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1
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Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet 2024:10.1038/s41588-024-01743-5. [PMID: 38811842 DOI: 10.1038/s41588-024-01743-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/04/2024] [Indexed: 05/31/2024]
Abstract
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
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Affiliation(s)
- Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob W Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Salvador Casaní-Galdón
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Jennifer M Umhoefer
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Katalin Sandor
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vinh Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian M Garrido
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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2
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Schlenker R, Schwalie PC, Dettling S, Huesser T, Irmisch A, Mariani M, Martínez Gómez JM, Ribeiro A, Limani F, Herter S, Yángüez E, Hoves S, Somandin J, Siebourg-Polster J, Kam-Thong T, de Matos IG, Umana P, Dummer R, Levesque MP, Bacac M. Myeloid-T cell interplay and cell state transitions associated with checkpoint inhibitor response in melanoma. MED 2024:S2666-6340(24)00127-2. [PMID: 38593812 DOI: 10.1016/j.medj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/23/2023] [Accepted: 03/17/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The treatment of melanoma, the deadliest form of skin cancer, has greatly benefited from immunotherapy. However, many patients do not show a durable response, which is only partially explained by known resistance mechanisms. METHODS We performed single-cell RNA sequencing of tumor immune infiltrates and matched peripheral blood mononuclear cells of 22 checkpoint inhibitor (CPI)-naive stage III-IV metastatic melanoma patients. After sample collection, the same patients received CPI treatment, and their response was assessed. FINDINGS CPI responders showed high levels of classical monocytes in peripheral blood, which preferentially transitioned toward CXCL9-expressing macrophages in tumors. Trajectories of tumor-infiltrating CD8+ T cells diverged at the level of effector memory/stem-like T cells, with non-responder cells progressing into a state characterized by cellular stress and apoptosis-related gene expression. Consistently, predicted non-responder-enriched myeloid-T/natural killer cell interactions were primarily immunosuppressive, while responder-enriched interactions were supportive of T cell priming and effector function. CONCLUSIONS Our study illustrates that the tumor immune microenvironment prior to CPI treatment can be indicative of response. In perspective, modulating the myeloid and/or effector cell compartment by altering the described cell interactions and transitions could improve immunotherapy response. FUNDING This research was funded by Roche Pharma Research and Early Development.
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Affiliation(s)
- Ramona Schlenker
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany.
| | | | - Steffen Dettling
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany
| | - Tamara Huesser
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marisa Mariani
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alison Ribeiro
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Florian Limani
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Sylvia Herter
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Emilio Yángüez
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Sabine Hoves
- Roche Innovation Center Munich, Roche Pharma Research and Early Development (pRED), Penzberg, Germany
| | - Jitka Somandin
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | | | | | | | - Pablo Umana
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marina Bacac
- Roche Innovation Center Zurich, pRED, Schlieren, Switzerland
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3
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Wienke J, Visser LL, Kholosy WM, Keller KM, Barisa M, Poon E, Munnings-Tomes S, Himsworth C, Calton E, Rodriguez A, Bernardi R, van den Ham F, van Hooff SR, Matser YAH, Tas ML, Langenberg KPS, Lijnzaad P, Borst AL, Zappa E, Bergsma FJ, Strijker JGM, Verhoeven BM, Mei S, Kramdi A, Restuadi R, Sanchez-Bernabeu A, Cornel AM, Holstege FCP, Gray JC, Tytgat GAM, Scheijde-Vermeulen MA, Wijnen MHWA, Dierselhuis MP, Straathof K, Behjati S, Wu W, Heck AJR, Koster J, Nierkens S, Janoueix-Lerosey I, de Krijger RR, Baryawno N, Chesler L, Anderson J, Caron HN, Margaritis T, van Noesel MM, Molenaar JJ. Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy. Cancer Cell 2024; 42:283-300.e8. [PMID: 38181797 PMCID: PMC10864003 DOI: 10.1016/j.ccell.2023.12.008] [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: 02/15/2023] [Revised: 11/10/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Pediatric patients with high-risk neuroblastoma have poor survival rates and urgently need more effective treatment options with less side effects. Since novel and improved immunotherapies may fill this need, we dissect the immunoregulatory interactions in neuroblastoma by single-cell RNA-sequencing of 24 tumors (10 pre- and 14 post-chemotherapy, including 5 pairs) to identify strategies for optimizing immunotherapy efficacy. Neuroblastomas are infiltrated by natural killer (NK), T and B cells, and immunosuppressive myeloid populations. NK cells show reduced cytotoxicity and T cells have a dysfunctional profile. Interaction analysis reveals a vast immunoregulatory network and identifies NECTIN2-TIGIT as a crucial immune checkpoint. Combined blockade of TIGIT and PD-L1 significantly reduces neuroblastoma growth, with complete responses (CR) in vivo. Moreover, addition of TIGIT+PD-L1 blockade to standard relapse treatment in a chemotherapy-resistant Th-ALKF1174L/MYCN 129/SvJ syngeneic model induces CR. In conclusion, our integrative analysis provides promising targets and a rationale for immunotherapeutic combination strategies.
