1
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Liang SQ, Navia A, Ramseier M, Zhou X, Martinez ML, Lee CC, Zhou C, Wu J, Xie J, Su Q, Wang D, Flotte TR, Anderson DG, Tarantal AF, Shalek A, Gao G, Xue W. AAV5 delivery of CRISPR/Cas9 mediates genome editing in the lungs of young rhesus monkeys. Hum Gene Ther 2024. [PMID: 38767512 DOI: 10.1089/hum.2024.035] [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: 05/22/2024] Open
Abstract
Genome editing has the potential to treat genetic diseases in a variety of tissues including the lung. We have previously developed and validated a dual adeno-associated virus (AAV) CRISPR platform that supports effective editing in the airways of mice. To validate this delivery vehicle in a large animal model, we have shown that intratracheal instillation of CRISPR/Cas9 in AAV5 can edit a housekeeping gene or a disease-related gene in the lungs of young rhesus monkeys. We observed up to 8% editing of ACE2 in lung lobes after single-dose administration. Single-nuclear RNA-sequencing revealed that AAV5 transduces multiple cell types in the caudal lung lobes, including alveolar cells, macrophages, fibroblasts, endothelial cells, and B cells. These results demonstrate that AAV5 is efficient in the delivery of CRISPR/Cas9 in the lung lobes of young rhesus monkeys.
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Affiliation(s)
- Shun-Qing Liang
- UMass Chan Medical School, RTI, Worcester, Massachusetts, United States;
| | - Andrew Navia
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States;
| | - Michelle Ramseier
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States;
| | - Xuntao Zhou
- UMass Chan Medical School, RTI, Worcester, Massachusetts, United States;
| | | | | | - Chen Zhou
- UMass Chan Medical School, RTI, Worcester, Massachusetts, United States;
| | - Joae Wu
- UMass Chan Medical School, RTI, Worcester, Massachusetts, United States;
| | - Jun Xie
- UMass Chan Medical School, RTI, Worcester, Massachusetts, United States;
| | - Qin Su
- University of Massachusetts Medical School, Gene Therapy Ctr & Vector Core, 368 Plantation St, AS6-2049-2049, Worcester, Massachusetts, United States, 01605;
| | - Dan Wang
- UMass Med School, Gene Therapy Center, 368 Plantation Street, ASC6-2011, Worcester, Massachusetts, United States, 01605;
| | - Terence R Flotte
- University of Massachusetts Medical School, Pediatrics, 55 Lake Avenue North, S1-340, Worcester, Massachusetts, United States, 01655;
| | - Daniel G Anderson
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States;
| | - Alice F Tarantal
- UC Davis, Pediatrics and Cell Biology and Human Anatomy, CNPRC, 1 Shields Avenue, Davis, California, United States, 95616-8542;
| | - Alex Shalek
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States;
| | - Guangping Gao
- University of Massachusetts Medical School, Gene Therapy Ctr & Vector Core, 368 Plantation St, AS6-2049-2049, Worcester, Massachusetts, United States, 01605
- United States;
| | - Wen Xue
- UMass Chan Medical School, RTI, Worcester, Massachusetts, United States;
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2
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Kaminski J, Fleming RA, Alvarez-Calderon F, Winschel MB, McGuckin C, Ho EE, Eng F, Rui X, Keskula P, Cagnin L, Charles J, Zavistaski JM, Margossian SP, Kapadia M, Rottman JB, Lane J, Baumeister SHC, Tkachev V, Shalek A, Kean LS, Gerdemann U. B-cell-directed CAR-T cell therapy activates CD8+ cytotoxic CARneg bystander T-cells in non-human primates and patients. Blood 2024:blood.2023022717. [PMID: 38558106 DOI: 10.1182/blood.2023022717] [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] [Received: 10/19/2023] [Revised: 02/23/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
CAR-T cells hold promise as a therapy for B-cell-derived malignancies, yet despite their impressive initial response rates, a significant proportion of patients ultimately experience relapse. While recent studies have explored the mechanisms of in vivo CAR-T cell function, little is understood about the activation of surrounding CARneg bystander T-cells and their potential to enhance tumor responses. We performed single-cell RNA-Seq (scRNA-Seq) on non-human primate (NHP) and patient-derived T-cells to identify the phenotypic and transcriptomic hallmarks of bystander activation of CARneg T-cells following B-cell targeted CAR-T cell therapy. Utilizing a highly translatable CD20 CAR NHP model, we observed a distinct population of activated CD8+ CARneg T-cells emerging during CAR-T cell expansion. These bystander CD8+ CARneg T-cells exhibited a unique transcriptional signature with upregulation of NK-cell markers (KIR3DL2, CD160, KLRD1), chemokines and chemokine receptors (CCL5, XCL1, CCR9), and downregulation of naive T-cell-associated genes (SELL, CD28). A transcriptionally similar population was identified in patients following Tisagenlecleucel infusion. Mechanistic studies revealed that IL-2 and IL-15 exposure induced bystander-like CD8+ T-cells in a dose dependent manner. In vitro activated and patient-derived T-cells with the bystander phenotype efficiently killed leukemic cells through a TCR-independent mechanism. Collectively, this dataset provides the first comprehensive identification and profiling of CARneg bystander CD8+ T-cells following B-cell targeting CAR-T cell therapy and suggests a novel mechanism through which CAR-T cell infusion might trigger enhanced anti-leukemic responses.
