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Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, Dyer MA. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv 2024:2024.01.07.574538. [PMID: 38260392 PMCID: PMC10802404 DOI: 10.1101/2024.01.07.574538] [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: 01/24/2024]
Abstract
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.
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Affiliation(s)
- Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chiara Caraccio
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amber Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ruth G Tatevossian
- Cancer Biomarkers Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jaimin Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marybeth Lupo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cynthia Cline
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- 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
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara Napolitano
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Grimaldi
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura Dellostritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Thorner
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
- Lead contacts
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Lead contacts
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2
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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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3
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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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4
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Kaur G, Porter CBM, Ashenberg O, Lee J, Riesenfeld SJ, Hofree M, Aggelakopoulou M, Subramanian A, Kuttikkatte SB, Attfield KE, Desel CAE, Davies JL, Evans HG, Avraham-Davidi I, Nguyen LT, Dionne DA, Neumann AE, Jensen LT, Barber TR, Soilleux E, Carrington M, McVean G, Rozenblatt-Rosen O, Regev A, Fugger L. Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade. Nat Commun 2022; 13:4398. [PMID: 35906236 PMCID: PMC9338297 DOI: 10.1038/s41467-022-32171-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Fetal growth restriction (FGR) affects 5-10% of pregnancies, and can have serious consequences for both mother and child. Prevention and treatment are limited because FGR pathogenesis is poorly understood. Genetic studies implicate KIR and HLA genes in FGR, however, linkage disequilibrium, genetic influence from both parents, and challenges with investigating human pregnancies make the risk alleles and their functional effects difficult to map. Here, we demonstrate that the interaction between the maternal KIR2DL1, expressed on uterine natural killer (NK) cells, and the paternally inherited HLA-C*0501, expressed on fetal trophoblast cells, leads to FGR in a humanized mouse model. We show that the KIR2DL1 and C*0501 interaction leads to pathogenic uterine arterial remodeling and modulation of uterine NK cell function. This initial effect cascades to altered transcriptional expression and intercellular communication at the maternal-fetal interface. These findings provide mechanistic insight into specific FGR risk alleles, and provide avenues of prevention and treatment.
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Affiliation(s)
- Gurman Kaur
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Lee
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Samantha J Riesenfeld
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria Aggelakopoulou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | - Subita Balaram Kuttikkatte
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kathrine E Attfield
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Christiane A E Desel
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- University Department of Neurology, University Hospital Magdeburg, Magdeburg, Germany
| | - Jessica L Davies
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hayley G Evans
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Inbal Avraham-Davidi
- 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
| | - Danielle A Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lise Torp Jensen
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas R Barber
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Elizabeth Soilleux
- Department of Pathology, Tennis Court Rd, University of Cambridge, Cambridge, England
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Genentech, 1 DNA Way, South San Francisco, CA, USA.
| | - Lars Fugger
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.
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5
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Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CFD, Liss AS, Ting DT, Jacks T, Regev A. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nat Genet 2022; 54:1178-1191. [PMID: 35902743 DOI: 10.1038/s41588-022-01134-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.