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Affiliation(s)
- Judith Wienke
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Lindy L Visser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Waleed M Kholosy
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Kaylee M Keller
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marta Barisa
- Cancer Section, Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Sophie Munnings-Tomes
- Cancer Section, Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Courtney Himsworth
- Cancer Section, Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Elizabeth Calton
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | | | - Ronald Bernardi
- Genentech, A Member of the Roche Group, South San Francisco, CA, USA
| | - Femke van den Ham
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Yvette A H Matser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Michelle L Tas
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anne L Borst
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Elisa Zappa
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | | | - Bronte M Verhoeven
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Amira Kramdi
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Restuadi Restuadi
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Alvaro Sanchez-Bernabeu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht University, Utrecht, the Netherlands
| | - Annelisa M Cornel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Juliet C Gray
- Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | | | | | - Marc H W A Wijnen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Karin Straathof
- University College London (UCL) Great Ormond Street Institute of Child Health, London, UK; UCL Cancer Institute, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht University, Utrecht, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht University, Utrecht, the Netherlands
| | - Jan Koster
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Amsterdam, the Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Isabelle Janoueix-Lerosey
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - John Anderson
- Cancer Section, Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, England, UK
| | | | | | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Division Imaging & Cancer, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
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4
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Shan F, Cillo AR, Cardello C, Yuan DY, Kunning SR, Cui J, Lampenfeld C, Williams AM, McDonough AP, Pennathur A, Luketich JD, Kirkwood JM, Ferris RL, Bruno TC, Workman CJ, Benos PV, Vignali DAA. Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells. Sci Immunol 2023; 8:eadf6717. [PMID: 37713508 PMCID: PMC11045170 DOI: 10.1126/sciimmunol.adf6717] [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: 11/05/2022] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Human regulatory T cells (Tregs) are crucial regulators of tissue repair, autoimmune diseases, and cancer. However, it is challenging to inhibit the suppressive function of Tregs for cancer therapy without affecting immune homeostasis. Identifying pathways that may distinguish tumor-restricted Tregs is important, yet the transcriptional programs that control intratumoral Treg gene expression, and that are distinct from Tregs in healthy tissues, remain largely unknown. We profiled single-cell transcriptomes of CD4+ T cells in tumors and peripheral blood from patients with head and neck squamous cell carcinomas (HNSCC) and those in nontumor tonsil tissues and peripheral blood from healthy donors. We identified a subpopulation of activated Tregs expressing multiple tumor necrosis factor receptor (TNFR) genes (TNFR+ Tregs) that is highly enriched in the tumor microenvironment (TME) compared with nontumor tissue and the periphery. TNFR+ Tregs are associated with worse prognosis in HNSCC and across multiple solid tumor types. Mechanistically, the transcription factor BATF is a central component of a gene regulatory network that governs key aspects of TNFR+ Tregs. CRISPR-Cas9-mediated BATF knockout in human activated Tregs in conjunction with bulk RNA sequencing, immunophenotyping, and in vitro functional assays corroborated the central role of BATF in limiting excessive activation and promoting the survival of human activated Tregs. Last, we identified a suite of surface molecules reflective of the BATF-driven transcriptional network on intratumoral Tregs in patients with HNSCC. These findings uncover a primary transcriptional regulator of highly suppressive intratumoral Tregs, highlighting potential opportunities for therapeutic intervention in cancer without affecting immune homeostasis.
