1
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Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. bioRxiv 2024:2024.02.29.582872. [PMID: 38496446 PMCID: PMC10942375 DOI: 10.1101/2024.02.29.582872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
- Present address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Andy Y. Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Wenxi Zhang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zhuang Miao
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Present address: Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Present address: Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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2
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Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, Qiu X, Wahlster L, Caulier A, Hussmann JA, Schnell A, Yost KE, Koblan LW, Martin-Rufino JD, Min J, Hammond A, Ssozi D, Bueno R, Mallidi H, Kreso A, Escabi J, Rideout WM, Jacks T, Hormoz S, van Galen P, Weissman JS, Sankaran VG. Deciphering cell states and genealogies of human haematopoiesis. Nature 2024; 627:389-398. [PMID: 38253266 PMCID: PMC10937407 DOI: 10.1038/s41586-024-07066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
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Affiliation(s)
- Chen Weng
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, P.R. China
| | - Dian Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Pharmacology and Therapeutics, Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael Poeschla
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew G Jones
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Genetics and Computer Science, BASE Research Initiative, Betty Irene Moore Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey A Hussmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandra Schnell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn E Yost
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke W Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jorge D Martin-Rufino
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Min
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alessandro Hammond
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Ssozi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Hari Mallidi
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Antonia Kreso
- Division of Cardiac Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Javier Escabi
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William M Rideout
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Sahand Hormoz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter van Galen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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3
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Rose JC, Wong ITL, Daniel B, Jones MG, Yost KE, Hung KL, Curtis EJ, Mischel PS, Chang HY. Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. bioRxiv 2023:2023.10.22.563489. [PMID: 37961138 PMCID: PMC10634728 DOI: 10.1101/2023.10.22.563489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.
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Affiliation(s)
- John C Rose
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew G Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ellis J Curtis
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul S Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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4
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Yu B, Shi Q, Belk JA, Yost KE, Parker KR, Li R, Liu BB, Huang H, Lingwood D, Greenleaf WJ, Davis MM, Satpathy AT, Chang HY. Engineered cell entry links receptor biology with single-cell genomics. Cell 2022; 185:4904-4920.e22. [PMID: 36516854 PMCID: PMC9789208 DOI: 10.1016/j.cell.2022.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/31/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter-clonal vs. intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.
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Affiliation(s)
- Bingfei Yu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Betty B Liu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Huang Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | | | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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5
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Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Hadlock J, Chen D, Dai CL, Yuan D, Su Y, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines (Basel) 2022; 11:5. [PMID: 36679852 PMCID: PMC9861578 DOI: 10.3390/vaccines11010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a different strain harboring the spike variant D614G. This case of reinfection was one of the first cases of reinfection reported in 2020. With antibody, B cell and T cell analytics, we show correlates of adaptive immunity at reinfection, including a differential response in neutralizing antibodies to a D614G pseudovirus. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.
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Affiliation(s)
- Jason D. Goldman
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E. Yost
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kelly Chun
- LabCorp Esoterix, Calabasas, CA 91301, USA
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Paula M. Manner
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Julie A. Wallick
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Heather A. Algren
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Kim M. Murray
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Jennifer Hadlock
- Providence St. Joseph Health, Renton, WA 98057, USA
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Daniel Chen
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Dan Yuan
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Joshua Jeharajah
- Division of Infectious Diseases, Polyclinic, Seattle, WA 98104, USA
| | - William R. Berrington
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - George P. Pappas
- Division of Pulmonology and Critical Care Medicine, Swedish Medical Center, Seattle, WA 98104, USA
| | - Sonam T. Nyatsatsang
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, DC 98109, USA
| | | | - John S. Pauk
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94304, USA
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6
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Foster DS, Januszyk M, Delitto D, Yost KE, Griffin M, Guo J, Guardino N, Delitto AE, Chinta M, Burcham AR, Nguyen AT, Bauer-Rowe KE, Titan AL, Salhotra A, Jones RE, da Silva O, Lindsay HG, Berry CE, Chen K, Henn D, Mascharak S, Talbott HE, Kim A, Nosrati F, Sivaraj D, Ransom RC, Matthews M, Khan A, Wagh D, Coller J, Gurtner GC, Wan DC, Wapnir IL, Chang HY, Norton JA, Longaker MT. Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin. Cancer Cell 2022; 40:1392-1406.e7. [PMID: 36270275 PMCID: PMC9669239 DOI: 10.1016/j.ccell.2022.09.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 07/27/2022] [Accepted: 09/26/2022] [Indexed: 01/09/2023]
Abstract
Cancer-associated fibroblasts (CAFs) are integral to the solid tumor microenvironment. CAFs were once thought to be a relatively uniform population of matrix-producing cells, but single-cell RNA sequencing has revealed diverse CAF phenotypes. Here, we further probed CAF heterogeneity with a comprehensive multiomics approach. Using paired, same-cell chromatin accessibility and transcriptome analysis, we provided an integrated analysis of CAF subpopulations over a complex spatial transcriptomic and proteomic landscape to identify three superclusters: steady state-like (SSL), mechanoresponsive (MR), and immunomodulatory (IM) CAFs. These superclusters are recapitulated across multiple tissue types and species. Selective disruption of underlying mechanical force or immune checkpoint inhibition therapy results in shifts in CAF subpopulation distributions and affected tumor growth. As such, the balance among CAF superclusters may have considerable translational implications. Collectively, this research expands our understanding of CAF biology, identifying regulatory pathways in CAF differentiation and elucidating therapeutic targets in a species- and tumor-agnostic manner.