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Affiliation(s)
- William L Hwang
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karthik A Jagadeesh
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jimmy A Guo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Hannah I Hoffman
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT MD/PhD and Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Payman Yadollahpour
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Rahul Mohan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | | | | | | | - George Eng
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Shiau
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William A Freed-Pastor
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina Kem
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clifton Rodrigues
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Debora Ciprani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge Roldan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vjola Jorgji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zackery Ely
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | - Jay S Loeffler
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David P Ryan
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin D Weekes
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rakesh K Jain
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer Y Wo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
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6
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Lobritz MA, Andrews IW, Braff D, Porter CBM, Gutierrez A, Furuta Y, Cortes LBG, Ferrante T, Bening SC, Wong F, Gruber C, Bakerlee C, Lambert G, Walker GC, Dwyer DJ, Collins JJ. Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality. Cell Chem Biol 2022; 29:276-286.e4. [PMID: 34990601 PMCID: PMC8857051 DOI: 10.1016/j.chembiol.2021.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/25/2021] [Revised: 10/11/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022]
Abstract
β-Lactam antibiotics disrupt the assembly of peptidoglycan (PG) within the bacterial cell wall by inhibiting the enzymatic activity of penicillin-binding proteins (PBPs). It was recently shown that β-lactam treatment initializes a futile cycle of PG synthesis and degradation, highlighting major gaps in our understanding of the lethal effects of PBP inhibition by β-lactam antibiotics. Here, we assess the downstream metabolic consequences of treatment of Escherichia coli with the β-lactam mecillinam and show that lethality from PBP2 inhibition is a specific consequence of toxic metabolic shifts induced by energy demand from multiple catabolic and anabolic processes, including accelerated protein synthesis downstream of PG futile cycling. Resource allocation into these processes is coincident with alterations in ATP synthesis and utilization, as well as a broadly dysregulated cellular redox environment. These results indicate that the disruption of normal anabolic-catabolic homeostasis by PBP inhibition is an essential factor for β-lactam antibiotic lethality.
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Affiliation(s)
- Michael A. Lobritz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA,Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA,Present address: Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland,These authors contributed equally
| | - Ian W. Andrews
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA,Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA,These authors contributed equally
| | - Dana Braff
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA,Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Present address: GRO Biosciences, Cambridge, MA 02139, USA
| | - Caroline B. M. Porter
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Arnaud Gutierrez
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA,Present address: Institut Cochin, INSERM U1016 – CNRS UMR8104 – Université Paris Descartes, 75014 Paris, France
| | - Yoshikazu Furuta
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Present address: Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Louis B. G. Cortes
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Sarah C. Bening
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Felix Wong
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Charley Gruber
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chris Bakerlee
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Guillaume Lambert
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel J. Dwyer
- Department of Cell Biology and Molecular Genetics, Institute for Physical Science and Technology, Department of Biomedical Engineering, and Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA,Corresponding authors: ,
| | - James J. Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA,Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA,Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA,Lead contact,Corresponding authors: ,
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7
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Bielecki P, Riesenfeld SJ, Hütter JC, Triglia ET, Kowalczyk MS, Ricardo-Gonzalez RR, Lian M, Vesely MCA, Kroehling L, Xu H, Slyper M, Muus C, Ludwig LS, Christian E, Tao L, Kedaigle AJ, Steach HR, York AG, Skadow MH, Yaghoubi P, Dionne D, Jarret A, McGee HM, Porter CBM, Licona-Limón P, Bailis W, Jackson R, Gagliani N, Gasteiger G, Locksley RM, Regev A, Flavell RA. Skin-resident innate lymphoid cells converge on a pathogenic effector state. Nature 2021; 592:128-132. [PMID: 33536623 PMCID: PMC8336632 DOI: 10.1038/s41586-021-03188-w] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/24/2020] [Indexed: 01/30/2023]
Abstract
Tissue-resident innate lymphoid cells (ILCs) help sustain barrier function and respond to local signals. ILCs are traditionally classified as ILC1, ILC2 or ILC3 on the basis of their expression of specific transcription factors and cytokines1. In the skin, disease-specific production of ILC3-associated cytokines interleukin (IL)-17 and IL-22 in response to IL-23 signalling contributes to dermal inflammation in psoriasis. However, it is not known whether this response is initiated by pre-committed ILCs or by cell-state transitions. Here we show that the induction of psoriasis in mice by IL-23 or imiquimod reconfigures a spectrum of skin ILCs, which converge on a pathogenic ILC3-like state. Tissue-resident ILCs were necessary and sufficient, in the absence of circulatory ILCs, to drive pathology. Single-cell RNA-sequencing (scRNA-seq) profiles of skin ILCs along a time course of psoriatic inflammation formed a dense transcriptional continuum-even at steady state-reflecting fluid ILC states, including a naive or quiescent-like state and an ILC2 effector state. Upon disease induction, the continuum shifted rapidly to span a mixed, ILC3-like subset also expressing cytokines characteristic of ILC2s, which we inferred as arising through multiple trajectories. We confirmed the transition potential of quiescent-like and ILC2 states using in vitro experiments, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and in vivo fate mapping. Our results highlight the range and flexibility of skin ILC responses, suggesting that immune activities primed in healthy tissues dynamically adapt to provocations and, left unchecked, drive pathological remodelling.
