1
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Ualiyeva S, Lemire E, Wong C, Perniss A, Boyd AA, Avilés EC, Minichetti DG, Maxfield A, Roditi R, Matsumoto I, Wang X, Deng W, Barrett NA, Buchheit KM, Laidlaw TM, Boyce JA, Bankova LG, Haber AL. A nasal cell atlas reveals heterogeneity of tuft cells and their role in directing olfactory stem cell proliferation. Sci Immunol 2024; 9:eabq4341. [PMID: 38306414 DOI: 10.1126/sciimmunol.abq4341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/08/2023] [Indexed: 02/04/2024]
Abstract
The olfactory neuroepithelium serves as a sensory organ for odors and forms part of the nasal mucosal barrier. Olfactory sensory neurons are surrounded and supported by epithelial cells. Among them, microvillous cells (MVCs) are strategically positioned at the apical surface, but their specific functions are enigmatic, and their relationship to the other specialized epithelial cells is unclear. Here, we establish that the family of MVCs comprises tuft cells and ionocytes in both mice and humans. Integrating analysis of the respiratory and olfactory epithelia, we define the distinct receptor expression of TRPM5+ tuft-MVCs compared with Gɑ-gustducinhigh respiratory tuft cells and characterize a previously undescribed population of glandular DCLK1+ tuft cells. To establish how allergen sensing by tuft-MVCs might direct olfactory mucosal responses, we used an integrated single-cell transcriptional and protein analysis. Inhalation of Alternaria induced mucosal epithelial effector molecules including Chil4 and a distinct pathway leading to proliferation of the quiescent olfactory horizontal basal stem cell (HBC) pool, both triggered in the absence of olfactory apoptosis. Alternaria- and ATP-elicited HBC proliferation was dependent on TRPM5+ tuft-MVCs, identifying these specialized epithelial cells as regulators of olfactory stem cell responses. Together, our data provide high-resolution characterization of nasal tuft cell heterogeneity and identify a function of TRPM5+ tuft-MVCs in directing the olfactory mucosal response to allergens.
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Affiliation(s)
- Saltanat Ualiyeva
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Evan Lemire
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caitlin Wong
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexander Perniss
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Amelia A Boyd
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Evelyn C Avilés
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Dante G Minichetti
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alice Maxfield
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women's Hospital and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Rachel Roditi
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women's Hospital and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | | | - Xin Wang
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wenjiang Deng
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nora A Barrett
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kathleen M Buchheit
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Tanya M Laidlaw
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joshua A Boyce
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lora G Bankova
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Adam L Haber
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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2
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Yuan F, Gasser GN, Lemire E, Montoro DT, Jagadeesh K, Zhang Y, Duan Y, Ievlev V, Wells KL, Rotti PG, Shahin W, Winter M, Rosen BH, Evans I, Cai Q, Yu M, Walsh SA, Acevedo MR, Pandya DN, Akurathi V, Dick DW, Wadas TJ, Joo NS, Wine JJ, Birket S, Fernandez CM, Leung HM, Tearney GJ, Verkman AS, Haggie PM, Scott K, Bartels D, Meyerholz DK, Rowe SM, Liu X, Yan Z, Haber AL, Sun X, Engelhardt JF. Transgenic ferret models define pulmonary ionocyte diversity and function. Nature 2023; 621:857-867. [PMID: 37730992 PMCID: PMC10533402 DOI: 10.1038/s41586-023-06549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 08/17/2023] [Indexed: 09/22/2023]
Abstract
Speciation leads to adaptive changes in organ cellular physiology and creates challenges for studying rare cell-type functions that diverge between humans and mice. Rare cystic fibrosis transmembrane conductance regulator (CFTR)-rich pulmonary ionocytes exist throughout the cartilaginous airways of humans1,2, but limited presence and divergent biology in the proximal trachea of mice has prevented the use of traditional transgenic models to elucidate ionocyte functions in the airway. Here we describe the creation and use of conditional genetic ferret models to dissect pulmonary ionocyte biology and function by enabling ionocyte lineage tracing (FOXI1-CreERT2::ROSA-TG), ionocyte ablation (FOXI1-KO) and ionocyte-specific deletion of CFTR (FOXI1-CreERT2::CFTRL/L). By comparing these models with cystic fibrosis ferrets3,4, we demonstrate that ionocytes control airway surface liquid absorption, secretion, pH and mucus viscosity-leading to reduced airway surface liquid volume and impaired mucociliary clearance in cystic fibrosis, FOXI1-KO and FOXI1-CreERT2::CFTRL/L ferrets. These processes are regulated by CFTR-dependent ionocyte transport of Cl- and HCO3-. Single-cell transcriptomics and in vivo lineage tracing revealed three subtypes of pulmonary ionocytes and a FOXI1-lineage common rare cell progenitor for ionocytes, tuft cells and neuroendocrine cells during airway development. Thus, rare pulmonary ionocytes perform critical CFTR-dependent functions in the proximal airway that are hallmark features of cystic fibrosis airway disease. These studies provide a road map for using conditional genetics in the first non-rodent mammal to address gene function, cell biology and disease processes that have greater evolutionary conservation between humans and ferrets.