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Affiliation(s)
- Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R. Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Daniel Y. Yuan
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sheryl R. Kunning
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Caleb Lampenfeld
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Asia M. Williams
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Alexandra P. McDonough
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Arjun Pennathur
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James D. Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John M. Kirkwood
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert L. Ferris
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tullia C. Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Creg J. Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Dario A. A. Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
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5
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Oh K, Yoo YJ, Torre-Healy LA, Rao M, Fassler D, Wang P, Caponegro M, Gao M, Kim J, Sasson A, Georgakis G, Powers S, Moffitt RA. Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype. Nat Commun 2023; 14:5226. [PMID: 37633924 PMCID: PMC10460409 DOI: 10.1038/s41467-023-40895-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Bulk analyses of pancreatic ductal adenocarcinoma (PDAC) samples are complicated by the tumor microenvironment (TME), i.e. signals from fibroblasts, endocrine, exocrine, and immune cells. Despite this, we and others have established tumor and stroma subtypes with prognostic significance. However, understanding of underlying signals driving distinct immune and stromal landscapes is still incomplete. Here we integrate 92 single cell RNA-seq samples from seven independent studies to build a reproducible PDAC atlas with a focus on tumor-TME interdependence. Patients with activated stroma are synonymous with higher myofibroblastic and immunogenic fibroblasts, and furthermore show increased M2-like macrophages and regulatory T-cells. Contrastingly, patients with 'normal' stroma show M1-like recruitment, elevated effector and exhausted T-cells. To aid interoperability of future studies, we provide a pretrained cell type classifier and an atlas of subtype-based signaling factors that we also validate in mouse data. Ultimately, this work leverages the heterogeneity among single-cell studies to create a comprehensive view of the orchestra of signaling interactions governing PDAC.
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Affiliation(s)
- Ki Oh
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Yun Jae Yoo
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Luke A Torre-Healy
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Manisha Rao
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
| | - Danielle Fassler
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Pei Wang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Michael Caponegro
- Department of Pharmacology, Stony Brook University, Stony Brook, NY, USA
| | - Mei Gao
- Department of Surgery, University of Kentucky and Markey Cancer Center, Lexington, KY, USA
| | - Joseph Kim
- Department of Surgery, University of Kentucky and Markey Cancer Center, Lexington, KY, USA
| | - Aaron Sasson
- Department of Surgery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Georgios Georgakis
- Department of Surgery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Scott Powers
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Richard A Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA.
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA.
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Tvingsholm SA, Frej MS, Rafa VM, Hansen UK, Ormhøj M, Tyron A, Jensen AWP, Kadivar M, Bentzen AK, Munk KK, Aasbjerg GN, Ternander JSH, Heeke C, Tamhane T, Schmess C, Funt SA, Kjeldsen JW, Kverneland AH, Met Ö, Draghi A, Jakobsen SN, Donia M, Marie Svane I, Hadrup SR. TCR-engaging scaffolds selectively expand antigen-specific T-cells with a favorable phenotype for adoptive cell therapy. J Immunother Cancer 2023; 11:e006847. [PMID: 37586765 PMCID: PMC10432666 DOI: 10.1136/jitc-2023-006847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Adoptive cell therapy (ACT) has shown promising results for the treatment of cancer and viral infections. Successful ACT relies on ex vivo expansion of large numbers of desired T-cells with strong cytotoxic capacity and in vivo persistence, which constitutes the greatest challenge to current ACT strategies. Here, in this study, we present a novel technology for ex vivo expansion of antigen-specific T-cells; artificial antigen-presenting scaffolds (Ag-scaffolds) consisting of a dextran-polysaccharide backbone, decorated with combinations of peptide-Major Histocompatibility Complex (pMHC), cytokines and co-stimulatory molecules, enabling coordinated stimulation of antigen-specific T-cells. METHODS The capacity of Ag-scaffolds to expand antigen-specific T-cells was explored in ex vivo cultures with peripheral blood mononuclear cells from healthy donors and patients with metastatic melanoma. The resulting T-cell products were assessed for phenotypic and functional characteristics. RESULTS We identified an optimal Ag-scaffold for expansion of T-cells for ACT, carrying pMHC and interleukin-2 (IL-2) and IL-21, with which we efficiently expanded both virus-specific and tumor-specific CD8+ T cells from peripheral blood of healthy donors and patients, respectively. The resulting T-cell products were characterized by a high frequency of antigen-specific cells with high self-renewal capacity, low exhaustion, a multifunctional cytokine profile upon antigen-challenge and superior tumor killing capacity. This demonstrates that the coordinated stimuli provided by an optimized stoichiometry of TCR engaging (pMHC) and stimulatory (cytokine) moieties is essential to obtain desired T-cell characteristics. To generate an 'off-the-shelf' multitargeting Ag-scaffold product of relevance to patients with metastatic melanoma, we identified the 30 most frequently recognized shared HLA-A0201-restricted melanoma epitopes in a cohort of 87 patients. By combining these in an Ag-scaffold product, we were able to expand tumor-specific T-cells from 60-70% of patients with melanoma, yielding a multitargeted T-cell product with up to 25% specific and phenotypically and functionally improved T cells. CONCLUSIONS Taken together, the Ag-scaffold represents a promising new technology for selective expansion of antigen-specific CD8+ T cells directly from blood, yielding a highly specific and functionally enhanced T-cell product for ACT.
