1
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Wu LW, Tao JJ, McDonnell D, Izar B. Pseudoprogression in a patient with metastatic melanoma treated with PD-1 and LAG-3 inhibition. Melanoma Res 2024:00008390-990000000-00144. [PMID: 38640504 DOI: 10.1097/cmr.0000000000000974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Pseudoprogression encapsulates a process of temporary radiographic growth followed by subsequent regression of metastatic melanoma lesions in response to immune checkpoint blockade (ICB), such as the combination of anti-programmed cell death protein 1 (PD-1) and anticytotoxic T-lymphocyte-associated antigen 4 therapy. This occurs in approximately 5-10% of ICB-treated patients, but has not yet been described in the context of novel combination therapies. Here, we report a case of an 89-year-old patient with metastatic melanoma to the liver, lung and lymph nodes, who underwent treatment with Opdualag (combining anti-PD-1 nivolumab and anti-lymphocyte-activation gene 3 relatlimab ICBs), and developed pseudoprogression after two cycles of therapy. The patient experienced a radiographic increase in liver metastatic lesion size, but was found to have a subsequent reduction in these lesions. The patient has been on therapy for 18 months without evidence of disease progression and continues to be clinically well-appearing.
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Affiliation(s)
- Lawrence W Wu
- Division of Hematology and Oncology, Department of Medicine
| | | | | | - Benjamin Izar
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
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2
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Rogava M, Aprati TJ, Chi WY, Melms JC, Hug C, Davis SH, Earlie EM, Chung C, Deshmukh SK, Wu S, Sledge G, Tang S, Ho P, Amin AD, Caprio L, Gurjao C, Tagore S, Ngo B, Lee MJ, Zanetti G, Wang Y, Chen S, Ge W, Melo LMN, Allies G, Rösler J, Gibney GT, Schmitz OJ, Sykes M, Creusot RJ, Tüting T, Schadendorf D, Röcken M, Eigentler TK, Molotkov A, Mintz A, Bakhoum SF, Beyaz S, Cantley LC, Sorger PK, Meckelmann SW, Tasdogan A, Liu D, Laughney AM, Izar B. Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nat Cancer 2024; 5:433-447. [PMID: 38286827 DOI: 10.1038/s43018-023-00704-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/08/2023] [Indexed: 01/31/2024]
Abstract
Liver metastasis (LM) confers poor survival and therapy resistance across cancer types, but the mechanisms of liver-metastatic organotropism remain unknown. Here, through in vivo CRISPR-Cas9 screens, we found that Pip4k2c loss conferred LM but had no impact on lung metastasis or primary tumor growth. Pip4k2c-deficient cells were hypersensitized to insulin-mediated PI3K/AKT signaling and exploited the insulin-rich liver milieu for organ-specific metastasis. We observed concordant changes in PIP4K2C expression and distinct metabolic changes in 3,511 patient melanomas, including primary tumors, LMs and lung metastases. We found that systemic PI3K inhibition exacerbated LM burden in mice injected with Pip4k2c-deficient cancer cells through host-mediated increase in hepatic insulin levels; however, this circuit could be broken by concurrent administration of an SGLT2 inhibitor or feeding of a ketogenic diet. Thus, this work demonstrates a rare example of metastatic organotropism through co-optation of physiological metabolic cues and proposes therapeutic avenues to counteract these mechanisms.
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Affiliation(s)
- Meri Rogava
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Tyler J Aprati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wei-Yu Chi
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Johannes C Melms
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Clemens Hug
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephanie H Davis
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ethan M Earlie
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charlie Chung
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Sharon Wu
- Caris Life Sciences, Phoenix, AZ, USA
| | | | - Stephen Tang
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Amit Dipak Amin
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lindsay Caprio
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carino Gurjao
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA
| | - Somnath Tagore
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA
| | - Bryan Ngo
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Lee
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Giorgia Zanetti
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yiping Wang
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sean Chen
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - William Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luiza Martins Nascentes Melo
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Gabriele Allies
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Jonas Rösler
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Goeffrey T Gibney
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Megan Sykes
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rémi J Creusot
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Thomas Tüting
- Laboratory for Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany
| | - Dirk Schadendorf
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Martin Röcken
- Department of Dermatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Thomas K Eigentler
- Department of Dermatology, Venerology and Allergology, Charité University Hospital, Berlin, Germany
| | - Andrei Molotkov
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sven W Meckelmann
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Alpaslan Tasdogan
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashley M Laughney
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Izar
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA.
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA.
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3
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Leuzzi G, Vasciaveo A, Taglialatela A, Chen X, Firestone TM, Hickman AR, Mao W, Thakar T, Vaitsiankova A, Huang JW, Cuella-Martin R, Hayward SB, Kesner JS, Ghasemzadeh A, Nambiar TS, Ho P, Rialdi A, Hebrard M, Li Y, Gao J, Gopinath S, Adeleke OA, Venters BJ, Drake CG, Baer R, Izar B, Guccione E, Keogh MC, Guerois R, Sun L, Lu C, Califano A, Ciccia A. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell 2024; 187:861-881.e32. [PMID: 38301646 PMCID: PMC10980358 DOI: 10.1016/j.cell.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/23/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.
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Affiliation(s)
- Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Vasciaveo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | | | - Wendy Mao
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanay Thakar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alina Vaitsiankova
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jordan S Kesner
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ali Ghasemzadeh
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander Rialdi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxime Hebrard
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jinmei Gao
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | | | - Charles G Drake
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lu Sun
- EpiCypher Inc., Durham, NC 27709, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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4
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Melms JC, Ho P, Rogava M, Izar B. From patient tissue correlates to molecular mechanisms of cancer immune evasion: the emerging role of CD58 and PD-L1 co-regulation via CMTM6. Genes Immun 2024; 25:82-84. [PMID: 38082156 DOI: 10.1038/s41435-023-00224-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/21/2023] [Accepted: 10/12/2023] [Indexed: 02/18/2024]
Abstract
Immune evasion is a hallmark of cancer, yet the underlying mechanisms are often unknown in many patients. Using single-cell transcriptomics analysis, we previously identified the co-stimulator CD58 as part of a cancer cell-intrinsic immune checkpoint resistance signature in patient melanoma tissue. We subsequently validated CD58 loss as a driver of immune evasion using a patient-derived co-culture model of cancer and cytotoxic tumor-infiltrating lymphocytes in a pooled single-cell perturbation experiment, where we additionally observed concurrent upregulation of PD-L1 protein expression in melanoma cells with CD58 loss. In our most recent study, we uncovered the mechanisms of immune evasion mediated by CD58 loss, including impaired T cell activation and infiltration within tumors, as well as inhibitory signaling by PD-L1 via a shared regulator, CMTM6. Thus, cancer cell-intrinsic reduction of CD58 represents a multi-faceted determinant of immune evasion. Furthermore, its reciprocal interaction with PD-L1 via CMTM6 provides critical insights into how co-inhibitory and co-stimulatory immune cues are regulated.
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Affiliation(s)
- Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY, 10032, USA
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY, 10032, USA
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY, 10032, USA
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY, 10032, USA.
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
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5
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Kumar D, Gurrapu S, Wang Y, Bae SY, Pandey PR, Chen H, Mondal J, Han H, Wu CJ, Karaiskos S, Yang F, Sahin A, Wistuba II, Gao J, Tripathy D, Gao H, Izar B, Giancotti FG. LncRNA Malat1 suppresses pyroptosis and T cell-mediated killing of incipient metastatic cells. Nat Cancer 2024; 5:262-282. [PMID: 38195932 DOI: 10.1038/s43018-023-00695-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/22/2023] [Indexed: 01/11/2024]
Abstract
The contribution of antitumor immunity to metastatic dormancy is poorly understood. Here we show that the long noncoding RNA Malat1 is required for tumor initiation and metastatic reactivation in mouse models of breast cancer and other tumor types. Malat1 localizes to nuclear speckles to couple transcription, splicing and mRNA maturation. In metastatic cells, Malat1 induces WNT ligands, autocrine loops to promote self-renewal and the expression of Serpin protease inhibitors. Through inhibition of caspase-1 and cathepsin G, SERPINB6B prevents gasdermin D-mediated induction of pyroptosis. In this way, SERPINB6B suppresses immunogenic cell death and confers evasion of T cell-mediated tumor lysis of incipient metastatic cells. On-target inhibition of Malat1 using therapeutic antisense nucleotides suppresses metastasis in a SERPINB6B-dependent manner. These results suggest that Malat1-induced expression of SERPINB6B can titrate pyroptosis and immune recognition at metastatic sites. Thus, Malat1 is at the nexus of tumor initiation, reactivation and immune evasion and represents a tractable and clinically relevant drug target.
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Affiliation(s)
- Dhiraj Kumar
- Cancer Metastasis Initiative, Herbert Irving Comprehensive Cancer Center and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
| | - Sreeharsha Gurrapu
- Cancer Metastasis Initiative, Herbert Irving Comprehensive Cancer Center and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Yan Wang
- Cancer Metastasis Initiative, Herbert Irving Comprehensive Cancer Center and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Seong-Yeon Bae
- Cancer Metastasis Initiative, Herbert Irving Comprehensive Cancer Center and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Poonam R Pandey
- Cancer Metastasis Initiative, Herbert Irving Comprehensive Cancer Center and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Hong Chen
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jayanta Mondal
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Hyunho Han
- Department of Urology, Urological Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Spyros Karaiskos
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Fei Yang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aysegul Sahin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Debasish Tripathy
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua Gao
- Shanghai Tenth People's Hospital, Advanced Institute of Translational Medicine, School of Medicine and Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA.
| | - Filippo G Giancotti
- Cancer Metastasis Initiative, Herbert Irving Comprehensive Cancer Center and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
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6
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Altorki NK, Walsh ZH, Melms JC, Port JL, Lee BE, Nasar A, Spinelli C, Caprio L, Rogava M, Ho P, Christos PJ, Saxena A, Elemento O, Bhinder B, Ager C, Amin AD, Sanfilippo NJ, Mittal V, Borczuk AC, Formenti SC, Izar B, McGraw TE. Author Correction: Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial. Nat Commun 2024; 15:225. [PMID: 38172131 PMCID: PMC10764801 DOI: 10.1038/s41467-023-44575-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Affiliation(s)
- Nasser K Altorki
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA.
| | - Zachary H Walsh
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Jeffery L Port
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Benjamin E Lee
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Abu Nasar
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Cathy Spinelli
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Paul J Christos
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Ashish Saxena
- Weill Cornell Medicine, Division of Hematology and Oncology, New York, New York, USA
| | - Olivier Elemento
- Weill Cornell Medicine, Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Department of Physiology and Biophysics, New York, New York, USA
| | - Bhavneet Bhinder
- Weill Cornell Medicine, Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Department of Physiology and Biophysics, New York, New York, USA
| | - Casey Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | | | - Vivek Mittal
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Alain C Borczuk
- Department of Pathology, Northwell Health, Greenvale, New York, New York, USA
| | - Silvia C Formenti
- Weill Cornell Medicine, Department of Radiation Oncology, New York, New York, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA.
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, New York, USA.
- Columbia Center for Translational Immunology, New York, New York, USA.
| | - Timothy E McGraw
- Weill Cornell Medicine, Department of Biochemistry, New York, New York, USA.
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7
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Altorki NK, Walsh ZH, Melms JC, Port JL, Lee BE, Nasar A, Spinelli C, Caprio L, Rogava M, Ho P, Christos PJ, Saxena A, Elemento O, Bhinder B, Ager C, Amin AD, Sanfilippo NJ, Mittal V, Borczuk AC, Formenti SC, Izar B, McGraw TE. Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial. Nat Commun 2023; 14:8435. [PMID: 38114518 PMCID: PMC10730562 DOI: 10.1038/s41467-023-44195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
We previously reported the results of a randomized phase II trial (NCT02904954) in patients with early-stage non-small cell lung cancer (NSCLC) who were treated with either two preoperative cycles of the anti-PD-L1 antibody durvalumab alone or combined with immunomodulatory doses of stereotactic radiation (DRT). The trial met its primary endpoint of major pathological response, which was significantly higher following DRT with no new safety signals. Here, we report on the prespecified secondary endpoint of disease-free survival (DFS) regardless of treatment assignment and the prespecified exploratory analysis of DFS in each arm of the trial. DFS at 2 and 3 years across patients in both arms of the trial were 73% (95% CI: 62.1-84.5) and 65% (95% CI: 52.5-76.9) respectively. For the exploratory endpoint of DFS in each arm of the trial, three-year DFS was 63% (95% CI: 46.0-80.4) in the durvalumab monotherapy arm compared to 67% (95% CI: 49.6-83.4) in the dual therapy arm. In addition, we report post hoc exploratory analysis of progression-free survival as well as molecular correlates of response and recurrence through high-plex immunophenotyping of sequentially collected peripheral blood and gene expression profiles from resected tumors in both treatment arms. Together, our results contribute to the evolving landscape of neoadjuvant treatment regimens for NSCLC and identify easily measurable potential biomarkers of response and recurrence.
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Affiliation(s)
- Nasser K Altorki
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA.
| | - Zachary H Walsh
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Jeffery L Port
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Benjamin E Lee
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Abu Nasar
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Cathy Spinelli
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Paul J Christos
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Ashish Saxena
- Weill Cornell Medicine, Division of Hematology and Oncology, New York, New York, USA
| | - Olivier Elemento
- Weill Cornell Medicine, Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Department of Physiology and Biophysics, New York, New York, USA
| | - Bhavneet Bhinder
- Weill Cornell Medicine, Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Department of Physiology and Biophysics, New York, New York, USA
| | - Casey Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA
| | | | - Vivek Mittal
- Weill Cornell Medicine, Department of Cardiothoracic Surgery, New York, New York, USA
| | - Alain C Borczuk
- Department of Pathology, Northwell Health, Greenvale, New York, New York, USA
| | - Silvia C Formenti
- Weill Cornell Medicine, Department of Radiation Oncology, New York, New York, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, New York, USA.
