, Gaida MM, García-Mulero S, Cabezas-Sáinz P, Batres-Ramos S, Barreto E, Sánchez-Tomero P, Vallespinós M, Ambler L, Lin ML, Aicher A, García García de Paredes A, de la Pinta C, Sanjuanbenito A, Ruz-Caracuel I, Rodríguez-Garrote M, Guerra C, Carrato A, de Cárcer G, Sánchez L, Nombela-Arrieta C, Espinet E, Sanchez-Arevalo Lobo VJ, Heeschen C, Sainz B. The Peptidoglycan Recognition Protein 1 confers immune evasive properties on pancreatic cancer stem cells. Gut 2024; 73:1489-1508. [PMID: 38754953 PMCID: PMC11347225 DOI: 10.1136/gutjnl-2023-330995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) has limited therapeutic options, particularly with immune checkpoint inhibitors. Highly chemoresistant 'stem-like' cells, known as cancer stem cells (CSCs), are implicated in PDAC aggressiveness. Thus, comprehending how this subset of cells evades the immune system is crucial for advancing novel therapies. DESIGN We used the KPC mouse model (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre) and primary tumour cell lines to investigate putative CSC populations. Transcriptomic analyses were conducted to pinpoint new genes involved in immune evasion. Overexpressing and knockout cell lines were established with lentiviral vectors. Subsequent in vitro coculture assays, in vivo mouse and zebrafish tumorigenesis studies, and in silico database approaches were performed. RESULTS Using the KPC mouse model, we functionally confirmed a population of cells marked by EpCAM, Sca-1 and CD133 as authentic CSCs and investigated their transcriptional profile. Immune evasion signatures/genes, notably the gene peptidoglycan recognition protein 1 (PGLYRP1), were significantly overexpressed in these CSCs. Modulating PGLYRP1 impacted CSC immune evasion, affecting their resistance to macrophage-mediated and T-cell-mediated killing and their tumourigenesis in immunocompetent mice. Mechanistically, tumour necrosis factor alpha (TNFα)-regulated PGLYRP1 expression interferes with the immune tumour microenvironment (TME) landscape, promoting myeloid cell-derived immunosuppression and activated T-cell death. Importantly, these findings were not only replicated in human models, but clinically, secreted PGLYRP1 levels were significantly elevated in patients with PDAC. CONCLUSIONS This study establishes PGLYRP1 as a novel CSC-associated marker crucial for immune evasion, particularly against macrophage phagocytosis and T-cell killing, presenting it as a promising target for PDAC immunotherapy.
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Affiliation(s)
- Juan Carlos López-Gil
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Department of Biochemistry, Autónoma University of Madrid (UAM), Madrid, Spain
| | - Susana García-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Laura Ruiz-Cañas
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Biobanco Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Diego Navarro
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Department of Biochemistry, Autónoma University of Madrid (UAM), Madrid, Spain
| | - Adrián Palencia-Campos
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Antonio Giráldez-Trujillo
- Grupo de Oncología Cutánea, Servicio de Anatomía Patológica, Hospiral Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Julie Earl
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
| | - Jorge Dorado
- Stem Cells and Cancer Group, Clinical Research Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Monfort-Vengut
- Cell Cycle and Cancer Biomarkers Laboratory, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
| | - Sonia Alcalá
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Department of Biochemistry, Autónoma University of Madrid (UAM), Madrid, Spain
| | - Matthias M Gaida
- Institute of Pathology, JGU-Mainz, University Medical Center Mainz, Mainz, Germany
- TRON, JGU-Mainz, Translational Oncology at the University Medical Center, Mainz, Germany
- Research Center for Immunotherapy, JGU-Mainz, University Medical Center Mainz, Mainz, Germany
| | - Sandra García-Mulero
- Department of Pathology and Experimental Therapy, Universidad de Barcelona Facultad de Medicina y Ciencias de La Salud, Barcelona, Spain
- Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), IDIBELL, Barcelona, Spain
| | - Pablo Cabezas-Sáinz
- Department of Zoology, Genetics and Physical Anthropology, Veterinary Faculty, Universidade de Santiago de Compostela, Lugo, Spain
| | - Sandra Batres-Ramos
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Emma Barreto
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
- School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Spain
| | - Patricia Sánchez-Tomero
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Mireia Vallespinós
- Stem Cells and Cancer Group, Clinical Research Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Leah Ambler
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Meng-Lay Lin
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alexandra Aicher
- Precision Immunotherapy, Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Ana García García de Paredes
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Gastroenterology and Hepatology, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | | | - Alfonso Sanjuanbenito
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