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Affiliation(s)
- Deshka S Foster
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Delitto
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Michelle Griffin
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason Guo
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nicholas Guardino
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrea E Delitto
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Malini Chinta
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Austin R Burcham
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alan T Nguyen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Khristian E Bauer-Rowe
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ashley L Titan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Ankit Salhotra
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - R Ellen Jones
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oscar da Silva
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hunter G Lindsay
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charlotte E Berry
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kellen Chen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dominic Henn
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shamik Mascharak
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heather E Talbott
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexia Kim
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fatemeh Nosrati
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dharshan Sivaraj
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - R Chase Ransom
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Matthews
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anum Khan
- Cell Sciences Imaging Facility, Stanford University, Stanford, CA 94305, USA
| | - Dhananjay Wagh
- Stanford Genomics Facility, Stanford University, Stanford, CA 94305, USA
| | - John Coller
- Stanford Genomics Facility, Stanford University, Stanford, CA 94305, USA
| | - Geoffrey C Gurtner
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Derrick C Wan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Irene L Wapnir
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Jeffrey A Norton
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA.
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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7
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Daniel B, Yost KE, Hsiung S, Sandor K, Xia Y, Qi Y, Hiam-Galvez KJ, Black M, J Raposo C, Shi Q, Meier SL, Belk JA, Giles JR, Wherry EJ, Chang HY, Egawa T, Satpathy AT. Divergent clonal differentiation trajectories of T cell exhaustion. Nat Immunol 2022; 23:1614-1627. [PMID: 36289450 DOI: 10.1038/s41590-022-01337-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
Chronic antigen exposure during viral infection or cancer promotes an exhausted T cell (Tex) state with reduced effector function. However, whether all antigen-specific T cell clones follow the same Tex differentiation trajectory remains unclear. Here, we generate a single-cell multiomic atlas of T cell exhaustion in murine chronic viral infection that redefines Tex phenotypic diversity, including two late-stage Tex subsets with either a terminal exhaustion (Texterm) or a killer cell lectin-like receptor-expressing cytotoxic (TexKLR) phenotype. We use paired single-cell RNA and T cell receptor sequencing to uncover clonal differentiation trajectories of Texterm-biased, TexKLR-biased or divergent clones that acquire both phenotypes. We show that high T cell receptor signaling avidity correlates with Texterm, whereas low avidity correlates with effector-like TexKLR fate. Finally, we identify similar clonal differentiation trajectories in human tumor-infiltrating lymphocytes. These findings reveal clonal heterogeneity in the T cell response to chronic antigen that influences Tex fates and persistence.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Sunnie Hsiung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Yu Xia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kamir J Hiam-Galvez
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mollie Black
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Colin J Raposo
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Quanming Shi
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Stefanie L Meier
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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8
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Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat Genet 2022; 54:1527-1533. [PMID: 36123406 PMCID: PMC9534767 DOI: 10.1038/s41588-022-01177-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 02/16/2022] [Accepted: 08/01/2022] [Indexed: 12/21/2022]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.
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Affiliation(s)
- Joshua T Lange
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Celine Y Chen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA, USA
| | - Jun Tang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcella L Erb
- University of California San Diego Light Microscopy Core Facility, Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China.
- Department of Mathematics, Queen Mary University of London, London, UK.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- ChEM-H, Stanford University, Stanford, CA, USA.