- Deparmtent of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, New York, USA.
- Columbia Center for Translational Immunology, New York, New York, USA.
| | - Timothy E McGraw
- Weill Cornell Medicine, Department of Biochemistry, New York, New York, USA.
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8
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Su J, Reynier JB, Fu X, Zhong G, Jiang J, Escalante RS, Wang Y, Aparicio L, Izar B, Knowles DA, Rabadan R. Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data. Genome Biol 2023; 24:291. [PMID: 38110959 PMCID: PMC10726548 DOI: 10.1186/s13059-023-03138-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution reveals plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allows for spatial mapping of reference populations with significantly reduced ambiguity.
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Affiliation(s)
- Jiayu Su
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Jean-Baptiste Reynier
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Xi Fu
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Guojie Zhong
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Jiahao Jiang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Yiping Wang
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Luis Aparicio
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Benjamin Izar
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Knowles
- Department of Systems Biology, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
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9
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Walsh ZH, Shah P, Kothapalli N, Nikolenyi G, Shah SB, Leuzzi G, Mu M, Ho P, Abuzaid S, Brodtman ZD, Vasan N, AlQuraishi M, Milner JD, Ciccia A, Melms JC, Izar B. Massively parallel base editing screens to map variant effects on anti-tumor hallmarks of primary human T cells. bioRxiv 2023:2023.12.13.571465. [PMID: 38168306 PMCID: PMC10760091 DOI: 10.1101/2023.12.13.571465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Base editing enables generation of single nucleotide variants, but large-scale screening in primary human T cells is limited due to low editing efficiency, among other challenges 1 . Here, we developed a high-throughput approach for high-efficiency and massively parallel adenine and cytosine base-editor screening in primary human T cells. We performed multiple large-scale screens editing 102 genes with central functions in T cells and full-length tiling mutagenesis of selected genes, and read out variant effects on hallmarks of T cell anti-tumor immunity, including activation, proliferation, and cytokine production. We discovered a broad landscape of gain- and loss-of-function mutations, including in PIK3CD and its regulatory subunit encoded by PIK3R1, LCK , AKT1, CTLA-4 and JAK1 . We identified variants that affected several (e.g., PIK3CD C416R) or only selected (e.g. LCK Y505C) hallmarks of T cell activity, and functionally validated several hits by probing downstream signaling nodes and testing their impact on T cell polyfunctionality and proliferation. Using primary human T cells in which we engineered a T cell receptor (TCR) specific to a commonly presented tumor testis antigen as a model for cellular immunotherapy, we demonstrate that base edits identified in our screens can tune specific or broad T cell functions and ultimately improve tumor elimination while exerting minimal off-target activity. In summary, we present the first large-scale base editing screen in primary human T cells and provide a framework for scalable and targeted base editing at high efficiency. Coupled with multi-modal phenotypic mapping, we accurately nominate variants that produce a desirable T cell state and leverage these synthetic proteins to improve models of cellular cancer immunotherapies.
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10
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In GK, Ribeiro JR, Yin J, Xiu J, Bustos MA, Ito F, Chow F, Zada G, Hwang L, Salama AKS, Park SJ, Moser JC, Darabi S, Domingo-Musibay E, Ascierto ML, Margolin K, Lutzky J, Gibney GT, Atkins MB, Izar B, Hoon DSB, VanderWalde AM. Multi-omic profiling reveals discrepant immunogenic properties and a unique tumor microenvironment among melanoma brain metastases. NPJ Precis Oncol 2023; 7:120. [PMID: 37964004 PMCID: PMC10646102 DOI: 10.1038/s41698-023-00471-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
Melanoma brain metastases (MBM) are clinically challenging to treat and exhibit variable responses to immune checkpoint therapies. Prior research suggests that MBM exhibit poor tumor immune responses and are enriched in oxidative phosphorylation. Here, we report results from a multi-omic analysis of a large, real-world melanoma cohort. MBM exhibited lower interferon-gamma (IFNγ) scores and T cell-inflamed scores compared to primary cutaneous melanoma (PCM) or extracranial metastases (ECM), which was independent of tumor mutational burden. Among MBM, there were fewer computationally inferred immune cell infiltrates, which correlated with lower TNF and IL12B mRNA levels. Ingenuity pathway analysis (IPA) revealed suppression of inflammatory responses and dendritic cell maturation pathways. MBM also demonstrated a higher frequency of pathogenic PTEN mutations and angiogenic signaling. Oxidative phosphorylation (OXPHOS) was enriched in MBM and negatively correlated with NK cell and B cell-associated transcriptomic signatures. Modulating metabolic or angiogenic pathways in MBM may improve responses to immunotherapy in this difficult-to-treat patient subset.
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Affiliation(s)
- Gino K In
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | | | - Jun Yin
- Caris Life Sciences, Phoenix, AZ, USA
| | | | - Matias A Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Fumito Ito
- Department of Surgery, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frances Chow
- Department of Neurology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Neurological Surgery, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gabriel Zada
- Department of Neurological Surgery, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lindsay Hwang
- LAC+USC Medical Center, Los Angeles, CA, USA
- Department of Radiation Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - April K S Salama
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Soo J Park
- Division of Hematology/Oncology, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Justin C Moser
- HonorHealth Research and Innovation Institute, Scottsdale, AZ, USA
| | - Sourat Darabi
- Hoag Family Cancer Institute, Hoag Hospital, Newport Beach, CA, USA
| | - Evidio Domingo-Musibay
- Department of Medicine, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Maria L Ascierto
- Rosalie and Harold Rae Brown Cancer Immunotherapy Research Program, Borstein Family Melanoma Program, Department of Translational Immunology, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Kim Margolin
- Department of Medical Oncology, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Jose Lutzky
- Sylvester Comprehensive Cancer Center, University of Miami Health System, Miami, FL, USA
| | - Geoffrey T Gibney
- Division of Hematology and Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Hospital, Washington, DC, USA
| | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Benjamin Izar
- Columbia University, Herbert Irving Comprehensive Cancer Center, New York, NY, USA
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Ari M VanderWalde
- Caris Life Sciences, Irving, TX, USA
- West Cancer Center and Research Institute, 514 Chickasawba St., Blytheville, Arkansas, 72315, USA
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11
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Wei AZ, Chen LN, Orloff M, Ariyan CE, Asgari M, Barker CA, Buchbinder E, Chandra S, Couts K, Frumovitz MM, Futreal A, Gershenwald JE, Hanna EY, Izar B, LeBlanc AK, Leitao MM, Lipson EJ, Liu D, McCarter M, McQuade JL, Najjar Y, Rapisuwon S, Selig S, Shoushtari AN, Yeh I, Schwartz GK, Guo J, Patel SP, Carvajal RD. Proceedings from the Melanoma Research Foundation Mucosal Melanoma Meeting (December 16, 2022, New York, USA). Pigment Cell Melanoma Res 2023; 36:542-556. [PMID: 37804122 DOI: 10.1111/pcmr.13139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/01/2023] [Accepted: 09/23/2023] [Indexed: 10/08/2023]
Abstract
Mucosal melanoma remains a rare cancer with high mortality and a paucity of therapeutic options. This is due in significant part to its low incidence leading to limited patient access to expert care and downstream clinical/basic science data for research interrogation. Clinical challenges such as delayed and at times inaccurate diagnoses, and lack of consensus tumor staging have added to the suboptimal outcomes for these patients. Clinical trials, while promising, have been difficult to activate and accrue. While individual institutions and investigators have attempted to seek solutions to such problems, international, national, and local partnership may provide the keys to more efficient and innovative paths forward. Furthermore, a mucosal melanoma coalition would provide a potential network for patients and caregivers to seek expert opinion and advice. The Melanoma Research Foundation Mucosal Melanoma Meeting (December 16, 2022, New York, USA) highlighted the current clinical challenges faced by patients, providers, and scientists, identified current and future clinical trial investigations in this rare disease space, and aimed to increase national and international collaboration among the mucosal melanoma community in an effort to improve patient outcomes. The included proceedings highlight the clinical challenges of mucosal melanoma, global clinical trial experience, basic science advances in mucosal melanoma, and future directions, including the creation of shared rare tumor registries and enhanced collaborations.
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Affiliation(s)
- Alexander Z Wei
- Columbia University Irving Medical Center, New York, New York, USA
| | - Lanyi N Chen
- Columbia University Irving Medical Center, New York, New York, USA
| | - Marlana Orloff
- Thomas Jefferson University Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Sunandana Chandra
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kasey Couts
- University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Ehab Y Hanna
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin Izar
- Columbia University Irving Medical Center, New York, New York, USA
| | - Amy K LeBlanc
- National Institute of Health, Bethesda, Maryland, USA
| | - Mario M Leitao
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, New York, USA
| | - Evan J Lipson
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Liu
- Dana-Farber Cancer Institute/Harvard Cancer Center, Boston, Massachusetts, USA
| | - Martin McCarter
- University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Yana Najjar
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | | | - Sara Selig
- Melanoma Research Foundation, CURE OM, Washington, DC, USA
| | | | - Iwei Yeh
- University of California, San Francisco, San Francisco, California, USA
| | | | - Jun Guo
- Peking University Cancer Hospital & Institute, Beijing, China
| | - Sapna P Patel
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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12
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Pavlick AC, Ariyan CE, Buchbinder EI, Davar D, Gibney GT, Hamid O, Hieken TJ, Izar B, Johnson DB, Kulkarni RP, Luke JJ, Mitchell TC, Mooradian MJ, Rubin KM, Salama AK, Shirai K, Taube JM, Tawbi HA, Tolley JK, Valdueza C, Weiss SA, Wong MK, Sullivan RJ. Society for Immunotherapy of Cancer (SITC) clinical practice guideline on immunotherapy for the treatment of melanoma, version 3.0. J Immunother Cancer 2023; 11:e006947. [PMID: 37852736 PMCID: PMC10603365 DOI: 10.1136/jitc-2023-006947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2023] [Indexed: 10/20/2023] Open
Abstract
Since the first approval for immune checkpoint inhibitors (ICIs) for the treatment of cutaneous melanoma more than a decade ago, immunotherapy has completely transformed the treatment landscape of this chemotherapy-resistant disease. Combination regimens including ICIs directed against programmed cell death protein 1 (PD-1) with anti-cytotoxic T lymphocyte antigen-4 (CTLA-4) agents or, more recently, anti-lymphocyte-activation gene 3 (LAG-3) agents, have gained regulatory approvals for the treatment of metastatic cutaneous melanoma, with long-term follow-up data suggesting the possibility of cure for some patients with advanced disease. In the resectable setting, adjuvant ICIs prolong recurrence-free survival, and neoadjuvant strategies are an active area of investigation. Other immunotherapy strategies, such as oncolytic virotherapy for injectable cutaneous melanoma and bispecific T-cell engager therapy for HLA-A*02:01 genotype-positive uveal melanoma, are also available to patients. Despite the remarkable efficacy of these regimens for many patients with cutaneous melanoma, traditional immunotherapy biomarkers (ie, programmed death-ligand 1 expression, tumor mutational burden, T-cell infiltrate and/or microsatellite stability) have failed to reliably predict response. Furthermore, ICIs are associated with unique toxicity profiles, particularly for the highly active combination of anti-PD-1 plus anti-CTLA-4 agents. The Society for Immunotherapy of Cancer (SITC) convened a panel of experts to develop this clinical practice guideline on immunotherapy for the treatment of melanoma, including rare subtypes of the disease (eg, uveal, mucosal), with the goal of improving patient care by providing guidance to the oncology community. Drawing from published data and clinical experience, the Expert Panel developed evidence- and consensus-based recommendations for healthcare professionals using immunotherapy to treat melanoma, with topics including therapy selection in the advanced and perioperative settings, intratumoral immunotherapy, when to use immunotherapy for patients with BRAFV600-mutated disease, management of patients with brain metastases, evaluation of treatment response, special patient populations, patient education, quality of life, and survivorship, among others.
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Affiliation(s)
| | - Charlotte E Ariyan
- Department of Surgery Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Diwakar Davar
- Hillman Cancer Center, University of Pittsburg Medical Center, Pittsburgh, Pennsylvania, USA
| | - Geoffrey T Gibney
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, District of Columbia, USA
| | - Omid Hamid
- The Angeles Clinic and Research Institute, A Cedars-Sinai Affiliate, Los Angeles, California, USA
| | - Tina J Hieken
- Department of Surgery and Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Medical Center, New York, New York, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rajan P Kulkarni
- Departments of Dermatology, Oncological Sciences, Biomedical Engineering, and Center for Cancer Early Detection Advanced Research, Knight Cancer Institute, OHSU, Portland, Oregon, USA
- Operative Care Division, VA Portland Health Care System (VAPORHCS), Portland, Oregon, USA
| | - Jason J Luke
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Tara C Mitchell
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Meghan J Mooradian
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Krista M Rubin
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - April Ks Salama
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, Carolina, USA
| | - Keisuke Shirai
- Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Janis M Taube
- Department of Dermatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - J Keith Tolley
- Patient Advocate, Melanoma Research Alliance, Washington, DC, USA
| | - Caressa Valdueza
- Cutaneous Oncology Program, Weill Cornell Medicine, New York, New York, USA
| | - Sarah A Weiss
- Department of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Michael K Wong
- Patient Advocate, Melanoma Research Alliance, Washington, DC, USA
| | - Ryan J Sullivan
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
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13
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DePinho R, Massagué J, Manji G, Rustgi AK, Izar B. Filippo Giancotti (1958-2023). Nat Cancer 2023; 4:1401-1402. [PMID: 37770653 DOI: 10.1038/s43018-023-00639-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Affiliation(s)
- Ronald DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gulam Manji
- Columbia University Irving Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, USA
| | - Anil K Rustgi
- Columbia University Irving Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, USA
| | - Benjamin Izar
- Columbia University Irving Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, USA.