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Affiliation(s)
| | - Ryan A Fleming
- Boston Children's Hospital, Boston, Massachusetts, United States
| | | | | | - Connor McGuckin
- Boston Children's Hospital, Boston, Massachusetts, United States
| | | | - Fay Eng
- 2seventy bio, Cambridge, Massachusetts, United States
| | - Xianliang Rui
- Boston Children's Hospital, Boston, Massachusetts, United States
| | - Paula Keskula
- Boston Children's Hospital, Boston, Massachusetts, United States
| | - Lorenzo Cagnin
- Boston Children's Hospital, Boston, Massachusetts, United States
| | - Joanne Charles
- Boston Children's Hospital, Boston, Massachusetts, United States
| | | | | | | | | | - Jennifer Lane
- Boston Children's Hospital, Boston, Massachusetts, United States
| | | | | | - Alex Shalek
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, United States
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3
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Alvarez-Breckenridge C, Prakadan S, Markson S, Kim A, Nayyar N, Kuter B, Mora J, Shaw B, Lee EQ, Chukwueke U, Cahill D, Sullivan R, Carter S, Shalek A, Brastianos P. IMMU-02. GENOMIC AND TRANSCRIPTOMIC CORRELATES OF IMMUNOTHERAPY RESPONSE WITHIN THE TUMOR MICROENVIRONMENT OF LEPTOMENINGEAL METASTASES. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.362] [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: 11/13/2022] Open
Abstract
Abstract
Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials utilizing either Pembrolizumab alone or the combination of Ipilimumab and Nivolumab. We investigated the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We isolated and sequenced 34,742 cells from both the malignant and immune compartment within CSF. Amongst the 19 patients included in the cohort, there were 13 pre-treatment and 24 post-treatment samples, and 9 patients were sampled across multiple timepoints. We detected dynamic changes in immune cell recruitment into the CSF and activation within 30 days of ICI, including increased effector T cell activation and IFN-gamma response pathways within T cells. Moreover, the overall level of IFN-gamma response and antigen processing within 30 days of ICI in malignant cells correlated with survival past clinical trial primary endpoint. Lastly, we observed evidence of longitudinal outgrowth of distinct immunogenic clones over the course of ICI. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and provides unique insights into the compartmental and temporal variation during the course of ICI. Moreover, our findings demonstrate the clinical utility of cell- free and single-cell genomic measurements for LMD research.
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Affiliation(s)
| | | | | | - Albert Kim
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Joana Mora
- Massachusetts General Hospital, Boston, MA, USA
| | - Brian Shaw
- Drexel University College of Medicine, Boston, MA, USA
| | | | | | | | | | - Scott Carter
- Broad Institute of Harvard and M.I.T., Boston, USA
| | - Alex Shalek
- Massachusetts Institute of Technology, Boston, USA
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4
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Rowe G, Morris V, Wang D, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, da Silva RV, Pikman Y, Harris M, Pimkin M, Shalek A, North T, Daley G, da Rocha EL. 2001 – PLASTICITY OF B-LYMPHOBLASTIC LEUKEMIA STEM CELLS. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Barreiro O, Loughhead SM, Pallis P, Eljalby M, Zwijnenburg T, Collado V, Ziegler C, Yosef N, Shalek A, Gerlach C, von Andrian UH. Endothelial immune surveillance by intravascular antigen-experienced CD8+ T cells as a novel mechanism of antiviral adaptive immunity. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.103.30] [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] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Following acute infection, pathogen-specific CD8+ T cells proliferate and divide in a heterogeneous manner, giving rise to effector and memory T cells with distinct migratory patterns. This migratory division of labor ensures that the host is efficiently scanned for ongoing or recurring infections. Recent evidence suggests that the presumed migratory behavior of the classical effector memory T cell subset needs revision. Here, we report that terminally differentiated effector and effector memory T cells adhere to and patrol the endothelium, while less differentiated T cells migrate into peripheral tissues. Interestingly, patrolling T cells have been observed at vascular beds such as the dermal microvasculature, where they concentrate in arterioles and preferentially migrate against the blood flow. Patrolling T cells survey the endothelium in the search for cognate antigen and, once encountered, cease their migration and establish long-lived interactions with peptide-presenting endothelial cells without inducing cytotoxicity. Finally, single-cell RNA-Seq analysis of patrolling CD8+ T effector cells and blockade experiments to prevent patrolling have unveiled a key and unexpected role for patrolling in the generation and maintenance of the intravascular CD8+ CX3CR1high KLRG-1+ effector memory T cell subset, which in turn is relevant for long-term protective immunity.