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Affiliation(s)
- Feng Yuan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Grace N Gasser
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Evan Lemire
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Yan Zhang
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yifan Duan
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Vitaly Ievlev
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kristen L Wells
- Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Pavana G Rotti
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Weam Shahin
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael Winter
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Bradley H Rosen
- Division of Pulmonary, Critical Care, Occupational, and Sleep Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Idil Evans
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Qian Cai
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Miao Yu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Susan A Walsh
- Department of Radiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael R Acevedo
- Department of Radiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Darpan N Pandya
- Department of Radiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Vamsidhar Akurathi
- Department of Radiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - David W Dick
- Department of Radiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Thaddeus J Wadas
- Department of Radiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nam Soo Joo
- Cystic Fibrosis Research Laboratory, Department of Psychology, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey J Wine
- Cystic Fibrosis Research Laboratory, Department of Psychology, Stanford University, Stanford, CA, USA
| | - Susan Birket
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Courtney M Fernandez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hui Min Leung
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alan S Verkman
- Department of Medicine, UCSF, San Francisco, CA, USA
- Department of Physiology, UCSF, San Francisco, CA, USA
| | - Peter M Haggie
- Department of Medicine, UCSF, San Francisco, CA, USA
- Department of Physiology, UCSF, San Francisco, CA, USA
| | - Kathleen Scott
- Office of Animal Resources, University of Iowa, Iowa City, IA, USA
| | - Douglas Bartels
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | | | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xiaoming Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Adam L Haber
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Xingshen Sun
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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3
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Kwok SJJ, Montoro DT, Haber AL, Yun SH, Vinarsky V. Single-cell transcriptomics of a dynamic cell behavior in murine airways. eLife 2023; 12:76645. [PMID: 37083555 PMCID: PMC10174686 DOI: 10.7554/elife.76645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/20/2023] [Indexed: 04/22/2023] Open
Abstract
Despite advances in high-dimensional cellular analysis, the molecular profiling of dynamic behaviors of cells in their native environment remains a major challenge. We present a method that allows us to couple physiological behaviors of cells in an intact murine tissue to deep molecular profiling of individual cells. This method enabled us to establish a novel molecular signature for a striking migratory cellular behavior following injury in murine airways.
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Affiliation(s)
| | | | | | - Seok-Hyun Yun
- Wellman Center for Photomedicine, Harvard Medical School, Cambridge, United States
| | - Vladimir Vinarsky
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States
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4
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Samuels EA, Taylor RA, Pendyal A, Shojaee A, Mainardi AS, Lemire ER, Venkatesh AK, Bernstein SL, Haber AL. Mapping emergency department asthma visits to identify poor-quality housing in New Haven, CT, USA: a retrospective cohort study. Lancet Public Health 2022; 7:e694-e704. [PMID: 35907420 PMCID: PMC9387147 DOI: 10.1016/s2468-2667(22)00143-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Housing conditions are a key driver of asthma incidence and severity. Previous studies have shown increased emergency department visits for asthma among residents living in poor-quality housing. Interventions to improve housing conditions have been shown to reduce emergency department visits for asthma, but identification and remediation of poor housing conditions is often delayed or does not occur. This study evaluates whether emergency department visits for asthma can be used to identify poor-quality housing to support proactive and early intervention. METHODS We conducted a retrospective cohort study of children and adults living in and around New Haven, CT, USA, who were seen for asthma in an urban, tertiary emergency department between March 1, 2013, and Aug 31, 2017. We geocoded and mapped patient addresses to city parcels, and calculated a composite estimate of the incidence of emergency department use for asthma for each parcel (Nv × Np/log2[P], where Nv is the estimated mean number of visits per patient, Np is the number of