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9
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Belk JA, Yao W, Ly N, Freitas KA, Chen YT, Shi Q, Valencia AM, Shifrut E, Kale N, Yost KE, Duffy CV, Daniel B, Hwee MA, Miao Z, Ashworth A, Mackall CL, Marson A, Carnevale J, Vardhana SA, Satpathy AT. Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. Cancer Cell 2022; 40:768-786.e7. [PMID: 35750052 PMCID: PMC9949532 DOI: 10.1016/j.ccell.2022.06.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022]
Abstract
T cell exhaustion limits antitumor immunity, but the molecular determinants of this process remain poorly understood. Using a chronic stimulation assay, we performed genome-wide CRISPR-Cas9 screens to systematically discover regulators of T cell exhaustion, which identified an enrichment of epigenetic factors. In vivo CRISPR screens in murine and human tumor models demonstrated that perturbation of the INO80 and BAF chromatin remodeling complexes improved T cell persistence in tumors. In vivo Perturb-seq revealed distinct transcriptional roles of each complex and that depletion of canonical BAF complex members, including Arid1a, resulted in the maintenance of an effector program and downregulation of exhaustion-related genes in tumor-infiltrating T cells. Finally, Arid1a depletion limited the acquisition of exhaustion-associated chromatin accessibility and led to improved antitumor immunity. In summary, we provide an atlas of the genetic regulators of T cell exhaustion and demonstrate that modulation of epigenetic state can improve T cell responses in cancer immunotherapy.
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Affiliation(s)
- Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Nghi Ly
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Katherine A Freitas
- Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA 94035, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94035, USA
| | - Yan-Ting Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Quanming Shi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alfredo M Valencia
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric Shifrut
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Nupura Kale
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kathryn E Yost
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Connor V Duffy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Zhuang Miao
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Crystal L Mackall
- Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Division of Pediatric Hematology/Oncology/Stem Cell Transplant and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94035, USA; Division of BMT and Cell Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94035, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Carnevale
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Santosh A Vardhana
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA 94035, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Wheeler JR, Whitney ON, Vogler TO, Nguyen ED, Pawlikowski B, Lester E, Cutler A, Elston T, Dalla Betta N, Parker KR, Yost KE, Vogel H, Rando TA, Chang HY, Johnson AM, Parker R, Olwin BB. RNA-binding proteins direct myogenic cell fate decisions. eLife 2022; 11:e75844. [PMID: 35695839 PMCID: PMC9191894 DOI: 10.7554/elife.75844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs), essential for skeletal muscle regeneration, cause muscle degeneration and neuromuscular disease when mutated. Why mutations in these ubiquitously expressed RBPs orchestrate complex tissue regeneration and direct cell fate decisions in skeletal muscle remains poorly understood. Single-cell RNA-sequencing of regenerating Mus musculus skeletal muscle reveals that RBP expression, including the expression of many neuromuscular disease-associated RBPs, is temporally regulated in skeletal muscle stem cells and correlates with specific stages of myogenic differentiation. By combining machine learning with RBP engagement scoring, we discovered that the neuromuscular disease-associated RBP Hnrnpa2b1 is a differentiation-specifying regulator of myogenesis that controls myogenic cell fate transitions during terminal differentiation in mice. The timing of RBP expression specifies cell fate transitions by providing post-transcriptional regulation of messenger RNAs that coordinate stem cell fate decisions during tissue regeneration.
