1
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Wu TTH, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner W, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. J Exp Med 2024; 221:e20232192. [PMID: 38597954 PMCID: PMC11009983 DOI: 10.1084/jem.20232192] [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: 11/28/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
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Affiliation(s)
- Timothy Ting-Hsuan Wu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yue Zhang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - SoRi Jang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanny J. Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aimee Beck
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron J. Wilk
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rob Bierman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B. Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christin S. Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
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2
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Liu S, Ezran C, Wang MFZ, Li Z, Awayan K, Long JZ, De Vlaminck I, Wang S, Epelbaum J, Kuo CS, Terrien J, Krasnow MA, Ferrell JE. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nat Commun 2024; 15:2188. [PMID: 38467625 PMCID: PMC10928088 DOI: 10.1038/s41467-024-46070-9] [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: 08/16/2022] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Hormones mediate long-range cell communication and play vital roles in physiology, metabolism, and health. Traditionally, endocrinologists have focused on one hormone or organ system at a time. Yet, hormone signaling by its very nature connects cells of different organs and involves crosstalk of different hormones. Here, we leverage the organism-wide single cell transcriptional atlas of a non-human primate, the mouse lemur (Microcebus murinus), to systematically map source and target cells for 84 classes of hormones. This work uncovers previously-uncharacterized sites of hormone regulation, and shows that the hormonal signaling network is densely connected, decentralized, and rich in feedback loops. Evolutionary comparisons of hormonal genes and their expression patterns show that mouse lemur better models human hormonal signaling than mouse, at both the genomic and transcriptomic levels, and reveal primate-specific rewiring of hormone-producing/target cells. This work complements the scale and resolution of classical endocrine studies and sheds light on primate hormone regulation.
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Affiliation(s)
- Shixuan Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Camille Ezran
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Michael F Z Wang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Zhengda Li
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle Awayan
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford, CA, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Sheng Wang
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Jacques Epelbaum
- Adaptive Mechanisms and Evolution (MECADEV), UMR 7179, National Center for Scientific Research, National Museum of Natural History, Brunoy, France
| | - Christin S Kuo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jérémy Terrien
- Adaptive Mechanisms and Evolution (MECADEV), UMR 7179, National Center for Scientific Research, National Museum of Natural History, Brunoy, France
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Angelakos CC, Girven KS, Liu Y, Gonzalez OC, Murphy KR, Jennings KJ, Giardino WJ, Zweifel LS, Suko A, Palmiter RD, Clark SD, Krasnow MA, Bruchas MR, de Lecea L. A cluster of neuropeptide S neurons regulates breathing and arousal. Curr Biol 2023; 33:5439-5455.e7. [PMID: 38056461 PMCID: PMC10842921 DOI: 10.1016/j.cub.2023.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/22/2023] [Revised: 08/31/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Neuropeptide S (NPS) is a highly conserved peptide found in all tetrapods that functions in the brain to promote heightened arousal; however, the subpopulations mediating these phenomena remain unknown. We generated mice expressing Cre recombinase from the Nps gene locus (NpsCre) and examined populations of NPS+ neurons in the lateral parabrachial area (LPBA), the peri-locus coeruleus (peri-LC) region of the pons, and the dorsomedial thalamus (DMT). We performed brain-wide mapping of input and output regions of NPS+ clusters and characterized expression patterns of the NPS receptor 1 (NPSR1). While the activity of all three NPS+ subpopulations tracked with vigilance state, only NPS+ neurons of the LPBA exhibited both increased activity prior to wakefulness and decreased activity during REM sleep, similar to the behavioral phenotype observed upon NPSR1 activation. Accordingly, we found that activation of the LPBA but not the peri-LC NPS+ neurons increased wake and reduced REM sleep. Furthermore, given the extended role of the LPBA in respiration and the link between behavioral arousal and breathing rate, we demonstrated that the LPBA but not the peri-LC NPS+ neuronal activation increased respiratory rate. Together, our data suggest that NPS+ neurons of the LPBA represent an unexplored subpopulation regulating breathing, and they are sufficient to recapitulate the sleep/wake phenotypes observed with broad NPS system activation.
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Affiliation(s)
- Christopher Caleb Angelakos
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Kasey S Girven
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington Center for the Neurobiology of Addiction, Pain, and Emotion, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Yin Liu
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oscar C Gonzalez
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Keith R Murphy
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Kim J Jennings
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - William J Giardino
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Larry S Zweifel
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Azra Suko
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington Center for the Neurobiology of Addiction, Pain, and Emotion, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Richard D Palmiter
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Stewart D Clark
- Department of Pharmacology and Toxicology, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Mark A Krasnow
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael R Bruchas
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington Center for the Neurobiology of Addiction, Pain, and Emotion, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA.
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4
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Abstract
Mammalian vocalizations are critical for communication and are produced through the process of phonation, in which expiratory muscles force air through the tensed vocal folds of the larynx, which vibrate to produce sound. Despite the importance of phonation, the motor circuits in the brain that control it remain poorly understood. In this study, we identified a subpopulation of ~160 neuropeptide precursor Nts (neurotensin)-expressing neurons in the mouse brainstem nucleus retroambiguus (RAm) that are robustly activated during both neonatal isolation cries and adult social vocalizations. The activity of these neurons is necessary and sufficient for vocalization and bidirectionally controls sound volume. RAm Nts neurons project to all brainstem and spinal cord motor centers involved in phonation and activate laryngeal and expiratory muscles essential for phonation and volume control. Thus, RAm Nts neurons form the core of a brain circuit for making sound and controlling its volume, which are two foundations of vocal communication.
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Affiliation(s)
- Avin Veerakumar
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua P Head
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Neurosciences Program, Stanford University, Stanford, CA, USA
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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5
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [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: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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6
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Savchuk S, Gentry K, Wang W, Carleton E, Yalçın B, Liu Y, Pavarino EC, LaBelle J, Toland AM, Woo PJ, Qu F, Filbin MG, Krasnow MA, Sabatini BL, Sage J, Monje M, Venkatesh HS. Neuronal-Activity Dependent Mechanisms of Small Cell Lung Cancer Progression. bioRxiv 2023:2023.01.19.524430. [PMID: 36711554 PMCID: PMC9882339 DOI: 10.1101/2023.01.19.524430] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Neural activity is increasingly recognized as a critical regulator of cancer growth. In the brain, neuronal activity robustly influences glioma growth both through paracrine mechanisms and through electrochemical integration of malignant cells into neural circuitry via neuron-to-glioma synapses, while perisynaptic neurotransmitter signaling drives breast cancer brain metastasis growth. Outside of the CNS, innervation of tumors such as prostate, breast, pancreatic and gastrointestinal cancers by peripheral nerves similarly regulates cancer progression. However, the extent to which the nervous system regulates lung cancer progression, either in the lung or when metastatic to brain, is largely unexplored. Small cell lung cancer (SCLC) is a lethal high-grade neuroendocrine tumor that exhibits a strong propensity to metastasize to the brain. Here we demonstrate that, similar to glioma, metastatic SCLC cells in the brain co-opt neuronal activity-regulated mechanisms to stimulate growth and progression. Optogenetic stimulation of cortical neuronal activity drives proliferation and invasion of SCLC brain metastases. In the brain, SCLC cells exhibit electrical currents and consequent calcium transients in response to neuronal activity, and direct SCLC cell membrane depolarization is sufficient to promote the growth of SCLC tumors. In the lung, vagus nerve transection markedly inhibits primary lung tumor formation, progression and metastasis, highlighting a critical role for innervation in overall SCLC initiation and progression. Taken together, these studies illustrate that neuronal activity plays a crucial role in dictating SCLC pathogenesis in both primary and metastatic sites.
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7
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Brownfield DG, de Arce AD, Ghelfi E, Gillich A, Desai TJ, Krasnow MA. Alveolar cell fate selection and lifelong maintenance of AT2 cells by FGF signaling. Nat Commun 2022; 13:7137. [PMID: 36414616 PMCID: PMC9681748 DOI: 10.1038/s41467-022-34059-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
Abstract
The lung's gas exchange surface is comprised of alveolar AT1 and AT2 cells that are corrupted in several common and deadly diseases. They arise from a bipotent progenitor whose differentiation is thought to be dictated by differential mechanical forces. Here we show the critical determinant is FGF signaling. Fgfr2 is expressed in the developing progenitors in mouse then restricts to nascent AT2 cells and remains on throughout life. Its ligands are expressed in surrounding mesenchyme and can, in the absence of exogenous mechanical cues, induce progenitors to form alveolospheres with intermingled AT2 and AT1 cells. FGF signaling directly and cell autonomously specifies AT2 fate; progenitors lacking Fgfr2 in vitro and in vivo exclusively acquire AT1 fate. Fgfr2 loss in AT2 cells perinatally results in reprogramming to AT1 identity, whereas loss or inhibition later in life triggers AT2 apoptosis and compensatory regeneration. We propose that Fgfr2 signaling selects AT2 fate during development, induces a cell non-autonomous AT1 differentiation signal, then continuously maintains AT2 identity and survival throughout life.
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Affiliation(s)
- Douglas G. Brownfield
- grid.168010.e0000000419368956Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307 USA ,grid.38142.3c000000041936754XMolecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66875.3a0000 0004 0459 167XPresent Address: Division of Pulmonary and Critical Care Medicine, Departments of Physiology and Biomedical Engineering and of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905 USA
| | - Alex Diaz de Arce
- grid.168010.e0000000419368956Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307 USA
| | - Elisa Ghelfi
- grid.38142.3c000000041936754XMolecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Astrid Gillich
- grid.168010.e0000000419368956Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307 USA
| | - Tushar J. Desai
- grid.168010.e0000000419368956Department of Internal Medicine and Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Mark A. Krasnow
- grid.168010.e0000000419368956Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307 USA
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8
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Veerakumar A, Yung AR, Liu Y, Krasnow MA. Molecularly defined circuits for cardiovascular and cardiopulmonary control. Nature 2022; 606:739-746. [PMID: 35650438 PMCID: PMC9297035 DOI: 10.1038/s41586-022-04760-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 07/12/2021] [Accepted: 04/13/2022] [Indexed: 01/29/2023]
Abstract
The sympathetic and parasympathetic nervous systems powerfully regulate internal organs1, but the molecular and functional diversity of their constituent neurons and circuits remains largely unknown. Here we use retrograde neuronal tracing, single-cell RNA sequencing, optogenetics, and physiological experiments to dissect the cardiac parasympathetic control circuit in mice. We show that cardiac-innervating neurons in the brainstem nucleus ambiguus (Amb) are comprised of two molecularly, anatomically, and functionally distinct subtypes. One we call ACV (ambiguus cardiovascular) neurons (~35 neurons per Amb), define the classical cardiac parasympathetic circuit. They selectively innervate a subset of cardiac parasympathetic ganglion neurons and mediate the baroreceptor reflex, slowing heart rate and atrioventricular node conduction in response to increased blood pressure. The other, ACP (ambiguus cardiopulmonary) neurons (~15 neurons per Amb) innervate cardiac ganglion neurons intermingled with and functionally indistinguishable from those innervated by ACV neurons, but surprisingly also innervate most or all lung parasympathetic ganglion neurons; clonal labeling shows individual ACP neurons innervate both organs. ACP neurons mediate the dive reflex, the simultaneous bradycardia and bronchoconstriction that follows water immersion. Thus, parasympathetic control of the heart is organized into two parallel circuits, one that selectively controls cardiac function (ACV circuit) and another that coordinates cardiac and pulmonary function (ACP circuit). This new understanding of cardiac control has implications for treating cardiac and pulmonary diseases and for elucidating the control and coordination circuits of other organs.