patients, and P is the estimated population). To determine whether parcel-level emergency department use for asthma was associated with public housing inspection scores, we used regression analyses, adjusting for neighbourhood-level and individual-level factors contributing to emergency department use for asthma. Public housing complex inspection scores were obtained from standardised home inspections, which are conducted every 1-3 years for publicly funded housing. We used a sliding-window approach to estimate how far in advance of a failed inspection the model could identify elevated use of emergency departments for asthma, using the city-wide 90th percentile as a cutoff for elevated incidence. FINDINGS 11 429 asthma-related emergency department visits from 6366 unique patients were included in the analysis. Mean patient age was 32·4 years (SD 12·8); 3836 (60·3%) patients were female, 2530 (39·7%) were male, 3461 (57·2%) were Medicaid-insured, and 2651 (41·6%) were Black. Incidence of emergency department use for asthma was strongly correlated with lower housing inspection scores (Pearson's r=-0·55 [95% CI -0·70 to -0·35], p=3·5 × 10-6), and this correlation persisted after adjustment for patient-level and neighbourhood-level demographics using a linear regression model (r=-0·54 [-0·69 to -0·33], p=7·1 × 10-6) and non-linear regression model (r=-0·44 [-0·62 to -0·21], p=3·8 × 10-4). Elevated asthma incidence rates were typically detected around a year before a housing complex failed a housing inspection. INTERPRETATION Emergency department visits for asthma are an early indicator of failed housing inspections. This approach represents a novel method for the early identification of poor housing conditions and could help to reduce asthma-related morbidity and mortality. FUNDING Harvard-National Institute of Environmental Health Sciences (NIEHS) Center for Environmental Health.
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Affiliation(s)
- Elizabeth A Samuels
- Department of Emergency Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | | | - Akshay Pendyal
- Novant Health Heart and Vascular Institute, Presbyterian Medical Center, Charlotte, NC, USA
| | - Abbas Shojaee
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Anne S Mainardi
- Department of Medicine, University of Tennessee Health Sciences Center, College of Medicine Chattanooga, Chattanooga, TN, USA
| | - Evan R Lemire
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Arjun K Venkatesh
- Department of Emergency Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Steven L Bernstein
- Emergency Medicine, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Adam L Haber
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, USA.
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5
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Ualiyeva S, Lemire E, Aviles EC, Wong C, Boyd AA, Lai J, Liu T, Matsumoto I, Barrett NA, Boyce JA, Haber AL, Bankova LG. Tuft cell-produced cysteinyl leukotrienes and IL-25 synergistically initiate lung type 2 inflammation. Sci Immunol 2021; 6:eabj0474. [PMID: 34932383 DOI: 10.1126/sciimmunol.abj0474] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Saltanat Ualiyeva
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Evan Lemire
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Evelyn C Aviles
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Caitlin Wong
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Amelia A Boyd
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Juying Lai
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Tao Liu
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Nora A Barrett
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joshua A Boyce
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Adam L Haber
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Lora G Bankova
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
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6
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Mou H, Yang Y, Riehs MA, Barrios J, Shivaraju M, Haber AL, Montoro DT, Gilmore K, Haas EA, Paunovic B, Rajagopal J, Vargas SO, Haynes RL, Fine A, Cardoso WV, Ai X. Airway basal stem cells generate distinct subpopulations of PNECs. Cell Rep 2021; 35:109011. [PMID: 33882306 PMCID: PMC8140387 DOI: 10.1016/j.celrep.2021.109011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/19/2019] [Revised: 11/04/2020] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Pulmonary neuroendocrine cells (PNECs) have crucial roles in airway physiology and immunity by producing bioactive amines and neuropeptides (NPs). A variety of human diseases exhibit PNEC hyperplasia. Given accumulated evidence that PNECs represent a heterogenous population of cells, we investigate how PNECs differ, whether the heterogeneity is similarly present in mouse and human cells, and whether specific disease involves discrete PNECs. Herein, we identify three distinct types of PNECs in human and mouse airways based on single and double positivity for TUBB3 and the established NP markers. We show that the three PNEC types exhibit significant differences in NP expression, homeostatic turnover, and response to injury and disease. We provide evidence that these differences parallel their distinct cell of origin from basal stem cells (BSCs) or other airway epithelial progenitors.