- Pancreatic and Biliopancreatic Surgery Unit, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Ignacio Ruz-Caracuel
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
- Ramon y Cajal University Hospital Anatomy Pathology Service, Madrid, Spain
- Molecular Pathology of Cancer Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Mercedes Rodríguez-Garrote
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
- Medical Oncology Service, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Carmen Guerra
- Experimental Oncology Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alfredo Carrato
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
- Medical Oncology Service, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Guillermo de Cárcer
- Cell Cycle and Cancer Biomarkers Laboratory, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
| | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, Veterinary Faculty, Universidade de Santiago de Compostela, Lugo, Spain
| | - César Nombela-Arrieta
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, Zürich, Switzerland
| | - Elisa Espinet
- Department of Pathology and Experimental Therapy, Universidad de Barcelona Facultad de Medicina y Ciencias de La Salud, Barcelona, Spain
- Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), IDIBELL, Barcelona, Spain
| | - Víctor Javier Sanchez-Arevalo Lobo
- Grupo de Oncología Cutánea, Servicio de Anatomía Patológica, Hospiral Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Grupo de Oncología Molecular, Instituto de Investigaciones Biosanitarias, Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Spain
| | - Christopher Heeschen
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute - FPO - IRCCS, Candiolo (TO), Italy
| | - Bruno Sainz
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Cancer Department, Instituto de Investigaciones Biomédicas (IIBM) Sols-Morreale CSIC-UAM, Madrid, Spain
- Biomarkers and Personalized Approach to Cancer Group (BIOPAC), Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Área Cáncer, Centro de Investigación Biomédica en Red (CIBERONC), ISCIII, Madrid, Spain
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Thakore PI, Schnell A, Huang L, Zhao M, Hou Y, Christian E, Zaghouani S, Wang C, Singh V, Singaraju A, Krishnan RK, Kozoriz D, Ma S, Sankar V, Notarbartolo S, Buenrostro JD, Sallusto F, Patsopoulos NA, Rozenblatt-Rosen O, Kuchroo VK, Regev A. BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H17 cells. Nat Immunol 2024; 25:1395-1410. [PMID: 39009838 DOI: 10.1038/s41590-024-01901-1] [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: 05/20/2022] [Accepted: 06/18/2024] [Indexed: 07/17/2024]
Abstract
Interleukin-17 (IL-17)-producing helper T (TH17) cells are heterogenous and consist of nonpathogenic TH17 (npTH17) cells that contribute to tissue homeostasis and pathogenic TH17 (pTH17) cells that mediate tissue inflammation. Here, we characterize regulatory pathways underlying TH17 heterogeneity and discover substantial differences in the chromatin landscape of npTH17 and pTH17 cells both in vitro and in vivo. Compared to other CD4+ T cell subsets, npTH17 cells share accessible chromatin configurations with regulatory T cells, whereas pTH17 cells exhibit features of both npTH17 cells and type 1 helper T (TH1) cells. Integrating single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), we infer self-reinforcing and mutually exclusive regulatory networks controlling different cell states and predicted transcription factors regulating TH17 cell pathogenicity. We validate that BACH2 promotes immunomodulatory npTH17 programs and restrains proinflammatory TH1-like programs in TH17 cells in vitro and in vivo. Furthermore, human genetics implicate BACH2 in multiple sclerosis. Overall, our work identifies regulators of TH17 heterogeneity as potential targets to mitigate autoimmunity.
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Affiliation(s)
- Pratiksha I Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Alexandra Schnell
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Linglin Huang
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Maryann Zhao
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yu Hou
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Elena Christian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah Zaghouani
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chao Wang
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology, University of Toronto and Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Vasundhara Singh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anvita Singaraju
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh Kumar Krishnan
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Deneen Kozoriz
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venkat Sankar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuele Notarbartolo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Infectious Diseases Unit, Milan, Italy
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Nikolaos A Patsopoulos
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham & Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay K Kuchroo
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
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