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Affiliation(s)
- Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. .,Celsius Therapeutics, Cambridge, MA, USA.
| | - Samantha J. Riesenfeld
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Correspondence to: A.R , R.A.F , P.B , and S.J.R
| | - Jan-Christian Hütter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Elena Torlai Triglia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Monika S. Kowalczyk
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Roberto R. Ricardo-Gonzalez
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA, Department of Medicine, Sandler Asthma Research Center University of California San Francisco, San Francisco, CA, USA
| | - Mi Lian
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maria C. Amezcua Vesely
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Howard Hughes Medical Institute
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hao Xu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Christoph Muus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Leif S. Ludwig
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Elena Christian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Liming Tao
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Amanda J. Kedaigle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Holly R. Steach
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Autumn G. York
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mathias H. Skadow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Parastou Yaghoubi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Abigail Jarret
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Heather M. McGee
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Sciences, La Jolla, CA 92037, USA
| | - Caroline B. M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Paula Licona-Limón
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City 04510
| | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Division of Protective Immunity, Children’s Hospital of Philadelphia, 19104, Philadelphia, PA, USA., Department of Pathology and Laboratory Medicine, University of Pennsylvania, 19104, Philadelphia, PA, USA
| | - Ruaidhrí Jackson
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicola Gagliani
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany, Department of Medicine, University Medical Center Hamburg-Eppendorf Hamburg-Eppendorf, 20246 Hamburg, Germany, Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and University Hospital, 17176 Stockholm, Sweden
| | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany
| | - Richard M. Locksley
- Department of Medicine, Sandler Asthma Research Center University of California San Francisco, San Francisco, CA, USA, Howard Hughes Medical Institute
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Howard Hughes Medical Institute, Correspondence to: A.R , R.A.F , P.B , and S.J.R
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8
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Boroughs AC, Larson RC, Marjanovic ND, Gosik K, Castano AP, Porter CBM, Lorrey SJ, Ashenberg O, Jerby L, Hofree M, Smith-Rosario G, Morris R, Gould J, Riley LS, Berger TR, Riesenfeld SJ, Rozenblatt-Rosen O, Choi BD, Regev A, Maus MV. A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq. Mol Ther 2020; 28:2577-2592. [PMID: 32755564 PMCID: PMC7704462 DOI: 10.1016/j.ymthe.2020.07.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 04/28/2020] [Revised: 06/26/2020] [Accepted: 07/21/2020] [Indexed: 01/22/2023] Open
Abstract
T cells engineered to express chimeric antigen receptors (CARs) targeting CD19 have produced impressive outcomes for the treatment of B cell malignancies, but different products vary in kinetics, persistence, and toxicity profiles based on the co-stimulatory domains included in the CAR. In this study, we performed transcriptional profiling of bulk CAR T cell populations and single cells to characterize the transcriptional states of human T cells transduced with CD3ζ, 4-1BB-CD3ζ (BBζ), or CD28-CD3ζ (28ζ) co-stimulatory domains at rest and after activation by triggering their CAR or their endogenous T cell receptor (TCR). We identified a transcriptional signature common across CARs with the CD3ζ signaling domain, as well as a distinct program associated with the 4-1BB co-stimulatory domain at rest and after activation. CAR T cells bearing BBζ had increased expression of human leukocyte antigen (HLA) class II genes, ENPP2, and interleukin (IL)-21 axis genes, and decreased PD1 compared to 28ζ CAR T cells. Similar to previous studies, we also found BBζ CAR CD8 T cells to be enriched in a central memory cell phenotype and fatty acid metabolism genes. Our data uncovered transcriptional signatures related to costimulatory domains and demonstrated that signaling domains included in CARs uniquely shape the transcriptional programs of T cells.