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Affiliation(s)
- Olga Barreiro
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
| | - Scott M Loughhead
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
| | - Paris Pallis
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
| | - Mahmoud Eljalby
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
| | | | - Victor Collado
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
| | | | - Nir Yosef
- 4Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley
| | - Alex Shalek
- 3Institute for Medical Engineering and Science, MIT
| | - Carmen Gerlach
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
- 2Department of Medicine, Karolinska Institute, Sweden
| | - Ulrich H von Andrian
- 1Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School
- 5Ragon Institute of MGH, MIT, and Harvard
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6
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Song H, Weinstein HN, Allegakoen P, Wadsworth M, Xie J, Yang H, Feng FY, Carroll PR, Wang B, Cooperberg MR, Shalek A, Huang FW. Single-cell analysis of cellular state heterogeneity in human localized prostate cancer. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.6_suppl.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
254 Background: Prostate cancer is the second most common malignancy in men worldwide. The development of cancer from prostate tissue involves complex interactions of tumor cells with surrounding epithelial and stromal cells and can occur multifocally, suggesting that prostate epithelial cells may undergo cellular state transitions towards carcinogenesis. Previous studies on localized prostate cancer molecular changes have focused on unsorted bulk tissue samples, leaving a gap in our understanding of the cellular heterogeneity in the tumor microenvironment. Single-cell analyses of tumor specimens have the potential to reveal, at unprecedented resolution, cellular composition, as well as instructive intercellular interactions. Methods: To characterize the localized prostate cancer tumor microenvironment, we performed single-cell RNA-sequencing (scRNA-seq) on prostate biopsies, radical prostatectomy specimens, and matched patient-derived organoids from localized prostate cancer patients. Results: Within prostate epithelial cells, we identified a population of club cells that may act as progenitor cells. Furthermore, we uncovered luminal-like epithelial cellular states augmented in androgen signaling across basal and club cell populations. By classifying tumor cells based on ERG expression status, we found that ERG- tumor cells, in contrast to ERG+ cells, share transcriptomic heterogeneity with surrounding luminal epithelial cells and are associated with common stromal and immune microenvironment responses. These results suggest that specific immune niches may arise based on TMPRSS2-ERG fusion status. Finally, we generated prostate epithelial organoids derived from matched localized prostate cancer patients and characterized their transcriptomic profiles by scRNA-seq. These patient-derived organoids recapitulated tumor-associated epithelial cell states but also harbored distinct cell types and states from their parent tissues. Conclusions: Our data from localized prostate cancer specimens and organoids provide diagnostically relevant insights and will help advance our understanding of the cancer cellular states associated with prostate carcinogenesis.
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Affiliation(s)
- Hanbing Song
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California, San Francisco, CA
| | - Hannah N.W. Weinstein
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California, San Francisco, CA
| | - Paul Allegakoen
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California, San Francisco, CA
| | | | - Jamie Xie
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California, San Francisco, CA
| | - Heiko Yang
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Felix Y Feng
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Peter R. Carroll
- Dept. of Urology, University of California San Francisco, San Francisco, CA
| | - Bruce Wang
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA
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7
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Winter PS, Raghavan S, Navia A, Williams H, DenAdel A, Kalekar R, Galvez-Reyes J, Lowder K, Mulugeta N, Raghavan M, Borah A, Ng R, Wang J, Reilly E, Ragon D, Brais L, Ng K, Cleary J, Crawford L, Manalis S, Nowak J, Wolpin B, Hahn W, Aguirre A, Shalek A. Abstract PR03: Subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-pr03] [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
The majority of patients with pancreatic ductal adenocarcinoma (PDAC) present at diagnosis with metastatic disease and have median survival times of less than 12 months. Recent studies have demonstrated that PDAC tumors with distinct transcriptional phenotypes are associated with different clinical outcomes. However, the mechanisms underlying this survival difference, the degree of cellular heterogeneity within a given tumor, and the subtype-specific contributions from the local immune microenvironment are not understood. In addition, there are ongoing efforts to understand if patient-derived organoid models can be used as functional surrogates for an individual patient’s disease. It remains unclear if patient transcriptional phenotypes are preserved in their matched organoid models. Here, we describe a pipeline that permits both direct characterization of the PDAC liver metastatic niche via single-cell RNA-sequencing and functional assessment of PDAC tumor biology in patient-matched organoid models. Starting from core needle biopsies of metastatic PDAC lesions containing 50-100k viable cells, we simultaneously perform: (1) single-cell RNA-sequencing using Seq-Well and (2) three-dimensional organoid culture generation. We have applied this approach to profile 23 patients and their matched early passage organoid models. Our pipeline yields high-quality single-cell measurements across diverse cell types—both malignant and non-malignant—enabling a principled dissection of tumor intrinsic and extrinsic factors. Evaluation of clinically relevant transcriptional signatures (e.g., Basal-like vs Classical) revealed extensive heterogeneity at the single-cell level. Single malignant cells are capable of co-expressing markers of both Basal-like and Classical states suggesting these phenotypes lie on a continuum rather than as discrete types. Basal cells express more stem-like features and inhabit a distinct microenvironment compared to their Classical counterparts. Microenvironmental composition differed on several levels between the two types, most notably their T/NK cell and macrophage populations with specific implications for subtype-specific microenvironmental directed therapy. Finally, we found that the microenvironment in traditional organoid culture selects against the Basal-like subtype and that these tumors are capable of significant phenotypic plasticity in vitro. We are able to recover Basal-like features by altering the organoid growth conditions. These findings suggest the need for distinct environments to support specific transcriptional subtypes in PDAC. Overall, our work provides a framework for the analysis of human cancers and their matched models using single-cell methods, and reveals novel, actionable insights into the heterogeneity and plasticity underlying survival in transcriptionally distinct forms of PDAC.
