1
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Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. Scalable genetic screening for regulatory circuits using compressed Perturb-seq. Nat Biotechnol 2023:10.1038/s41587-023-01964-9. [PMID: 37872410 PMCID: PMC11035494 DOI: 10.1038/s41587-023-01964-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/22/2023] [Indexed: 10/25/2023]
Abstract
Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique in functional genomics, but they are limited in scale by cost and combinatorial complexity. In this study, we modified the design of Perturb-seq by incorporating algorithms applied to random, low-dimensional observations. Compressed Perturb-seq measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq with an order of magnitude cost reduction and greater power to learn genetic interactions. We identified known and novel regulators of immune responses and uncovered evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing genome-wide association studies. Our framework enables new scales of interrogation for a foundational method in functional genomics.
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Affiliation(s)
- Douglas Yao
- Program in Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, MA, USA
| | - Loic Binan
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jon Bezney
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Brooke Simonton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jahanara Freedman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chris J Frangieh
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kushal Dey
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Alexander Gusev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Genentech, South San Francisco, CA, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Program in Bioinformatics, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
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2
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Strebinger D, Frangieh CJ, Friedrich MJ, Faure G, Macrae RK, Zhang F. Cell type-specific delivery by modular envelope design. Nat Commun 2023; 14:5141. [PMID: 37612276 PMCID: PMC10447438 DOI: 10.1038/s41467-023-40788-8] [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: 02/03/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
The delivery of genetic cargo remains one of the largest obstacles to the successful translation of experimental therapies, in large part due to the absence of targetable delivery vectors. Enveloped delivery modalities use viral envelope proteins, which determine tropism and induce membrane fusion. Here we develop DIRECTED (Delivery to Intended REcipient Cells Through Envelope Design), a modular platform that consists of separate fusion and targeting components. To achieve high modularity and programmable cell type specificity, we develop multiple strategies to recruit or immobilize antibodies on the viral envelope, including a chimeric antibody binding protein and a SNAP-tag enabling the use of antibodies or other proteins as targeting molecules. Moreover, we show that fusogens from multiple viral families are compatible with DIRECTED and that DIRECTED components can target multiple delivery chassis (e.g., lentivirus and MMLV gag) to specific cell types, including primary human T cells in PBMCs and whole blood.
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Affiliation(s)
- Daniel Strebinger
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chris J Frangieh
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mirco J Friedrich
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Guilhem Faure
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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3
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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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4
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Wilkinson ME, Frangieh CJ, Macrae RK, Zhang F. Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription. Science 2023; 380:301-308. [PMID: 37023171 PMCID: PMC10499050 DOI: 10.1126/science.adg7883] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 01/20/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
Non-long terminal repeat (non-LTR) retrotransposons, or long interspersed nuclear elements (LINEs), are an abundant class of eukaryotic transposons that insert into genomes by target-primed reverse transcription (TPRT). During TPRT, a target DNA sequence is nicked and primes reverse transcription of the retrotransposon RNA. Here, we report the cryo-electron microscopy structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target. The target DNA sequence is unwound at the insertion site and recognized by an upstream motif. An extension of the reverse transcriptase (RT) domain recognizes the retrotransposon RNA and guides the 3' end into the RT active site to template reverse transcription. We used Cas9 to retarget R2 in vitro to non-native sequences, suggesting future use as a reprogrammable RNA-based gene-insertion tool.
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Affiliation(s)
- Max E. Wilkinson
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Chris J. Frangieh
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
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5
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Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations. bioRxiv 2023:2023.01.23.525200. [PMID: 36747806 PMCID: PMC9900787 DOI: 10.1101/2023.01.23.525200] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as a key technique in functional genomics, but are limited in scale by cost and combinatorial complexity. Here, we reimagine Perturb-seq's design through the lens of algorithms applied to random, low-dimensional observations. We present compressed Perturb-seq, which measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq at 4 to 20-fold reduced cost, with greater power to learn genetic interactions. We identify known and novel regulators of immune responses and uncover evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing GWAS or trans-eQTL studies. Our framework enables new scales of interrogation for a foundational method in functional genomics.
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Affiliation(s)
- Douglas Yao
- Program in Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, MA
| | - Loic Binan
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jon Bezney
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
- Current address: Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Brooke Simonton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jahanara Freedman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Chris J Frangieh
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
| | - Kushal Dey
- Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | - Alexander Gusev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA
- These authors jointly supervised this work
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
- Current address: Genentech, South San Francisco, CA
- These authors jointly supervised this work
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA
- Department of Biology, Boston University, Boston, MA
- Department of Biomedical Engineering, Boston University, Boston, MA
- Program in Bioinformatics, Boston University, Boston, MA
- Biological Design Center, Boston University, Boston, MA
- These authors jointly supervised this work
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6
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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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7
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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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8
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Frangieh CJ, Melms JC, Thakore PI, Geiger-Schuller KR, Ho P, Luoma AM, Cleary B, Jerby-Arnon L, Malu S, Cuoco MS, Zhao M, Ager CR, Rogava M, Hovey L, Rotem A, Bernatchez C, Wucherpfennig KW, Johnson BE, Rozenblatt-Rosen O, Schadendorf D, Regev A, Izar B. Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nat Genet 2021; 53:332-341. [PMID: 33649592 PMCID: PMC8376399 DOI: 10.1038/s41588-021-00779-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [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: 08/13/2020] [Accepted: 01/04/2021] [Indexed: 01/05/2023]
Abstract
Resistance to immune checkpoint inhibitors (ICIs) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-sequencing (Perturb-CITE-seq), enabling pooled clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 perturbations with single-cell transcriptome and protein readouts. In patient-derived melanoma cells and autologous tumor-infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICI resistance (ICR). We recover known mechanisms of resistance, including defects in the interferon-γ (IFN-γ)-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and new ones, including loss/downregulation of CD58. Loss of CD58 conferred immune evasion in multiple co-culture models and was downregulated in tumors of melanoma patients with ICR. CD58 protein expression was not induced by IFN-γ signaling, and CD58 loss conferred immune evasion without compromising major histocompatibility complex (MHC) expression, suggesting that it acts orthogonally to known mechanisms of ICR. This work provides a framework for the deciphering of complex mechanisms by large-scale perturbation screens with multimodal, single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion.