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14
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Hegewisch-Solloa E, Melsen JE, Ravichandran H, Rendeiro AF, Freud AG, Mundy-Bosse B, Melms JC, Eisman SE, Izar B, Grunstein E, Connors TJ, Elemento O, Horowitz A, Mace EM. Mapping human natural killer cell development in pediatric tonsil by imaging mass cytometry and high-resolution microscopy. bioRxiv 2023:2023.09.05.556371. [PMID: 37732282 PMCID: PMC10508773 DOI: 10.1101/2023.09.05.556371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Natural killer (NK) cells develop from CD34+ progenitors in a stage-specific manner defined by changes in cell surface receptor expression and function. Secondary lymphoid tissues, including tonsil, are sites of human NK cell development. Here we present new insights into human NK cell development in pediatric tonsil using cyclic immunofluorescence and imaging mass cytometry. We show that NK cell subset localization and interactions are dependent on NK cell developmental stage and tissue residency. NK cell progenitors are found in the interfollicular domain in proximity to cytokine-expressing stromal cells that promote proliferation and maturation. Mature NK cells are primarily found in the T-cell rich parafollicular domain engaging in cell-cell interactions that differ depending on their stage and tissue residency. The presence of local inflammation results in changes in NK cell interactions, abundance, and localization. This study provides the first comprehensive atlas of human NK cell development in secondary lymphoid tissue.
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Affiliation(s)
- Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Janine E Melsen
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Hiranmayi Ravichandran
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - André F Rendeiro
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Aharon G Freud
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, 10032
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032
| | - Shira E Eisman
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, 10032
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032
- Program for Mathematical Genomics, Columbia University, New York, NY, 10032
| | - Eli Grunstein
- Department of Otolaryngology - Head and Neck Surgery, Columbia University Medical Center, New York, New York 10032
| | - Thomas J Connors
- Department of Pediatrics, Division of Pediatric Critical Care and Hospital Medicine, Columbia University Irving Medical Center, New York, NY 10024
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
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15
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Ager CR, Zhang M, Chaimowitz M, Bansal S, Tagore S, Obradovic A, Jugler C, Rogava M, Melms JC, McCann P, Spina C, Drake CG, Dallos MC, Izar B. KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response. J Immunother Cancer 2023; 11:e006782. [PMID: 37657842 PMCID: PMC10476134 DOI: 10.1136/jitc-2023-006782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/03/2023] Open
Abstract
Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To thoroughly characterize the temporal nature of antitumor immune responses, we developed a 34-parameter spectral flow cytometry panel and performed high-throughput analyses in critical contexts. We leveraged two distinct preclinical models that recapitulate cancer immunoediting (NPK-C1) and immune checkpoint blockade (ICB) response (MC38), respectively, and profiled multiple relevant tissues at and around key inflection points of immune surveillance and escape and/or ICB response. Machine learning-driven data analysis revealed a pattern of KLRG1 expression that uniquely identified intratumoral effector CD4 T cell populations that constitutively associate with tumor burden across tumor models, and are lost in tumors undergoing regression in response to ICB. Similarly, a Helios-KLRG1+ subset of tumor-infiltrating regulatory T cells was associated with tumor progression from immune equilibrium to escape and was also lost in tumors responding to ICB. Validation studies confirmed KLRG1 signatures in human tumor-infiltrating CD4 T cells associate with disease progression in renal cancer. These findings nominate KLRG1+ CD4 T cell populations as subsets for further investigation in cancer immunity and demonstrate the utility of longitudinal spectral flow profiling as an engine of dynamic biomarker discovery.
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Affiliation(s)
- Casey R Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Mingxuan Zhang
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Molecular Pathology and Therapeutics, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew Chaimowitz
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Shruti Bansal
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Somnath Tagore
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Aleksandar Obradovic
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Collin Jugler
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Patrick McCann
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Catherine Spina
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Charles G Drake
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
- Janssen Research and Development, Janssen Pharmaceuticals, Spring House, Pennsylvania, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew C Dallos
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Columbia University Irving Medical Center, New York, New York, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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16
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Li J, Hubisz MJ, Earlie EM, Duran MA, Hong C, Varela AA, Lettera E, Deyell M, Tavora B, Havel JJ, Phyu SM, Amin AD, Budre K, Kamiya E, Cavallo JA, Garris C, Powell S, Reis-Filho JS, Wen H, Bettigole S, Khan AJ, Izar B, Parkes EE, Laughney AM, Bakhoum SF. Non-cell-autonomous cancer progression from chromosomal instability. Nature 2023; 620:1080-1088. [PMID: 37612508 PMCID: PMC10468402 DOI: 10.1038/s41586-023-06464-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/20/2023] [Indexed: 08/25/2023]
Abstract
Chromosomal instability (CIN) is a driver of cancer metastasis1-4, yet the extent to which this effect depends on the immune system remains unknown. Using ContactTracing-a newly developed, validated and benchmarked tool to infer the nature and conditional dependence of cell-cell interactions from single-cell transcriptomic data-we show that CIN-induced chronic activation of the cGAS-STING pathway promotes downstream signal re-wiring in cancer cells, leading to a pro-metastatic tumour microenvironment. This re-wiring is manifested by type I interferon tachyphylaxis selectively downstream of STING and a corresponding increase in cancer cell-derived endoplasmic reticulum (ER) stress response. Reversal of CIN, depletion of cancer cell STING or inhibition of ER stress response signalling abrogates CIN-dependent effects on the tumour microenvironment and suppresses metastasis in immune competent, but not severely immune compromised, settings. Treatment with STING inhibitors reduces CIN-driven metastasis in melanoma, breast and colorectal cancers in a manner dependent on tumour cell-intrinsic STING. Finally, we show that CIN and pervasive cGAS activation in micronuclei are associated with ER stress signalling, immune suppression and metastasis in human triple-negative breast cancer, highlighting a viable strategy to identify and therapeutically intervene in tumours spurred by CIN-induced inflammation.
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Affiliation(s)
- Jun Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa J Hubisz
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Ethan M Earlie
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Mercedes A Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christy Hong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Austin A Varela
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Emanuele Lettera
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Deyell
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Su M Phyu
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Amit Dipak Amin
- Columbia Center for Translational Immunology, New York, NY, USA
- Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Karolina Budre
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Erina Kamiya
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Julie-Ann Cavallo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Garris
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Atif J Khan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Izar
- Columbia Center for Translational Immunology, New York, NY, USA
- Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Eileen E Parkes
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Ashley M Laughney
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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17
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Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B. The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell 2023; 41:1207-1221.e12. [PMID: 37327789 PMCID: PMC10524902 DOI: 10.1016/j.ccell.2023.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023]
Abstract
The cell-autonomous balance of immune-inhibitory and -stimulatory signals is a critical process in cancer immune evasion. Using patient-derived co-cultures, humanized mouse models, and single-cell RNA-sequencing of patient melanomas biopsied before and on immune checkpoint blockade, we find that intact cancer cell-intrinsic expression of CD58 and ligation to CD2 is required for anti-tumor immunity and is predictive of treatment response. Defects in this axis promote immune evasion through diminished T cell activation, impaired intratumoral T cell infiltration and proliferation, and concurrently increased PD-L1 protein stabilization. Through CRISPR-Cas9 and proteomics screens, we identify and validate CMTM6 as critical for CD58 stability and upregulation of PD-L1 upon CD58 loss. Competition between CD58 and PD-L1 for CMTM6 binding determines their rate of endosomal recycling over lysosomal degradation. Overall, we describe an underappreciated yet critical axis of cancer immunity and provide a molecular basis for how cancer cells balance immune inhibitory and stimulatory cues.
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Affiliation(s)
- Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chris J Frangieh
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, the Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Shivem B Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Zachary Walsh
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Oleksandr Kyrysyuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY 10032, USA
| | - Casey R Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Immunology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Giorgia Zanetti
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Michael Mu
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Hijab Fatima
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Emily K Moore
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Medicine, Division of Rheumatology, Columbia University, New York, NY 10032, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven L Reiner
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Chantale Bernatchez
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Department of Surgery, Columbia University, New York, NY 10032, USA
| | - Emily M Mace
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, 45147 Essen, Germany
| | | | - Parin Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
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18
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Tagore S, Caprio L, Amin AD, Barrera I, Melms J, Luthria K, Wang Y, Georgis Y, Jaiswal A, Lagos GG, Walsh Z, Shah P, Biermann J, Sheikh N, Ramaradj P, Anandasabapathy N, Hibshoosh H, Schwartz G, Henick B, Taylor A, Chen F, Izar B. Abstract 3517: Multi-modal single-cell and spatial genomics reveals genomic, adaptive and microenvironmental features of human non-small cell lung cancer brain metastasis. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Non-small cell lung cancer (NSCLC) accounts for nearly half of all newly diagnosed patients with brain metastasis (BM), followed by melanoma and breast carcinomas. The presence of BM is associated with reduced response to several modern cancer therapies and a poor prognosis, but the underlying molecular underpinnings remain poorly understood. Here, we performed multi-modal single-nucleus RNA, T cell receptor, single-cell spatial, and whole-genome sequencing (WGS) of 44 primary NSCLC tumors (PTs) and BMs. Through combination of WGS with inferred copy-number alterations (CNAs) and gene expression snRNA-seq, we robustly identify malignant cells despite the presence of healthy cell mosaicism. We find a strong association of chromosomal instability (CIN) and brain-metastatic organotropism. Through integration with clinical information and thousands of publicly available whole-exome sequencing (WES) profiles obtained from patients with NSCLC, we validate this observation and show that CIN progressively increases from PTs to extracranial metastases (ECMs) and is the highest in BMs. Using non-negative matrix factorization, we identify recurrent transcriptional hallmarks cancer metastasis, and additionally find that cancer cells from BMs strongly enrich for a neuronal-like cell state. At single-cell resolution, we indeed identify a rare cancer cell population genomically define by very high CIN, and transcriptionally characterized by a program of epithelial-to-mesenchymal transition (EMT), neuronal-like differentiation, and loss of lineage attribution. We show in our data and external scRNA-seq data that this cell state does not ecist in healthy lungs, progressively enriches from PTs to ECMs, and is most abundant in BMs, suggesting that these cells may indeed give rise to BMs. Furthermore, through integration of snRNA/TCR-seq and spatial transcriptomics, we find distinct tumor-microenvironments across disease sites, including, nearly exclusive expansion of tissue-resident myeloid cells in PTs, while BMs are largely dominated by dense infiltration with monocyte-derived macrophages and granulocytes, impaired T cell infiltration, activation and clonal expansion. Lastly, spatial transcriptomics also recurrent, cell-type specific patterns of geographic variability in key pathways, including antigen presentation, EMT, oxidative phosphorylation, and inflammatory response and associated cellular micro-niches. Together, this work identifies cellular, genomic, and transcriptional features of NSCLC BMs and has important therapeutic implications for novel therapies, in particular immunomodulatory approaches targeting cell types/states unique to disease sites.
Citation Format: Somnath Tagore, Lindsay Caprio, Amit Dipak Amin, Irving Barrera, Johannes Melms, Karan Luthria, Yiping Wang, Yohanna Georgis, Abhi Jaiswal, Galina G. Lagos, Zachary Walsh, Parin Shah, Jana Biermann, Neha Sheikh, Priyanka Ramaradj, Niroshana Anandasabapathy, Hanina Hibshoosh, Gary Schwartz, Brian Henick, Alison Taylor, Fei Chen, Benjamin Izar. Multi-modal single-cell and spatial genomics reveals genomic, adaptive and microenvironmental features of human non-small cell lung cancer brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3517.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Fei Chen
- 1Columbia University, New York, NY
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19
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Ager C, Chaimowitz M, Bansal S, Rogava M, Melms J, Spina C, Abate-Shen C, Drake CG, Dallos M, Izar B. Abstract 4115: KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with immune escape and immunotherapy response. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To better capture the dynamic and compartmentalized nature of antitumor immune responses, we generated longitudinal “temporal atlases” of productive versus non-productive antitumor immune responses in murine tumor models. We utilized a 34-parameter full spectrum flow cytometry panel to comprehensively profile immune composition within tumors, draining and non-draining lymph nodes, and blood in and around key inflection points of tumor regression or progression. We leveraged two distinct preclinical models for this; the NPK-C1 ectopic prostate cancer model to map dynamics of spontaneous cancer immunoediting, and anti-PD-1 treated MC38 tumors to study response or non-response to immune checkpoint blockade (ICB). We utilized UMAP and FlowSOM algorithms for iterative dimensionality reduction and clustering, respectively, to reveal novel phenotypes associated with productive versus non-productive immunity across model systems, tissues, and time points. We discovered expression of KLRG1 within the intratumoral CD4 T cell compartment was highly associated with tumor progression and response to ICB. Specifically, both FoxP3+ Tregs and FoxP3- Tconv cells within tumors accumulated KLRG1 expression through disease progression, but this was not observed in CD4 T cell or other immune subsets residing in lymph nodes or circulating in blood. Among all intratumoral clusters, KLRG1+ Tconv were the only subset significantly correlated with tumor burden at each time point tested and across both models. KLRG1+ Tconv were significantly enriched in NPK-C1 tumors undergoing progression to escape versus those under immune-mediated equilibrium (p=0.0004) and were lost in animals undergoing curative responses to ICB (p=0.003). In the Treg compartment, unsupervised clustering revealed a KLRG1+Helios- tumor Treg subset that was positively correlated with transition from equilibrium to escape in the NPK-C1 model (p=0.005). Also indicating a potential functional significance, this phenotype was absent in tumors undergoing curative responses to ICB (p=0.0002). Systematic investigation of the functional characteristics, transcriptional programming, and translational significance of intratumoral KLRG1+ CD4 T cell subsets is ongoing. Together, these findings identify KLRG1+ CD4 T cell populations as subsets for further investigation in cancer and demonstrate the utility of longitudinal full spectrum flow cytometry profiling as an engine of dynamic biomarker and/or target discovery in immuno-oncology.