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Affiliation(s)
| | | | - Vibeke Mindahl Rafa
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Maria Ormhøj
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Alexander Tyron
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Agnete W P Jensen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Mohammad Kadivar
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Kamilla K Munk
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Gitte N Aasbjerg
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Christina Heeke
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Schmess
- NMI Natural and Medical Science Institute, University of Tübingen, Tubingen, Germany
| | - Samuel A Funt
- Deptartment of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Julie Westerlin Kjeldsen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Anders Handrup Kverneland
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Özcan Met
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Copenhagen, Denmark
| | - Arianna Draghi
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Søren Nyboe Jakobsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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Xu X, Sun R, Li Y, Wang J, Zhang M, Xiong X, Xie D, Jin X, Zhao M. Comprehensive bioinformatic analysis of the expression and prognostic significance of TSC22D domain family genes in adult acute myeloid leukemia. BMC Med Genomics 2023; 16:117. [PMID: 37237254 DOI: 10.1186/s12920-023-01550-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND TSC22D domain family genes, including TSC22D1-4, play a principal role in cancer progression. However, their expression profiles and prognostic significance in adult acute myeloid leukemia (AML) remain unknown. METHODS The online databases, including HPA, CCLE, EMBL-EBI, GEPIA2, BloodSpot, GENT2, UCSCXenaShiny, GSCALite, cBioportal, and GenomicScape, utilized the data of TCGA and GEO to investigate gene expression, mutation, copy number variation (CNV), and prognostic significance of the TSC22D domain family in adult AML. Computational analysis of resistance (CARE) was used to explore the effect of TSC22D3 expression on drug response. Functional enrichment analysis of TSC22D3 was performed in the TRRUST Version 2 database. The STRING, Pathway Commons, and AnimalTFDB3.0 databases were used to investigate the protein-protein interaction (PPI) network of TSC22D3. Harmonizome was used to predict target genes and kinases regulated by TSC22D3. The StarBase v2.0 and CancermiRNome databases were used to predict miRNAs regulated by TSC22D3. UCSCXenaShiny was used to investigate the correlation between TSC22D3 expression and immune infiltration. RESULTS Compared with normal adult hematopoietic stem cells (HSCs), the expression of TSC22D3 and TSC22D4 in adult AML tissues was markedly up-regulated, whereas TSC22D1 expression was markedly down-regulated. The expression of TSC22D1 and TSC22D3 was significantly increased in adult AML tissues compared to normal adult tissues. High TSC22D3 expression was significantly associated with poor overall survival (OS) and event-free survival (EFS) in adult AML patients. Univariate and multivariate Cox analysis showed that overexpression of TSC22D3 was independently associated with adverse OS of adult AML patients. High TSC22D3 expression had a adverse impact on OS and EFS of adult AML patients in the chemotherapy group. TSC22D3 expression correlated with drug resistance to BCL2 inhibitors. Functional enrichment analysis indicated that TSC22D3 might promote AML progression. MIR143-3p sponging TSC22D3 might have anti-leukemia effect in adult AML. CONCLUSIONS A significant increase in TSC22D3 expression was observed in adult AML tissues compared to normal adult HSCs and tissues. The prognosis of adult AML patients with high TSC22D3 expression was unfavorable, which could severe as a new prognostic biomarker and potential target for adult AML.
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Affiliation(s)
- XiaoQiang Xu
- The First Central Clinical School, Tianjin Medical University, Tianjin, 300192, China
- Department of Hematology, Shanxi Fenyang Hospital, Fenyang, 032200, China
| | - Rui Sun
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - YuanZhang Li
- The First Central Clinical School, Tianjin Medical University, Tianjin, 300192, China
| | - JiaXi Wang
- The First Central Clinical School, Tianjin Medical University, Tianjin, 300192, China
| | - Meng Zhang
- The First Central Clinical School, Tianjin Medical University, Tianjin, 300192, China
| | - Xia Xiong
- The First Central Clinical School, Tianjin Medical University, Tianjin, 300192, China
| | - DanNi Xie
- The First Central Clinical School, Tianjin Medical University, Tianjin, 300192, China
| | - Xin Jin
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, China
| | - MingFeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, China.