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Affiliation(s)
- Angela C Boroughs
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca C Larson
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Nemanja D Marjanovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Kirk Gosik
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Ana P Castano
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Selena J Lorrey
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Livnat Jerby
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Robert Morris
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Lauren S Riley
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Trisha R Berger
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Samantha J Riesenfeld
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Bryan D Choi
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
| | - Marcela V Maus
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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9
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Marjanovic ND, Hofree M, Chan JE, Canner D, Wu K, Trakala M, Hartmann GG, Smith OC, Kim JY, Evans KV, Hudson A, Ashenberg O, Porter CBM, Bejnood A, Subramanian A, Pitter K, Yan Y, Delorey T, Phillips DR, Shah N, Chaudhary O, Tsankov A, Hollmann T, Rekhtman N, Massion PP, Poirier JT, Mazutis L, Li R, Lee JH, Amon A, Rudin CM, Jacks T, Regev A, Tammela T. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. Cancer Cell 2020; 38:229-246.e13. [PMID: 32707077 PMCID: PMC7745838 DOI: 10.1016/j.ccell.2020.06.012] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [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: 08/01/2019] [Revised: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
Tumor evolution from a single cell into a malignant, heterogeneous tissue remains poorly understood. Here, we profile single-cell transcriptomes of genetically engineered mouse lung tumors at seven stages, from pre-neoplastic hyperplasia to adenocarcinoma. The diversity of transcriptional states increases over time and is reproducible across tumors and mice. Cancer cells progressively adopt alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). Accordingly, HPCS cells prospectively isolated from mouse tumors and human patient-derived xenografts display high capacity for differentiation and proliferation. The HPCS program is associated with poor survival across human cancers and demonstrates chemoresistance in mice. Our study reveals a central principle underpinning intra-tumoral heterogeneity and motivates therapeutic targeting of the HPCS.
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Affiliation(s)
- Nemanja Despot Marjanovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Computational and Systems Biology PhD Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason E Chan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Canner
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katherine Wu
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marianna Trakala
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Griffin G Hartmann
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olivia C Smith
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jonathan Y Kim
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kelly Victoria Evans
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Anna Hudson
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alborz Bejnood
- Klarman Cell Observatory, 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
| | - Kenneth Pitter
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yan Yan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Toni Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Devan R Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nisargbhai Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ojasvi Chaudhary
- The Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Tsankov
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Travis Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pierre P Massion
- Department of Medicine and Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John T Poirier
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- The Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruifang Li
- Epigenetics Technology Innovation Lab, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; The Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Tuomas Tammela
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology, Weill-Cornell Medical College, New York, NY 10065, USA.