Citation Format: Casey Ager, Matthew Chaimowitz, Shruti Bansal, Meri Rogava, Johannes Melms, Catherine Spina, Cory Abate-Shen, Charles G. Drake, Matthew Dallos, Benjamin Izar. KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with immune escape and immunotherapy response. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4115.
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Hou D, Castro B, Dapash M, Zolp A, Katz J, Arrieta V, Biermann J, Melms J, Kueckelhaus J, Benotmane J, Youngblood M, Rashidi A, Billingham L, Dmello C, Vazquez-Cervantes G, Lopez-Rosas A, Han Y, Patel R, Chia TY, Sun L, Prins R, Izar B, Heiland DH, Zhang P, Sonabend A, Miska J, Lesniak M, Zhao J, Lee-Chang C. B-cells Drive Response to PD-1 Blockade in Glioblastoma Upon Neutralization of TGFβ-mediated Immunosuppression. Res Sq 2023:rs.3.rs-2399170. [PMID: 36711497 PMCID: PMC9882679 DOI: 10.21203/rs.3.rs-2399170/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Immunotherapy has revolutionized cancer treatment but has yet to be translated into brain tumors. Studies in other solid tumors suggest a central role of B-cell immunity in driving immune-checkpoint-blockade efficacy. Using single-cell and single-nuclei transcriptomics of human glioblastoma and melanoma brain metastasis, we found that tumor-associated B-cells have high expression of checkpoint molecules, known to block B-cell-receptor downstream effector function such as plasmablast differentiation and antigen-presentation. We also identified TGFβ-1/TGFβ receptor-2 interaction as a crucial modulator of B-cell suppression. Treatment of glioblastoma patients with pembrolizumab induced expression of B-cell checkpoint molecules and TGFβ-receptor-2. Abrogation of TGFβ using different conditional knockouts expanded germinal-center-like intratumoral B-cells, enhancing immune-checkpoint-blockade efficacy. Finally, blocking αVβ8 integrin (which controls the release of active TGFβ) and PD-1 significantly increased B-cell-dependent animal survival and immunological memory. Our study highlights the importance of intratumoral B-cell immunity and a remodeled approach to boost the effects of immunotherapy against brain tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jason Miska
- University of Miami Miller School of Medicine
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21
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Ager CR, Zhang M, Chaimowitz M, Bansal S, Obradovic A, Rogava M, Melms JC, McCann P, Spina C, Drake CG, Dallos MC, Izar B. KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response. bioRxiv 2023:2023.01.01.522340. [PMID: 36711647 PMCID: PMC9881861 DOI: 10.1101/2023.01.01.522340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To thoroughly characterize the temporal nature of antitumor immune responses, we developed a 34-parameter spectral flow cytometry panel and performed high-throughput analyses in critical contexts. We leveraged two distinct preclinical models that recapitulate cancer immunoediting (NPK-C1) and immune checkpoint blockade (ICB) response (MC38), respectively, and profiled multiple relevant tissues at and around key inflection points of immune surveillance and escape and/or ICB response. Machine learning-driven data analysis revealed a pattern of KLRG1 expression that uniquely identified intratumoral effector CD4 T cell populations that constitutively associate with tumor burden across tumor models, and are lost in tumors undergoing regression in response to ICB. Similarly, a Helios - KLRG1 + subset of tumor-infiltrating regulatory T cells (Tregs) was associated with tumor progression from immune equilibrium to escape, and were also lost in tumors responding to ICB. Validation studies confirmed KLRG1 signatures in human tumorinfiltrating CD4 T cells associate with disease progression in renal cancer. These findings nominate KLRG1 + CD4 T cell populations as subsets for further investigation in cancer immunity and demonstrate the utility of longitudinal spectral flow profiling as an engine of dynamic biomarker and/or target discovery.
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Wang Y, Fan JL, Melms JC, Amin AD, Georgis Y, Barrera I, Ho P, Tagore S, Abril-Rodríguez G, He S, Jin Y, Biermann J, Hofree M, Caprio L, Berhe S, Khan SA, Henick BS, Ribas A, Macosko EZ, Chen F, Taylor AM, Schwartz GK, Carvajal RD, Azizi E, Izar B. Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nat Genet 2023; 55:19-25. [PMID: 36624340 PMCID: PMC10155259 DOI: 10.1038/s41588-022-01268-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 11/11/2022] [Indexed: 01/10/2023]
Abstract
Single-cell genomics enables dissection of tumor heterogeneity and molecular underpinnings of drug response at an unprecedented resolution1-11. However, broad clinical application of these methods remains challenging, due to several practical and preanalytical challenges that are incompatible with typical clinical care workflows, namely the need for relatively large, fresh tissue inputs. In the present study, we show that multimodal, single-nucleus (sn)RNA/T cell receptor (TCR) sequencing, spatial transcriptomics and whole-genome sequencing (WGS) are feasible from small, frozen tissues that approximate routinely collected clinical specimens (for example, core needle biopsies). Compared with data from sample-matched fresh tissue, we find a similar quality in the biological outputs of snRNA/TCR-seq data, while reducing artifactual signals and compositional biases introduced by fresh tissue processing. Profiling sequentially collected melanoma samples from a patient treated in the KEYNOTE-001 trial12, we resolved cellular, genomic, spatial and clonotype dynamics that represent molecular patterns of heterogeneous intralesional evolution during anti-programmed cell death protein 1 therapy. To demonstrate applicability to banked biospecimens of rare diseases13, we generated a single-cell atlas of uveal melanoma liver metastasis with matched WGS data. These results show that single-cell genomics from archival, clinical specimens is feasible and provides a framework for translating these methods more broadly to the clinical arena.
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Affiliation(s)
- Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, NY, USA
| | - Joy Linyue Fan
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yohanna Georgis
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Somnath Tagore
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gabriel Abril-Rodríguez
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Siyu He
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Yinuo Jin
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, NY, USA
| | - Matan Hofree
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Simon Berhe
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shaheer A Khan
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Brian S Henick
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Alison M Taylor
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Richard D Carvajal
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA.
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
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Yeku O, D. Shepard, Patel M, Fleming G, Vaena D, Rasco D, Chmielowski B, Sharma M, Hamilton E, Sullivan R, Papadopoulos K, Izar B, Cojocaru G, Ophir E, Ferre P, Dumbrava E. 159P COM701 in combination with nivolumab demonstrates preliminary antitumor activity in patients with platinum-resistant epithelial ovarian cancer. Immuno-Oncology and Technology 2022. [DOI: 10.1016/j.iotech.2022.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Moroney J, Yeku O, Fleming G, Emens L, Vaena D, Dumbrava E, Rasco D, Sharma M, Papadopoulos K, Patnaik A, Sullivan R, Adewoye H, Ophir E, Cojocaru G, Ferre P, Izar B, Gaillard S. 158P Triple blockade of the DNAM-axis with COM701 + BMS-986207 + nivolumab demonstrates preliminary antitumor activity in patients with platinum-resistant OVCA. Immuno-Oncology and Technology 2022. [DOI: 10.1016/j.iotech.2022.100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nguyen T, Shang E, Shu C, Akman H, Izar B, Westhoff MA, Karpel-Massler G, Bruce J, Canoll P, Siegelin M. TMET-38. LOSS OF FUNCTION OF CDK7 IS SYNTHETICALLY LETHAL WITH FATTY ACID OXIDATION INHIBITION IN GLIOBLASTOMA. Neuro Oncol 2022. [PMCID: PMC9661204 DOI: 10.1093/neuonc/noac209.1043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
CDK7 has been identified as a potential drug target for glioblastoma (GBM), a highly lethal primary brain tumor. However, resistance to therapy develops quickly, which may be facilitated by drug-induced reprogramming of metabolism. By combination of a transcriptome and metabolite screening analyses followed by carbon tracing (U-13C-Glucose, U-13C-Glutamine and U-13C-Palmitic acid) and extracellular flux analysis we demonstrated that both genetic and pharmacological (YKL-5-124 and THZ1) CDK7 inhibition elicited substantial metabolic reprogramming. Specifically, CDK7i elicited an increase of oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO) manifested by enhanced labeling of citric acid cycle intermediates from palmitic acid. Consistently, the combination treatment of CDK7i inhibitors with blockers of FAO (etomoxir) or cellular respiration (gamitrinib) exerted substantial synergistic growth inhibition in patient derived xenograft as well as neurosphere GBM cultures, which was mainly driven by a collapse of oxidative energy metabolism. In turn, exogenous administration of adenosine triphosphate partially rescued from the cell death induced by the combination treatment. Moreover, the combination treatment activated intrinsic apoptosis through a reduction of both Mcl-1 and Bcl-xL as demonstrated by rescue experiments. Finally, the combined administration of YKL-5-124 and etomoxir extended overall in an orthotopic patient-derived xenograft model of GBM. In summary, these data support that simultaneous targeting of CDK7 and FAO might be a potential novel therapy against GBM.
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Affiliation(s)
| | | | - Chang Shu
- Columbia University , New York, NY , USA
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Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LTY, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. bioRxiv 2022:2022.10.27.514070. [PMID: 36324805 PMCID: PMC9628199 DOI: 10.1101/2022.10.27.514070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
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Affiliation(s)
- Yered Pita-Juarez
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dimitra Karagkouni
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Kalavros
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, HMS Initiative for RNA Medicine / Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam L Essene
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Olga R Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Disha Skelton-Badlani
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Pourya Naderi
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Pinzhu Huang
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Liuliu Pan
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Tallulah S Andrews
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Carly G K Ziegler
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Andriy Myloserdnyy
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Rachel Chen
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Andy Nam
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Yan Liang
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Molly Veregge
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Zachary Kramer
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Christopher Jacobs
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Yusuf Yalcin
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Devan Phillips
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Michal Slyper
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | | | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Victoria M Tran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen J Fleming
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sonya A MacParland
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, Toronto, ON, Canada
| | - Nasser Imad
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric Miller
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Linus T-Y Tsai
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Winston Hide
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Gyongyi Szabo
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Jonathan Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Alex K Shalek
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Yury Popov
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Z Gordon Jiang
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA
| | - Ioannis S Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, HMS Initiative for RNA Medicine / Beth Israel Deaconess Medical Center, Boston, MA, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
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Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LTY, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. bioRxiv 2022. [PMID: 36324805 DOI: 10.1101/2022.08.06.503037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
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28
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Li Y, Goldberg EM, Chen X, Xu X, McGuire JT, Leuzzi G, Karagiannis D, Tate T, Farhangdoost N, Horth C, Dai E, Li Z, Zhang Z, Izar B, Que J, Ciccia A, Majewski J, Yoon AJ, Ailles L, Mendelsohn CL, Lu C. Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas. Mol Cell 2022; 82:3901-3918.e7. [PMID: 36206767 PMCID: PMC9588679 DOI: 10.1016/j.molcel.2022.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/06/2022]
Abstract
How cancer-associated chromatin abnormalities shape tumor-immune interaction remains incompletely understood. Recent studies have linked DNA hypomethylation and de-repression of retrotransposons to anti-tumor immunity through the induction of interferon response. Here, we report that inactivation of the histone H3K36 methyltransferase NSD1, which is frequently found in squamous cell carcinomas (SCCs) and induces DNA hypomethylation, unexpectedly results in diminished tumor immune infiltration. In syngeneic and genetically engineered mouse models of head and neck SCCs, NSD1-deficient tumors exhibit immune exclusion and reduced interferon response despite high retrotransposon expression. Mechanistically, NSD1 loss results in silencing of innate immunity genes, including the type III interferon receptor IFNLR1, through depletion of H3K36 di-methylation (H3K36me2) and gain of H3K27 tri-methylation (H3K27me3). Inhibition of EZH2 restores immune infiltration and impairs the growth of Nsd1-mutant tumors. Thus, our work uncovers a druggable chromatin cross talk that regulates the viral mimicry response and enables immune evasion of DNA hypomethylated tumors.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Elizabeth M Goldberg
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xinjing Xu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John T McGuire
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tiffany Tate
- Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nargess Farhangdoost
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Esther Dai
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhiguo Zhang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianwen Que
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Angela J Yoon
- Division of Oral and Maxillofacial Pathology, Columbia University College of Dental Medicine and Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Laurie Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Cathy Lee Mendelsohn
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Filliol A, Saito Y, Nair A, Dapito DH, Yu LX, Ravichandra A, Bhattacharjee S, Affo S, Fujiwara N, Su H, Sun Q, Savage TM, Wilson-Kanamori JR, Caviglia JM, Chin L, Chen D, Wang X, Caruso S, Kang JK, Amin AD, Wallace S, Dobie R, Yin D, Rodriguez-Fiallos OM, Yin C, Mehal A, Izar B, Friedman RA, Wells RG, Pajvani UB, Hoshida Y, Remotti HE, Arpaia N, Zucman-Rossi J, Karin M, Henderson NC, Tabas I, Schwabe RF. Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis. Nature 2022; 610:356-365. [PMID: 36198802 PMCID: PMC9949942 DOI: 10.1038/s41586-022-05289-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/30/2022] [Indexed: 01/21/2023]
Abstract
Hepatocellular carcinoma (HCC), the fourth leading cause of cancer mortality worldwide, develops almost exclusively in patients with chronic liver disease and advanced fibrosis1,2. Here we interrogated functions of hepatic stellate cells (HSCs), the main source of liver fibroblasts3, during hepatocarcinogenesis. Genetic depletion, activation or inhibition of HSCs in mouse models of HCC revealed their overall tumour-promoting role. HSCs were enriched in the preneoplastic environment, where they closely interacted with hepatocytes and modulated hepatocarcinogenesis by regulating hepatocyte proliferation and death. Analyses of mouse and human HSC subpopulations by single-cell RNA sequencing together with genetic ablation of subpopulation-enriched mediators revealed dual functions of HSCs in hepatocarcinogenesis. Hepatocyte growth factor, enriched in quiescent and cytokine-producing HSCs, protected against hepatocyte death and HCC development. By contrast, type I collagen, enriched in activated myofibroblastic HSCs, promoted proliferation and tumour development through increased stiffness and TAZ activation in pretumoural hepatocytes and through activation of discoidin domain receptor 1 in established tumours. An increased HSC imbalance between cytokine-producing HSCs and myofibroblastic HSCs during liver disease progression was associated with increased HCC risk in patients. In summary, the dynamic shift in HSC subpopulations and their mediators during chronic liver disease is associated with a switch from HCC protection to HCC promotion.