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Affiliation(s)
- Hongmei Mou
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Boston, MA 02114, USA.
| | - Ying Yang
- Columbia Center for Human Development and Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Molly A Riehs
- Department of Pathology, Boston Children's Hospital, MA 02115, USA
| | - Juliana Barrios
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Manjunatha Shivaraju
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam L Haber
- Computational Biology and Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Daniel T Montoro
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kimberly Gilmore
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elisabeth A Haas
- Department of Research, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Brankica Paunovic
- San Diego County Office of the Medical Examiner, San Diego, CA 92123, USA
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, MA 02115, USA
| | - Robin L Haynes
- Department of Pathology, Boston Children's Hospital, MA 02115, USA
| | - Alan Fine
- Pulmonary Division, Boston University School of Medicine, Boston, MA 02118, USA
| | - Wellington V Cardoso
- Columbia Center for Human Development and Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Xingbin Ai
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA.
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7
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Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams TS, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo AS, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CG. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med 2021; 27:546-559. [PMID: 33654293 PMCID: PMC9469728 DOI: 10.1038/s41591-020-01227-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/23/2020] [Indexed: 02/01/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
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Affiliation(s)
- Christoph Muus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard, University, Cambridge, MA 02138
| | - Malte D. Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, , Neuherberg, Germany
| | - Gokcen Eraslan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lisa Sikkema
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Eeshit Dhaval Vaishnav
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Elizabeth Thu Duong
- University of California San Diego, Department of Pediatrics, Division of Respiratory Medicine
| | - Evgenij Fiskin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Elena Torlai Triglia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Peiwen Cai
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital,Boston, MA, USA; Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Sijia Chen
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Jian Shu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Adam L. Haber
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA. Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Hattie Chung
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel T. Montoro
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Taylor S. Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Samuel J. Allon
- Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Zaneta Andrusivova
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
| | - Ilias Angelidis
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Bassler
- Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | | | - Inbal Benhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Emelie Braun
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
| | - Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ
| | - Steven Callori
- Department of Medicine, Boston University School of Medicine; Bioinformatic Program, Boston University
| | - Mark Chaffin
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | - Evgeny Chichelnitskiy
- Institute of Transplant Immunology, Hannover Medical School, MHH, Carl-Neuberg Str. 1, 30625 Hannover, Germany, phone +40 511 532 9745; fax +40 511 532 8090; German Center for Infectious Diseases DZIF, TTU-IICH 07.801
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA, 92093
| | - Thomas M. Conlon
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael S. Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Anna S.E. Cuomo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Marie Deprez
- Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, 06560, France
| | - Grant Duclos
- Boston University School of Medicine, Boston, MA 02118, USA
| | | | - David S. Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Astrid Gillich
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Bruno Giotti
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Minzhe Guo
- Divisions of Pulmonary Biology; Perinatal Institute, Cincinnati Children's Hospital Medical Center
| | | | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Peng He
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Xiaomeng Hou
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Lijuan Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
| | - Yan Hu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Aurora, CO, USA 80045
| | - Alok Jaiswal
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lu Ji
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Theodoro S. Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Christin S. Kuo
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Ludvig Larsson
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
| | | | - Kyungtae Lim
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Monika Litviňuková
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Leif S. Ludwig
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Division of Hematology / Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Soeren Lukassen
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; Berlin Institute of Health (BIH), Center for Digital Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wendy Luo
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Elo Madissoon
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK; Wellcome Sanger Institute, Cellular Genetics Programme Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Kasidet Manakongtreecheep
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sylvie Leroy
- Université Côte d’Azur, Pulmonology Department, CHU Nice, NICE, France; Institut de Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Christoph H. Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ian M. Mbano
- Africa Health Research Institute,Durban, South Africa. School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of Kwazulu Natal, Durban, South Africa
| | - Alexi M. McAdams
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
| | - Ahmad N. Nabhan
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Sarah K. Nyquist
- Computational and Systems Biology, CSAIL, Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Lolita Penland
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Olivier B. Poirion
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Sergio Poli