Citation Format: Peter S. Winter, Srivatsan Raghavan, Andrew Navia, Hannah Williams, Alan DenAdel, Radha Kalekar, Jennyfer Galvez-Reyes, Kristen Lowder, Nolawit Mulugeta, Manisha Raghavan, Ashir Borah, Raymond Ng, Junning Wang, Emma Reilly, Dorisanne Ragon, Lauren Brais, Kimmie Ng, James Cleary, Lorin Crawford, Scott Manalis, Jonathan Nowak, Brian Wolpin, William Hahn, Andrew Aguirre, Alex Shalek. Subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PR03.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kimmie Ng
- 2Dana-Farber Cancer Institute, Boston, MA,
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8
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Rowe G, Morris V, Marion W, Hughes T, Sousa P, Sensharma P, Harris M, Pikman Y, North T, Shalek A, Daley G, da Rocha EL. 3126 – SINGLE CELL SEQUENCING OF MLL-REARRANGED LEUKEMIA REVEALS MECHANISMS OF LEUKEMIA INITIATING CELL PLASTICITY. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Winchell CG, Maiello P, Nyquist S, Shalek A, Lin P, Flynn JL. Defining the role of CD8 T cell subsets in tuberculosis in non-human primates. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.82.29] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Tuberculosis (TB) is the number one cause of death by a single infectious agent with no protective vaccine available. Challenges in vaccine development are partially attributed to a deficiency in knowledge regarding specific immune cells’ contribution to protection. CD8 T cells comprise ~30–40% of T cells in the lung granuloma, an organized collection of immune cells that is a hallmark of Mycobacterium tuberculosis (Mtb) infection. However, few studies have explored the diversity, function and contribution to protection of CD8 subsets during TB. We investigated the roles of conventional CD8αβ T cells and unconventional CD8αα T cells during early Mtb infection. Cynomolgus macaques were CD8-depleted using anti-CD8α or anti-CD8β antibodies prior to and during Mtb infection and necropsied at 6 weeks post-infection. CD8α depleted NHPs (CD8αα and CD8αβ depletion) had higher bacterial burdens, worse pathology and overall poorer disease outcome compared to IgG controls, while CD8β depleted (CD8αβ only depletion) displayed an intermediate phenotype. This provides the first evidence for an important early role for non-conventional CD8 T cells in TB. Using spectral flow cytometry we identified multiple CD8 subsets and assessed their functions in granulomas for the first time in NHPs. After CD8α depletion, the repertoire of CD8 subsets dramatically changed in granulomas. This was associated with functional alterations in other immune cell populations which we validated and expanded upon using single-cell RNA sequencing. These studies provide a functional immune landscape of early events in Mtb granulomas as well as the effects of CD8 depletion, shedding light on the protective potential of CD8 T cell subsets during primary Mtb infection.
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10
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Walesky C, Kolb K, Winston C, Henderson J, Kruft B, Fleming I, Ko S, Monga SP, Mueller F, Apte U, Shalek A, Goessling W. Functional Compensation Precedes Recovery of Tissue Mass Following Acute Liver Injury. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chad Walesky
- Harvard Medical School/Brigham and Women’s Hospital
| | | | | | | | | | | | - Sungjin Ko
- University of Pittsburgh School of Medicine
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11
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Ocwieja K, Stanton A, Richards A, Antonucci J, Hughes T, Shalek A, Jaenisch R, Gehrke L. 973. Single-cell RNA Sequencing Analysis of Zika Virus Infection in Human Stem Cell-Derived Cerebral Organoids. Open Forum Infect Dis 2019. [PMCID: PMC6808757 DOI: 10.1093/ofid/ofz359.075] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The molecular mechanisms underpinning the neurologic and congenital pathologies caused by Zika virus (ZIKV) infection remain poorly understood. One barrier has been the lack of relevant model systems for the developing human brain; however, thanks to advances in the stem cell field, we can now evaluate ZIKV central nervous system infections in human stem cell-derived cerebral organoids which recapitulate complex 3-dimensional neural architecture.
Methods
We apply Seq-Well—a simple, portable platform for massively parallel single-cell RNA sequencing—to characterize cerebral organoids infected with ZIKV. Using this sequencing method, and published transcriptional profiles, we identify multiple cellular populations in our organoids, including neuroprogenitor cells, intermediate progenitor cells, and terminally differentiated neurons. We detect and quantify host mRNA transcripts and viral RNA with single-cell resolution, defining transcriptional features of uninfected cells and infected cells.
Results
In this model of the developing brain, we identify preferred tropisms of ZIKV infection and pronounced effects on cell division, differentiation, and death. Our data additionally reveal differences in cellular populations and gene expression within organoids infected by historic and contemporary ZIKV strains from a variety of geographic locations. This finding might help explain phenotypic differences attributed to the viruses, including variable propensity to cause microcephaly.