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Affiliation(s)
- Joshua R Wheeler
- Department of Biochemistry, University of ColoradoBoulderUnited States
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
- Howard Hughes Medical Institute, University of ColoradoBoulderUnited States
- Department of Pathology, Stanford UniversityStanfordUnited States
- Department of Neuropathology, Stanford UniversityStanfordUnited States
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Thomas O Vogler
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
- Department of Surgery, University of ColoradoAuroraUnited States
| | - Eric D Nguyen
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
- Molecular Biology Program and Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Bradley Pawlikowski
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Evan Lester
- Department of Biochemistry, University of ColoradoBoulderUnited States
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Alicia Cutler
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Tiffany Elston
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Nicole Dalla Betta
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Kevin R Parker
- Center for Personal and Dynamic Regulomes, Stanford UniversityPalo AltoUnited States
| | - Kathryn E Yost
- Center for Personal and Dynamic Regulomes, Stanford UniversityPalo AltoUnited States
| | - Hannes Vogel
- Department of Pathology, Stanford UniversityStanfordUnited States
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of MedicineStanfordUnited States
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of MedicineStanfordUnited States
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care SystemPalo AltoUnited States
| | - Howard Y Chang
- Center for Personal and Dynamic Regulomes, Stanford UniversityPalo AltoUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Aaron M Johnson
- Molecular Biology Program and Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- University of Colorado School of Medicine, RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Roy Parker
- Howard Hughes Medical Institute, University of ColoradoBoulderUnited States
| | - Bradley B Olwin
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
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11
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Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021; 600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [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: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joshua T Lange
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Celine Chen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria E Valieva
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ivy Tsz-Lo Wong
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor V Duffy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jun Tang
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jordan Friedlein
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Paul S Mischel
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Foster DS, Januszyk M, Yost KE, Chinta M, Titan AL, Wapnir IL, Gurtner GC, Chang HY, Norton JA, Longaker MT. Cancer-Associated Fibroblasts Share Highly Conserved Phenotypes and Functions Across Tumor Types and Species. J Am Coll Surg 2021. [DOI: 10.1016/j.jamcollsurg.2021.07.504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Foster DS, Januszyk M, Yost KE, Chinta MS, Gulati GS, Nguyen AT, Burcham AR, Salhotra A, Ransom RC, Henn D, Chen K, Mascharak S, Tolentino K, Titan AL, Jones RE, da Silva O, Leavitt WT, Marshall CD, des Jardins-Park HE, Hu MS, Wan DC, Wernig G, Wagh D, Coller J, Norton JA, Gurtner GC, Newman AM, Chang HY, Longaker MT. Integrated spatial multiomics reveals fibroblast fate during tissue repair. Proc Natl Acad Sci U S A 2021; 118:e2110025118. [PMID: 34620713 PMCID: PMC8521719 DOI: 10.1073/pnas.2110025118] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [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] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive, in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing across both time and space. We employ a stented wound model that recapitulates human tissue repair kinetics and multiple Rainbow transgenic lines to precisely track fibroblast fate during the physiologic response to skin injury. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to reveal potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and thereby reexamine the canonical phases of wound healing. These findings have broad implications for the study of tissue repair in complex organ systems.
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Affiliation(s)
- Deshka S Foster
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305
| | - Malini S Chinta
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Alan T Nguyen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Austin R Burcham
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Ankit Salhotra
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - R Chase Ransom
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Dominic Henn
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Kellen Chen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Shamik Mascharak
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305
| | - Ashley L Titan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - R Ellen Jones
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Oscar da Silva
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - W Tripp Leavitt
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Clement D Marshall
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Heather E des Jardins-Park
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael S Hu
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Derrick C Wan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Gerlinde Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Dhananjay Wagh
- Stanford Functional Genomics Facility, Stanford University, Stanford, CA 94305
| | - John Coller
- Stanford Functional Genomics Facility, Stanford University, Stanford, CA 94305
| | - Jeffrey A Norton
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Geoffrey C Gurtner
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305;
- HHMI, Stanford University, Stanford, CA 94305
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305;
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
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14
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Maas-Bauer K, Lohmeyer JK, Hirai T, Ramos TL, Fazal FM, Litzenburger UM, Yost KE, Ribado JV, Kambham N, Wenokur AS, Lin PY, Alvarez M, Mavers M, Baker J, Bhatt AS, Chang HY, Simonetta F, Negrin RS. Invariant natural killer T-cell subsets have diverse graft-versus-host-disease-preventing and antitumor effects. Blood 2021; 138:858-870. [PMID: 34036317 PMCID: PMC8432044 DOI: 10.1182/blood.2021010887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 01/19/2021] [Accepted: 04/22/2021] [Indexed: 11/20/2022] Open
Abstract
Invariant natural killer T (iNKT) cells are a T-cell subset with potent immunomodulatory properties. Experimental evidence in mice and observational studies in humans indicate that iNKT cells have antitumor potential as well as the ability to suppress acute and chronic graft-versus-host-disease (GVHD). Murine iNKT cells differentiate during thymic development into iNKT1, iNKT2, and iNKT17 sublineages, which differ transcriptomically and epigenomically and have subset-specific developmental requirements. Whether distinct iNKT sublineages also differ in their antitumor effect and their ability to suppress GVHD is currently unknown. In this work, we generated highly purified murine iNKT sublineages, characterized their transcriptomic and epigenomic landscape, and assessed specific functions. We show that iNKT2 and iNKT17, but not iNKT1, cells efficiently suppress T-cell activation in vitro and mitigate murine acute GVHD in vivo. Conversely, we show that iNKT1 cells display the highest antitumor activity against murine B-cell lymphoma cells both in vitro and in vivo. Thus, we report for the first time that iNKT sublineages have distinct and different functions, with iNKT1 cells having the highest antitumor activity and iNKT2 and iNKT17 cells having immune-regulatory properties. These results have important implications for the translation of iNKT cell therapies to the clinic for cancer immunotherapy as well as for the prevention and treatment of GVHD.