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Affiliation(s)
- Aveline Filliol
- Department of Medicine, Columbia University, New York, NY, USA
| | - Yoshinobu Saito
- Department of Medicine, Columbia University, New York, NY, USA
| | - Ajay Nair
- Department of Medicine, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Dianne H Dapito
- Department of Medicine, Columbia University, New York, NY, USA
| | - Le-Xing Yu
- Department of Medicine, Columbia University, New York, NY, USA
| | - Aashreya Ravichandra
- Department of Medicine, Columbia University, New York, NY, USA
- Klinikum Rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | | | - Silvia Affo
- Department of Medicine, Columbia University, New York, NY, USA
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Harold C. Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Su
- Department of Pharmacology, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Qiuyan Sun
- Department of Medicine, Columbia University, New York, NY, USA
| | - Thomas M Savage
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John R Wilson-Kanamori
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Jorge M Caviglia
- Department of Medicine, Columbia University, New York, NY, USA
- Department of Health and Nutrition Sciences, Brooklyn College, City University of New York, New York, NY, USA
| | - LiKang Chin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical Engineering, Widener University, Chester, PA, USA
| | - Dongning Chen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaobo Wang
- Department of Medicine, Columbia University, New York, NY, USA
| | - Stefano Caruso
- Functional Genomics of Solid Tumors Laboratory, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France
| | - Jin Ku Kang
- Department of Medicine, Columbia University, New York, NY, USA
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Amit Dipak Amin
- Department of Medicine, Columbia University, New York, NY, USA
| | - Sebastian Wallace
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Deqi Yin
- Department of Medicine, Columbia University, New York, NY, USA
| | | | - Chuan Yin
- Department of Medicine, Columbia University, New York, NY, USA
- Department of Gastroenterology, Changzheng Hospital, Shanghai, China
| | - Adam Mehal
- Department of Medicine, Columbia University, New York, NY, USA
| | - Benjamin Izar
- Department of Medicine, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, and Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rebecca G Wells
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Utpal B Pajvani
- Department of Medicine, Columbia University, New York, NY, USA
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Harold C. Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Helen E Remotti
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas Arpaia
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica Zucman-Rossi
- Functional Genomics of Solid Tumors Laboratory, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France
| | - Michael Karin
- Department of Pharmacology, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ira Tabas
- Department of Medicine, Columbia University, New York, NY, USA
- Institute of Human Nutrition, Columbia University, New York, NY, USA
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology, Columbia University, New York, NY, USA
| | - Robert F Schwabe
- Department of Medicine, Columbia University, New York, NY, USA.
- Institute of Human Nutrition, Columbia University, New York, NY, USA.
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30
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Khan S, Patel SP, Shoushtari AN, Ambrosini G, Cremers S, Lee S, Franks L, Singh-Kandah S, Hernandez S, Sender N, Vuolo K, Nesson A, Mundi P, Izar B, Schwartz GK, Carvajal RD. Intermittent MEK inhibition for the treatment of metastatic uveal melanoma. Front Oncol 2022; 12:975643. [PMID: 36249046 PMCID: PMC9557946 DOI: 10.3389/fonc.2022.975643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Uveal melanoma (UM) is associated with poor outcomes in the metastatic setting and harbors activating mutations resulting in upregulation of MAPK signaling in almost all cases. The efficacy of selumetinib, an oral allosteric inhibitor of MEK1/2, was limited when administered at a continual dosing schedule of 75 mg BID. Preclinical studies demonstrate that intermittent MEK inhibition reduces compensatory pathway activation and promotes T cell activation. We hypothesized that intermittent dosing of selumetinib would reduce toxicity, allow for the administration of increased doses, and achieve more complete pathway inhibition, thus resulting in improved antitumor activity. Methods We conducted a phase Ib trial of selumetinib using an intermittent dosing schedule in patients with metastatic UM. The primary objective was to estimate the maximum tolerated dose (MTD) and assess safety and tolerability. Secondary objectives included assessment of the overall response rate (RR), progression-free survival (PFS) and overall survival (OS). Tumor biopsies were collected at baseline, on day 3 (on treatment), and between days 11-14 (off treatment) from 9 patients for pharmacodynamic (PD) assessments. Results 29 patients were enrolled and received at least one dose of selumetinib across 4 dose levels (DL; DL1: 100 mg BID; DL2: 125 mg BID; DL3: 150 mg BID; DL4: 175 mg BID). All patients experienced a treatment-related adverse event (TRAE), with 5/29 (17%) developing a grade 3 or higher TRAE. Five dose limiting toxicities (DLT) were observed: 2/20 in DL2, 2/5 in DL3, 1/1 in DL4. The estimated MTD was 150 mg BID (DL3), with an estimated probability of toxicity of 29% (90% probability interval 16%-44%). No responses were observed; 11/29 patients achieved a best response of stable disease (SD). The median PFS and OS were 1.8 months (95% CI 1.7, 4.5) and 7.1 months (95% CI 5.3, 11.5). PD analysis demonstrated at least partial pathway inhibition in all samples at day 3, with reactivation between days 11-14 in 7 of those cases. Conclusions We identified 150 mg BID as the MTD of intermittent selumetinib, representing a 100% increase over the continuous dose MTD (75 mg BID). However, no significant clinical efficacy was observed using this dosing schedule.
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Affiliation(s)
- Shaheer Khan
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
- *Correspondence: Shaheer Khan,
| | - Sapna P. Patel
- Department of Melanoma Medical Oncology University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Grazia Ambrosini
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Serge Cremers
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Shing Lee
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lauren Franks
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shahnaz Singh-Kandah
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Susana Hernandez
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Naomi Sender
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Kristina Vuolo
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Alexandra Nesson
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Prabhjot Mundi
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Benjamin Izar
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Gary K. Schwartz
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
| | - Richard D. Carvajal
- Department of Medicine Columbia University Irving Medical Center, New York, NY, United States
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Bose S, Caldwell B, Amin AD, Melms J, Tagore S, Ingham M, Izar B, Schwartz GK. Abstract PR006: Multi-modal single-cell profiling of sarcomas from archival tissue reveals mechanisms of resistance to immune checkpoint inhibitors. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-pr006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Single-cell genomics is an enabling technology that may inform the molecular underpinnings of drug response and resistance in patient biopsies. These methods are difficult to implement in the study of rare diseases such as sarcomas due to specimen requirements and technical limitations. Here, we evolved novel methods that we recently reported in melanoma (Wang, Fan, et al., bioRxiv, 2022) which enable single-nucleus RNA, T cell receptor (snRNA/TCR-seq), and pool-matched whole-genome sequencing (WGS) from archival frozen sarcoma tissue. This enabled profiling of 75,716 cells and 788 matched TCR clonotypes from six patients with intimal sarcoma (INS) and undifferentiated pleomorphic sarcoma (UPS), including two matched pair samples from pre/post-immune checkpoint inhibitor (ICI). Our analysis revealed substantial transcriptional cancer cell heterogeneity driven by varying copy number alterations (CNAs). In one patient with INS with a complete response to ICI followed by an isolated recurrence, we identified a rare cancer cell clone defined by CNA (confirmed with WGS) and resulting transcriptional outputs that pre-existed and emerged during resistance. Furthermore, in a UPS patient with intrinsic resistance to ICI, we find adequate T cell clonal expansion, activation, and differentiation, suggesting appropriate T cell response to ICI dampened by intrinsic mechanisms of ICI resistance within the cancer cells. Non-negative matrix factorization (NMF) analysis identified cell states associated with either intrinsic or adaptive resistance to ICI that was distinct from resistance to doxorubicin. These observations are consistent with those previously reported from sequential biopsies obtained from KEYNOTE-001 in metastatic melanoma (Wang, Fan, et al., bioRxiv, 2022), which also revealed emergence of pre-existing populations of resistant clones defined by their underlying aneuploidy patterns. Together, these results demonstrate feasibility of implementing single-cell genomics from archival tissue to study sarcoma and propel our understanding of drug resistance. Conceptually, this work suggests that large-scale CNAs may allow us to identify cell sub-populations associated with ICI resistance in sarcoma and in other diseases.
Citation Format: Sminu Bose, Blake Caldwell, Amit Dipak Amin, Johannes Melms, Somnath Tagore, Matthew Ingham, Benjamin Izar, Gary K. Schwartz. Multi-modal single-cell profiling of sarcomas from archival tissue reveals mechanisms of resistance to immune checkpoint inhibitors [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR006.
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Affiliation(s)
- Sminu Bose
- 1Columbia University Medical Center, New York, NY
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32
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Anderson AC, Yanai I, Yates LR, Wang L, Swarbrick A, Sorger P, Santagata S, Fridman WH, Gao Q, Jerby L, Izar B, Shang L, Zhou X. Spatial transcriptomics. Cancer Cell 2022; 40:895-900. [PMID: 36099884 DOI: 10.1016/j.ccell.2022.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spatial transcriptomics, with other spatial technologies, has enabled scientists to dissect the organization and interaction of different cell types within the tumor microenvironment. We asked experts to discuss some aspects of this technology from revealing the tumor microenvironment and heterogeneity, to tracking tumor evolution, to guiding tumor therapy, to current technical challenges.
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33
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Hamid O, Sato T, Davar D, Callahan M, Thistlethwaite F, Aljumaily R, Johnson M, Arkenau HT, Ileana Dumbrava E, Izar B, Chen H, Marshall S, Yuan Y, Deo M, Stanhope S, Collins L, Mundy R, Abdullah S, Lopez J. 728O Results from phase I dose escalation of IMC-F106C, the first PRAME × CD3 ImmTAC bispecific protein in solid tumors. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Alvarez-Breckenridge C, Markson SC, Stocking JH, Nayyar N, Lastrapes M, Strickland MR, Kim AE, de Sauvage M, Dahal A, Larson JM, Mora JL, Navia AW, Klein RH, Kuter BM, Gill CM, Bertalan M, Shaw B, Kaplan A, Subramanian M, Jain A, Kumar S, Danish H, White M, Shahid O, Pauken KE, Miller BC, Frederick DT, Hebert C, Shaw M, Martinez-Lage M, Frosch M, Wang N, Gerstner E, Nahed BV, Curry WT, Carter B, Cahill DP, Boland GM, Izar B, Davies MA, Sharpe AH, Suvà ML, Sullivan RJ, Brastianos PK, Carter SL. Microenvironmental Landscape of Human Melanoma Brain Metastases in Response to Immune Checkpoint Inhibition. Cancer Immunol Res 2022; 10:996-1012. [PMID: 35706413 DOI: 10.1158/2326-6066.cir-21-0870] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/12/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Melanoma-derived brain metastases (MBM) represent an unmet clinical need because central nervous system progression is frequently an end stage of the disease. Immune checkpoint inhibitors (ICI) provide a clinical opportunity against MBM; however, the MBM tumor microenvironment (TME) has not been fully elucidated in the context of ICI. To dissect unique elements of the MBM TME and correlates of MBM response to ICI, we collected 32 fresh MBM and performed single-cell RNA sequencing of the MBM TME and T-cell receptor clonotyping on T cells from MBM and matched blood and extracranial lesions. We observed myeloid phenotypic heterogeneity in the MBM TME, most notably multiple distinct neutrophil states, including an IL8-expressing population that correlated with malignant cell epithelial-to-mesenchymal transition. In addition, we observed significant relationships between intracranial T-cell phenotypes and the distribution of T-cell clonotypes intracranially and peripherally. We found that the phenotype, clonotype, and overall number of MBM-infiltrating T cells were associated with response to ICI, suggesting that ICI-responsive MBMs interact with peripheral blood in a manner similar to extracranial lesions. These data identify unique features of the MBM TME that may represent potential targets to improve clinical outcomes for patients with MBM.