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Affiliation(s)
- Avin Veerakumar
- Department of Biochemistry, Wall Center for Pulmonary Vascular Disease, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrea R Yung
- Department of Biochemistry, Wall Center for Pulmonary Vascular Disease, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yin Liu
- Department of Biochemistry, Wall Center for Pulmonary Vascular Disease, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Krasnow
- Department of Biochemistry, Wall Center for Pulmonary Vascular Disease, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Gillich A, Brownfield DG, Travaglini KJ, Zhang F, Farmer CG, St. Julien KR, Tan SY, Gu M, Zhou B, Feinstein JA, Metzger RJ, Krasnow MA. Dissecting alveolar patterning and maintenance at single‐cell resolution. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.i7444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Astrid Gillich
- BiochemistryStanford University School of MedicineStanfordCA
- Howard Hughes Medical InstituteStanfordCA
| | - Douglas G. Brownfield
- BiochemistryStanford University School of MedicineStanfordCA
- Howard Hughes Medical InstituteStanfordCA
| | - Kyle J. Travaglini
- BiochemistryStanford University School of MedicineStanfordCA
- Howard Hughes Medical InstituteStanfordCA
| | - Fan Zhang
- Vera Moulton Wall Center for Pulmonary Vascular DiseaseStanford University School of MedicineStanfordCA
| | | | - Krystal R. St. Julien
- BiochemistryStanford University School of MedicineStanfordCA
- Howard Hughes Medical InstituteStanfordCA
| | - Serena Y. Tan
- PathologyStanford University School of MedicineStanfordCA
| | - Mingxia Gu
- PediatricsStanford University School of MedicineStanfordCA
| | - Bin Zhou
- Chinese Academy of SciencesShanghai
| | | | | | - Mark A. Krasnow
- BiochemistryStanford University School of MedicineStanfordCA
- Howard Hughes Medical InstituteStanfordCA
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10
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Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, Aaron KA, Concepcion W, Gardner JM, Kelly B, Neidlinger N, Wang Z, Crasta S, Kolluru S, Morri M, Pisco AO, Tan SY, Travaglini KJ, Xu C, Alcántara-Hernández M, Almanzar N, Antony J, Beyersdorf B, Burhan D, Calcuttawala K, Carter MM, Chan CKF, Chang CA, Chang S, Colville A, Crasta S, Culver RN, Cvijović I, D'Amato G, Ezran C, Galdos FX, Gillich A, Goodyer WR, Hang Y, Hayashi A, Houshdaran S, Huang X, Irwin JC, Jang S, Juanico JV, Kershner AM, Kim S, Kiss B, Kolluru S, Kong W, Kumar ME, Kuo AH, Leylek R, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Morri M, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Phansalkar R, Pisco AO, Puluca N, Qi Z, Rao P, Raquer-McKay H, Schaum N, Scott B, Seddighzadeh B, Segal J, Sen S, Sikandar S, Spencer SP, Steffes LC, Subramaniam VR, Swarup A, Swift M, Travaglini KJ, Van Treuren W, Trimm E, Veizades S, Vijayakumar S, Vo KC, Vorperian SK, Wang W, Weinstein HNW, Winkler J, Wu TTH, Xie J, Yung AR, Zhang Y, Detweiler AM, Mekonen H, Neff NF, Sit RV, Tan M, Yan J, Bean GR, Charu V, Forgó E, Martin BA, Ozawa MG, Silva O, Tan SY, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Detweiler AM, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, de Morree A, Olivieri JE, Park M, Pisco AO, Ravikumar N, Salzman J, Stanley G, Swift M, Tan M, Tan W, Tarashansky AJ, Vanheusden R, Vorperian SK, Wang P, Wang S, Xing G, Xu C, Yosef N, Alcántara-Hernández M, Antony J, Chan CKF, Chang CA, Colville A, Crasta S, Culver R, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Kershner AM, Kong W, Kumar ME, Kuo AH, Leylek R, Liu S, Loeb GB, Lu WJ, Maltzman JS, Metzger RJ, de Morree A, Neuhöfer P, Perez K, Phansalkar R, Qi Z, Rao P, Raquer-McKay H, Sasagawa K, Scott B, Sinha R, Song H, Spencer SP, Swarup A, Swift M, Travaglini KJ, Trimm E, Veizades S, Vijayakumar S, Wang B, Wang W, Winkler J, Xie J, Yung AR, Artandi SE, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Krasnow M, Kuo CS, Nguyen P, Quake SR, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wang B, Wu A, Wu SM, Wyss-Coray T. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science 2022; 376:eabl4896. [PMID: 35549404 PMCID: PMC9812260 DOI: 10.1126/science.abl4896] [Citation(s) in RCA: 225] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.
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11
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Kuo CS, Darmanis S, Diaz de Arce A, Liu Y, Almanzar N, Wu TTH, Quake SR, Krasnow MA. Neuroendocrinology of the lung revealed by single-cell RNA sequencing. eLife 2022; 11:78216. [PMID: 36469459 PMCID: PMC9721618 DOI: 10.7554/elife.78216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Pulmonary neuroendocrine cells (PNECs) are sensory epithelial cells that transmit airway status to the brain via sensory neurons and locally via calcitonin gene-related peptide (CGRP) and γ- aminobutyric acid (GABA). Several other neuropeptides and neurotransmitters have been detected in various species, but the number, targets, functions, and conservation of PNEC signals are largely unknown. We used scRNAseq to profile hundreds of the rare mouse and human PNECs. This revealed over 40 PNEC neuropeptide and peptide hormone genes, most cells expressing unique combinations of 5-18 genes. Peptides are packaged in separate vesicles, their release presumably regulated by the distinct, multimodal combinations of sensors we show are expressed by each PNEC. Expression of the peptide receptors predicts an array of local cell targets, and we show the new PNEC signal angiotensin directly activates one subtype of innervating sensory neuron. Many signals lack lung targets so may have endocrine activity like those of PNEC-derived carcinoid tumors. PNECs are an extraordinarily rich and diverse signaling hub rivaling the enteroendocrine system.
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Affiliation(s)
- Christin S Kuo
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States,Department of Biochemistry and Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Spyros Darmanis
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Alex Diaz de Arce
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Yin Liu
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Nicole Almanzar
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Timothy Ting-Hsuan Wu
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Stephen R Quake
- Department of Bioengineering, Stanford UniversityStanfordUnited States,Chan-Zuckerburg BiohubSan FranciscoUnited States
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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12
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Olivieri JE, Dehghannasiri R, Wang PL, Jang S, de Morree A, Tan SY, Ming J, Ruohao Wu A, Quake SR, Krasnow MA, Salzman J. RNA splicing programs define tissue compartments and cell types at single-cell resolution. eLife 2021; 10:e70692. [PMID: 34515025 PMCID: PMC8563012 DOI: 10.7554/elife.70692] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 05/26/2021] [Accepted: 09/10/2021] [Indexed: 02/05/2023] Open
Abstract
The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10X Chromium data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in SAT1. Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically.
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Affiliation(s)
- Julia Eve Olivieri
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Roozbeh Dehghannasiri
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Peter L Wang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - SoRi Jang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of MedicineStanfordUnited States
| | - Serena Y Tan
- Department of Pathology, Stanford University Medical CenterStanfordUnited States
| | - Jingsi Ming
- Academy for Statistics and Interdisciplinary Sciences, Faculty of Economics and Management,East China Normal UniversityShanghaiChina
- Department of Mathematics, The Hong Kong University of Science and TechnologyHong KongChina
| | - Angela Ruohao Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and TechnologyHong KongChina
| | - Stephen R Quake
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Mark A Krasnow
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
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13
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Rakotonanahary RJL, Andriambolamanana H, Razafinjato B, Raza-Fanomezanjanahary EM, Ramanandraitsiory V, Ralaivavikoa F, Tsirinomen'ny Aina A, Rahajatiana L, Rakotonirina L, Haruna J, Cordier LF, Murray MB, Cowley G, Jordan D, Krasnow MA, Wright PC, Gillespie TR, Docherty M, Loyd T, Evans MV, Drake JM, Ngonghala CN, Rich ML, Popper SJ, Miller AC, Ihantamalala FA, Randrianambinina A, Ramiandrisoa B, Rakotozafy E, Rasolofomanana A, Rakotozafy G, Andriamahatana Vololoniaina MC, Andriamihaja B, Garchitorena A, Rakotonirina J, Mayfield A, Finnegan KE, Bonds MH. Integrating Health Systems and Science to Respond to COVID-19 in a Model District of Rural Madagascar. Front Public Health 2021; 9:654299. [PMID: 34368043 PMCID: PMC8333873 DOI: 10.3389/fpubh.2021.654299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/31/2021] [Indexed: 11/17/2022] Open
Abstract
There are many outstanding questions about how to control the global COVID-19 pandemic. The information void has been especially stark in the World Health Organization Africa Region, which has low per capita reported cases, low testing rates, low access to therapeutic drugs, and has the longest wait for vaccines. As with all disease, the central challenge in responding to COVID-19 is that it requires integrating complex health systems that incorporate prevention, testing, front line health care, and reliable data to inform policies and their implementation within a relevant timeframe. It requires that the population can rely on the health system, and decision-makers can rely on the data. To understand the process and challenges of such an integrated response in an under-resourced rural African setting, we present the COVID-19 strategy in Ifanadiana District, where a partnership between Malagasy Ministry of Public Health (MoPH) and non-governmental organizations integrates prevention, diagnosis, surveillance, and treatment, in the context of a model health system. These efforts touch every level of the health system in the district-community, primary care centers, hospital-including the establishment of the only RT-PCR lab for SARS-CoV-2 testing outside of the capital. Starting in March of 2021, a second wave of COVID-19 occurred in Madagascar, but there remain fewer cases in Ifanadiana than for many other diseases (e.g., malaria). At the Ifanadiana District Hospital, there have been two deaths that are officially attributed to COVID-19. Here, we describe the main components and challenges of this integrated response, the broad epidemiological contours of the epidemic, and how complex data sources can be developed to address many questions of COVID-19 science. Because of data limitations, it still remains unclear how this epidemic will affect rural areas of Madagascar and other developing countries where health system utilization is relatively low and there is limited capacity to diagnose and treat COVID-19 patients. Widespread population based seroprevalence studies are being implemented in Ifanadiana to inform the COVID-19 response strategy as health systems must simultaneously manage perennial and endemic disease threats.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
| | | | - Demetrice Jordan
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
| | - Mark A. Krasnow
- Centre Valbio, Ranomafana, Madagascar
- Department of Biochemistry, Stanford University, Stanford, CA, United States
| | - Patricia C. Wright