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Affiliation(s)
- 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
| | - Johannes C Melms
- Columbia Center for Translational Immunology, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Pratiksha I Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn R Geiger-Schuller
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Cleary
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Shruti Malu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Immunitas Therapeutics, Waltham, MA, USA
| | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maryann Zhao
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Casey R Ager
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Meri Rogava
- Columbia Center for Translational Immunology, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Lila Hovey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
- AstraZeneca, Waltham, MA, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, Essen, Germany
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Genentech, South San Francisco, CA, USA.
| | - Benjamin Izar
- Columbia Center for Translational Immunology, New York, NY, USA.
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
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9
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Bashyam A, Frangieh CJ, Raigani S, Sogo J, Bronson RT, Uygun K, Yeh H, Ausiello DA, Cima MJ. A portable single-sided magnetic-resonance sensor for the grading of liver steatosis and fibrosis. Nat Biomed Eng 2020; 5:240-251. [PMID: 33257853 DOI: 10.1038/s41551-020-00638-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/28/2020] [Indexed: 12/19/2022]
Abstract
Low-cost non-invasive diagnostic tools for staging the progression of non-alcoholic chronic liver failure from fatty liver disease to steatohepatitis are unavailable. Here, we describe the development and performance of a portable single-sided magnetic-resonance sensor for grading liver steatosis and fibrosis using diffusion-weighted multicomponent T2 relaxometry. In a diet-induced mouse model of non-alcoholic fatty liver disease, the sensor achieved overall accuracies of 92% (Cohen's kappa, κ = 0.89) and 86% (κ = 0.78) in the ex vivo grading of steatosis and fibrosis, respectively. Localization of the measurements in living mice through frequency-dependent spatial encoding led to an overall accuracy of 87% (κ = 0.81) for the grading of steatosis. In human liver samples, the sensor graded steatosis with an overall accuracy of 93% (κ = 0.88). The use of T2 relaxometry as a sensitive measure in fully automated low-cost magnetic-resonance devices at the point of care would alleviate the accessibility and cost limits of magnetic-resonance imaging for diagnosing liver disease and assessing liver health before liver transplantation.
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Affiliation(s)
- Ashvin Bashyam
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chris J Frangieh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Siavash Raigani
- Division of Transplantation, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Jeremy Sogo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Division of Immunology, Harvard Medical School, Boston, MA, USA
| | - Korkut Uygun
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Heidi Yeh
- Division of Transplantation, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Dennis A Ausiello
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Center for Assessment Technology and Continuous Health, Massachusetts General Hospital, Boston, MA, USA
| | - Michael J Cima
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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10
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Bashyam A, Frangieh CJ, Li M, Cima MJ. Dehydration assessment via a portable, single sided magnetic resonance sensor. Magn Reson Med 2019; 83:1390-1404. [PMID: 31631380 DOI: 10.1002/mrm.28004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE Undiagnosed dehydration compromises health outcomes across many populations. Existing dehydration diagnostics require invasive bodily fluid sampling or are easily confounded by fluid and electrolyte intake, environment, and physical activity limiting widespread adoption. We present a portable MR sensor designed to measure intramuscular fluid shifts to identify volume depletion. METHODS Fluid loss is induced via a mouse model of thermal dehydration (37°C; 15-20% relative humidity). We demonstrate quantification of fluid loss induced by hyperosmotic dehydration with multicomponent T2 relaxometry using both a benchtop NMR system and MRI localized to skeletal muscle tissue. We then describe a miniaturized (~1000 cm3 ) portable (~4 kg) MR sensor (0.28 T) designed to identify dehydration-induced fluid loss. T2 relaxometry measurements were performed using a Carr-Purcell-Meiboom-Gill pulse sequence in ~4 min. RESULTS T2 values from the portable MR sensor exhibited strong (R2 = 0.996) agreement with benchtop NMR spectrometer. Thermal dehydration induced weight loss of 4 to 11% over 5 to 10 h. Fluid loss induced by thermal dehydration was accurately identified via whole-animal NMR and skeletal muscle. The portable MR sensor accurately identified dehydration via multicomponent T2 relaxometry. CONCLUSION Performing multicomponent T2 relaxometry localized to the skeletal muscle with a miniaturized MR sensor provides a noninvasive, physiologically relevant measure of dehydration induced fluid loss in a mouse model. This approach offers sensor portability, reduced system complexity, fully automated operation, and low cost compared with MRI. This approach may serve as a versatile and portable point of care technique for dehydration monitoring.
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Affiliation(s)
- Ashvin Bashyam
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Chris J Frangieh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthew Li
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael J Cima
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
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