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - CanCan Qi
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rachel Queen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Bioscience West Building, Newcastle upon Tyne NE1 3 BZ, UK
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA, United States.; Department of Cardiology, University Heart & Vascular Center, University of Hamburg, Hamburg, Germany
| | - Ivan Rosas
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Conor V. Shea
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Xingyi Shi
- Department of Medicine, Boston University School of Medicine; Bioinformatic Program, Boston University
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Rene V. Sit
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Kamil Slowikowski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Neal P. Smith
- Massachusetts General Hospital Center for Immunology and Inflammatory Diseases
| | - Alex Sountoulidis
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute
| | - Maximilian Strunz
- Comprehensive Pneumology Center (CPC) and Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Dawei Sun
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Carlos Talavera-López
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peng Tan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jessica Tantivit
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Nathan R. Tucker
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142; Masonic Medical Research Institute, Utica, NY, USA 13501
| | - Katherine A. Vernon
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marc H. Wadsworth
- Institute for Medical Engineering and Science, Department of Chemistry & Koch Institute for Integrative Cancer Research, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xiuting Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Ke Xu
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - William Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Carly G.K. Ziegler
- Harvard-MIT Health Sciences and Technology, Institute for Medical Engineering and Science, Koch Institute for Integrative Cancer Research, MIT; Broad Institute of MIT and Harvard; Ragon Institute of MGH, MIT and Harvard
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8
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Montoro DT, Haber AL, Rood JE, Regev A, Rajagopal J. A Synthesis Concerning Conservation and Divergence of Cell Types across Epithelia. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035733. [PMID: 32122885 DOI: 10.1101/cshperspect.a035733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Advances in single-cell RNA-seq (scRNA-seq) and computational analysis have enabled the systematic interrogation of the cellular composition of tissues. Combined with tools from developmental biology, cell biology, and genetics, these approaches are revealing fundamental aspects of tissue geometry and physiology, including the distribution, origins, and inferred functions of specialized cell types, and the dynamics of cellular turnover and differentiation. By comparing different tissues, such studies can delineate shared and specialized features of cell types and their lineage. Here, we compare two developmentally related murine epithelia, the airway and the small intestinal epithelia, which are both derived from the embryonic endodermal gut tube. We examine how airway and intestine generate and functionalize common archetypal cell types to fulfill similar shared physiologic functionalities. We point to cases in which similar cell types are repurposed to accommodate each tissue's unique physiologic role, and highlight tissue-specific cells whose specializations contribute to the distinct functional roles of each organ. We discuss how archetypal and unique cell types are incorporated within a cellular lineage, and how the regulation of the proportions of these cell types enables tissue-level organization to meet functional demands and maintain homeostasis.
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Affiliation(s)
- Daniel T Montoro
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Jennifer E Rood
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jayaraj Rajagopal
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Howard Hughes Medical Institute Faculty Scholar, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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9
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Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell 2020; 178:714-730.e22. [PMID: 31348891 DOI: 10.1016/j.cell.2019.06.029] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/25/2019] [Accepted: 06/18/2019] [Indexed: 11/29/2022]
Abstract
Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4+ enterocytes, microfold-like cells, and IL13RA2+IL11+ inflammatory fibroblasts, which we associate with resistance to anti-TNF treatment. Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs. Many UC risk genes are cell type specific and co-regulated within relatively few gene modules, suggesting convergence onto limited sets of cell types and pathways. Using this observation, we nominate and infer functions for specific risk genes across GWAS loci. Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways.
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Affiliation(s)
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Department of Molecular Biology, MGH, Boston, MA, USA
| | - Jose Ordovas-Montanes
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Keri M Sullivan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Daniel B Graham
- Department of Molecular Biology, MGH, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Rebecca H Herbst
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Elizabeth Andrews
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Gabriella Velonias
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | | | - Sanja Vickovic
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Junmei Yao
- Center for Computational and Integrative Biology, MGH, Boston, MA, USA
| | | | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, MGH, Boston, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | | | - Hailiang Huang
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Analytical and Translational Genetics Unit, MGH, Boston, MA, USA
| | | | - John J Garber
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Hamed Khalili
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - A Nicole Desch
- Broad Institute, Cambridge, MA, USA; Center for Computational and Integrative Biology, MGH, Boston, MA, USA
| | - Mark J Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Analytical and Translational Genetics Unit, MGH, Boston, MA, USA; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA.
| | - Alex K Shalek
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | - Ramnik J Xavier
- Department of Molecular Biology, MGH, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA; Center for Computational and Integrative Biology, MGH, Boston, MA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA.