- Centre Valbio, Ranomafana, Madagascar
- Institute for the Conservation of Tropical Environments, Stony Brook University, Stony Brook, NY, United States
- Department of Anthropology, Stony Brook University, Stony Brook, NY, United States
| | - Thomas R. Gillespie
- Centre Valbio, Ranomafana, Madagascar
- Department of Environmental Sciences and Program in Population Biology, Ecology, and Evolutionary Biology, Emory University, Atlanta, GA, United States
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | | | | | - Michelle V. Evans
- Odum School of Ecology and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - John M. Drake
- Odum School of Ecology and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Calistus N. Ngonghala
- Department of Mathematics, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Center for African Studies, University of Florida, Gainesville, FL, United States
| | - Michael L. Rich
- PIVOT NGO, Ranomafana, Madagascar
- Brigham and Women's Hospital, Boston, MA, United States
- Partners in Health, Boston, MA, United States
| | - Stephen J. Popper
- PIVOT NGO, Ranomafana, Madagascar
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Ann C. Miller
- PIVOT NGO, Ranomafana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
| | | | | | | | | | | | | | | | | | - Andres Garchitorena
- PIVOT NGO, Ranomafana, Madagascar
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Julio Rakotonirina
- Faculty of Medicine, University of Antananarivo, Antananarivo, Madagascar
| | - Alishya Mayfield
- PIVOT NGO, Ranomafana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
- Brigham and Women's Hospital, Boston, MA, United States
| | - Karen E. Finnegan
- PIVOT NGO, Ranomafana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
| | - Matthew H. Bonds
- PIVOT NGO, Ranomafana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
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14
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Li P, Li SB, Wang X, Phillips CD, Schwarz LA, Luo L, de Lecea L, Krasnow MA. Brain Circuit of Claustrophobia-like Behavior in Mice Identified by Upstream Tracing of Sighing. Cell Rep 2021; 31:107779. [PMID: 32553161 PMCID: PMC8576489 DOI: 10.1016/j.celrep.2020.107779] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 08/04/2018] [Revised: 04/04/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Emotions are distinct patterns of behavioral and physiological responses triggered by stimuli that induce different brain states. Elucidating the circuits is difficult because of challenges in interrogating emotional brain states and their complex outputs. Here, we leverage the recent discovery in mice of a neural circuit for sighing, a simple, quantifiable output of various emotions. We show that mouse confinement triggers sighing, and this "claustrophobic" sighing, but not accompanying tachypnea, requires the same medullary neuromedin B (Nmb)-expressing neurons as physiological sighing. Retrograde tracing from the Nmb neurons identified 12 forebrain centers providing presynaptic input, including hypocretin (Hcrt)-expressing lateral hypothalamic neurons. Confinement activates Hcrt neurons, and optogenetic activation induces sighing and tachypnea whereas pharmacologic inhibition suppresses both responses. The effect on sighing is mediated by HCRT directly on Nmbneurons. We propose that this HCRT-NMB neuropeptide relay circuit mediates claustrophobic sighing and that activated Hcrt neurons are a claustrophobia brain state that directly controls claustrophobic outputs.
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Affiliation(s)
- Peng Li
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Life Sciences Institute, Departments of Biologic and Materials Sciences and of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Shi-Bin Li
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Xuenan Wang
- Life Sciences Institute, Departments of Biologic and Materials Sciences and of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chrystian D Phillips
- Life Sciences Institute, Departments of Biologic and Materials Sciences and of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsay A Schwarz
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Mark A Krasnow
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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15
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Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J, Berry GJ, Shrager JB, Metzger RJ, Kuo CS, Neff N, Weissman IL, Quake SR, Krasnow MA. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 2020; 587:619-625. [PMID: 33208946 PMCID: PMC7704697 DOI: 10.1038/s41586-020-2922-4] [Citation(s) in RCA: 508] [Impact Index Per Article: 127.0] [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: 08/24/2019] [Accepted: 08/26/2020] [Indexed: 12/11/2022]
Abstract
Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.
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Affiliation(s)
- Kyle J Travaglini
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Ahmad N Nabhan
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Genentech, South San Francisco, CA, USA
| | - Lolita Penland
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Calico Life Sciences, South San Francisco, CA, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Rene V Sit
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Stephen Chang
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephanie D Conley
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yasuo Mori
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Jun Seita
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Medical Sciences Innovation Hub Program, RIKEN, Tokyo, Japan
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ross J Metzger
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christin S Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Mark A Krasnow
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA.
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16
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Gillich A, Zhang F, Farmer CG, Travaglini KJ, Tan SY, Gu M, Zhou B, Feinstein JA, Krasnow MA, Metzger RJ. Capillary cell-type specialization in the alveolus. Nature 2020; 586:785-789. [PMID: 33057196 PMCID: PMC7721049 DOI: 10.1038/s41586-020-2822-7] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/22/2020] [Indexed: 01/01/2023]
Abstract
In the mammalian lung, an apparently homogenous mesh of capillary vessels surrounds each alveolus, forming the vast respiratory surface across which oxygen transfers to the blood1. Here we use single-cell analysis to elucidate the cell types, development, renewal and evolution of the alveolar capillary endothelium. We show that alveolar capillaries are mosaics; similar to the epithelium that lines the alveolus, the alveolar endothelium is made up of two intermingled cell types, with complex 'Swiss-cheese'-like morphologies and distinct functions. The first cell type, which we term the 'aerocyte', is specialized for gas exchange and the trafficking of leukocytes, and is unique to the lung. The other cell type, termed gCap ('general' capillary), is specialized to regulate vasomotor tone, and functions as a stem/progenitor cell in capillary homeostasis and repair. The two cell types develop from bipotent progenitors, mature gradually and are affected differently in disease and during ageing. This cell-type specialization is conserved between mouse and human lungs but is not found in alligator or turtle lungs, suggesting it arose during the evolution of the mammalian lung. The discovery of cell type specialization in alveolar capillaries transforms our understanding of the structure, function, regulation and maintenance of the air-blood barrier and gas exchange in health, disease and evolution.
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Affiliation(s)
- Astrid Gillich
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Fan Zhang
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Colleen G Farmer
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Kyle J Travaglini
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Serena Y Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingxia Gu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jeffrey A Feinstein
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ross J Metzger
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Ouadah Y, Rojas ER, Riordan DP, Capostagno S, Kuo CS, Krasnow MA. Rare Pulmonary Neuroendocrine Cells Are Stem Cells Regulated by Rb, p53, and Notch. Cell 2020; 179:403-416.e23. [PMID: 31585080 DOI: 10.1016/j.cell.2019.09.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [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: 07/26/2018] [Revised: 04/29/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023]
Abstract
Pulmonary neuroendocrine (NE) cells are neurosensory cells sparsely distributed throughout the bronchial epithelium, many in innervated clusters of 20-30 cells. Following lung injury, NE cells proliferate and generate other cell types to promote epithelial repair. Here, we show that only rare NE cells, typically 2-4 per cluster, function as stem cells. These fully differentiated cells display features of classical stem cells. Most proliferate (self-renew) following injury, and some migrate into the injured area. A week later, individual cells, often just one per cluster, lose NE identity (deprogram), transit amplify, and reprogram to other fates, creating large clonal repair patches. Small cell lung cancer (SCLC) tumor suppressors regulate the stem cells: Rb and p53 suppress self-renewal, whereas Notch marks the stem cells and initiates deprogramming and transit amplification. We propose that NE stem cells give rise to SCLC, and transformation results from constitutive activation of stem cell renewal and inhibition of deprogramming.
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Affiliation(s)
- Youcef Ouadah
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Enrique R Rojas
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel P Riordan
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah Capostagno
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Christin S Kuo
- Department of Pediatrics, Division of Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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18
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Cable J, Fuchs E, Weissman I, Jasper H, Glass D, Rando TA, Blau H, Debnath S, Oliva A, Park S, Passegué E, Kim C, Krasnow MA. Adult stem cells and regenerative medicine-a symposium report. Ann N Y Acad Sci 2019; 1462:27-36. [PMID: 31655007 DOI: 10.1111/nyas.14243] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022]
Abstract
Adult stem cells are rare, undifferentiated cells found in all tissues of the body. Although normally kept in a quiescent, nondividing state, these cells can proliferate and differentiate to replace naturally dying cells within their tissue and to repair its wounds in response to injury. Due to their proliferative nature and ability to regenerate tissue, adult stem cells have the potential to treat a variety of degenerative diseases as well as aging. In addition, since stem cells are often thought to be the source of malignant tumors, understanding the mechanisms that keep their proliferative abilities in check can pave the way for new cancer therapies. While adult stem cells have had limited practical and clinical applications to date, several clinical trials of stem cell-based therapies are underway. This report details recent research presented at the New York Academy of Sciences on March 14, 2019 on understanding the factors that regulate stem cell activity and differentiation, with the hope of translating these findings into the clinic.