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10
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Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su MJ, Shah P, Iwanicki M, Walker SR, Kanodia A, Melms JC, Mei S, Lin JR, Porter CBM, Slyper M, Waldman J, Jerby-Arnon L, Ashenberg O, Brinker TJ, Mills C, Rogava M, Vigneau S, Sorger PK, Garraway LA, Konstantinopoulos PA, Liu JF, Matulonis U, Johnson BE, Rozenblatt-Rosen O, Rotem A, Regev A. A single-cell landscape of high-grade serous ovarian cancer. Nat Med 2020; 26:1271-1279. [PMID: 32572264 PMCID: PMC7723336 DOI: 10.1038/s41591-020-0926-0] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [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: 07/01/2019] [Accepted: 05/07/2020] [Indexed: 01/04/2023]
Abstract
Malignant abdominal fluid (ascites) frequently develops in women with advanced high-grade serous ovarian cancer (HGSOC) and is associated with drug resistance and a poor prognosis1. To comprehensively characterize the HGSOC ascites ecosystem, we used single-cell RNA sequencing to profile ~11,000 cells from 22 ascites specimens from 11 patients with HGSOC. We found significant inter-patient variability in the composition and functional programs of ascites cells, including immunomodulatory fibroblast sub-populations and dichotomous macrophage populations. We found that the previously described immunoreactive and mesenchymal subtypes of HGSOC, which have prognostic implications, reflect the abundance of immune infiltrates and fibroblasts rather than distinct subsets of malignant cells2. Malignant cell variability was partly explained by heterogeneous copy number alteration patterns or expression of a stemness program. Malignant cells shared expression of inflammatory programs that were largely recapitulated in single-cell RNA sequencing of ~35,000 cells from additionally collected samples, including three ascites, two primary HGSOC tumors and three patient ascites-derived xenograft models. Inhibition of the JAK/STAT pathway, which was expressed in both malignant cells and cancer-associated fibroblasts, had potent anti-tumor activity in primary short-term cultures and patient-derived xenograft models. Our work contributes to resolving the HSGOC landscape3-5 and provides a resource for the development of novel therapeutic approaches.
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Affiliation(s)
- Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Columbia University Medical Center, Columbia Center for Translational Immunology, New York, NY, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elizabeth H Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Idan Alter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Christopher Rodman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel Leeson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marcin Iwanicki
- Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Sarah R Walker
- Molecular, Cellular, and Biomedical Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Abhay Kanodia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johannes C Melms
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaolin Mei
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Slyper
- 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
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Caitlin Mills
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Meri Rogava
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sébastien Vigneau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | - Joyce F Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ursula Matulonis
- Department of Medical Oncology, 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
| | | | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ludwig Center for Cancer Research at MIT, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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11
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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020; 26:1307. [PMID: 32587393 PMCID: PMC7417328 DOI: 10.1038/s41591-020-0976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Isaac Wakiro
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jingyi Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sébastien Vigneau
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara Napolitano
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Asa Karlstrom
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon Gritsch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Nomura
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Satyen H Gohil
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ofir Cohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bo Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.,Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Ludwig Center for Cancer Research at Harvard, Boston, MA, USA.,Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Rizwan Haq
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth H Stover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael R Clay
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Natalie B Collins
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikhil Wagle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020; 26:792-802. [PMID: 32405060 PMCID: PMC7220853 DOI: 10.1038/s41591-020-0844-1] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/20/2020] [Indexed: 01/20/2023]
Abstract
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.
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Affiliation(s)
- Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Isaac Wakiro
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jingyi Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sébastien Vigneau
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara Napolitano
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Asa Karlstrom
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon Gritsch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Nomura
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Satyen H Gohil
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ofir Cohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bo Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA, USA
- Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Rizwan Haq
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth H Stover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael R Clay
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Natalie B Collins
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikhil Wagle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity 2020; 51:696-708.e9. [PMID: 31618654 DOI: 10.1016/j.immuni.2019.09.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/06/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022]
Abstract
Signaling abnormalities in immune responses in the small intestine can trigger chronic type 2 inflammation involving interaction of multiple immune cell types. To systematically characterize this response, we analyzed 58,067 immune cells from the mouse small intestine by single-cell RNA sequencing (scRNA-seq) at steady state and after induction of a type 2 inflammatory reaction to ovalbumin (OVA). Computational analysis revealed broad shifts in both cell-type composition and cell programs in response to the inflammation, especially in group 2 innate lymphoid cells (ILC2s). Inflammation induced the expression of exon 5 of Calca, which encodes the alpha-calcitonin gene-related peptide (α-CGRP), in intestinal KLRG1+ ILC2s. α-CGRP antagonized KLRG1+ ILC2s proliferation but promoted IL-5 expression. Genetic perturbation of α-CGRP increased the proportion of intestinal KLRG1+ ILC2s. Our work highlights a model where α-CGRP-mediated neuronal signaling is critical for suppressing ILC2 expansion and maintaining homeostasis of the type 2 immune machinery.