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10
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Howitt MR, Cao YG, Gologorsky MB, Li JA, Haber AL, Biton M, Lang J, Michaud M, Regev A, Garrett WS. The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis. Immunohorizons 2020; 4:23-32. [PMID: 31980480 PMCID: PMC7197368 DOI: 10.4049/immunohorizons.1900099] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 01/06/2023] Open
Abstract
Tuft cells are an epithelial cell type critical for initiating type 2 immune responses to parasites and protozoa in the small intestine. To respond to these stimuli, intestinal tuft cells use taste chemosensory signaling pathways, but the role of taste receptors in type 2 immunity is poorly understood. In this study, we show that the taste receptor TAS1R3, which detects sweet and umami in the tongue, also regulates tuft cell responses in the distal small intestine. BALB/c mice, which have an inactive form of TAS1R3, as well as Tas1r3-deficient C57BL6/J mice both have severely impaired responses to tuft cell–inducing signals in the ileum, including the protozoa Tritrichomonas muris and succinate. In contrast, TAS1R3 is not required to mount an immune response to the helminth Heligmosomoides polygyrus, which infects the proximal small intestine. Examination of uninfected Tas1r3−/− mice revealed a modest reduction in the number of tuft cells in the proximal small intestine but a severe decrease in the distal small intestine at homeostasis. Together, these results suggest that TAS1R3 influences intestinal immunity by shaping the epithelial cell landscape at steady-state. ImmunoHorizons, 2020, 4: 23–32.
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Affiliation(s)
- Michael R Howitt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115; .,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Pathology, Stanford University, Stanford, CA 94305
| | - Y Grace Cao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | | | - Jessica A Li
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Adam L Haber
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Moshe Biton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jessica Lang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Monia Michaud
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142; and
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115; .,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115.,Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
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11
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Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ. Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1. J Immunol 2019; 203:1820-1829. [PMID: 31451676 PMCID: PMC6761021 DOI: 10.4049/jimmunol.1800419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
Abstract
The clear role of autophagy in human inflammatory diseases such as Crohn disease was first identified by genome-wide association studies and subsequently dissected in multiple mechanistic studies. ATG16L1 has been particularly well studied in knockout and hypomorph settings as well as models recapitulating the Crohn disease-associated T300A polymorphism. Interestingly, ATG16L1 has a single homolog, ATG16L2, which is independently implicated in diseases, including Crohn disease and systemic lupus erythematosus. However, the contribution of ATG16L2 to canonical autophagy pathways and other cellular functions is poorly understood. To better understand its role, we generated and analyzed the first, to our knowledge, ATG16L2 knockout mouse. Our results show that ATG16L1 and ATG16L2 contribute very distinctly to autophagy and cellular ontogeny in myeloid, lymphoid, and epithelial lineages. Dysregulation of any of these lineages could contribute to complex diseases like Crohn disease and systemic lupus erythematosus, highlighting the value of examining cell-specific effects. We also identify a novel genetic interaction between ATG16L2 and epithelial ATG16L1. These findings are discussed in the context of how these genes may contribute distinctly to human disease.
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Affiliation(s)
- Bernard Khor
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and.,Pathology Service, Massachusetts General Hospital, Boston, MA 02114
| | - Kara L Conway
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Abdifatah S Omar
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Moshe Biton
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Adam L Haber
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Noga Rogel
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leigh A Baxt
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jakob Begun
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Petric Kuballa
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - John D Gagnon
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kara G Lassen
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and
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12
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Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz ÖH. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell 2019; 178:1115-1131.e15. [PMID: 31442404 PMCID: PMC6732196 DOI: 10.1016/j.cell.2019.07.048] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/03/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023]
Abstract
Little is known about how metabolites couple tissue-specific stem cell function with physiology. Here we show that, in the mammalian small intestine, the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2), the gene encoding the rate-limiting enzyme in the production of ketone bodies, including beta-hydroxybutyrate (βOHB), distinguishes self-renewing Lgr5+ stem cells (ISCs) from differentiated cell types. Hmgcs2 loss depletes βOHB levels in Lgr5+ ISCs and skews their differentiation toward secretory cell fates, which can be rescued by exogenous βOHB and class I histone deacetylase (HDAC) inhibitor treatment. Mechanistically, βOHB acts by inhibiting HDACs to reinforce Notch signaling, instructing ISC self-renewal and lineage decisions. Notably, although a high-fat ketogenic diet elevates ISC function and post-injury regeneration through βOHB-mediated Notch signaling, a glucose-supplemented diet has the opposite effects. These findings reveal how control of βOHB-activated signaling in ISCs by diet helps to fine-tune stem cell adaptation in homeostasis and injury.