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Affiliation(s)
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, New York
| | - Irving Weissman
- Pathology Stem Cell Institute, Stanford University, Stanford, California
| | | | | | - Thomas A Rando
- Neurology & Neurological Sciences, Stanford University, Stanford, California
| | - Helen Blau
- Microbiology and Immunology - Baxter Labs, Stanford University, Stanford, California
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | | | - Sangbum Park
- Department of Genetics, Yale University, New Haven, Connecticut
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, New York
| | - Carla Kim
- Dana Farber/Harvard Cancer Center, Boston, Massachusetts.,Division of Hematology/Oncology, Stem Cell Program, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts.,Genetics Department, Harvard Medical School, Boston, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University, Stanford, California
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19
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Schaum N, Karkanias J, Neff NF, May AP, Quake SR, Wyss-Coray T, Darmanis S, Batson J, Botvinnik O, Chen MB, Chen S, Green F, Jones R, Maynard A, Penland L, Pisco AO, Sit RV, Stanley GM, Webber JT, Zanini F, Baghel AS, Bakerman I, Bansal I, Berdnik D, Bilen B, Brownfield D, Cain C, Chen MB, Chen S, Cho M, Cirolia G, Conley SD, Darmanis S, Demers A, Demir K, de Morree A, Divita T, du Bois H, Dulgeroff LBT, Ebadi H, Espinoza FH, Fish M, Gan Q, George BM, Gillich A, Green F, Genetiano G, Gu X, Gulati GS, Hang Y, Hosseinzadeh S, Huang A, Iram T, Isobe T, Ives F, Jones R, Kao KS, Karnam G, Kershner AM, Kiss BM, Kong W, Kumar ME, Lam J, Lee DP, Lee SE, Li G, Li Q, Liu L, Lo A, Lu WJ, Manjunath A, May AP, May KL, May OL, Maynard A, McKay M, Metzger RJ, Mignardi M, Min D, Nabhan AN, Neff NF, Ng KM, Noh J, Patkar R, Peng WC, Penland L, Puccinelli R, Rulifson EJ, Schaum N, Sikandar SS, Sinha R, Sit RV, Szade K, Tan W, Tato C, Tellez K, Travaglini KJ, Tropini C, Waldburger L, van Weele LJ, Wosczyna MN, Xiang J, Xue S, Youngyunpipatkul J, Zanini F, Zardeneta ME, Zhang F, Zhou L, Bansal I, Chen S, Cho M, Cirolia G, Darmanis S, Demers A, Divita T, Ebadi H, Genetiano G, Green F, Hosseinzadeh S, Ives F, Lo A, May AP, Maynard A, McKay M, Neff NF, Penland L, Sit RV, Tan W, Waldburger L, oungyunpipatkul JY, Batson J, Botvinnik O, Castro P, Croote D, Darmanis S, DeRisi JL, Karkanias J, Pisco AO, Stanley GM, Webber JT, Zanini F, Baghel AS, Bakerman I, Batson J, Bilen B, Botvinnik O, Brownfield D, Chen MB, Darmanis S, Demir K, de Morree A, Ebadi H, Espinoza FH, Fish M, Gan Q, George BM, Gillich A, Gu X, Gulati GS, Hang Y, Huang A, Iram T, Isobe T, Karnam G, Kershner AM, Kiss BM, Kong W, Kuo CS, Lam J, Lehallier B, Li G, Li Q, Liu L, Lu WJ, Min D, Nabhan AN, Ng KM, Nguyen PK, Patkar R, Peng WC, Penland L, Rulifson EJ, Schaum N, Sikandar SS, Sinha R, Szade K, Tan SY, Tellez K, Travaglini KJ, Tropini C, van Weele LJ, Wang BM, Wosczyna MN, Xiang J, Yousef H, Zhou L, Batson J, Botvinnik O, Chen S, Darmanis S, Green F, May AP, Maynard A, Pisco AO, Quake SR, Schaum N, Stanley GM, Webber JT, Wyss-Coray T, Zanini F, Beachy PA, Chan CKF, de Morree A, George BM, Gulati GS, Hang Y, Huang KC, Iram T, Isobe T, Kershner AM, Kiss BM, Kong W, Li G, Li Q, Liu L, Lu WJ, Nabhan AN, Ng KM, Nguyen PK, Peng WC, Rulifson EJ, Schaum N, Sikandar SS, Sinha R, Szade K, Travaglini KJ, Tropini C, Wang BM, Weinberg K, Wosczyna MN, Wu SM, Yousef H, Barres BA, Beachy PA, Chan CKF, Clarke MF, Darmanis S, Huang KC, Karkanias J, Kim SK, Krasnow MA, Kumar ME, Kuo CS, May AP, Metzger RJ, Neff NF, Nusse R, Nguyen PK, Rando TA, Sonnenburg J, Wang BM, Weinberg K, Weissman IL, Wu SM, Quake SR, Wyss-Coray T. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 2018; 562:367-372. [PMID: 30283141 PMCID: PMC6642641 DOI: 10.1038/s41586-018-0590-4] [Citation(s) in RCA: 1466] [Impact Index Per Article: 244.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.
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Affiliation(s)
- Nicholas Schaum
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jim Karkanias
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Andrew P. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
- Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
| | | | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Michelle B. Chen
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Steven Chen
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Foad Green
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Robert Jones
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | | | | | - Rene V. Sit
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Geoffrey M. Stanley
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ankit S Baghel
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Isaac Bakerman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
| | - Ishita Bansal
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Daniela Berdnik
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Biter Bilen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Douglas Brownfield
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Corey Cain
- Flow Cytometry Core, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
| | - Michelle B. Chen
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Steven Chen
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Min Cho
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Giana Cirolia
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Stephanie D. Conley
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | | | - Aaron Demers
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Kubilay Demir
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Tessa Divita
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Haley du Bois
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Laughing Bear Torrez Dulgeroff
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Hamid Ebadi
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - F. Hernán Espinoza
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Matt Fish
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Qiang Gan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Benson M. George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Foad Green
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Xueying Gu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Gunsagar S. Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Albin Huang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Taichi Isobe
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Feather Ives
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Robert Jones
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Kevin S. Kao
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Guruswamy Karnam
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Aaron M. Kershner
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Bernhard M. Kiss
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - William Kong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Maya E. Kumar
- Sean N. Parker Center for Asthma and Allergy Research, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Pulmonary and Critical Care, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan Lam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Davis P. Lee
- Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
| | - Song E. Lee
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Guang Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Qingyun Li
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Annie Lo
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Wan-Jin Lu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Anoop Manjunath
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Andrew P. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Kaia L. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Oliver L. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Marina McKay
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Ross J. Metzger
- Vera Moulton Wall Center for Pulmonary and Vascular Disease, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
| | - Marco Mignardi
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Dullei Min
- Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
| | - Ahmad N. Nabhan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Katharine M. Ng
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Joseph Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Rasika Patkar
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Weng Chuan Peng
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - Eric J. Rulifson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Nicholas Schaum
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Shaheen S. Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Rene V. Sit
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Krzysztof Szade
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Medical Biotechnology, Faculty of Biophysics, Biochemistry and Biotechnology, Jagiellonian University, Poland
| | - Weilun Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Cristina Tato
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Krissie Tellez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Carolina Tropini
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Linda J. van Weele
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Michael N. Wosczyna
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Jinyi Xiang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Soso Xue
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Macy E. Zardeneta
- Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
| | - Fan Zhang
- Vera Moulton Wall Center for Pulmonary and Vascular Disease, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
| | - Lu Zhou
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
| | - Ishita Bansal
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Steven Chen
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Min Cho
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Giana Cirolia
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Aaron Demers
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Tessa Divita
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Hamid Ebadi
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Foad Green
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Feather Ives
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Annie Lo
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Andrew P. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Marina McKay
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Rene V. Sit
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Weilun Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | | | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Paola Castro
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Derek Croote
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California USA
| | - Jim Karkanias
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Geoffrey M. Stanley
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ankit S. Baghel
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Isaac Bakerman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Biter Bilen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | | | - Douglas Brownfield
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle B. Chen
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Kubilay Demir
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Hamid Ebadi
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - F. Hernán Espinoza
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Matt Fish
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Qiang Gan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Benson M. George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Xueying Gu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Gunsagar S. Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Albin Huang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Taichi Isobe
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Guruswamy Karnam
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Aaron M. Kershner
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Bernhard M. Kiss
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - William Kong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Christin S. Kuo
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
| | - Jonathan Lam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Guang Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Qingyun Li
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Wan-Jin Lu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Dullei Min
- Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
| | - Ahmad N. Nabhan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Katharine M. Ng
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Patricia K. Nguyen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Rasika Patkar
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Weng Chuan Peng
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Eric J. Rulifson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Nicholas Schaum
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Shaheen S. Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Krzysztof Szade
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Medical Biotechnology, Faculty of Biophysics, Biochemistry and Biotechnology, Jagiellonian University, Poland
| | - Serena Y. Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Krissie Tellez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Carolina Tropini
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Linda J. van Weele
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Bruce M. Wang
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Michael N. Wosczyna
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Jinyi Xiang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Hanadie Yousef
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Lu Zhou
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Steven Chen
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Foad Green
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Andrew P. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | | | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Nicholas Schaum
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Geoffrey M. Stanley
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
- Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
| | - Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Philip A. Beachy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Charles K. F. Chan
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, California USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Benson M. George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Gunsagar S. Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Taichi Isobe
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Aaron M. Kershner
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Bernhard M. Kiss
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - William Kong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Guang Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Qingyun Li
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Wan-Jin Lu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Ahmad N. Nabhan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Katharine M. Ng
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Patricia K. Nguyen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Weng Chuan Peng
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Eric J. Rulifson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Nicholas Schaum
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Shaheen S. Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Krzysztof Szade
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Medical Biotechnology, Faculty of Biophysics, Biochemistry and Biotechnology, Jagiellonian University, Poland
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Carolina Tropini
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Bruce M. Wang
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Kenneth Weinberg
- Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
| | - Michael N. Wosczyna
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Sean M. Wu
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Hanadie Yousef
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Ben A. Barres
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
| | - Philip A. Beachy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Charles K. F. Chan
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, California USA
| | - Michael F. Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | | | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jim Karkanias
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine and Stanford Diabetes Research Center, Stanford University, Stanford, California USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
| | - Maya E. Kumar
- Sean N. Parker Center for Asthma and Allergy Research, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Pulmonary and Critical Care, Stanford University School of Medicine, Stanford, California, USA
| | - Christin S. Kuo
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
| | - Andrew P. May
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Ross J. Metzger
- Vera Moulton Wall Center for Pulmonary and Vascular Disease, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
| | - Norma F. Neff
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Roel Nusse
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Patricia K. Nguyen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Thomas A. Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
- Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
| | - Justin Sonnenburg
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Bruce M. Wang
- Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
| | - Kenneth Weinberg
- Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Sean M. Wu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
- Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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20
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21
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Madelaine R, Sloan SA, Huber N, Notwell JH, Leung LC, Skariah G, Halluin C, Paşca SP, Bejerano G, Krasnow MA, Barres BA, Mourrain P. MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis. Cell Rep 2018; 20:1533-1542. [PMID: 28813666 DOI: 10.1016/j.celrep.2017.07.051] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [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: 03/30/2017] [Revised: 06/30/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
Abstract
In the developing brain, neurons expressing VEGF-A and blood vessels grow in close apposition, but many of the molecular pathways regulating neuronal VEGF-A and neurovascular system development remain to be deciphered. Here, we show that miR-9 links neurogenesis and angiogenesis through the formation of neurons expressing VEGF-A. We found that miR-9 directly targets the transcription factors TLX and ONECUTs to regulate VEGF-A expression. miR-9 inhibition leads to increased TLX and ONECUT expression, resulting in VEGF-A overexpression. This untimely increase of neuronal VEGF-A signal leads to the thickening of blood vessels at the expense of the normal formation of the neurovascular network in the brain and retina. Thus, this conserved transcriptional cascade is critical for proper brain development in vertebrates. Because of this dual role on neural stem cell proliferation and angiogenesis, miR-9 and its downstream targets are promising factors for cellular regenerative therapy following stroke and for brain tumor treatment.
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Affiliation(s)
- Romain Madelaine
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Steven A Sloan
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Nina Huber
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - James H Notwell
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Louis C Leung
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Gemini Skariah
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Caroline Halluin
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Sergiu P Paşca
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Mark A Krasnow
- HHMI and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ben A Barres
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Philippe Mourrain
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; INSERM 1024, École Normale Supérieure, Paris 75005, France.