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Affiliation(s)
- Kristina Maas-Bauer
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
- Department of Hematology, Oncology, and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany
| | - Juliane K Lohmeyer
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | - Toshihito Hirai
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | - Teresa Lopes Ramos
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | | | | | | | | | | | - Arielle S Wenokur
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | - Po-Yu Lin
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | - Maite Alvarez
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | - Melissa Mavers
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
- Division of Stem Cell Transplantation and Regenerative Medicine, Bass Center for Childhood Cancer and Blood Diseases, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA
| | - Jeanette Baker
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
| | - Ami S Bhatt
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
- Department of Genetics, and
- Division of Hematology and
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes
- Howard Hughes Medical Institute, Stanford University, Stanford, CA
| | - Federico Simonetta
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland; and
- Translational Research Center for Oncohematology, Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Robert S Negrin
- Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA
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15
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Raju S, Xia Y, Daniel B, Yost KE, Bradshaw E, Tonc E, Verbaro DJ, Kometani K, Yokoyama WM, Kurosaki T, Satpathy AT, Egawa T. Identification of a T-bet hi Quiescent Exhausted CD8 T Cell Subpopulation That Can Differentiate into TIM3 +CX3CR1 + Effectors and Memory-like Cells. J Immunol 2021; 206:2924-2936. [PMID: 34088768 DOI: 10.4049/jimmunol.2001348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/12/2021] [Indexed: 11/19/2022]
Abstract
Persistent Ag induces a dysfunctional CD8 T cell state known as "exhaustion" characterized by PD-1 expression. Nevertheless, exhausted CD8 T cells retain functionality through continued differentiation of progenitor into effector cells. However, it remains ill-defined how CD8 T cell effector responses are sustained in situ. In this study, we show using the mouse chronic lymphocytic choriomeningitis virus infection model that CX3CR1+ CD8 T cells contain a T-bet-dependent TIM3-PD-1lo subpopulation that is distinct from the TIM3+CX3CR1+PD-1+ proliferative effector subset. The TIM3-CX3CR1+ cells are quiescent and express a low but significant level of the transcription factor TCF-1, demonstrating similarity to TCF-1hi progenitor CD8 T cells. Furthermore, following the resolution of lymphocytic choriomeningitis virus viremia, a substantial proportion of TCF-1+ memory-like CD8 T cells show evidence of CX3CR1 expression during the chronic phase of the infection. Our results suggest a subset of the CX3CR1+ exhausted population demonstrates progenitor-like features that support the generation of the CX3CR1+ effector pool from the TCF-1hi progenitors and contribute to the memory-like pool following the resolution of viremia.
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Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Yu Xia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Kathryn E Yost
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Elliot Bradshaw
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Elena Tonc
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Daniel J Verbaro
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Kohei Kometani
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Wayne M Yokoyama
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Tomohiro Kurosaki
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan.,Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; and
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO;
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16
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Affiliation(s)
- Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Abstract
Simultaneous profiling of multiomic modalities within a single cell is a grand challenge for single-cell biology. While there have been impressive technical innovations demonstrating feasibility-for example, generating paired measurements of single-cell transcriptome (single-cell RNA sequencing [scRNA-seq]) and chromatin accessibility (single-cell assay for transposase-accessible chromatin using sequencing [scATAC-seq])-widespread application of joint profiling is challenging due to its experimental complexity, noise, and cost. Here, we introduce BABEL, a deep learning method that translates between the transcriptome and chromatin profiles of a single cell. Leveraging an interoperable neural network model, BABEL can predict single-cell expression directly from a cell's scATAC-seq and vice versa after training on relevant data. This makes it possible to computationally synthesize paired multiomic measurements when only one modality is experimentally available. Across several paired single-cell ATAC and gene expression datasets in human and mouse, we validate that BABEL accurately translates between these modalities for individual cells. BABEL also generalizes well to cell types within new biological contexts not seen during training. Starting from scATAC-seq of patient-derived basal cell carcinoma (BCC), BABEL generated single-cell expression that enabled fine-grained classification of complex cell states, despite having never seen BCC data. These predictions are comparable to analyses of experimental BCC scRNA-seq data for diverse cell types related to BABEL's training data. We further show that BABEL can incorporate additional single-cell data modalities, such as protein epitope profiling, thus enabling translation across chromatin, RNA, and protein. BABEL offers a powerful approach for data exploration and hypothesis generation.