Conclusion
Overall, our work provides insight into normal and diseased human brain development, and suggests that both virus replication and host response mechanisms underlie the neuropathology of ZIKV infection.
Disclosures
All Authors: No reported Disclosures.
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Affiliation(s)
- Karen Ocwieja
- Boston Children’s Hospital, Somerville, Massachusetts
| | - Alexandra Stanton
- Graduate Program in Virology, Harvard University, Cambridge, Massachusetts
| | | | - Jenna Antonucci
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Travis Hughes
- Virology Graduate Program, Harvard Medical School, Cambridge, Massachusetts
| | - Alex Shalek
- Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Lee Gehrke
- Massachusetts Institute of Technology, Harvard Medical School, Cambridge, Massachusetts
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12
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Reitman Z, Paolella B, Bergthold G, Pelton K, Becker S, Jones R, Sinai C, Malkin H, Huang Y, Grimmet L, Herbert Z, Sun Y, Weatherbee J, Qian K, Condurat AL, Alberta J, Daley J, Rozenblatt-Rozen O, Segal R, Haas-Kogan D, Filbin M, Suva M, Regev A, Stiles C, Kieran M, Goumnerova L, Ligon K, Shalek A, Beroukhim R, Bandopadhayay P. LGG-05. SINGLE CELL RNA SEQUENCING REVEALS MITOGENIC AND PROGENITOR GENE PROGRAMS IN BRAF-REARRANGED PILOCYTIC ASTROCYTOMAS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | - Ying Huang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Yu Sun
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kenin Qian
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - John Daley
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | | | - Mario Suva
- Massachusetts General Hospital, Boston, MA, USA
| | - Aviv Regev
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Mark Kieran
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Keith Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex Shalek
- Massachusetts Institute of Technology, Boston, MA, USA
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13
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Walesky C, Kolb K, Winston C, Henderson J, Apte U, Mueller F, Shalek A, Goessling W. Single Cell RNA‐sequencing (scRNA‐seq) Reveals Reprogramming and Functional Compensation Preceding Cellular Recovery in Multiple Models of Acute Liver Injury. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.369.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chad Walesky
- Medicine/GeneticsHarvard Medical School/Brigham and Women's HospitalBostonMA
| | - Kellie Kolb
- Broad Institute of MIT and HarvardCambridgeMA
| | - Carolyn Winston
- Medicine/GeneticsHarvard Medical School/Brigham and Women's HospitalBostonMA
| | - Jake Henderson
- Medicine/GeneticsHarvard Medical School/Brigham and Women's HospitalBostonMA
| | - Udayan Apte
- Pharmacology, Toxicology and TherapeuticsUniversity of Kansas Medical CenterKansas CityKS
| | | | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeMA
| | - Wolfram Goessling
- Medicine/GeneticsHarvard Medical School/Brigham and Women's HospitalBostonMA
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14
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Alvarez-Breckenridge C, Prakadan S, Lee E, Tolaney S, Nayak L, Lin N, Bihun I, Chukwueke U, Oh K, White M, Gerstner E, Lawrence D, Cohen J, Giobbie-Hurder A, Cahill D, Carter S, Shalek A, Sullivan R, Brastianos P. CMET-20. EVIDENCE OF CNS RESPONSE OF PEMBROLIZUMAB FOR LEPTOMENINGEAL CARCINOMATOSIS AT A SINGLE CELL RESOLUTION. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Eudocia Lee
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Nancy Lin
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Kevin Oh
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | | | - Daniel Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Shalek
- Massachusetts Institute of Technology, Boston, MA, USA
| | | | - Priscilla Brastianos
- Divisions of Neuro-Oncology and Hematology/Oncology, Departments of Medicine and Neurology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
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15
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van Galen P, Hovestadt V, Griffin G, Verga J, Wadsworth M, Hughes T, Stephansky J, Pastika TI, Story JL, Pinkus G, Pozdnyakova O, Graubert T, Shalek A, Aster J, Lane A, Bernstein B. Single-Cell Analysis of AML Reveals Determinants of Disease Progression and Immune Evasion. Exp Hematol 2018. [DOI: 10.1016/j.exphem.2018.06.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Reitman Z, Paolella B, Bergthold G, Pelton K, Becker S, Jones R, Herbert Z, Grimmett L, Daley J, Filbin M, Suva M, Goumnerova L, Wright K, Chi S, Kieran M, Regev A, Shalek A, Ligon KL, Beroukhim R, Bandopadhayay P. LGG-13. RESOLVING TRANSCRIPTIONAL PROFILES IN BRAF-REARRANGED PILOCYTIC ASTROCYTOMA USING SINGLE CELL RNA SEQUENCING. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zachary Reitman
- Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Boston, MA, USA
| | | | | | | | | | | | - Zach Herbert
- Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Boston, MA, USA
| | | | - John Daley
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Mariella Filbin
- Dana Farber Cancer Institute, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mario Suva
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Susan Chi
- Boston Children’s Hospital, Boston, MA, USA
| | | | - Aviv Regev