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Affiliation(s)
- Christopher Alvarez-Breckenridge
- Departments of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Samuel C Markson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jackson H Stocking
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Naema Nayyar
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Matt Lastrapes
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Matthew R Strickland
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Albert E Kim
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Magali de Sauvage
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Ashish Dahal
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Juliana M Larson
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Joana L Mora
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Andrew W Navia
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, Massachusetts
| | - Robert H Klein
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Benjamin M Kuter
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Corey M Gill
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Mia Bertalan
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Brian Shaw
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Alexander Kaplan
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Megha Subramanian
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Aarushi Jain
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Swaminathan Kumar
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Husain Danish
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical Center, New York, New York
| | - Michael White
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | - Osmaan Shahid
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen E Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Brian C Miller
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dennie T Frederick
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christine Hebert
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - McKenzie Shaw
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Maria Martinez-Lage
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Matthew Frosch
- C. S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nancy Wang
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
| | | | - Brian V Nahed
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
| | - William T Curry
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Bob Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Genevieve Marie Boland
- Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Benjamin Izar
- Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York
- Columbia Center for Translational Immunology, New York, New York
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Mario L Suvà
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ryan J Sullivan
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Priscilla K Brastianos
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Scott L Carter
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
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Jaiswal A, Verma A, Dannenfelser R, Melssen M, Tirosh I, Izar B, Kim T, Nirschl C, Devi S, Olson W, Slingluff C, Engelhard V, Garraway L, Regev A, Yoon C, Troyanskaya O, Elemento O, Suarez-Farinas M, Anandasabapathy N. 037 A systems immunology approach to classify melanoma tumor infiltrating lymphocytes (TILs) informs and models overall survival. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022; 185:2591-2608.e30. [PMID: 35803246 PMCID: PMC9677434 DOI: 10.1016/j.cell.2022.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/08/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma; yet, our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs) and matched spatial single-cell transcriptomics and T cell receptor (TCR)-seq. Cancer cells from MBM were more chromosomally unstable, adopted a neuronal-like cell state, and enriched for spatially variably expressed metabolic pathways. Key observations were validated in independent patient cohorts, patient-derived MBM/ECM xenograft models, RNA/ATAC-seq, proteomics, and multiplexed imaging. Integrated spatial analyses revealed distinct geography of putative cancer immune evasion and evidence for more abundant intra-tumoral B to plasma cell differentiation in lymphoid aggregates in MBM. MBM harbored larger fractions of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with distinct expression of immune checkpoints. This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.
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Affiliation(s)
- Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Lindsay A Caprio
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alcida Karz
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Irving Barrera
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Miguel A Ibarra-Arellano
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Massimo Andreatta
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kristjan H Gretarsson
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Varun Sahu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Vaibhav S Mangipudy
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Trang T T Nguyen
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ajay Nair
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter D Koch
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Matei Banu
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nelson Humala
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Daniel H Vaccaro
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Blake Caldwell
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Florian Wünnemann
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Margot Chazotte
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Simon Berhe
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Joseph Driver
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ingham
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shaheer A Khan
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Suthee Rapisuwon
- Division of Hematology/Oncology, Medstar Washington Cancer Institute, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Craig L Slingluff
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Thomas Eigentler
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venereology and Allergology, 10117, Berlin, Germany
| | - Martin Röcken
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Richard Carvajal
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albert Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Samuel F Bakhoum
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Markus Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Santiago J Carmona
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90024, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Praveen Agrawal
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Denis Schapiro
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Ho P, Melms J, Rogava M, Shah S, Izar B. Abstract 2165: CD58:CD2 - a multi-dimensional axis in cancer immunotherapy resistance. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
While immune checkpoint blockade therapy has transformed the treatment of metastatic melanoma, most patients exhibit resistance to these therapies, often by unknown mechanisms. We previously found an association of cancer cell autonomous loss of CD58, which encodes a co-stimulatory/adhesion molecule, with immunotherapy resistance in patients. Here, we investigate the mechanistic molecular underpinnings of this observation. In patient-derived melanoma cells co-cultured with autologous tumor infiltrating lymphocytes (TILs), we found that CD58:CD2 ligation is specifically required for TIL-mediated killing and promotes T cell cytokine production. Furthermore, CD58 co-stimulation of TILs enhances their proliferation and activation compared to traditional methods of co-stimulation via CD28. We additionally examined the role of CD58 in vivo. Given that there is no known mouse homolog for CD58, we utilized a humanized mouse model in which hIL-2-expressing NOD/Shi-scid/IL-2Rγnull mice were implanted with patient-derived WT or CD58 knockout (KO) melanoma cells, followed by adoptive cell transfer (ACT) of autologous TILs. We found that CD58 KO tumors were resistant to ACT and had significantly lower TIL infiltration and proliferation compared to WT tumors, and that these effects were rescued by re-expressing CD58. We had previously found that CD58 loss concurrently leads to higher expression of PD-L1, suggesting that enhanced co-inhibitory PD-1/PD-L1 signaling could additionally contribute to cancer immune evasion. To understand CD58/PD-L1 co-regulation, we first sought to delineate genetic and protein-protein regulation of CD58. We performed a genome-wide CRISPR/Cas9 KO screen with FACS enrichment, as well as unbiased CD58 co-immunoprecipitation mass spectrometry screens and identified CMTM6 as a key regulator of CD58. Importantly, CMTM6 was previously identified as a regulator of PD-L1 maintenance, positioning it as a potential candidate for regulating both co-stimulatory (CD58) and co-inhibitory (PD-L1) signals in cancer cells. Indeed, we find that both PD-L1 and CD58 are regulated by CMTM6 at the level of lysosomal degradation. Furthermore, in cells with CD58/CMTM6 double-KO, CMTM6 is required for CD58/PD-L1 co-regulation, which is restored with re-expression of CMTM6. We therefore propose a model in which CD58 regulates PD-L1 by modulating its level of binding to CMTM6; in the absence of CD58, additional CMTM6 is available to bind PD-L1 and thereby stabilize its expression. In summary, we define a central role of the CD58:CD2 axis in tumor immunity and propose that loss of CD58 confers cancer immune evasion through impaired T cell toxicity, tumor infiltration, and concurrent CMTM6-dependent PD-L1 upregulation.
Citation Format: Patricia Ho, Johannes Melms, Meri Rogava, Shivem Shah, Benjamin Izar. CD58:CD2 - a multi-dimensional axis in cancer immunotherapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2165.
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Li J, Hubisz M, Earlie E, Duran MA, Lettera E, Phyu SM, Amin AD, Deyell M, Kamiya E, Budre K, Cavallo JA, Garris C, Wen H, Izar B, Parkes E, Laughney A, Bakhoum S. Abstract 3822: Chromosomal instability shapes the tumor microenvironment through a chronic ER-stress response. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chromosomal instability (CIN) is a cancer hallmark associated with cancer metastasis and immune evasion. Yet, it is unclear how CIN modulates the tumor-microenvironment (TME). Here we show that CIN results in a protumor TME with enrichment of immune-suppressive macrophages, a granulocytic infiltrate, and exhausted T cells. Using ContactTracing, a newly developed computational tool to infer conditionally dependent cell-cell interactions from single cell RNA sequence data, we identify tumor ligands induced by the ER stress response in cancer cells as central mediators of immune suppression. Mechanistically, CIN-dependent chronic activation of the cytosolic DNA sensing cGAS-STING pathway promotes ER-stress-dependent transcription. Suppression of CIN or depletion of cancer cell STING reduces ER-stress and restores CIN-induced changes on the TME. Correspondingly, chronic STING activation in human breast cancer patients is associated with reduced tumor infiltrating lymphocytes and increased metastasis. Remarkably, pharmacologic inhibition of chronically active STING or depletion of downstream ER stress signaling suppresses metastasis in syngeneic models of melanoma, breast, and colorectal cancers, thereby demonstrating a viable therapeutic strategy for chromosomally unstable cancers.
Citation Format: Jun Li, Melissa Hubisz, Ethan Earlie, Mercedes A. Duran, Emanuele Lettera, Su M. Phyu, Amit D. Amin, Matthew Deyell, Erina Kamiya, Karolina Budre, Julie-Ann Cavallo, Christopher Garris, Hannah Wen, Benjamin Izar, Eileen Parkes, Ashley Laughney, Samuel Bakhoum. Chromosomal instability shapes the tumor microenvironment through a chronic ER-stress response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3822.
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Affiliation(s)
- Jun Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Su M. Phyu
- 3University of Oxford, Oxford, United Kingdom
| | - Amit D. Amin
- 4Columbia University Medical Center, New York, NY
| | | | | | | | | | | | - Hannah Wen
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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39
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Melms JC, Biermann J, Amin AD, Wang Y, Tagore S, Andreatta M, Nair A, Rogava M, Ho P, Caprio LA, Walsh ZH, Shah S, Vacarro DH, Caldwell B, Luoma AM, Driver J, Ingham M, Rapisuwon S, Wargo J, Slinguff CL, Macosco EZ, Chen F, Carvajal R, Atkins MB, Davies MA, Azizi E, Carmona SJ, Hibshoosh H, Canoll PD, Bruce JN, Bi WL, Schwartz GK, Izar B. Abstract 984: Dissecting the ecosystem of treatment-naïve melanoma brain metastasis using multi-modal single-cell analysis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Brain metastases are the most frequent malignancies in the brain and are associated with significant morbidity and mortality. Melanoma brain metastases (MBM) occur in most patients with advanced melanoma and are challenging to treat. Our understanding of the treatment-naïve landscape of MBM is still rudimentary, and there are no site-specific molecular therapies available. To gain comprehensive insights into the niche-specific biology of MBM, we performed multi-modal profiling of fresh and frozen samples using single-cell RNA-seq, single-cell TCR-seq, single-nuclei RNA-seq, and spatial transcriptional profiling. We evolved single-nucleus RNA-seq processing methods to enable profiling of minute amounts of archival, frozen specimens and compared data quality and structure between matched fresh and frozen MBM. We curated a treatment-naïve single-transcriptome atlas of MBM, collected either fresh samples over 1 year or profiled frozen samples dating back more than 15 years, and compared these samples to extracranial melanoma metastases (ECMM). In total, we profiled 25 samples with more than 114,000 transcriptomes. We identified more than 20 different cell types, including diverse tumor-infiltrating T-cell subsets and rare dendritic cell types, and tissue-specific cell types, such as activated microglia. Tumor cells in MBM showed an increase in copy number alterations (CNAs) compared to ECMM, which we validated using an external dataset of whole exome sequencing (WES) data including both MBM and ECMM. MBM-derived tumor cells show enrichment of genes involved in neuronal development and function, and site-specific metabolic programs (e.g., oxidative phosphorylation). Comparison with an external bulk RNA-seq dataset validated enriched key genes in MBM and ECMM as putative dependencies. We recovered cell-cell interactions between tumor and brain-resident cells involved in brain development, homeostasis, and disease. Similar to ECMM, the tumor microenvironment of MBM contained CD8+ T cells across a spectrum of differentiation, exhaustion and expansion, which was associated with loss of TCF7 expression and adoption of a TOX+ cell state. CD4+ T cells included T regulatory, T helper and T follicular-helper-like expression profiles. Plasma cells showed spatially localized expansion and limited heterogeneity. Myeloid cells largely adopted pro-tumorigenic cell states, including microglia, the brain-resident myeloid cells, which showed an activation trajectory characterized by expression of SPP1 (osteopontin). Spatial transcriptional analysis revealed restricted expression of antigen presentation genes with only a subset of these locations showing a type I interferon response. In summary, this work presents a multi-modal single-cell approach to dissect and compare the landscape of treatment-naïve MBM and ECMM.
Citation Format: Johannes C. Melms, Jana Biermann, Amit Dipak Amin, Yiping Wang, Somnath Tagore, Massimo Andreatta, Ajay Nair, Meri Rogava, Patricia Ho, Lindsay A. Caprio, Zachary H. Walsh, Shivem Shah, Daniel H. Vacarro, Blake Caldwell, Adrienne M. Luoma, Joseph Driver, Matthew Ingham, Suthee Rapisuwon, Jennifer Wargo, Craig L. Slinguff, Evan Z. Macosco, Fei Chen, Richard Carvajal, Michael B. Atkins, Michael A. Davies, Elham Azizi, Santiago J. Carmona, Hanina Hibshoosh, Peter D. Canoll, Jeffrey N. Bruce, Wenya L. Bi, Gary K. Schwartz, Benjamin Izar. Dissecting the ecosystem of treatment-naïve melanoma brain metastasis using multi-modal single-cell analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 984.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joseph Driver
- 4Brigham and Women' Hospital. Harvard Medical School, Boston, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wenya L. Bi
- 4Brigham and Women' Hospital. Harvard Medical School, Boston, NY
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Rogava M, Melms JC, Davis S, Hug C, Ngo B, Lee MJ, Ho P, Amin AD, Wang Y, Chen S, Ge W, Liu D, Tüting T, Röcken M, Eigentler TK, Bakhoum SF, Molotkov A, Mintz A, Cantley LC, Sorger PK, Izar B. Abstract 981: A genetic-metabolic axis of metastatic liver organotropism. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic and adaptive determinants of organ-specific metastasis are poorly understood. A model of sequential acquisition of divergent somatic mutations is insufficient to explain metastasis. Liver metastasis (LM) occurs frequently and is associated with a poor prognosis and reduced therapy response in several cancers, including in patients with melanoma and lung cancer. To identify drivers of metastatic niches, we used a syngeneic mouse melanoma model which recapitulates genomic, metastatic and therapy response patterns seen in patients. We performed a large-scale in vivo CRISPR-Cas9 knockout screen and identified perturbations that promote LM, but not primary tumor growth or metastasis to other organs (e.g. lung). The “top hit” in this screen associated with LM was loss Pip4k2c. We generated Pip4k2cKO cells and show that in otherwise isogenic melanoma cell lines, loss of Pip4k2c led to increased baseline and insulin-induced activation of the PI3K/AKT pathway, and increased invasive capacity. Rescuing Pip4k2cKO with full-length (Pip4k2cRec) or allosteric domain deficient (Pip4k2cAD) Pip4k2c ORFs, we show that hyperactivation of the PI3K/AKT pathway in is mediated by loss of the allosteric domain function, and not loss of the kinase domain of Pip4k2c. Treatment with different PI3K inhibitors effectively abrogated the pathway, but was partly bypassed in the presence of insulin in Pip4k2cKO and Pip4k2cAD, but not parental or Pip4k2cRec cells. Upon tail vein injection, Pip4k2cKO cells produced a significantly increased LM burden compared to parental cells, and this effect was rescued in Pip4k2cRec but not Pip4k2cAD, further affirming that loss of allosteric domain was required for this phenotype. We reasoned that Pip4k2cKO cells preferentially colonized the liver by co-opting the insulin-rich milieu in this organ. To test this, we used shRNA targeted against the insulin receptor (Insr) generated Pip4k2cKO/InsrshIR and showed that Insr was required but not sufficient to enhance LM burden. Given the promising in vitro activity of PI3K inhibitors, we next tested whether these could abrogate LM in vivo. Surprisingly, we found a substantial increase in LM burden in mice with Pip4k2cKO-bearing LM treated with PI3K inhibition compared to vehicle treated animals. We show that this paradoxical observation was due to host-mediated increased in glucose and insulin in response to PI3K inhibitor, which promoted a forward loop of increased liver metastasis. Breaking this loop with either ketogenic diet or treatment with a SGLT2 inhibitor in turn rescued increased these host responses and resulted in reduced LM burden in combination with PI3K inhibition. In summary, we identify a novel mechanism of metastatic liver organotropism and pharmacological and dietary combinations to reduced liver metastatic burden. Given the expanding use of PI3K inhibitors, our findings may have important clinical implications.