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Affiliation(s)
- Kevin E Wu
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathryn E Yost
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | - Howard Y Chang
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305;
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
| | - James Zou
- Department of Computer Science, Stanford University, Stanford, CA 94305;
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
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18
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Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Jean GH, Stevens BA, Lee JY, Rustagi A, Rogers AJ, Powell AE, Hunter M, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Nadeau KC, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2. Cell Host Microbe 2020; 28:516-525.e5. [PMID: 32941787 PMCID: PMC7470783 DOI: 10.1016/j.chom.2020.09.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [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: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
B cells are critical for the production of antibodies and protective immunity to viruses. Here we show that patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronavirus disease 2019 (COVID-19) display early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify convergence of antibody sequences across SARS-CoV-2-infected patients, highlighting stereotyped naive responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and SARS-CoV.
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Affiliation(s)
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Grace H Jean
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail E Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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19
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Parker KR, Migliorini D, Perkey E, Yost KE, Bhaduri A, Bagga P, Haris M, Wilson NE, Liu F, Gabunia K, Scholler J, Montine TJ, Bhoj VG, Reddy R, Mohan S, Maillard I, Kriegstein AR, June CH, Chang HY, Posey AD, Satpathy AT. Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies. Cell 2020; 183:126-142.e17. [PMID: 32961131 PMCID: PMC7640763 DOI: 10.1016/j.cell.2020.08.022] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [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: 05/06/2019] [Revised: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
CD19-directed immunotherapies are clinically effective for treating B cell malignancies but also cause a high incidence of neurotoxicity. A subset of patients treated with chimeric antigen receptor (CAR) T cells or bispecific T cell engager (BiTE) antibodies display severe neurotoxicity, including fatal cerebral edema associated with T cell infiltration into the brain. Here, we report that mural cells, which surround the endothelium and are critical for blood-brain-barrier integrity, express CD19. We identify CD19 expression in brain mural cells using single-cell RNA sequencing data and confirm perivascular staining at the protein level. CD19 expression in the brain begins early in development alongside the emergence of mural cell lineages and persists throughout adulthood across brain regions. Mouse mural cells demonstrate lower levels of Cd19 expression, suggesting limitations in preclinical animal models of neurotoxicity. These data suggest an on-target mechanism for neurotoxicity in CD19-directed therapies and highlight the utility of human single-cell atlases for designing immunotherapies.
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MESH Headings
- Animals
- Antibodies, Bispecific/immunology
- Antigens, CD19/immunology
- B-Lymphocytes/immunology
- Blood-Brain Barrier/immunology
- Blood-Brain Barrier/metabolism
- Brain/immunology
- Brain/metabolism
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Epithelial Cells/metabolism
- Humans
- Immunotherapy/adverse effects
- Immunotherapy/methods
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Muscle, Smooth, Vascular/metabolism
- Neoplasms
- Receptors, Antigen, T-Cell/immunology
- Receptors, Chimeric Antigen/immunology
- Single-Cell Analysis/methods
- T-Lymphocytes/immunology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Denis Migliorini
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Translational Research in Onco-Hematology and Department of Oncology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Eric Perkey
- Graduate Program in Cellular and Molecular Biology and Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Division of Hematology-Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Puneet Bagga
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohammad Haris
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Functional and Molecular Imaging Laboratory, Research Branch, Sidra Medicine, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Neil E Wilson
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Liu
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Khatuna Gabunia
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John Scholler
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijay G Bhoj
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravinder Reddy
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suyash Mohan
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Carl H June
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Avery D Posey
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Ansuman T Satpathy
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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20
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Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Su Y, Hadlock J, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. medRxiv 2020:2020.09.22.20192443. [PMID: 32995830 PMCID: PMC7523175 DOI: 10.1101/2020.09.22.20192443] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [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: 02/04/2023]
Abstract
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a new strain harboring the spike variant D614G. With antibody and B cell analytics, we show correlates of adaptive immunity, including a differential response to D614G. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.