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22
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Nabhan AN, Brownfield DG, Harbury PB, Krasnow MA, Desai TJ. Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells. Science 2018; 359:1118-1123. [PMID: 29420258 DOI: 10.1126/science.aam6603] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/20/2017] [Accepted: 01/23/2018] [Indexed: 01/03/2023]
Abstract
Alveoli, the lung's respiratory units, are tiny sacs where oxygen enters the bloodstream. They are lined by flat alveolar type 1 (AT1) cells, which mediate gas exchange, and AT2 cells, which secrete surfactant. Rare AT2s also function as alveolar stem cells. We show that AT2 lung stem cells display active Wnt signaling, and many of them are near single, Wnt-expressing fibroblasts. Blocking Wnt secretion depletes these stem cells. Daughter cells leaving the Wnt niche transdifferentiate into AT1s: Maintaining Wnt signaling prevents transdifferentiation, whereas abrogating Wnt signaling promotes it. Injury induces AT2 autocrine Wnts, recruiting "bulk" AT2s as progenitors. Thus, individual AT2 stem cells reside in single-cell fibroblast niches providing juxtacrine Wnts that maintain them, whereas injury induces autocrine Wnts that transiently expand the progenitor pool. This simple niche maintains the gas exchange surface and is coopted in cancer.
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Affiliation(s)
- Ahmad N Nabhan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Douglas G Brownfield
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Pehr B Harbury
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Tushar J Desai
- Department of Internal Medicine, Division of Pulmonary and Critical Care, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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23
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Ezran C, Karanewsky CJ, Pendleton JL, Sholtz A, Krasnow MR, Willick J, Razafindrakoto A, Zohdy S, Albertelli MA, Krasnow MA. The Mouse Lemur, a Genetic Model Organism for Primate Biology, Behavior, and Health. Genetics 2017; 206:651-664. [PMID: 28592502 PMCID: PMC5499178 DOI: 10.1534/genetics.116.199448] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 04/08/2017] [Indexed: 01/24/2023] Open
Abstract
Systematic genetic studies of a handful of diverse organisms over the past 50 years have transformed our understanding of biology. However, many aspects of primate biology, behavior, and disease are absent or poorly modeled in any of the current genetic model organisms including mice. We surveyed the animal kingdom to find other animals with advantages similar to mice that might better exemplify primate biology, and identified mouse lemurs (Microcebus spp.) as the outstanding candidate. Mouse lemurs are prosimian primates, roughly half the genetic distance between mice and humans. They are the smallest, fastest developing, and among the most prolific and abundant primates in the world, distributed throughout the island of Madagascar, many in separate breeding populations due to habitat destruction. Their physiology, behavior, and phylogeny have been studied for decades in laboratory colonies in Europe and in field studies in Malagasy rainforests, and a high quality reference genome sequence has recently been completed. To initiate a classical genetic approach, we developed a deep phenotyping protocol and have screened hundreds of laboratory and wild mouse lemurs for interesting phenotypes and begun mapping the underlying mutations, in collaboration with leading mouse lemur biologists. We also seek to establish a mouse lemur gene "knockout" library by sequencing the genomes of thousands of mouse lemurs to identify null alleles in most genes from the large pool of natural genetic variants. As part of this effort, we have begun a citizen science project in which students across Madagascar explore the remarkable biology around their schools, including longitudinal studies of the local mouse lemurs. We hope this work spawns a new model organism and cultivates a deep genetic understanding of primate biology and health. We also hope it establishes a new and ethical method of genetics that bridges biological, behavioral, medical, and conservation disciplines, while providing an example of how hands-on science education can help transform developing countries.
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Affiliation(s)
- Camille Ezran
- Department of Biochemistry
- Howard Hughes Medical Institute, and
| | | | | | - Alex Sholtz
- Department of Biochemistry
- Howard Hughes Medical Institute, and
| | - Maya R Krasnow
- Department of Biochemistry
- Howard Hughes Medical Institute, and
| | - Jason Willick
- Department of Biochemistry
- Howard Hughes Medical Institute, and
| | - Andriamahery Razafindrakoto
- Department of Animal Biology, Faculty of Science, University of Antananarivo, Antananarivo 101, BP 566, Madagascar, and
| | - Sarah Zohdy
- School of Forestry and Wildlife Sciences and College of Veterinary Medicine, Auburn University, Alabama 36849
| | - Megan A Albertelli
- Department of Comparative Medicine, Stanford University School of Medicine, California 94305
| | - Mark A Krasnow
- Department of Biochemistry
- Howard Hughes Medical Institute, and
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24
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Yackle K, Schwarz LA, Kam K, Sorokin JM, Huguenard JR, Feldman JL, Luo L, Krasnow MA. Breathing control center neurons that promote arousal in mice. Science 2017; 355:1411-1415. [PMID: 28360327 DOI: 10.1126/science.aari7984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 02/01/2017] [Indexed: 05/19/2023]
Abstract
Slow, controlled breathing has been used for centuries to promote mental calming, and it is used clinically to suppress excessive arousal such as panic attacks. However, the physiological and neural basis of the relationship between breathing and higher-order brain activity is unknown. We found a neuronal subpopulation in the mouse preBötzinger complex (preBötC), the primary breathing rhythm generator, which regulates the balance between calm and arousal behaviors. Conditional, bilateral genetic ablation of the ~175 Cdh9/Dbx1 double-positive preBötC neurons in adult mice left breathing intact but increased calm behaviors and decreased time in aroused states. These neurons project to, synapse on, and positively regulate noradrenergic neurons in the locus coeruleus, a brain center implicated in attention, arousal, and panic that projects throughout the brain.
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Affiliation(s)
- Kevin Yackle
- Howard Hughes Medical Institute, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lindsay A Schwarz
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kaiwen Kam
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Jordan M Sorokin
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Jack L Feldman
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mark A Krasnow
- Howard Hughes Medical Institute, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
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25
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Yackle K, Schwarz LA, Kam K, Sorokin JM, Huguenard JR, Feldman JL, Luo L, Krasnow MA. Breathing control center neurons that promote arousal in mice. Science 2017; 355:1411-1415. [PMID: 28360327 DOI: 10.1126/science.aai7984] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022]
Abstract
Slow, controlled breathing has been used for centuries to promote mental calming, and it is used clinically to suppress excessive arousal such as panic attacks. However, the physiological and neural basis of the relationship between breathing and higher-order brain activity is unknown. We found a neuronal subpopulation in the mouse preBötzinger complex (preBötC), the primary breathing rhythm generator, which regulates the balance between calm and arousal behaviors. Conditional, bilateral genetic ablation of the ~175 Cdh9/Dbx1 double-positive preBötC neurons in adult mice left breathing intact but increased calm behaviors and decreased time in aroused states. These neurons project to, synapse on, and positively regulate noradrenergic neurons in the locus coeruleus, a brain center implicated in attention, arousal, and panic that projects throughout the brain.
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Affiliation(s)
- Kevin Yackle
- Howard Hughes Medical Institute, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lindsay A Schwarz
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kaiwen Kam
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Jordan M Sorokin
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Jack L Feldman
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mark A Krasnow
- Howard Hughes Medical Institute, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Bunn PA, Minna JD, Augustyn A, Gazdar AF, Ouadah Y, Krasnow MA, Berns A, Brambilla E, Rekhtman N, Massion PP, Niederst M, Peifer M, Yokota J, Govindan R, Poirier JT, Byers LA, Wynes MW, McFadden DG, MacPherson D, Hann CL, Farago AF, Dive C, Teicher BA, Peacock CD, Johnson JE, Cobb MH, Wendel HG, Spigel D, Sage J, Yang P, Pietanza MC, Krug LM, Heymach J, Ujhazy P, Zhou C, Goto K, Dowlati A, Christensen CL, Park K, Einhorn LH, Edelman MJ, Giaccone G, Gerber DE, Salgia R, Owonikoko T, Malik S, Karachaliou N, Gandara DR, Slotman BJ, Blackhall F, Goss G, Thomas R, Rudin CM, Hirsch FR. Small Cell Lung Cancer: Can Recent Advances in Biology and Molecular Biology Be Translated into Improved Outcomes? J Thorac Oncol 2016; 11:453-74. [PMID: 26829312 PMCID: PMC4836290 DOI: 10.1016/j.jtho.2016.01.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Paul A Bunn
- University of Colorado Cancer Center, Aurora, Colorado
| | - John D Minna
- University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Adi F Gazdar
- University of Texas Southwestern Medical Center, Dallas, Texas
| | | | | | - Anton Berns
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Jun Yokota
- Institute of Predictive and Personalized Medicine of Cancer, Barcelona, Spain; National Cancer Center Research Institute, Tokyo, Japan
| | | | - John T Poirier
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lauren A Byers
- University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Murry W Wynes
- International Association for the Study of Lung Cancer, Aurora, Colorado
| | | | | | | | - Anna F Farago
- Massachusetts General Hospital, Boston, Massachusetts
| | - Caroline Dive
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | | | | | - Jane E Johnson
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Melanie H Cobb
- University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - David Spigel
- Sara Cannon Research Institute, Nashville, Tennessee
| | | | - Ping Yang
- Mayo Clinic Cancer Center, Rochester, Minnesota
| | | | - Lee M Krug
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Heymach
- University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Caicun Zhou
- Cancer Institute of Tongji University Medical School, Shanghai, China
| | - Koichi Goto
- National Cancer Center Hospital East, Chiba, Japan
| | - Afshin Dowlati
- Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio
| | | | - Keunchil Park
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Martin J Edelman
- University of Maryland, Greenebaum Cancer Center, Baltimore, Maryland
| | | | - David E Gerber
- University of Texas Southwestern Medical Center, Dallas, Texas
| | | | | | | | | | - David R Gandara
- University of California Davis Comprehensive Cancer Center, Davis, California
| | - Ben J Slotman
- Vrije Universiteit Medical Center, Amsterdam, Netherlands
| | | | | | | | | | - Fred R Hirsch
- University of Colorado Cancer Center, Aurora, Colorado.
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27
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Abstract
Macrophages are specialized phagocytic cells, present in all tissues, which engulf and digest pathogens, infected and dying cells, and debris, and can recruit and regulate other immune cells and the inflammatory response and aid in tissue repair. Macrophage subpopulations play distinct roles in these processes and in disease, and are typically recognized by differences in marker expression, immune function, or tissue of residency. Although macrophage subpopulations in the brain have been found to have distinct developmental origins, the extent to which development contributes to macrophage diversity between tissues and within tissues is not well understood. Here, we investigate the development and maintenance of mouse lung macrophages by marker expression patterns, genetic lineage tracing and parabiosis. We show that macrophages populate the lung in three developmental waves, each giving rise to a distinct lineage. These lineages express different markers, reside in different locations, renew in different ways, and show little or no interconversion. Thus, development contributes significantly to lung macrophage diversity and targets each lineage to a different anatomical domain.