Citation Format: Meri Rogava, Johannes C. Melms, Stephanie Davis, Clemens Hug, Bryan Ngo, Michael J. Lee, Patricia Ho, Amit Dipak Amin, Yiping Wang, Sean Chen, William Ge, David Liu, Thomas Tüting, Martin Röcken, Thomas K. Eigentler, Samuel F. Bakhoum, Andrei Molotkov, Akiva Mintz, Lewis C. Cantley, Peter K. Sorger, Benjamin Izar. A genetic-metabolic axis of metastatic liver organotropism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 981.
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Affiliation(s)
| | | | | | | | - Bryan Ngo
- 3Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - William Ge
- 4Dana-Farber Cancer Institute, Boston, MA
| | - David Liu
- 4Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Akiva Mintz
- 8Columbia University Medical Center, New York, NY
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Spigel D, Spira A, Zamarin D, McDermott DF, Luke J, Heymach JV, Previs R, Sullivan R, Gandhi L, Azrilevich A, Rizvi N, Oft M, Busby N, Izar B. Abstract CT244: A phase 1a/1b study of STK-012, an α/β IL-2 receptor selective partial agonist as monotherapy and in combination with pembrolizumab in advanced solid tumors (NCT05098132). Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-ct244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: High dose intravenous (IV) interleukin-2 (IL-2) induces complete responses in certain cancers, but its use is limited due to toxicities including severe hypotension and capillary leak syndrome (CLS), and the requirement for inpatient administration. Recent approaches to develop IL-2 therapies with an expanded therapeutic index have targeted the dimeric form (β/γ) of the IL-2 receptor, which is predominantly expressed on naïve T cells and NK cells, rather than the high affinity trimeric form (α/β/γ), predominantly expressed on antigen activated T cells and Tregs. Preclinical data support the hypothesis that this “non-α” approach favors activating cells that serve as principal mediators of toxicity (NK cells) over antitumor activity (antigen activated T cells). STK-012 is a pegylated, α/β-IL-2R selective partial agonist engineered to preferentially stimulate antigen-activated CD25+ T cells and avoid systemic NK and naïve T cell activation. In syngeneic tumor models, subcutaneously (SQ) injected STK-012 mouse surrogate demonstrated reduced toxicities and improved efficacy relative to mouse wild-type IL-2 or a non-α IL-2. In cynomolgus monkeys, acute lung inflammation was induced by aldesleukin and non-α-IL-2, but not by STK-012. STK-012 is in development as monotherapy and in combination with pembrolizumab for the treatment of advanced solid tumors.
Methods: This is a first-in-human, open-label, dose escalation and expansion study in adults with advanced solid tumors (NCT05098132). The objectives of this study are to evaluate the safety, pharmacokinetics, immunogenicity, preliminary efficacy, and pharmacodynamics of STK-012 as monotherapy and in combination with pembrolizumab. Dose escalation will follow a standard 3+3 design for STK-012 monotherapy and in combination with pembrolizumab. STK-012 will be dosed SQ weekly, and pembrolizumab will be dosed IV every 3 weeks. Eligible participants for dose escalation include individuals with non-small cell lung cancer, head and neck squamous cell cancer, malignant melanoma, renal cell carcinoma, ovarian cancer, cervical cancer and microsatellite instability-high or mismatch repair deficient cancers who are relapsed/refractory to, intolerant to, or refuse standard of care treatment. Expansion cohorts will enroll participants at selected dose(s) and indications on the basis of dose escalation findings. The primary endpoint of safety includes outcomes such as adverse events and dose-limiting toxicities. Efficacy, a secondary endpoint, will include assessments of tumor response according to RECIST v1.1. Exploratory biomarker assessments will include peripheral and tumor measures of immune cell populations and relevant gene/protein expression. Enrollment in STK-012 monotherapy dose escalation has been initiated.
Citation Format: David Spigel, Alexander Spira, Dmitriy Zamarin, David F. McDermott, Jason Luke, John V. Heymach, Rebecca Previs, Ryan Sullivan, Leena Gandhi, Alex Azrilevich, Naiyer Rizvi, Martin Oft, Natalie Busby, Benjamin Izar. A phase 1a/1b study of STK-012, an α/β IL-2 receptor selective partial agonist as monotherapy and in combination with pembrolizumab in advanced solid tumors (NCT05098132) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT244.
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Affiliation(s)
| | | | | | | | - Jason Luke
- 5University of Pittsburgh Medical Center, Pittsbrugh, PA
| | | | | | | | | | | | | | | | | | - Benjamin Izar
- 11Columbia University Irving Medical Center, New York, NY
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Caldwell B, Bose S, Amin AD, Tagore S, Melms JC, Berhe S, Ingham M, Schwartz GK, Izar B. Multi-modal single-cell profiling of sarcomas from archival tissue reveals mechanisms of resistance to immune checkpoint inhibitors. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e23518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e23518 Background: Single-cell RNA-seq is an enabling technology that may inform the molecular underpinnings of drug response and resistance in patient biopsies. This method is difficult to implement in the study of rare diseases such as sarcomas due to specimen requirements and technical limitations. Methods: Here, we evolved novel methods that we recently reported in melanoma ( Wang, Fan, et al., bioRxiv, 2022), which enable single-nucleus RNA, T cell receptor (snRNA/TCR)-seq, and pool-matched whole-genome sequencing (WGS) from archival, frozen sarcoma tissue. Results: This enabled profiling of 75,716 cells and 788 matched TCR clonotypes from six patients with intimal sarcoma (INS) and undifferentiated pleomorphic sarcomas (UPS), including two matched pair samples from pre/post-immune checkpoint inhibitor (ICI). Our analysis revealed substantial transcriptional cancer cell heterogeneity driven by varying copy number alterations (CNAs). In one patient with INS with a complete response to ICI followed by an isolated recurrence, we identified a rare cancer cell clone defined by CNA (confirmed with WGS) and resulting transcriptional outputs that pre-existed and emerged during resistance. Furthermore, in a patient with UPS with intrinsic resistance to ICI, we find adequate T cell clonal expansion and activation, suggesting appropriate T cell response to ICI dampened by intrinsic mechanisms of ICI resistance within the cancer cells. Non-negative matrix factorization (NMF) analysis identified cell states associated with either intrinsic or adaptive resistance to ICI that was distinct from resistance to doxorubicin. These observations are consistent with those previously reported from sequential biopsies obtained from KEYNOTE-001 in metastatic melanoma ( Wang, Fan, et al., bioRxiv, 2022), which also revealed emergence of pre-existing populations of resistant clones defined by their underlying aneuploidy patterns. Conclusions: Together, these results demonstrate feasibility of implementing single-cell genomics from archival tissue to study sarcoma and propel our understanding of drug resistance. Conceptually, this work suggests that large-scale CNAs may drive cell sub-populations associated with ICI resistance in sarcoma and in other diseases.
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Affiliation(s)
| | - Sminu Bose
- Columbia University Medical Center, New York, NY
| | | | | | | | - Simon Berhe
- Columbia University Medical Center, New York, NY
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Jaiswal A, Verma A, Dannenfelser R, Melssen M, Tirosh I, Izar B, Kim TG, Nirschl CJ, Devi KSP, Olson WC, Slingluff CL, Engelhard VH, Garraway L, Regev A, Minkis K, Yoon CH, Troyanskaya O, Elemento O, Suárez-Fariñas M, Anandasabapathy N. An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes. Cancer Cell 2022; 40:524-544.e5. [PMID: 35537413 PMCID: PMC9122099 DOI: 10.1016/j.ccell.2022.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
There is a need for better classification and understanding of tumor-infiltrating lymphocytes (TILs). Here, we applied advanced functional genomics to interrogate 9,000 human tumors and multiple single-cell sequencing sets using benchmarked T cell states, comprehensive T cell differentiation trajectories, human and mouse vaccine responses, and other human TILs. Compared with other T cell states, enrichment of T memory/resident memory programs was observed across solid tumors. Trajectory analysis of single-cell melanoma CD8+ TILs also identified a high fraction of memory/resident memory-scoring TILs in anti-PD-1 responders, which expanded post therapy. In contrast, TILs scoring highly for early T cell activation, but not exhaustion, associated with non-response. Late/persistent, but not early activation signatures, prognosticate melanoma survival, and co-express with dendritic cell and IFN-γ response programs. These data identify an activation-like state associated to poor response and suggest successful memory conversion, above resuscitation of exhaustion, is an under-appreciated aspect of successful anti-tumoral immunity.
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Affiliation(s)
- Abhinav Jaiswal
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10026, USA
| | - Akanksha Verma
- Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ruth Dannenfelser
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Marit Melssen
- Division of Surgical Oncology - Breast and Melanoma Surgery, Department of Surgery, Human Immune Therapy Center, Cancer Center, University of Virginia, Charlottesville, VA 22908, USA; Carter Immunology Center, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Herbert Irving Comprehensive Cancer Center, Columbia Center for Translational Immunology and Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Tae-Gyun Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, South Korea
| | - Christopher J Nirschl
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - K Sanjana P Devi
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA
| | - Walter C Olson
- Division of Surgical Oncology - Breast and Melanoma Surgery, Department of Surgery, Human Immune Therapy Center, Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Craig L Slingluff
- Division of Surgical Oncology - Breast and Melanoma Surgery, Department of Surgery, Human Immune Therapy Center, Cancer Center, University of Virginia, Charlottesville, VA 22908, USA; Carter Immunology Center, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Victor H Engelhard
- Carter Immunology Center, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Levi Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Center for Cancer for Cancer Precision Medicine, Boston, MA 02115, USA; Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kira Minkis
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA
| | - Charles H Yoon
- Brigham and Women's Hospital, Department of Surgical Oncology Harvard Medical School, Boston, MA 02115, USA
| | - Olga Troyanskaya
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Simons Center for Data Analysis, Simons Foundation, New York, NY 10010, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Niroshana Anandasabapathy
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10026, USA; Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10026, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10026, USA.
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Garrido A, Kim E, Teijeiro A, Sánchez Sánchez P, Gallo R, Nair A, Matamala Montoya M, Perna C, Vicent GP, Muñoz J, Campos-Olivas R, Melms JC, Izar B, Schwabe RF, Djouder N. Histone acetylation of bile acid transporter genes plays a critical role in cirrhosis. J Hepatol 2022; 76:850-861. [PMID: 34958836 PMCID: PMC8934297 DOI: 10.1016/j.jhep.2021.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/01/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Owing to the lack of genetic animal models that adequately recreate key clinical characteristics of cirrhosis, the molecular pathogenesis of cirrhosis has been poorly characterized, and treatments remain limited. Hence, we aimed to better elucidate the pathological mechanisms of cirrhosis using a novel murine model. METHODS We report on the first murine genetic model mimicking human cirrhosis induced by hepatocyte-specific elimination of microspherule protein 1 (MCRS1), a member of non-specific lethal (NSL) and INO80 chromatin-modifier complexes. Using this genetic tool with other mouse models, cell culture and human samples, combined with quantitative proteomics, single nuclei/cell RNA sequencing and chromatin immunoprecipitation assays, we investigated mechanisms of cirrhosis. RESULTS MCRS1 loss in mouse hepatocytes modulates the expression of bile acid (BA) transporters - with a pronounced downregulation of Na+-taurocholate cotransporting polypeptide (NTCP) - concentrating BAs in sinusoids and thereby activating hepatic stellate cells (HSCs) via the farnesoid X receptor (FXR), which is predominantly expressed in human and mouse HSCs. Consistently, re-expression of NTCP in mice reduces cirrhosis, and genetic ablation of FXR in HSCs suppresses fibrotic marks in mice and in vitro cell culture. Mechanistically, deletion of a putative SANT domain from MCRS1 evicts histone deacetylase 1 from its histone H3 anchoring sites, increasing histone acetylation of BA transporter genes, modulating their expression and perturbing BA flow. Accordingly, human cirrhosis displays decreased nuclear MCRS1 and NTCP expression. CONCLUSIONS Our data reveal a previously unrecognized function of MCRS1 as a critical histone acetylation regulator, maintaining gene expression and liver homeostasis. MCRS1 loss induces acetylation of BA transporter genes, perturbation of BA flow, and consequently, FXR activation in HSCs. This axis represents a central and universal signaling event in cirrhosis, which has significant implications for cirrhosis treatment. LAY SUMMARY By genetic ablation of MCRS1 in mouse hepatocytes, we generate the first genetic mouse model of cirrhosis that recapitulates human features. Herein, we demonstrate that the activation of the bile acid/FXR axis in liver fibroblasts is key in cirrhosis development.