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Affiliation(s)
- Heping Xu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China.
| | - Jiarui Ding
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Antonia Wallrapp
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Marcin Tabaka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sai Ma
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shujie Fu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Xuanxuan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | | | - Chienwen Su
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Danielle Dionne
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lan T Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ariel Lefkovith
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick R Burkett
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Hai Ning Shi
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | | | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
| | - Vijay K Kuchroo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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14
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Halder V, Porter CBM, Chavez A, Shapiro RS. Author Correction: Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nat Protoc 2019; 14:2595. [PMID: 30976123 DOI: 10.1038/s41596-019-0157-3] [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: 11/09/2022]
Abstract
The version of this paper originally published contained reference errors. The sentence "To dissect complex genetic interactions in C. albicans, a CRISPR-Cas9-based Gene Drive Array (GDA) was developed" incorrectly cited ref. 13, and should have cited ref. 14. In addition, the reference included as ref. 13 in the original paper was incorrect, and should have been the following: Shapiro, R. S., Chavez, A. & Collins, J. J. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat. Rev. Microbiol. 16, 333-339 (2018). This reference should have been cited after the sentence "Recent innovations in CRISPR-Cas9-based genome editing have facilitated such genetic interaction analyses." The original reference 13 (Gerami-Nejad, M., Zacchi, L. F., McClellan, M., Matter, K. & Berman, J. Shuttle vectors for facile gap repair cloning and integration into a neutral locus in Candida albicans. Microbiology 159, 565-579 (2013)) should have been cited later in the paper, and is now in the reference list as ref. 27. As a result, original references 27-33 have been renumbered in the reference list and in the text. These changes have been made in the PDF and HTML versions of the protocol.
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Affiliation(s)
- Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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15
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Halder V, Porter CBM, Chavez A, Shapiro RS. Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nat Protoc 2019; 14:955-975. [PMID: 30737491 DOI: 10.1038/s41596-018-0122-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 08/30/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
The study of fungal pathogens is of immediate importance, yet progress is hindered by the technical challenges of genetic manipulation. For Candida species, their inability to maintain plasmids, unusual codon usage, and inefficient homologous recombination are among the obstacles limiting efficient genetic manipulation. New advances in genomic biotechnologies-particularly CRISPR-based tools-have revolutionized genome editing for many fungal species. Here, we present a protocol for CRISPR-Cas9-based manipulation in Candida albicans using a modified gene-drive-based strategy that takes ~1 month to complete. We detail the generation of Candida-optimized Cas9-based plasmids for gene deletion, an efficient transformation protocol using C. albicans haploids, and an optimized mating strategy to generate homozygous single- and double-gene diploid mutants. We further describe protocols for quantifying cell growth and analysis pipelines to calculate fitness and genetic interaction scores for genetic mutants. This protocol overcomes previous limitations associated with genetic manipulation in C. albicans and advances researchers' ability to perform genetic analysis in this pathogen; the protocol also has broad applicability to other mating-competent microorganisms.