- Boston Children’s Hospital, Boston, MA, USA
| | - Alex Shalek
- Massachusetts Institute of Technology, Boston, MA, USA
| | | | | | - Pratiti Bandopadhayay
- Dana Farber Cancer Institute, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
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17
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Brastianos PK, Prakadan S, Alvarez-Breckenridge C, Lee EQ, Tolaney SM, Nayak L, Lin NU, Navia A, Bihun I, Chukwueke UN, Oh KS, White M, Gerstner ER, Lawrence DP, Cohen JV, Giobbie-Hurder A, Cahill DP, Shalek A, Carter SL, Sullivan RJ. Phase II study of pembrolizumab in leptomeningeal carcinomatosis. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.2007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | - Andrew Navia
- Massachusetts Institute of Technology, Cambridge, MA
| | | | | | | | | | | | - Donald P. Lawrence
- Massachusetts General Hospital and Dana-Farber Cancer Institute, Boston, MA
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18
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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19
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1156] [Impact Index Per Article: 165.1] [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: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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Paolella B, Bandopadhayay P, Bergthold G, Shalek A, Pelton K, Ramkissoon S, Sinai C, Malkin H, Herbert Z, Sun Y, Alberta J, Brown M, Daley J, Lazo-Kallanian S, Goumnerova L, Kieran M, Ligon K, Beroukhim R. LGG-05. SINGLE-CELL RNA SEQUENCING OF PEDIATRIC LOW-GRADE GLIOMAS REVEALS INTRATUMORAL HETEROGENEITY. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Izar B, Stover E, Tirosh I, Rotem A, Shah P, Rodman C, Prakadan S, Wadsworth M, Su MJ, Leeson R, Palakurthi S, Liu J, Matulonis U, Shalek A, Rozenblatt-Rosen O, Regev A, Garraway L. Abstract AP19: SINGLE–CELL RNA–SEQUENCING OF PATIENT–DERIVED OVARIAN CANCER CELLS AND PATIENT–DERIVED XENOGRAFT MODELS. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.ovcasymp16-ap19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND AND PURPOSE: Genetic heterogeneity is a hallmark of ovarian cancer (OvCa) biology and underlies treatment resistance. Macroscopic and or treatment resistant microscopic residual disease (MRD) after debulking surgery and chemotherapy are the source for disease recurrence and death in these patients. Current profiling methods are unable adequately reflect heterogeneity, and transcriptional programs associated with treatment resistance and MRD remain elusive. To elucidate transcriptional heterogeneity and potential mechanisms of drug-resistance, we isolated OvCa cells from patients with malignant ascites using flow-cytometry. We applied single-cell RNA-sequencing (sc-RNA-seq) to ascites-derived cells from patients with OvCa. We picked OvCa spheroids and profiled these separately. To investigate MRD, we used three PDX-models stably expressing mCherry, treated with carboplatin, and harvested tumor cells for sc-RNA-seq at three time points (pre-treatment, at time of MRD as determined by bio-luminescence imaging, and disease relapse).
SUMMARY OF RESULTS: We successfully sequenced 770 single-cell transcriptomes from 6 individuals with treatment-resistant OvCa, including 3 patients with sequential samples. We mapped the landscape of chromosomal aberrations by inferred large-scale copy number variations (CNVs) at a single-cell level. We observed significant inter-tumor heterogeneity and started to deconstruct the genomic architecture of individual patients. Using experimentally validated gene sets, we determined the cell cycle state of individual cells and identified transcriptional programs related to the cell cycle as significant bias in publically available bulk RNA-sequencing data. Principal component analysis revealed the expression of a stem-ness signature, including CD133, ALDH1A and AXL, in a sub-set of non-cycling cells. An important driver of transcriptional heterogeneity common to patients included in this study was the expression of gene sets related to inflammatory pathways, such as the NFkB and JAK/STAT pathways. Hierarchical clustering of 42 spheroid profiles identified four major clusters, including a highly “inflamed” phenotype. Therapeutic inhibition of the STAT pathway abrogated the capacity of spheroid formation on an ultra-low attachment surface, indicating its importance for metastasis. We have successfully isolated thousands of individual cells for single-cell profiling from PDX models treated with carboplatin. These cells were collected at three time points, including at the MRD stage. We have successfully sequenced 100 cells from this collection and were able to generate whole-transcriptome data comparable to that of freshly isolated patient cells and thousands of single cells are currently undergoing sequencing.
CONCLUSION: We have successfully applied single-cell RNA-sequencing to patient-derived ovarian cancer cells and PDX-models. Single-cell transcriptomes enabled inference of genomic information, genetic and transcriptional heterogeneity, cell cycle state, and programs related to stem-ness and inflammation, providing a unique and comprehensive perspective on ovarian cancer cell states. Ongoing profiling of carboplatin-resistant cells captured at the minimal residual disease stage in PDX-models will provide a unique opportunity to understand treatment resistance which ultimately leads to cancer recurrence.