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Single B Cell Gene Co-Expression Networks Implicated in Prognosis, Proliferation, and Therapeutic Responses in Non-Small Cell Lung Cancer Bulk Tumors. Cancers (Basel) 2022; 14:cancers14133123. [PMID: 35804895 PMCID: PMC9265014 DOI: 10.3390/cancers14133123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/14/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary This study presents novel insights on dysregulated B cell proliferation networks in non-small cell lung cancer (NSCLC). Within this network, a nine-gene signature demonstrated prognostic and predictive indications in more than 1400 NSCLC patients using their gene and protein expression profiles in bulk tumors. Furthermore, novel therapeutic candidates are identified to improve NSCLC treatment outcomes. Abstract In NSCLC, there is a pressing need for immunotherapy predictive biomarkers. The processes underlying B-cell dysfunction, as well as their prognostic importance in NSCLC, are unknown. Tumor-specific B-cell gene co-expression networks were constructed by comparing the Boolean implication modeling of single-cell RNA sequencing of NSCLC tumor B cells and normal B cells. Proliferation genes were selected from the networks using in vitro CRISPR-Cas9/RNA interfering (RNAi) screening data in more than 92 human NSCLC epithelial cell lines. The prognostic and predictive evaluation was performed using public NSCLC transcriptome and proteome profiles. A B cell proliferation and prognostic gene co-expression network was present only in normal lung B cells and missing in NSCLC tumor B cells. A nine-gene signature was identified from this B cell network that provided accurate prognostic stratification using bulk NSCLC tumor transcriptome (n = 1313) and proteome profiles (n = 103). Multiple genes (HLA-DRA, HLA-DRB1, OAS1, and CD74) differentially expressed in NSCLC B cells, peripheral blood lymphocytes, and tumor T cells had concordant prognostic indications at the mRNA and protein expression levels. The selected genes were associated with drug sensitivity/resistance to 10 commonly used NSCLC therapeutic regimens. Lestaurtinib was discovered as a potential repositioning drug for treating NSCLC.
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Zhou M, Zhou S, Han K, Zhang J, Chen Q, Tian C, Zhu H, Jiang M, Min D. Th1 immune maturation effects of Nocardia rubra cell-wall skeleton via PI3K/Akt/PAX8 regulatory axis. Sci Prog 2022; 105:368504221092901. [PMID: 35473474 PMCID: PMC10450467 DOI: 10.1177/00368504221092901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nocardia rubra cell-wall skeleton (Nr-CWS) is reported as an external immunotherapeutic enhancer with the advantage of antitumor effect on human cancers. However, the immune regulatory role of Nr-CWS is not fully illustrated. We studied mouse CD4+ T lymphocytes isolated from mice spleen were induced by Nr-CWS and observed that the differentiation of Th1 CD4+ T cells and the cytokines of IL-2, TNF-α, IFN-γ were all enhanced by Nr-CWS. Furthermore, RNA sequencing was conducted to investigate the different mRNA profiling induced by Nr-CWS. We observed that paired box 8 (PAX8) was significantly up-regulated in Nr-CWS-treated Th1 cells compared to control. As a transcription factor, chromatin immunoprecipitation sequencing was carried out to study the genome-wide distribution of PAX8. Interestingly, we found that the binding domain of PAX8 was elevated by Nr-CWS, and the target genes associated with these binding sites showed a positive correlation between their transcription and PAX8 binding strength. Finally, we determined that Nr-CWS could enhance the activity of the PI3 K/Akt signaling pathway. Akt agonist could mimic the effect of Nr-CWS for PAX8 up-regulation, while Akt inhibitor compromised the expression of PAX8. Taken together, we determined a novel role of Nr-CWS in boosting the activity of Th1 maturation via the PI3 K/Akt/PAX8 axis.
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Affiliation(s)
- Meixiang Zhou
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Shuping Zhou
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Kun Han
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Jie Zhang
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Qingyu Chen
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Cong Tian
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Hongling Zhu
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Mengyi Jiang
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Daliu Min
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
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