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Affiliation(s)
- Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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16
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Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nat Microbiol 2018; 3:73-82. [PMID: 29062088 PMCID: PMC5832965 DOI: 10.1038/s41564-017-0043-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/15/2017] [Indexed: 11/09/2022]
Abstract
Candida albicans is the leading cause of fungal infections; yet, complex genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based 'gene drive array' platform to facilitate efficient genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different gene drive disabling a gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We generate double-gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how genetic networks shift under diverse conditions. This platform transforms our ability to perform genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Alejandro Chavez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, 10032, NY, USA
| | - Caroline B M Porter
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Meagan Hamblin
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christian S Kaas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Expression Technologies 2, Novo Nordisk A/S, Maaloev, 2760, Denmark
| | - James E DiCarlo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA
| | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
| | - Xiaoli Xu
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
| | | | | | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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17
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Meylan S, Porter CBM, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM, Collins JJ. Carbon Sources Tune Antibiotic Susceptibility in Pseudomonas aeruginosa via Tricarboxylic Acid Cycle Control. Cell Chem Biol 2017; 24:195-206. [PMID: 28111098 DOI: 10.1016/j.chembiol.2016.12.015] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [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: 08/05/2016] [Revised: 11/21/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
Abstract
Metabolically dormant bacteria present a critical challenge to effective antimicrobial therapy because these bacteria are genetically susceptible to antibiotic treatment but phenotypically tolerant. Such tolerance has been attributed to impaired drug uptake, which can be reversed by metabolic stimulation. Here, we evaluate the effects of central carbon metabolite stimulations on aminoglycoside sensitivity in the pathogen Pseudomonas aeruginosa. We identify fumarate as a tobramycin potentiator that activates cellular respiration and generates a proton motive force by stimulating the tricarboxylic acid (TCA) cycle. In contrast, we find that glyoxylate induces phenotypic tolerance by inhibiting cellular respiration with acetyl-coenzyme A diversion through the glyoxylate shunt, despite drug import. Collectively, this work demonstrates that TCA cycle activity is important for both aminoglycoside uptake and downstream lethality and identifies a potential strategy for potentiating aminoglycoside treatment of P. aeruginosa infections.
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Affiliation(s)
- Sylvain Meylan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biological Engineering, Institute for Medical Engineering & Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Caroline B M Porter
- Department of Biological Engineering, Institute for Medical Engineering & Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason H Yang
- Department of Biological Engineering, Institute for Medical Engineering & Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Arnaud Gutierrez
- Department of Biological Engineering, Institute for Medical Engineering & Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael A Lobritz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biological Engineering, Institute for Medical Engineering & Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jihye Park
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sun H Kim
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Samuel M Moskowitz
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biological Engineering, Institute for Medical Engineering & Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Program, Health Sciences and Technology, Cambridge, MA 02139, USA.
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18
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Belenky P, Ye JD, Porter CBM, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Cell Rep 2015; 13:968-80. [PMID: 26565910 DOI: 10.1016/j.celrep.2015.09.059] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [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: 07/30/2015] [Revised: 09/04/2015] [Accepted: 09/17/2015] [Indexed: 01/16/2023] Open
Abstract
Understanding how antibiotics impact bacterial metabolism may provide insight into their mechanisms of action and could lead to enhanced therapeutic methodologies. Here, we profiled the metabolome of Escherichia coli after treatment with three different classes of bactericidal antibiotics (?-lactams, aminoglycosides, quinolones). These treatments induced a similar set of metabolic changes after 30 min that then diverged into more distinct profiles at later time points. The most striking changes corresponded to elevated concentrations of central carbon metabolites, active breakdown of the nucleotide pool, reduced lipid levels, and evidence of an elevated redox state. We examined potential end-target consequences of these metabolic perturbations and found that antibiotic-treated cells exhibited cytotoxic changes indicative of oxidative stress, including higher levels of protein carbonylation, malondialdehyde adducts, nucleotide oxidation, and double-strand DNA breaks. This work shows that bactericidal antibiotics induce a complex set of metabolic changes that are correlated with the buildup of toxic metabolic by-products.
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Affiliation(s)
- Peter Belenky
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA; Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting Street, Providence, RI 02912, USA.
| | - Jonathan D Ye
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA
| | - Caroline B M Porter
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Nadia R Cohen
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Michael A Lobritz
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Saloni Jain
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting Street, Providence, RI 02912, USA
| | - Eric G Schwarz
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA.
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