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Affiliation(s)
- Jason D. Goldman
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kathryn E. Yost
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Paula M. Manner
- Providence St. Joseph Health, Renton, WA, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA
| | - Julie A. Wallick
- Providence St. Joseph Health, Renton, WA, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA
| | - Heather A. Algren
- Providence St. Joseph Health, Renton, WA, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA
| | | | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Jennifer Hadlock
- Providence St. Joseph Health, Renton, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | | | - William R. Berrington
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - George P. Pappas
- Division of Pulmonology and Critical Care Medicine, Swedish Medical Center, Seattle, WA, USA
| | - Sonam T. Nyatsatsang
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | | | - John S. Pauk
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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21
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Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Stevens B, Lee JY, Rustagi A, Rogers AJ, Powell AE, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. bioRxiv 2020:2020.07.08.194456. [PMID: 32676593 PMCID: PMC7359515 DOI: 10.1101/2020.07.08.194456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/04/2022]
Abstract
During virus infection B cells are critical for the production of antibodies and protective immunity. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify extensive convergence of antibody sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses.
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Affiliation(s)
- Sandra C. A. Nielsen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Katherine J. L. Jackson
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- These authors contributed equally
| | - Ramona A. Hoh
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Theodore S. Jardetzky
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Peter S. Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | | | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
- Lead Contact
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22
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Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho SW, Mistry A, Longaker MT, Khavari PA, Batey RT, Wuttke DS, Chang HY. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. eLife 2020; 9:e54508. [PMID: 32379046 PMCID: PMC7282817 DOI: 10.7554/elife.54508] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 12/17/2019] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen loss activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.
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Affiliation(s)
- Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Meagan Y Nakamoto
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Brian J Zarnegar
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - James P Broughton
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Ryan C Ransom
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Ankit Salhotra
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Surya D Nagaraja
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Seung-Woo Cho
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Anil Mistry
- Novartis Institute for Biomedical ResearchCambridgeUnited States
| | - Michael T Longaker
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Robert T Batey
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Deborah S Wuttke
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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23
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Yost KE, Chang HY, Satpathy AT. Tracking the immune response with single-cell genomics. Vaccine 2019; 38:4487-4490. [PMID: 31859202 DOI: 10.1016/j.vaccine.2019.11.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023]
Abstract
The immune system is composed of a diverse array of cell types, each with a specialized role in orchestrating the immune response to pathogens or cancer. Even within a single cell 'type,' individual cells can access a wide spectrum of differentiation and activation states, which reflect the physiological response of each cell to the tissue environment and immune stimuli. Thus, the cellular diversity of the immune system is inherently quite complex and understanding this complexity has greatly benefited from technologies that measure immune responses at single-cell resolution, in addition to the systems-level response as a whole. In this Commentary, we focus on recent work at the interface of immunology and single-cell genomics and highlight advances in technologies and their application to immune cells. In particular, we highlight recent single-cell genomic profiling studies of T cells, since somatic rearrangements in the T cell receptor (TCR) loci enable the tracking of clonal T cell responses through space and time. Finally, we discuss opportunities for future use of these technologies in understanding vaccination and the basis for effective vaccine-induced immunity.
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Affiliation(s)
- Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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24
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Yost KE, Satpathy AT, Wells DK, Qi Y, Wang C, Kageyama R, McNamara KL, Granja JM, Sarin KY, Brown RA, Gupta RK, Curtis C, Bucktrout SL, Davis MM, Chang ALS, Chang HY. Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat Med 2019; 25:1251-1259. [PMID: 31359002 PMCID: PMC6689255 DOI: 10.1038/s41591-019-0522-3] [Citation(s) in RCA: 807] [Impact Index Per Article: 161.4] [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: 04/18/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of patients with cancer1. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear2-4. Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Tracking T cell receptor clones and transcriptional phenotypes revealed coupling of tumor recognition, clonal expansion and T cell dysfunction marked by clonal expansion of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, the expansion of T cell clones did not derive from pre-existing tumor-infiltrating T lymphocytes; instead, the expanded clones consisted of novel clonotypes that had not previously been observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells and evident in patients with basal or squamous cell carcinoma. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.