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Affiliation(s)
- Chia-Wei Cheng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Moshe Biton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Adam L. Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Nuray Gunduz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey 06800
| | - George Eng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Liam T. Gaynor
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston MA, 02215, USA
| | - Surya Tripathi
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Gizem Calibasi-Kocal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Vincent L. Butty
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Marta Moreno
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Ameena M Iqbal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | | | - Shinya Imada
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University,1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Mehmet Sefa Ulutas
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, Siirt University, Science and Arts Faculty, 56100 Siirt, Turkey
| | | | - Mark T. Whary
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Stuart S. Levine
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Yasemin Basbinar
- Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Richard O. Hynes
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Laurie A. Boyer
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - James G. Fox
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Christopher Terranova
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kunal Rai
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria M. Mihaylova
- The Ohio State Comprehensive Cancer Center, Department of Biological Chemistry and Pharmacology, Ohio State University, 308 Wiseman Hall, Columbus, OH 43210, USA
| | - Aviv Regev
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Ömer H. Yilmaz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, MIT, Cambridge, Massachusetts 02139, USA,Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,Lead Contact,Correspondence: Ömer H. Yilmaz () (Ö.H.Y)
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13
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Myers SA, Rhoads A, Cocco AR, Peckner R, Haber AL, Schweitzer LD, Krug K, Mani DR, Clauser KR, Rozenblatt-Rosen O, Hacohen N, Regev A, Carr SA. Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells. Mol Cell Proteomics 2019; 18:995-1009. [PMID: 30792265 DOI: 10.1074/mcp.ra118.001259] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [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: 12/04/2018] [Revised: 02/15/2019] [Indexed: 12/27/2022] Open
Abstract
Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact the appropriate responses to extracellular queues. Transcriptional profiling has proven invaluable to our understanding of cellular responses; however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein levels in steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited and widely used analytical tool for studying global protein abundances. Typical proteomic workflows are often limited by the amount of sample input that is required for deep and quantitative proteome profiling. This is especially true if the cells of interest need to be purified by fluorescence-activated cell sorting (FACS) and one wants to avoid ex vivo culturing. To address this need, we developed an easy to implement, streamlined workflow that enables quantitative proteome profiling from roughly 2 μg of protein input per experimental condition. Utilizing a combination of facile cell collection from cell sorting, solid-state isobaric labeling and multiplexing of peptides, and small-scale fractionation, we profiled the proteomes of 12 freshly isolated, primary murine immune cell types. Analyzing half of the 3e5 cells collected per cell type, we quantified over 7000 proteins across 12 key immune cell populations directly from their resident tissues. We show that low input proteomics is precise, and the data generated accurately reflects many aspects of known immunology, while expanding the list of cell-type specific proteins across the cell types profiled. The low input proteomics methods we developed are readily adaptable and broadly applicable to any cell or sample types and should enable proteome profiling in systems previously unattainable.
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Affiliation(s)
- Samuel A Myers
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;.
| | - Andrew Rhoads
- ¶Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Alexandra R Cocco
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Ryan Peckner
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Adam L Haber
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - Karsten Krug
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - D R Mani
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Karl R Clauser
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Orit Rozenblatt-Rosen
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Nir Hacohen
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; ‖Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;; **Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Aviv Regev
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;; ‡‡Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140
| | - Steven A Carr
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;.
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14
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Adiconis X, Haber AL, Simmons SK, Moonshine AL, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ. Author Correction: Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Nat Methods 2018; 15:1126. [PMID: 30459407 DOI: 10.1038/s41592-018-0237-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The original version of this paper contained an incorrect primer sequence. In the Methods subsection "Rampage libraries," the text for modification 3 stated that the reverse primer used for library indexing was 5'-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGT-3'. The correct sequence of the oligonucleotide used is 5'-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'. This error has been corrected in the PDF and HTML versions of the paper.
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Affiliation(s)
- Xian Adiconis
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Zhe Ji
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Xi Shi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Justin Jacques
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The David H. Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joshua Z Levin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell 2018; 175:1307-1320.e22. [PMID: 30392957 DOI: 10.1016/j.cell.2018.10.008] [Citation(s) in RCA: 324] [Impact Index Per Article: 54.0] [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: 03/22/2018] [Revised: 07/13/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
Abstract
In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5+ ISCs. We show that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5+ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5+ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5+ ISCs, thus, orchestrate tissue-wide responses to external signals.