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Affiliation(s)
- Serena Y S Tan
- Department of Biochemistry and HHMI, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Mark A Krasnow
- Department of Biochemistry and HHMI, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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28
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Li P, Janczewski WA, Yackle K, Kam K, Pagliardini S, Krasnow MA, Feldman JL. The peptidergic control circuit for sighing. Nature 2016; 530:293-297. [PMID: 26855425 DOI: 10.1038/nature16964] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/30/2015] [Indexed: 02/06/2023]
Abstract
Sighs are long, deep breaths expressing sadness, relief or exhaustion. Sighs also occur spontaneously every few minutes to reinflate alveoli, and sighing increases under hypoxia, stress, and certain psychiatric conditions. Here we use molecular, genetic, and pharmacologic approaches to identify a peptidergic sigh control circuit in murine brain. Small neural subpopulations in a key breathing control centre, the retrotrapezoid nucleus/parafacial respiratory group (RTN/pFRG), express bombesin-like neuropeptide genes neuromedin B (Nmb) or gastrin-releasing peptide (Grp). These project to the preBötzinger Complex (preBötC), the respiratory rhythm generator, which expresses NMB and GRP receptors in overlapping subsets of ~200 neurons. Introducing either neuropeptide into preBötC or onto preBötC slices, induced sighing or in vitro sigh activity, whereas elimination or inhibition of either receptor reduced basal sighing, and inhibition of both abolished it. Ablating receptor-expressing neurons eliminated basal and hypoxia-induced sighing, but left breathing otherwise intact initially. We propose that these overlapping peptidergic pathways comprise the core of a sigh control circuit that integrates physiological and perhaps emotional input to transform normal breaths into sighs.
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Affiliation(s)
- Peng Li
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305
| | - Wiktor A Janczewski
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095
| | - Kevin Yackle
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305
| | - Kaiwen Kam
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095
| | - Silvia Pagliardini
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305
| | - Jack L Feldman
- Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095
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29
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Chang AJ, Ortega FE, Riegler J, Madison DV, Krasnow MA. Oxygen regulation of breathing through an olfactory receptor activated by lactate. Nature 2015; 527:240-4. [PMID: 26560302 PMCID: PMC4765808 DOI: 10.1038/nature15721] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [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: 07/09/2015] [Accepted: 08/28/2015] [Indexed: 12/25/2022]
Abstract
Animals have evolved homeostatic responses to changes in oxygen availability that act on different time scales. Although the hypoxia-inducible factor (HIF) transcriptional pathway that controls long term responses to low oxygen (hypoxia) has been established1, the pathway that mediates acute responses to hypoxia in mammals is not well understood. Here we show that the olfactory receptor Olfr78 is highly and selectively expressed in oxygen-sensitive glomus cells of the carotid body, a chemosensory organ at the carotid artery bifurcation that monitors blood oxygen and stimulates breathing within seconds when oxygen declines2. Olfr78 mutants fail to increase ventilation in hypoxia but respond normally to hypercapnia. Glomus cells are present in normal numbers and appear structurally intact, but hypoxia-induced carotid body activity is diminished. Lactate, a metabolite that rapidly accumulates in hypoxia and induces hyperventilation3–6, activates Olfr78 in heterologous expression experiments, induces calcium transients in glomus cells, and stimulates carotid sinus nerve activity through Olfr78. We propose that in addition to its role in olfaction, Olfr78 acts as a hypoxia sensor in the breathing circuit by sensing lactate produced when oxygen levels decline.
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Affiliation(s)
- Andy J Chang
- Department of Biochemistry, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, California 94305-5307, USA
| | - Fabian E Ortega
- Department of Biochemistry, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, California 94305-5307, USA
| | - Johannes Riegler
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Daniel V Madison
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, California 94305-5307, USA
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30
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Kuo CS, Krasnow MA. Formation of a Neurosensory Organ by Epithelial Cell Slithering. Cell 2015; 163:394-405. [PMID: 26435104 DOI: 10.1016/j.cell.2015.09.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/08/2015] [Accepted: 08/11/2015] [Indexed: 11/25/2022]
Abstract
Epithelial cells are normally stably anchored, maintaining their relative positions and association with the basement membrane. Developmental rearrangements occur through cell intercalation, and cells can delaminate during epithelial-mesenchymal transitions and metastasis. We mapped the formation of lung neuroepithelial bodies (NEBs), innervated clusters of neuroendocrine/neurosensory cells within the bronchial epithelium, revealing a targeted mode of cell migration that we named "slithering," in which cells transiently lose epithelial character but remain associated with the membrane while traversing neighboring epithelial cells to reach cluster sites. Immunostaining, lineage tracing, clonal analysis, and live imaging showed that NEB progenitors, initially distributed randomly, downregulate adhesion and polarity proteins, crawling over and between neighboring cells to converge at diametrically opposed positions at bronchial branchpoints, where they reestablish epithelial structure and express neuroendocrine genes. There is little accompanying progenitor proliferation or apoptosis. Activation of the slithering program may explain why lung cancers arising from neuroendocrine cells are highly metastatic.
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Affiliation(s)
- Christin S Kuo
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305-5307, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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31
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Peterson SJ, Krasnow MA. Subcellular trafficking of FGF controls tracheal invasion of Drosophila flight muscle. Cell 2014; 160:313-23. [PMID: 25557078 DOI: 10.1016/j.cell.2014.11.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/07/2014] [Accepted: 11/15/2014] [Indexed: 11/16/2022]
Abstract
To meet the extreme oxygen demand of insect flight muscle, tracheal (respiratory) tubes ramify not only on its surface, as in other tissues, but also within T-tubules and ultimately surrounding every mitochondrion. Although this remarkable physiological specialization has long been recognized, its cellular and molecular basis is unknown. Here, we show that Drosophila tracheoles invade flight muscle T-tubules through transient surface openings. Like other tracheal branching events, invasion requires the Branchless FGF pathway. However, localization of the FGF chemoattractant changes from all muscle membranes to T-tubules as invasion begins. Core regulators of epithelial basolateral membrane identity localize to T-tubules, and knockdown of AP-1γ, required for basolateral trafficking, redirects FGF from T-tubules to surface, increasing tracheal surface ramification and preventing invasion. We propose that tracheal invasion is controlled by an AP-1-dependent switch in FGF trafficking. Thus, subcellular targeting of a chemoattractant can direct outgrowth to specific domains, including inside the cell.
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Affiliation(s)
- Soren J Peterson
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Mark A Krasnow
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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Kumar ME, Bogard PE, Espinoza FH, Menke DB, Kingsley DM, Krasnow MA. Mesenchymal cells. Defining a mesenchymal progenitor niche at single-cell resolution. Science 2014; 346:1258810. [PMID: 25395543 DOI: 10.1126/science.1258810] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Most vertebrate organs are composed of epithelium surrounded by support and stromal tissues formed from mesenchyme cells, which are not generally thought to form organized progenitor pools. Here, we use clonal cell labeling with multicolor reporters to characterize individual mesenchymal progenitors in the developing mouse lung. We observe a diversity of mesenchymal progenitor populations with different locations, movements, and lineage boundaries. Airway smooth muscle (ASM) progenitors map exclusively to mesenchyme ahead of budding airways. Progenitors recruited from these tip pools differentiate into ASM around airway stalks; flanking stalk mesenchyme can be induced to form an ASM niche by a lateral bud or by an airway tip plus focal Wnt signal. Thus, mesenchymal progenitors can be organized into localized and carefully controlled domains that rival epithelial progenitor niches in regulatory sophistication.
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Affiliation(s)
- Maya E Kumar
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Patrick E Bogard
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - F Hernán Espinoza
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, GA 30602-2607, USA. Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - David M Kingsley
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Mark A Krasnow
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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Desai TJ, Brownfield DG, Krasnow MA. Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature 2014; 507:190-4. [PMID: 24499815 DOI: 10.1038/nature12930] [Citation(s) in RCA: 671] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/03/2013] [Indexed: 12/28/2022]
Abstract
Alveoli are gas-exchange sacs lined by squamous alveolar type (AT) 1 cells and cuboidal, surfactant-secreting AT2 cells. Classical studies suggested that AT1 arise from AT2 cells, but recent studies propose other sources. Here we use molecular markers, lineage tracing and clonal analysis to map alveolar progenitors throughout the mouse lifespan. We show that, during development, AT1 and AT2 cells arise directly from a bipotent progenitor, whereas after birth new AT1 cells derive from rare, self-renewing, long-lived, mature AT2 cells that produce slowly expanding clonal foci of alveolar renewal. This stem-cell function is broadly activated by AT1 injury, and AT2 self-renewal is selectively induced by EGFR (epidermal growth factor receptor) ligands in vitro and oncogenic Kras(G12D) in vivo, efficiently generating multifocal, clonal adenomas. Thus, there is a switch after birth, when AT2 cells function as stem cells that contribute to alveolar renewal, repair and cancer. We propose that local signals regulate AT2 stem-cell activity: a signal transduced by EGFR-KRAS controls self-renewal and is hijacked during oncogenesis, whereas another signal controls reprogramming to AT1 fate.
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Affiliation(s)
- Tushar J Desai
- 1] Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA [2] Department of Internal Medicine, Division of Pulmonary and Critical Care, Stanford University School of Medicine, Stanford, California 94305-5307, USA
| | - Douglas G Brownfield
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA
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Abstract
Although there has been progress identifying adult stem and progenitor cells and the signals that control their proliferation and differentiation, little is known about the substrates and signals that guide them out of their niche. By examining Drosophila tracheal outgrowth during metamorphosis, we show that progenitors follow a stereotyped path out of the niche, tracking along a subset of tracheal branches destined for destruction. The embryonic tracheal inducer branchless FGF (fibroblast growth factor) is expressed dynamically just ahead of progenitor outgrowth in decaying branches. Knockdown of branchless abrogates progenitor outgrowth, whereas misexpression redirects it. Thus, reactivation of an embryonic tracheal inducer in decaying branches directs outgrowth of progenitors that replace them. This explains how the structure of a newly generated tissue is coordinated with that of the old.