Citation Format: Benjamin Izar, Elizabeth Stover, Itay Tirosh, Asaf Rotem, Parin Shah, Chris Rodman, Sanjay Prakadan, Marc Wadsworth, Mei-Ju Su, Rachel Leeson, Sangeetha Palakurthi, Joyce Liu, Ursula Matulonis, Alex Shalek, Orit Rozenblatt-Rosen, Aviv Regev, Levi Garraway. SINGLE–CELL RNA–SEQUENCING OF PATIENT–DERIVED OVARIAN CANCER CELLS AND PATIENT–DERIVED XENOGRAFT MODELS [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr AP19.
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Affiliation(s)
- Benjamin Izar
- 1Dana-Farber Cancer Institute, Boston, MA
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | - Elizabeth Stover
- 1Dana-Farber Cancer Institute, Boston, MA
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | | | - Asaf Rotem
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | - Parin Shah
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | - Mei-Ju Su
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | - Joyce Liu
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | - Aviv Regev
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Levi Garraway
- 1Dana-Farber Cancer Institute, Boston, MA
- 2Broad Institute of Harvard and MIT, Cambridge, MA
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Suarez-Farinas M, Devi K, Dannenfelser R, Izar B, Prakadan S, Zhu Q, Yoon C, Regev A, Garraway L, Shalek A, Troyansakaya O, Anandasabapathy N. 065 Highly conserved tissue immune signatures are co-opted in cancer. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Izar B, Tirsh I, Prakadan S, Wadsworth M, Treacy D, Trombetta J, Rotem A, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Jane-Valbuena J, Rozenblatt-Rosen O, Yoon C, Shalek A, Regev A, Garraway L. Abstract 4380: Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-sequencing. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4380] [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
Tumors are heterogeneous ecosystems composed of genetically and epigenetically distinct cancer cell populations embedded in an intricate tumor microenvironment. The complexity and cell-to-cell interactions within this system pose a tremendous therapeutic challenge and opportunity. Due to technical constraints, current profiling technologies only provide average signals that do not reflect this intrinsic genetic and phenotypic variability.
Here, we applied single-cell RNA-sequencing to examine 4,645 single cells isolated from 19 freshly procured melanomas, profiling malignant, immune and stromal cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, stem-like cells, spatial context, and a drug treatment resistance program. All tumors harbored malignant cells from two distinct transcriptional cell states, such that treatment-sensitive “MITF-high” tumors also contained drug-resistant “AXL-high” tumor cells; similar heterogeneity was present in 18 established melanoma cell lines. The frequency of AXL-high cells increased in post-relapse resistant tumors following treatment with BRAF/MEK inhibitors. Using multiplexed, quantitative single-cell immunofluorescence analysis and FACS, we validated these observations in melanoma cell lines treated with BRAF±MEK inhibitors. Signatures of cell types identified from single-cell analysis revealed distinct patterns of the tumor microenvironment. We inferred cell-to-cell interactions between stromal, immune and malignant cells, and identified factors, including known secreted gene products (e.g. CXCL12) and several complement factors. We validated the association between cancer-associated fibroblast (CAF)-expressed complement factor 3 (C3) and TIL infiltration in an independent set of 308 melanomas. Finally, analysis of TILs revealed T-cell activation dependent and independent exhaustion programs that varied among patients dependent on their exposure to treatment with immune checkpoint-inhibitors. In addition to co-expression of several known co-inhibitory receptors, including PD1, CTLA-4, and TIM-3, we identified common markers associated with cytotoxicity-independent T-cell exhaustion across patients. To identify potential T-cell clones, we classified single T-cells by their isoforms of the V and J segments of the alpha and beta TCR chains, allowing us to identify expanded T-cell clones. We found that clonally expanded T-cells expressed a strong exhaustion program, while non-expanded T-cells lacked this phenotype.
This study represents the most comprehensive single-cell genomics analysis in humans to date and begins to unravel the cellular ecosystem of tumors. Single-cell genomics offer new insights with implications for both targeted and immune therapies by simultaneously profiling numerous aspects of a tumor with a single assay.
Citation Format: Benjamin Izar, Itay Tirsh, Sanjay Prakadan, Marc Wadsworth, Daniel Treacy, John Trombetta, Asaf Rotem, Christine Lian, George Murphy, Mohammad Fallahi-Sichani, Ken Dutton-Regester, Jia-Ren Lin, Judit Jane-Valbuena, Orit Rozenblatt-Rosen, Charles Yoon, Alex Shalek, Aviv Regev, Levi Garraway. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4380.