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Affiliation(s)
- Moshe Biton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Semir Beyaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Chien-Wen Su
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zuojia Chen
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chuan Wu
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jose Ordovas-Montanes
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - David Alvarez
- Department of Microbiology & Immunobiology and Center for Immune Imaging, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca H Herbst
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA
| | - Mei Zhang
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Itay Tirosh
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lan T Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Michael E Xifaras
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Alex K Shalek
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - Ulrich H von Andrian
- Department of Microbiology & Immunobiology and Center for Immune Imaging, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel B Graham
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hai Ning Shi
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Vijay Kuchroo
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Omer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.
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16
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Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 2018; 560:319-324. [PMID: 30069044 PMCID: PMC6295155 DOI: 10.1038/s41586-018-0393-7] [Citation(s) in RCA: 684] [Impact Index Per Article: 114.0] [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: 07/31/2017] [Accepted: 06/21/2018] [Indexed: 12/16/2022]
Abstract
The airways of the lung are the primary sites of disease in asthma and cystic fibrosis. Here we study the cellular composition and hierarchy of the mouse tracheal epithelium by single-cell RNA-sequencing (scRNA-seq) and in vivo lineage tracing. We identify a rare cell type, the Foxi1+ pulmonary ionocyte; functional variations in club cells based on their location; a distinct cell type in high turnover squamous epithelial structures that we term 'hillocks'; and disease-relevant subsets of tuft and goblet cells. We developed 'pulse-seq', combining scRNA-seq and lineage tracing, to show that tuft, neuroendocrine and ionocyte cells are continually and directly replenished by basal progenitor cells. Ionocytes are the major source of transcripts of the cystic fibrosis transmembrane conductance regulator in both mouse (Cftr) and human (CFTR). Knockout of Foxi1 in mouse ionocytes causes loss of Cftr expression and disrupts airway fluid and mucus physiology, phenotypes that are characteristic of cystic fibrosis. By associating cell-type-specific expression programs with key disease genes, we establish a new cellular narrative for airways disease.
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Affiliation(s)
- Daniel T Montoro
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Vladimir Vinarsky
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Susan E Birket
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL, USA
| | - Feng Yuan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sijia Chen
- Department of Experimental Immunology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - Hui Min Leung
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jorge Villoria
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Purushothama Rao Tata
- Department of Cell Biology, Duke University, Durham, NC, USA
- Duke Cancer Institute, Duke University, Durham, NC, USA
- Division of Pulmonary Critical Care, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Regeneration Next, Duke University, Durham, NC, USA
| | - Hongmei Mou
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Manjunatha Shivaraju
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Hermann Bihler
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Martin Mense
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Guillermo J Tearney
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL, USA
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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Fung PK, Haber AL, Robinson PA. Neural field theory of plasticity in the cerebral cortex. J Theor Biol 2012; 318:44-57. [PMID: 23036915 DOI: 10.1016/j.jtbi.2012.09.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 08/20/2012] [Accepted: 09/21/2012] [Indexed: 11/25/2022]
Abstract
A generalized timing-dependent plasticity rule is incorporated into a recent neural field theory to explore synaptic plasticity in the cerebral cortex, with both excitatory and inhibitory populations included. Analysis in the time and frequency domains reveals that cortical network behavior gives rise to a saddle-node bifurcation and resonant frequencies, including a gamma-band resonance. These system resonances constrain cortical synaptic dynamics and divide it into four classes, which depend on the type of synaptic plasticity window. Depending on the dynamical class, synaptic strengths can either have a stable fixed point, or can diverge in the absence of a separate saturation mechanism. Parameter exploration shows that time-asymmetric plasticity windows, which are signatures of spike-timing dependent plasticity, enable the richest variety of synaptic dynamics to occur. In particular, we predict a zone in parameter space which may allow brains to attain the marginal stability phenomena observed experimentally, although additional regulatory mechanisms may be required to maintain these parameters.
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Affiliation(s)
- P K Fung
- School of Physics, The University of Sydney, NSW 2006, Australia.
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18
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Haber AL, Griffiths KR, Jamting ÅK, Emslie KR. Addition of gold nanoparticles to real-time PCR: effect on PCR profile and SYBR Green I fluorescence. Anal Bioanal Chem 2008; 392:887-96. [DOI: 10.1007/s00216-008-2358-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 08/14/2008] [Accepted: 08/18/2008] [Indexed: 11/24/2022]
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