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Affiliation(s)
- Feng Chen
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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Affiliation(s)
- Tushar J Desai
- Department of Medicine, Division of Pulmonary and Critical Care, Stanford University School of Medicine, Stanford, California 94305-5307, USA
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Tan FE, Vladar EK, Ma L, Fuentealba LC, Hoh R, Hernán Espinoza F, Axelrod JD, Alvarez-Buylla A, Stearns T, Kintner C, Krasnow MA. Myb promotes centriole amplification and later steps of the multiciliogenesis program. J Cell Sci 2013. [DOI: 10.1242/jcs.143099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tan FE, Vladar EK, Ma L, Fuentealba LC, Hoh R, Espinoza FH, Axelrod JD, Alvarez-Buylla A, Stearns T, Kintner C, Krasnow MA. Myb promotes centriole amplification and later steps of the multiciliogenesis program. Development 2013; 140:4277-86. [PMID: 24048590 PMCID: PMC3787764 DOI: 10.1242/dev.094102] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transcriptional control of primary cilium formation and ciliary motility are beginning to be understood, but little is known about the transcriptional programs that control cilium number and other structural and functional specializations. One of the most intriguing ciliary specializations occurs in multiciliated cells (MCCs), which amplify their centrioles to nucleate hundreds of cilia per cell, instead of the usual monocilium. Here we report that the transcription factor MYB, which promotes S phase and drives cycling of a variety of progenitor cells, is expressed in postmitotic epithelial cells of the mouse airways and ependyma destined to become MCCs. MYB is expressed early in multiciliogenesis, as progenitors exit the cell cycle and amplify their centrioles, then switches off as MCCs mature. Conditional inactivation of Myb in the developing airways blocks or delays centriole amplification and expression of FOXJ1, a transcription factor that controls centriole docking and ciliary motility, and airways fail to become fully ciliated. We provide evidence that MYB acts in a conserved pathway downstream of Notch signaling and multicilin, a protein related to the S-phase regulator geminin, and upstream of FOXJ1. MYB can activate endogenous Foxj1 expression and stimulate a cotransfected Foxj1 reporter in heterologous cells, and it can drive the complete multiciliogenesis program in Xenopus embryonic epidermis. We conclude that MYB has an early, crucial and conserved role in multiciliogenesis, and propose that it promotes a novel S-like phase in which centriole amplification occurs uncoupled from DNA synthesis, and then drives later steps of multiciliogenesis through induction of Foxj1.
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Affiliation(s)
- Fraser E Tan
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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Wang H, St. Julien KR, Stevenson DK, Hoffmann TJ, Witte JS, Lazzeroni LC, Krasnow MA, Quaintance CC, Oehlert JW, Jelliffe-Pawlowski LL, Gould JB, Shaw GM, O’Brodovich HM. A genome-wide association study (GWAS) for bronchopulmonary dysplasia. Pediatrics 2013; 132:290-7. [PMID: 23897914 PMCID: PMC3727675 DOI: 10.1542/peds.2013-0533] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Twin studies suggest that heritability of moderate-severe bronchopulmonary dysplasia (BPD) is 53% to 79%, we conducted a genome-wide association study (GWAS) to identify genetic variants associated with the risk for BPD. METHODS The discovery GWAS was completed on 1726 very low birth weight infants (gestational age = 25(0)-29(6/7) weeks) who had a minimum of 3 days of intermittent positive pressure ventilation and were in the hospital at 36 weeks' postmenstrual age. At 36 weeks' postmenstrual age, moderate-severe BPD cases (n = 899) were defined as requiring continuous supplemental oxygen, whereas controls (n = 827) inhaled room air. An additional 795 comparable infants (371 cases, 424 controls) were a replication population. Genomic DNA from case and control newborn screening bloodspots was used for the GWAS. The replication study interrogated single-nucleotide polymorphisms (SNPs) identified in the discovery GWAS and those within the HumanExome beadchip. RESULTS Genotyping using genomic DNA was successful. We did not identify SNPs associated with BPD at the genome-wide significance level (5 × 10(-8)) and no SNP identified in previous studies reached statistical significance (Bonferroni-corrected P value threshold .0018). Pathway analyses were not informative. CONCLUSIONS We did not identify genomic loci or pathways that account for the previously described heritability for BPD. Potential explanations include causal mutations that are genetic variants and were not assayed or are mapped to many distributed loci, inadequate sample size, race ethnicity of our study population, or case-control differences investigated are not attributable to underlying common genetic variation.
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Affiliation(s)
| | - Krystal R. St. Julien
- Biochemistry, and,Howard Hughes Medical Institute, Stanford University School of Medicine, Palo Alto, California
| | | | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, and Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - John S. Witte
- Department of Epidemiology and Biostatistics, and Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | | | - Mark A. Krasnow
- Biochemistry, and,Howard Hughes Medical Institute, Stanford University School of Medicine, Palo Alto, California
| | | | | | - Laura L. Jelliffe-Pawlowski
- California Genetic Disease Screening Program of the California Department of Public Health, Richmond, California; and
| | - Jeffrey B. Gould
- Departments of Pediatrics,,California Perinatal Quality Care Collaborative, California
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St. Julien KR, Jelliffe-Pawlowski LL, Shaw GM, Stevenson DK, O’Brodovich HM, Krasnow MA. High quality genome-wide genotyping from archived dried blood spots without DNA amplification. PLoS One 2013; 8:e64710. [PMID: 23737996 PMCID: PMC3667813 DOI: 10.1371/journal.pone.0064710] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 12/18/2012] [Accepted: 04/17/2013] [Indexed: 11/19/2022] Open
Abstract
Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.
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Affiliation(s)
- Krystal R. St. Julien
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Laura L. Jelliffe-Pawlowski
- California Genetic Disease Screening Program of the California Department of Public Health, Richmond, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hugh M. O’Brodovich
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A. Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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40
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Greif DM, Kumar M, Lighthouse JK, Hum J, An A, Ding L, Red-Horse K, Espinoza FH, Olson L, Offermanns S, Krasnow MA. Radial construction of an arterial wall. Dev Cell 2013; 23:482-93. [PMID: 22975322 DOI: 10.1016/j.devcel.2012.07.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 05/24/2012] [Accepted: 07/16/2012] [Indexed: 01/04/2023]
Abstract
Some of the most serious diseases involve altered size and structure of the arterial wall. Elucidating how arterial walls are built could aid understanding of these diseases, but little is known about how concentric layers of muscle cells and the outer adventitial layer are assembled and patterned around endothelial tubes. Using histochemical, clonal, and genetic analysis in mice, here we show that the pulmonary artery wall is constructed radially, from the inside out, by two separate but coordinated processes. One is sequential induction of successive cell layers from surrounding mesenchyme. The other is controlled invasion of outer layers by inner layer cells through developmentally regulated cell reorientation and radial migration. We propose that a radial signal gradient controls these processes and provide evidence that PDGF-B and at least one other signal contribute. Modulation of such radial signaling pathways may underlie vessel-specific differences and pathological changes in arterial wall size and structure.
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Affiliation(s)
- Daniel M Greif
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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41
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Abstract
Epithelia are classified as either simple, a single cell layer thick, or stratified (multilayered). Stratified epithelia arise from simple epithelia during development, and transcription factor p63 functions as a key positive regulator of epidermal stratification. Here we show that deletion of integrin beta 1 (Itgb1) in the developing mouse airway epithelium abrogates airway branching and converts this monolayer epithelium into a multilayer epithelium with more than 10 extra layers. Mutant lung epithelial cells change mitotic spindle orientation to seed outer layers, and cells in different layers become molecularly and functionally distinct, hallmarks of normal stratification. However, mutant lung epithelial cells do not activate p63 and do not switch to the stratified keratin profile of epidermal cells. These data, together with previous data implicating Itgb1 in regulation of epidermal stratification, suggest that the simple-versus-stratified developmental decision may involve not only stratification inducers like p63 but suppressors like Itgb1 that prevent simple epithelia from inappropriately activating key steps in the stratification program.
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Affiliation(s)
- Jichao Chen
- Department of Biochemistry and HHMI, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (JC); (MAK)
| | - Mark A. Krasnow
- Department of Biochemistry and HHMI, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (JC); (MAK)
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Ghabrial AS, Levi BP, Krasnow MA. A systematic screen for tube morphogenesis and branching genes in the Drosophila tracheal system. PLoS Genet 2011; 7:e1002087. [PMID: 21750678 PMCID: PMC3131284 DOI: 10.1371/journal.pgen.1002087] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 04/05/2011] [Indexed: 01/10/2023] Open
Abstract
Many signaling proteins and transcription factors that induce and pattern organs have been identified, but relatively few of the downstream effectors that execute morphogenesis programs. Because such morphogenesis genes may function in many organs and developmental processes, mutations in them are expected to be pleiotropic and hence ignored or discarded in most standard genetic screens. Here we describe a systematic screen designed to identify all Drosophila third chromosome genes (∼40% of the genome) that function in development of the tracheal system, a tubular respiratory organ that provides a paradigm for branching morphogenesis. To identify potentially pleiotropic morphogenesis genes, the screen included analysis of marked clones of homozygous mutant tracheal cells in heterozygous animals, plus a secondary screen to exclude mutations in general “house-keeping” genes. From a collection including more than 5,000 lethal mutations, we identified 133 mutations representing ∼70 or more genes that subdivide the tracheal terminal branching program into six genetically separable steps, a previously established cell specification step plus five major morphogenesis and maturation steps: branching, growth, tubulogenesis, gas-filling, and maintenance. Molecular identification of 14 of the 70 genes demonstrates that they include six previously known tracheal genes, each with a novel function revealed by clonal analysis, and two well-known growth suppressors that establish an integral role for cell growth control in branching morphogenesis. The rest are new tracheal genes that function in morphogenesis and maturation, many through cytoskeletal and secretory pathways. The results suggest systematic genetic screens that include clonal analysis can elucidate the full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ such as the Drosophila tracheal system. Elucidating the genetic programs that control formation and maintenance of body organs is a central goal of developmental biology, and understanding how these programs go awry in disease has important implications for medicine. Many such organogenesis genes have been identified, but most are early-acting “patterning genes” encoding signaling proteins and gene regulators that control expression of a poorly characterized set of downstream “morphogenesis genes,” which encode proteins that generate the remarkable organ forms and structures of the constituent cells. We screened ∼40% of the fruit fly Drosophila genome for mutations that affect tracheal (respiratory) system development. We included steps to bypass complexities from mutant effects on other tissues and steps to exclude mutations in general cell “housekeeping genes.” We isolated mutations in ∼70 genes that identify major steps in the organogenesis program including an integral cell growth control step. Many of the new tracheal genes are “morphogenesis genes” that encode proteins involved in cell structure or intracellular transport. The results suggest that genetic screens can elucidate a full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ.
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Affiliation(s)
- Amin S. Ghabrial
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Cell and Developmental Biology, University Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ASG); (MAK)
| | - Boaz P. Levi
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A. Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (ASG); (MAK)
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London NR, Zhu W, Bozza FA, Smith MCP, Greif DM, Sorensen LK, Chen L, Kaminoh Y, Chan AC, Passi SF, Day CW, Barnard DL, Zimmerman GA, Krasnow MA, Li DY. Targeting Robo4-dependent Slit signaling to survive the cytokine storm in sepsis and influenza. Sci Transl Med 2010; 2:23ra19. [PMID: 20375003 DOI: 10.1126/scitranslmed.3000678] [Citation(s) in RCA: 248] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The innate immune system provides a first line of defense against invading pathogens by releasing multiple inflammatory cytokines, such as interleukin-1beta and tumor necrosis factor-alpha, which directly combat the infectious agent and recruit additional immune responses. This exuberant cytokine release paradoxically injures the host by triggering leakage from capillaries, tissue edema, organ failure, and shock. Current medical therapies target individual pathogens with antimicrobial agents or directly either blunt or boost the host's immune system. We explored a third approach: activating with the soluble ligand Slit an endothelium-specific, Robo4-dependent signaling pathway that strengthens the vascular barrier, diminishing deleterious aspects of the host's response to the pathogen-induced cytokine storm. This approach reduced vascular permeability in the lung and other organs and increased survival in animal models of bacterial endotoxin exposure, polymicrobial sepsis, and H5N1 influenza. Thus, enhancing the resilience of the host vascular system to the host's innate immune response may provide a therapeutic strategy for treating multiple infectious agents.