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Affiliation(s)
- Amanda Garrido
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Eunjeong Kim
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Ana Teijeiro
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Paula Sánchez Sánchez
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Rosa Gallo
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Ajay Nair
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - María Matamala Montoya
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Cristian Perna
- Department of Pathology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, 28034, Spain
| | - Guillermo P Vicent
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, 08028, Spain
| | - Javier Muñoz
- Biotechnology Programme, Proteomics Core Unit, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain; Present address: Biocruces Bizkaia Health Research Institute. Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Ramón Campos-Olivas
- Structural Biology Programme, Spectroscopyand Nuclear Magnetic Resonance Unit, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Irving Medical Center, Columbia University, New York, NY 10032, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Irving Medical Center, Columbia University, New York, NY 10032, USA
| | - Robert F Schwabe
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Nabil Djouder
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain.
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Palmer AC, Izar B, Hwangbo H, Sorger PK. Predictable Clinical Benefits without Evidence of Synergy in Trials of Combination Therapies with Immune-Checkpoint Inhibitors. Clin Cancer Res 2022; 28:368-377. [PMID: 35045958 DOI: 10.1158/1078-0432.ccr-21-2275] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/06/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Combinations of immune-checkpoint inhibitors (ICI) with other cancer therapies have been approved for advanced cancers in multiple indications, and numerous trials are under way to test new combinations. However, the mechanisms that account for the superiority of approved ICI combinations relative to their constituent monotherapies remain unknown. EXPERIMENTAL DESIGN We analyzed 13 phase III clinical trials testing combinations of ICIs with each other or other drugs in patients with advanced melanoma and lung, breast, gastric, kidney, and head and neck cancers. The clinical activity of the individual constituent therapies, measured in the same or a closely matched trial cohort, was used to compute progression-free survival (PFS) curves expected under a model of independent drug action. To identify additive or synergistic efficacy, PFS expected under this null model was compared with observed PFS by Cox regression. RESULTS PFS elicited by approved combination therapies with ICIs could be accurately predicted from monotherapy data using the independent drug action model (Pearson r = 0.98, P < 5 × 10-9, N = 4,173 patients, 8 types of cancer). We found no evidence of drug additivity or synergy except in one trial in which such interactions might have extended median PFS by 9 days. CONCLUSIONS Combining ICIs with other cancer therapies affords predictable and clinically meaningful benefit by providing patients with multiple chances of response to a single agent. Conversely, there exists no evidence in phase III trials that other therapies interact with and enhance the activity of ICIs. These findings can inform the design and testing of new ICI combination therapies while emphasizing the importance of developing better predictors (biomarkers) of ICI response.
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Affiliation(s)
- Adam C Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts
| | - Benjamin Izar
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, Columbia Center for Translational Tumor Immunology, New York, New York
| | - Haeun Hwangbo
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts.
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Huang H, Fang Y, Jiang M, Zhang Y, Biermann J, Melms JC, Danielsson JA, Yang Y, Qiang L, Liu J, Zhou Y, Wang M, Hu Z, Wang TC, Saqi A, Sun J, Matsumoto I, Cardoso WV, Emala CW, Zhu J, Izar B, Mou H, Que J. Contribution of Trp63CreERT2-labeled cells to alveolar regeneration is independent of tuft cells. eLife 2022; 11:78217. [PMID: 36129169 PMCID: PMC9553211 DOI: 10.7554/elife.78217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/18/2022] [Indexed: 11/13/2022] Open
Abstract
Viral infection often causes severe damage to the lungs, leading to the appearance of ectopic basal cells (EBCs) and tuft cells in the lung parenchyma. Thus far, the roles of these ectopic epithelial cells in alveolar regeneration remain controversial. Here, we confirm that the ectopic tuft cells are originated from EBCs in mouse models and COVID-19 lungs. The differentiation of tuft cells from EBCs is promoted by Wnt inhibition while suppressed by Notch inhibition. Although progenitor functions have been suggested in other organs, pulmonary tuft cells don't proliferate or give rise to other cell lineages. Consistent with previous reports, Trp63CreERT2 and KRT5-CreERT2-labeled ectopic EBCs do not exhibit alveolar regeneration potential. Intriguingly, when tamoxifen was administrated post-viral infection, Trp63CreERT2 but not KRT5-CreERT2 labels islands of alveolar epithelial cells that are negative for EBC biomarkers. Furthermore, germline deletion of Trpm5 significantly increases the contribution of Trp63CreERT2-labeled cells to the alveolar epithelium. Although Trpm5 is known to regulate tuft cell development, complete ablation of tuft cell production fails to improve alveolar regeneration in Pou2f3-/- mice, implying that Trpm5 promotes alveolar epithelial regeneration through a mechanism independent of tuft cells.
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Affiliation(s)
- Huachao Huang
- Columbia Center for Human Development, Department of Medicine, Columbia University Medical CenterNew YorkUnited States,Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical CenterNew YorkUnited States
| | - Yinshan Fang
- Columbia Center for Human Development, Department of Medicine, Columbia University Medical CenterNew YorkUnited States,Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical CenterNew YorkUnited States
| | - Ming Jiang
- Institute of Genetics, the Children's Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Yihan Zhang
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Jana Biermann
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical CenterNew YorkUnited States,Columbia Center for Translational Immunology, Columbia University Irving Medical CenterNew YorkUnited States
| | - Johannes C Melms
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical CenterNew YorkUnited States,Columbia Center for Translational Immunology, Columbia University Irving Medical CenterNew YorkUnited States
| | - Jennifer A Danielsson
- Department of Anesthesiology, Columbia University Irving Medical CenterNew YorkUnited States
| | - Ying Yang
- Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Li Qiang
- Department of Pathology & Cell Biology, Columbia University Medical CenterNew YorkUnited States
| | - Jia Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of SciencesWuhanChina
| | - Yiwu Zhou
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and TechnologyWuhanChina
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of SciencesWuhanChina
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of SciencesWuhanChina
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical CenterNew YorkUnited States
| | - Anjali Saqi
- Department of Pathology & Cell Biology, Columbia University Medical CenterNew YorkUnited States
| | - Jie Sun
- Carter Immunology Center, the University of VirginiaCharlottesvilleUnited States
| | | | - Wellington V Cardoso
- Columbia Center for Human Development, Department of Medicine, Columbia University Medical CenterNew YorkUnited States,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical CenterNew YorkUnited States
| | - Charles W Emala
- Department of Anesthesiology, Columbia University Irving Medical CenterNew YorkUnited States
| | - Jian Zhu
- Department of Pathology, Ohio State University College of MedicineColumbusUnited States
| | - Benjamin Izar
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical CenterNew YorkUnited States,Columbia Center for Translational Immunology, Columbia University Irving Medical CenterNew YorkUnited States
| | - Hongmei Mou
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Jianwen Que
- Columbia Center for Human Development, Department of Medicine, Columbia University Medical CenterNew YorkUnited States,Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical CenterNew YorkUnited States
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47
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Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Tsai EJ, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. Author Correction: A molecular single-cell lung atlas of lethal COVID-19. Nature 2021; 598:E2. [PMID: 34625743 PMCID: PMC8498978 DOI: 10.1038/s41586-021-03921-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Huachao Huang
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ajay Nair
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chris J Frangieh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Aveline Filliol
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yinshan Fang
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Mariano G Clausi
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - George A Alba
- Department of Medicine, Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean W Chen
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Daniel T Montoro
- Cell Circuits, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam E Kornberg
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Arnold S Han
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA
| | - Niroshana Anandasabapathy
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xinzheng V Guo
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - Jay H Lefkowitch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Marboe
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Stephen M Lagana
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Emily J Tsai
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Glen S Markowitz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert F Schwabe
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jianwen Que
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA.
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
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48
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Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N. Spatially organized multicellular immune hubs in human colorectal cancer. Cell 2021; 184:4734-4752.e20. [PMID: 34450029 PMCID: PMC8772395 DOI: 10.1016/j.cell.2021.08.003] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]
Abstract
Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd individuals. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across tumors from affected individuals and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T cell-attracting chemokines. By identifying interacting cellular programs, we reveal the logic underlying spatially organized immune-malignant cell networks.
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Affiliation(s)
- Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan H Chen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Pathology, MGH, Boston, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Joshua D Pirl
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Pathology, MGH, Boston, MA, USA
| | - Alborz Bejnood
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William H Ge
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Katherine H Xu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Sherry X Chao
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, HMS, Boston, MA, USA
| | | | - David J Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | | | | | - Toni Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Max Klapholz
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Ofir Cohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Julian Albers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Mei-Ju Su
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Jason Yeung
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | | | | | | | - Tabea Moll
- Clinical Research Center, MGH, Boston, MA, USA
| | | | | | | | - Laura K DelloStritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | | | | | - Emma K Hill
- Clinical Research Center, DFCI, Boston, MA, USA
| | | | | | | | - Abhay Kanodia
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Ellen Z Todres
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, MGH, Boston, MA, USA
| | - Benjamin Izar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Conner D Lambden
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA
| | | | | | | | | | | | | | | | | | - Shuji Ogino
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Pathology, BWH, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, HMS, Boston, MA, USA
| | - Arlene H Sharpe
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA; Department of Immunology, Blavatnik Institute, HMS, Boston, MA, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Linda T Nieman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Genevieve M Boland
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Surgery, MGH, Boston, MA, USA
| | - Andrew J Aguirre
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medical Oncology, DFCI, Boston, MA, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, HMS and Brigham and Women's Hospital (BWH), Boston, MA, USA.
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA.
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Immunology, HMS, Boston, MA, USA.
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49
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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021; 595:107-113. [PMID: 33915569 PMCID: PMC8919505 DOI: 10.1038/s41586-021-03570-8] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]
Abstract
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.
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Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Harvard Medical School, Boston, MA 02115, USA,Massachusetts Institute of Technology, Cambridge, MA
02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public
Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Division of Infectious Diseases, Department of Medicine,
Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki,
Finland,Analytical & Translational Genetics Unit,
Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Systems Biology, Harvard Medical School,
Boston, MA 02115, USA,FAS Center for Systems Biology, Department of Organismic
and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical
Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Genetics and BASE Initiative, Stanford
University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Joshua Gould
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki,
Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115,Harvard-MIT Division of Health Sciences and Technology,
Cambridge MA,Department of Pathology, Harvard Medical School, Boston,
MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA,Center for Regenerative Medicine, Massachusetts General
Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine,
Brigham and Women’s Hospital, Boston, MA, USA
| | - Rajat M. Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public
Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of
MIT and Harvard, Cambridge, MA
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston,
MA 02115, USA,Department of Molecular Biology and Center for
Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA,Department of Immunology and Infectious Diseases, Harvard
T.H. Chan School of Public Health, Harvard University, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Massachusetts Consortium on Pathogen Readiness, Boston,
MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering,
Harvard University
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138,Wyss Institute for Biologically Inspired Engineering,
Harvard University,Vascular Biology Program and Department of Surgery,
Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Z. Gordon Jiang
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY,Herbert Irving Comprehensive Cancer Center, Columbia
University Irving Medical Center, New York, NY,Program for Mathematical Genomics, Columbia University
Irving Medical Center, New York, NY
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA,Harvard Medical School, Boston, MA 02115, USA,Harvard Stem Cell Institute, Cambridge, MA, USA,Program in Computational & Systems Biology,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Program in Immunology, Harvard Medical School, Boston, MA
02115, USA,Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
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50
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Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. A molecular single-cell lung atlas of lethal COVID-19. Nature 2021; 595:114-119. [PMID: 33915568 PMCID: PMC8814825 DOI: 10.1038/s41586-021-03569-1] [Citation(s) in RCA: 324] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 01/21/2023]
Abstract
Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection1,2, but the host response at the lung tissue level is poorly understood. Here we performed single-nucleus RNA sequencing of about 116,000 nuclei from the lungs of nineteen individuals who died of COVID-19 and underwent rapid autopsy and seven control individuals. Integrated analyses identified substantial alterations in cellular composition, transcriptional cell states, and cell-to-cell interactions, thereby providing insight into the biology of lethal COVID-19. The lungs from individuals with COVID-19 were highly inflamed, with dense infiltration of aberrantly activated monocyte-derived macrophages and alveolar macrophages, but had impaired T cell responses. Monocyte/macrophage-derived interleukin-1β and epithelial cell-derived interleukin-6 were unique features of SARS-CoV-2 infection compared to other viral and bacterial causes of pneumonia. Alveolar type 2 cells adopted an inflammation-associated transient progenitor cell state and failed to undergo full transition into alveolar type 1 cells, resulting in impaired lung regeneration. Furthermore, we identified expansion of recently described CTHRC1+ pathological fibroblasts3 contributing to rapidly ensuing pulmonary fibrosis in COVID-19. Inference of protein activity and ligand-receptor interactions identified putative drug targets to disrupt deleterious circuits. This atlas enables the dissection of lethal COVID-19, may inform our understanding of long-term complications of COVID-19 survivors, and provides an important resource for therapeutic development.
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Affiliation(s)
- Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Huachao Huang
- Columbia Center for Human Development, New York, NY, USA,Division of Digestive and Liver Diseases, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Ajay Nair
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - André F. Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chris J. Frangieh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Adrienne M. Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Aveline Filliol
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yinshan Fang
- Columbia Center for Human Development, New York, NY, USA,Division of Digestive and Liver Diseases, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Mariano G. Clausi
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - George A. Alba
- Department of Medicine, Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA
| | - Sean W. Chen
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA
| | - Daniel T. Montoro
- Cell Circuits, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Arnold S. Han
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Mathieu F. Bakhoum
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA
| | - Niroshana Anandasabapathy
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Dermatology, Weill Cornell Medical College, New York, NY, USA,Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xinzheng V. Guo
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - Jay H. Lefkowitch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Marboe
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Stephen M. Lagana
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Glen S. Markowitz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert F. Schwabe
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Robert E. Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Jianwen Que
- Columbia Center for Human Development, New York, NY, USA,Division of Digestive and Liver Diseases, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,Herbert Irving Comprehensive Cancer Center, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar.,,
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,Herbert Irving Comprehensive Cancer Center, New York, NY, USA,Program for Mathematical Genomics, Columbia University, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar.,,
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