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Affiliation(s)
- Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Robin Kageyama
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Katherine L McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Ryanne A Brown
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Rohit K Gupta
- Stanford Biobank, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mark M Davis
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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25
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Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, Wang L, Yin Y, Giresi PG, Chang ALS, Zheng GXY, Greenleaf WJ, Chang HY. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 2019; 37:925-936. [PMID: 31375813 PMCID: PMC7299161 DOI: 10.1038/s41587-019-0206-z] [Citation(s) in RCA: 457] [Impact Index Per Article: 91.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/01/2019] [Indexed: 02/08/2023]
Abstract
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | | | - Jean Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | - Li Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | | | | | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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26
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Yost KE, Clatterbuck Soper SF, Walker RL, Pineda MA, Zhu YJ, Ester CD, Showman S, Roschke AV, Waterfall JJ, Meltzer PS. Rapid and reversible suppression of ALT by DAXX in osteosarcoma cells. Sci Rep 2019; 9:4544. [PMID: 30872698 PMCID: PMC6418139 DOI: 10.1038/s41598-019-41058-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 11/07/2018] [Accepted: 02/07/2019] [Indexed: 01/19/2023] Open
Abstract
Many tumors maintain chromosome-ends through a telomerase-independent, DNA-templated mechanism called alternative lengthening of telomeres (ALT). While ALT occurs in only a subset of tumors, it is strongly associated with mutations in the genes ATRX and DAXX, which encode components of an H3.3 histone chaperone complex. The role of ATRX and DAXX mutations in potentiating the mechanism of ALT remains incompletely understood. Here we characterize an osteosarcoma cell line, G292, with wild-type ATRX but a unique chromosome translocation resulting in loss of DAXX function. While ATRX and DAXX form a complex in G292, this complex fails to localize to nuclear PML bodies. We demonstrate that introduction of wild type DAXX suppresses the ALT phenotype and restores the localization of ATRX/DAXX to PML bodies. Using an inducible system, we show that ALT-associated PML bodies are disrupted rapidly following DAXX induction and that ALT is again restored following withdrawal of DAXX.
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Affiliation(s)
- Kathryn E Yost
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sarah F Clatterbuck Soper
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marbin A Pineda
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuelin J Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Corbin D Ester
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Soyeon Showman
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anna V Roschke
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joshua J Waterfall
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. .,Translational Research Department & INSERM U830, Institut Curie, Paris, France.
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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27
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Soper SFC, Yost KE, Walker RL, Pineda MA, Zhu YJ, Waterfall JJ, Meltzer PS. Abstract 1466: DAXX localizes ATRX to suppress alternative lengthening of telomeres in osteosarcoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To maintain genome stability, proliferating cells must add telomere sequence to counteract the chromosome end replication problem. In normal cells, telomeres are lengthened through the action of the enzyme telomerase. In about 10-15% of tumors, however, telomeres are lengthened through a telomerase-independent mechanism known as Alternative Lengthening of Telomeres or ALT. Many tumors that use ALT have poor prognoses, so ALT represents an appealing therapeutic target. It has been previously observed that ALT tumors frequently carry mutations in ATRX, which partners with the protein DAXX in a chromatin remodeling complex that deposits histone variant H3.3. How these mutations facilitate the ALT pathway is not well understood. Previous work in our lab identified an ALT-positive osteosarcoma cell line, G292, in which ATRX is wild-type but DAXX has undergone a fusion event with the non-canonical kinesin KIFC3. The DAXX-KIFC3 fusion leads to a loss of DAXX function, and inducible restoration of wild-type DAXX reversibly abrogates ALT in this cell line. We observe that expression of wild-type DAXX results in localization of ATRX to PML bodies, increased occupancy of ATRX at telomeric chromatin, and higher levels of histone H3.3 at telomeres. We conclude that full-length DAXX is required for the functional localization of ATRX to telomeres. Leveraging this our inducible system, we continue to probe the role of the ATRX/DAXX complex in suppressing ALT.
Citation Format: Sarah Faith Clatterbuck Soper, Kathryn E. Yost, Robert L. Walker, Marbin A. Pineda, Yuelin J. Zhu, Joshua J. Waterfall, Paul S. Meltzer. DAXX localizes ATRX to suppress alternative lengthening of telomeres in osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1466.
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Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell 2018; 173:1398-1412.e22. [PMID: 29731168 PMCID: PMC5984165 DOI: 10.1016/j.cell.2018.03.068] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [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: 10/17/2017] [Revised: 02/08/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.
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MESH Headings
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- CRISPR-Cas Systems
- Carcinogenesis/genetics
- Cell Line, Tumor
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromatin
- DNA, Neoplasm/genetics
- Enhancer Elements, Genetic
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, myc
- Humans
- Mice
- Mice, Inbred NOD
- Mutation
- Neoplasm Transplantation
- Promoter Regions, Genetic
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transcription, Genetic
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Affiliation(s)
- Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Y Grace Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeewon Kim
- Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Jing He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Stephanie A Nevins
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Program, CRUK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 2QQ, UK
| | - S John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA 94121, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
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