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Affiliation(s)
- Benjamin Izar
- 1Dana-Farber Cancer Institute, Broad Institute of Harvard and MIT, Boston, MA
| | - Itay Tirsh
- 2Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | | | - Asaf Rotem
- 1Dana-Farber Cancer Institute, Broad Institute of Harvard and MIT, Boston, MA
| | | | | | | | | | | | | | | | | | - Alex Shalek
- 7MIT, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Aviv Regev
- 7MIT, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Levi Garraway
- 1Dana-Farber Cancer Institute, Broad Institute of Harvard and MIT, Boston, MA
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24
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Izar B, Tirosh I, Prakadan S, Wadsworth M, Rotem A, Trombetta J, Shah P, Dutton-Regester K, Fallahi M, Ren-Lin J, Murphy G, Lian C, Sorger P, Bertagnolli MM, Rozenblatt-Rosen O, Yoon CH, Shalek A, Regev A, Garraway LA. Implementation of single-cell genomics as a translational tool in patients with metastatic melanoma. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.11503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Asaf Rotem
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Parin Shah
- Dana-Farber Cancer Institute, Boston, MA
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Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D. Oct1 and OCA-B are selectively required for CD4 memory T cell function. J Biophys Biochem Cytol 2015. [DOI: 10.1083/jcb.2112oia234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D. Oct1 and OCA-B are selectively required for CD4 memory T cell function. J Exp Med 2015; 212:2115-31. [PMID: 26481684 PMCID: PMC4647264 DOI: 10.1084/jem.20150363] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/25/2015] [Indexed: 12/31/2022] Open
Abstract
Shakya et al. identify the transcription factor Oct1 and its cofactor OCA-B as central mediators for generating memory T cell responses in mice. Epigenetic changes are crucial for the generation of immunological memory. Failure to generate or maintain these changes will result in poor memory responses. Similarly, augmenting or stabilizing the correct epigenetic states offers a potential method of enhancing memory. Yet the transcription factors that regulate these processes are poorly defined. We find that the transcription factor Oct1 and its cofactor OCA-B are selectively required for the in vivo generation of CD4+ memory T cells. More importantly, the memory cells that are formed do not respond properly to antigen reencounter. In vitro, both proteins are required to maintain a poised state at the Il2 target locus in resting but previously stimulated CD4+ T cells. OCA-B is also required for the robust reexpression of multiple other genes including Ifng. ChIPseq identifies ∼50 differentially expressed direct Oct1 and OCA-B targets. We identify an underlying mechanism involving OCA-B recruitment of the histone lysine demethylase Jmjd1a to targets such as Il2, Ifng, and Zbtb32. The findings pinpoint Oct1 and OCA-B as central mediators of CD4+ T cell memory.
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Affiliation(s)
- Arvind Shakya
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Alon Goren
- Broad Technology Labs, The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Alex Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 Department of Physics, Harvard University, Cambridge, MA 02138 The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Cody N German
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Jeremy Snook
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Vijay K Kuchroo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Nir Yosef
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Raymond C Chan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Aviv Regev
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Matthew A Williams
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
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Lamothe P, Ranasinghe S, Crawford F, White J, Clayton G, Power K, Garcia-Beltran W, Allen T, Shalek A, Kappler J, Walker B. Characterizing the T cell receptor clonotype repertoire of an atypical HLA class II-restricted CD8 T cell response in HIV-1 infection (VIR6P.1170). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.149.10] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
CD8 T cells targeting peptides presented by human leukocyte antigen (HLA) class II are atypical. Little is known about how the CD8 T cell receptor (TCR) recognizes peptides on HLA class II. We analyzed the TCR repertoire of a class II-restricted CD8 T cells targeting a HIV peptide. We identified an atypical HIV-specific CD8 response to DV16 peptide on HLA-DRB1*11. We sequenced the TCR of the class II-tetramer sorted cells. To measure the binding kinetics of the TCR with the peptide-MHC we used surface plasmon resonance (SPR). Analysis of 68 sequences showed that TCR-beta repertoire has a single TRBV2*01 clonotype. We looked at 64 sequences of TCRalpha and found that the repertoire had two clonotypes: TRAV26-1*02 and TRAV6*02. SPR revealed that only the TRAV6 was able to bind to the peptide-MHC. We studied 27 sequences of the CD4 T cells targeting the same MHC class II-peptide. We observed a polyclonal response of 16 clonotypes. 13 clonotypes used the same TRBV2*01 gene but had different rearrangements. Interestingly, two of these sequences are exactly the same as the dominant clonotype from the CD8 response. We found that the TCR is shared between CD8 and CD4 T cells targeting the same class II HLA-peptide. These data suggest that atypical CD8 cells express two different TCR alpha, possibly due to inefficient allelic exclusion during development. The use of the same TRBV2*01 by different CD4 clonotypes may suggest an atypical docking of TCR in the binding with peptide-HLA.
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Affiliation(s)
- Pedro Lamothe
- 1Ragon Inst. of MGH, MIT and Harvard, Cambridge, MA
- 2Biological Sciences in Public Health, Harvard Univ., Boston, MA
| | | | | | | | | | - Karen Power
- 1Ragon Inst. of MGH, MIT and Harvard, Cambridge, MA
| | | | - Todd Allen
- 1Ragon Inst. of MGH, MIT and Harvard, Cambridge, MA
| | - Alex Shalek
- 1Ragon Inst. of MGH, MIT and Harvard, Cambridge, MA
- 3MIT, Cambridge, MA
| | - John Kappler
- 4National Jewish Health, Denver, CO
- 5Howard Hughes Med. Inst., Cambridge, MA
| | - Bruce Walker
- 1Ragon Inst. of MGH, MIT and Harvard, Cambridge, MA
- 5Howard Hughes Med. Inst., Cambridge, MA
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