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Affiliation(s)
- Nyall R London
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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Espinoza H, Krasnow MA. Large scale analysis of gene expression in the murine embryonic lung. Dev Biol 2010. [DOI: 10.1016/j.ydbio.2010.05.280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
During Drosophila metamorphosis, most larval cells die. Pupal and adult tissues form from imaginal cells, tissue-specific progenitors allocated in embryogenesis that remain quiescent during embryonic and larval life. Clonal analysis and fate mapping of single, identified cells show that tracheal system remodeling at metamorphosis involves a classical imaginal cell population and a population of differentiated, functional larval tracheal cells that reenter the cell cycle and regain developmental potency. In late larvae, both populations are activated and proliferate, spread over and replace old branches, and diversify into various stalk and coiled tracheolar cells under control of fibroblast growth factor signaling. Thus, Drosophila pupal/adult tissue progenitors can arise both by early allocation of multipotent cells and late return of differentiated cells to a multipotent state, even within a single tissue.
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Affiliation(s)
- Molly Weaver
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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46
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Babcock DT, Brock AR, Fish GS, Wang Y, Perrin L, Krasnow MA, Galko MJ. Circulating blood cells function as a surveillance system for damaged tissue in Drosophila larvae. Proc Natl Acad Sci U S A 2008; 105:10017-22. [PMID: 18632567 PMCID: PMC2474562 DOI: 10.1073/pnas.0709951105] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Indexed: 02/08/2023] Open
Abstract
Insects have an open circulatory system in which the heart pumps blood (hemolymph) into the body cavity, where it directly bathes the internal organs and epidermis. The blood contains free and tissue-bound immune cells that function in the inflammatory response. Here, we use live imaging of transgenic Drosophila larvae with fluorescently labeled blood cells (hemocytes) to investigate the circulatory dynamics of larval blood cells and their response to tissue injury. We find that, under normal conditions, the free cells rapidly circulate, whereas the tissue-bound cells are sessile. After epidermal wounding, tissue-bound cells around the wound site remain sessile and unresponsive, whereas circulating cells are rapidly recruited to the site of damage by adhesive capture. After capture, these cells distribute across the wound, appear phagocytically active, and are subsequently released back into circulation by the healing epidermis. The results demonstrate that circulating cells function as a surveillance system that monitors larval tissues for damage, and that adhesive capture, an important mechanism of recruitment of circulating cells to inflammatory sites in vertebrates, is shared by insects and vertebrates despite the vastly different architectures of their circulatory systems.
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Affiliation(s)
| | - Amanda R. Brock
- *Department of Biochemistry and Molecular Biology
- Genes and Development Graduate Program, University of Texas Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030
| | - Greg S. Fish
- Howard Hughes Medical Institute and
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305-5307; and
| | - Yan Wang
- *Department of Biochemistry and Molecular Biology
| | - Laurent Perrin
- Institut de Biologie du Développement de Marseille–Luminy, Centre National de la Recherche Scientifique–Université de la Méditéranée, Parc Scientifique de Luminy, 13288 Marseille Cedex 9, France
| | - Mark A. Krasnow
- Howard Hughes Medical Institute and
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305-5307; and
| | - Michael J. Galko
- *Department of Biochemistry and Molecular Biology
- Genes and Development Graduate Program, University of Texas Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305-5307; and
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Levi BP, Ghabrial AS, Krasnow MA. Drosophila talin and integrin genes are required for maintenance of tracheal terminal branches and luminal organization. Development 2006; 133:2383-93. [PMID: 16720877 DOI: 10.1242/dev.02404] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Epithelial tubes that compose many organs are typically long lasting, except under specific developmental and physiological conditions when network remodeling occurs. Although there has been progress elucidating mechanisms of tube formation, little is known of the mechanisms that maintain tubes and destabilize them during network remodeling. Here, we describe Drosophila tendrils mutations that compromise maintenance of tracheal terminal branches, fine gauge tubes formed by tracheal terminal cells that ramify on and adhere tightly to tissues in order to supply them with oxygen. Homozygous tendrils terminal cell clones have fewer terminal branches than normal but individual branches contain multiple convoluted lumens. The phenotype arises late in development: terminal branches bud and form lumens normally early in development, but during larval life lumens become convoluted and mature branches degenerate. Their lumens, however, are retained in the remaining branches, resulting in the distinctive multi-lumen phenotype. Mapping and molecular studies demonstrate that tendrils is allelic to rhea, which encodes Drosophila talin, a large cytoskeletal protein that links integrins to the cytoskeleton. Terminal cells mutant for myospheroid, the major Drosophila beta-integrin, or doubly mutant for multiple edematous wings and inflated alpha-integrins, also show the tendrils phenotype, and localization of myospheroid beta-integrin protein is disrupted in tendrils mutant terminal cells. The results provide evidence that integrin-talin adhesion complexes are necessary to maintain tracheal terminal branches and luminal organization. Similar complexes may stabilize other tubular networks and may be targeted for inactivation during network remodeling events.
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Affiliation(s)
- Boaz P Levi
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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48
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Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance mechanism that degrades transcripts containing premature translation termination codons, and it also influences expression of certain wild-type transcripts. Although the biochemical mechanisms of NMD have been studied intensively, its developmental functions and importance are less clear. Here, we describe the isolation and characterization of Drosophila “photoshop” mutations, which increase expression of green fluorescent protein and other transgenes. Mapping and molecular analyses show that photoshop mutations are loss-of-function mutations in the Drosophila homologs of NMD genes Upf1, Upf2, and Smg1. We find that Upf1 and Upf2 are broadly active during development, and they are required for NMD as well as for proper expression of dozens of wild-type genes during development and for larval viability. Genetic mosaic analysis shows that Upf1 and Upf2 are required for growth and/or survival of imaginal cell clones, but this defect can be overcome if surrounding wild-type cells are eliminated. By contrast, we find that the PI3K-related kinase Smg1 potentiates but is not required for NMD or for viability, implying that the Upf1 phosphorylation cycle that is required for mammalian and Caenorhabditis elegans NMD has a more limited role during Drosophila development. Finally, we show that the SV40 3′ UTR, present in many Drosophila transgenes, targets the transgenes for regulation by the NMD pathway. The results establish that the Drosophila NMD pathway is broadly active and essential for development, and one critical function of the pathway is to endow proliferating imaginal cells with a competitive growth advantage that prevents them from being overtaken by other proliferating cells. Cells possess a variety of surveillance mechanisms that detect and dispose of defective gene products. One such system is the nonsense-mediated mRNA decay (NMD) pathway, which degrades aberrant mRNAs containing nonsense mutations or other premature translation stop signals. In a genetic screen in Drosophila, the authors identified a set of mutations they call “photoshop” mutations because they increase expression of green fluorescent protein transgenes such that cells expressing green fluorescent protein are more easily visualized. They found that the photoshop mutations are mutations in three different genes implicated in NMD. Using these mutations, they show that the NMD pathway not only degrades mutant mRNAs but also influences expression of many transgenes and dozens of endogenous genes during development and is essential for development beyond the larval stage. One important function of the pathway is to provide proliferating cells with a competitive growth advantage that prevents them from being overtaken by other proliferating cells during development. Thus, the Drosophila NMD pathway has critical cellular and developmental roles beyond the classical surveillance function of eliminating mutant transcripts.
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Affiliation(s)
- Mark M Metzstein
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A Krasnow
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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49
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Ghabrial AS, Krasnow MA. Social interactions among epithelial cells during tracheal branching morphogenesis. Nature 2006; 441:746-9. [PMID: 16760977 DOI: 10.1038/nature04829] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [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: 10/30/2005] [Accepted: 04/19/2006] [Indexed: 11/09/2022]
Abstract
Many organs are composed of tubular networks that arise by branching morphogenesis in which cells bud from an epithelium and organize into a tube. Fibroblast growth factors (FGFs) and other signalling molecules have been shown to guide branch budding and outgrowth, but it is not known how epithelial cells coordinate their movements and morphogenesis. Here we use genetic mosaic analysis in Drosophila melanogaster to show that there are two functionally distinct classes of cells in budding tracheal branches: cells at the tip that respond directly to Branchless FGF and lead branch outgrowth, and trailing cells that receive a secondary signal to follow the lead cells and form a tube. These roles are not pre-specified; rather, there is competition between cells such that those with the highest FGF receptor activity take the lead positions, whereas those with less FGF receptor activity assume subsidiary positions and form the branch stalk. Competition appears to involve Notch-mediated lateral inhibition that prevents extra cells from assuming the lead. There may also be cooperation between budding cells, because in a mosaic epithelium, cells that cannot respond to the chemoattractant, or respond only poorly, allow other cells in the epithelium to move ahead of them.
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Affiliation(s)
- Amin S Ghabrial
- Howard Hughes Medical Institute, Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305-5307, USA
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50
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Jarvis LA, Toering SJ, Simon MA, Krasnow MA, Smith-Bolton RK. Sprouty proteins are in vivo targets of Corkscrew/SHP-2 tyrosine phosphatases. Development 2006; 133:1133-42. [PMID: 16481357 DOI: 10.1242/dev.02255] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Drosophila Corkscrew protein and its vertebrate ortholog SHP-2(now known as Ptpn11) positively modulate receptor tyrosine kinase (RTK)signaling during development, but how these tyrosine phosphatases promote tyrosine kinase signaling is not well understood. Sprouty proteins are tyrosine-phosphorylated RTK feedback inhibitors, but their regulation and mechanism of action are also poorly understood. Here, we show that Corkscrew/SHP-2 proteins control Sprouty phosphorylation and function. Genetic experiments demonstrate that Corkscrew/SHP-2 and Sprouty proteins have opposite effects on RTK-mediated developmental events in Drosophilaand an RTK signaling process in cultured mammalian cells, and the genes display dose-sensitive genetic interactions. In cultured cells, inactivation of SHP-2 increases phosphorylation on the critical tyrosine of Sprouty 1. SHP-2 associates in a complex with Sprouty 1 in cultured cells and in vitro,and a purified SHP-2 protein dephosphorylates the critical tyrosine of Sprouty 1. Substrate-trapping forms of Corkscrew bind Sprouty in cultured Drosophila cells and the developing eye. These results identify Sprouty proteins as in vivo targets of Corkscrew/SHP-2 tyrosine phosphatases and show how Corkscrew/SHP-2 proteins can promote RTK signaling by inactivating a feedback inhibitor. We propose that this double-negative feedback circuit shapes the output profile of RTK signaling events.
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Affiliation(s)
- Lesley A Jarvis
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5307 USA
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