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Uytingco CR, Chew J, Hartnett AD, Weisenfeld N, Williams SR, Ziraldo SB, Meschi F, Miller K, Yin Y. Spatially resolved transcriptomics in the APPSWE [Tg2576] mouse model of Alzheimer’s disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.061888] [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: 12/24/2022]
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Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature 2020; 588:670-675. [PMID: 33238290 PMCID: PMC8003326 DOI: 10.1038/s41586-020-3014-1] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/18/2020] [Indexed: 12/17/2022]
Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate the investigation of pathologies such as interstitial lung disease, cancer and coronavirus disease 2019 (COVID-19) pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we describe the development of a long-term feeder-free, chemically defined culture system for distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids were able to differentiate into AT1 cells, and basal cell organoids developed lumens lined with differentiated club and ciliated cells. Single-cell analysis of KRT5+ cells in basal organoids revealed a distinct population of ITGA6+ITGB4+ mitotic cells, whose offspring further segregated into a TNFRSF12Ahi subfraction that comprised about ten per cent of KRT5+ basal cells. This subpopulation formed clusters within terminal bronchioles and exhibited enriched clonogenic organoid growth activity. We created distal lung organoids with apical-out polarity to present ACE2 on the exposed external surface, facilitating infection of AT2 and basal cultures with SARS-CoV-2 and identifying club cells as a target population. This long-term, feeder-free culture of human distal lung organoids, coupled with single-cell analysis, identifies functional heterogeneity among basal cells and establishes a facile in vitro organoid model of human distal lung infections, including COVID-19-associated pneumonia.
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Affiliation(s)
- Ameen A Salahudeen
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Shannon S Choi
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Rustagi
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Junjie Zhu
- Stanford University School of Engineering, Department of Electrical Engineering, Stanford, CA, USA
| | - Vincent van Unen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean M de la O
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mar Margalef-Català
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - António J M Santos
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jihang Ju
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arpit Batish
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tatsuya Usui
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vincent Luca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benedict Anchang
- Division of Biomedical Data Science, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Monica Nagendran
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Khanh Nguyen
- Division of Gastroenterology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel J Hart
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Pehr B Harbury
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey S Glenn
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chiara Sabatti
- Division of Biomedical Data Science, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel R Amieva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Blish
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Calvin J Kuo
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Salahudeen AA, Choi SS, Rustagi A, Zhu J, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, van Unen V, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.27.212076. [PMID: 32743583 PMCID: PMC7386503 DOI: 10.1101/2020.07.27.212076] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange and is affected by disorders including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. Investigations of these localized pathologies have been hindered by a lack of 3D in vitro human distal lung culture systems. Further, human distal lung stem cell identification has been impaired by quiescence, anatomic divergence from mouse and lack of lineage tracing and clonogenic culture. Here, we developed robust feeder-free, chemically-defined culture of distal human lung progenitors as organoids derived clonally from single adult human alveolar epithelial type II (AT2) or KRT5 + basal cells. AT2 organoids exhibited AT1 transdifferentiation potential, while basal cell organoids progressively developed lumens lined by differentiated club and ciliated cells. Organoids consisting solely of club cells were not observed. Upon single cell RNA-sequencing (scRNA-seq), alveolar organoids were composed of proliferative AT2 cells; however, basal organoid KRT5 + cells contained a distinct ITGA6 + ITGB4 + mitotic population whose proliferation segregated to a TNFRSF12A hi subfraction. Clonogenic organoid growth was markedly enriched within the TNFRSF12A hi subset of FACS-purified ITGA6 + ITGB4 + basal cells from human lung or derivative organoids. In vivo, TNFRSF12A + cells comprised ~10% of KRT5 + basal cells and resided in clusters within terminal bronchioles. To model COVID-19 distal lung disease, we everted the polarity of basal and alveolar organoids to rapidly relocate differentiated club and ciliated cells from the organoid lumen to the exterior surface, thus displaying the SARS-CoV-2 receptor ACE2 on the outwardly-facing apical aspect. Accordingly, basal and AT2 apical-out organoids were infected by SARS-CoV-2, identifying club cells as a novel target population. This long-term, feeder-free organoid culture of human distal lung alveolar and basal stem cells, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and exemplifies progenitor identification within a slowly proliferating human tissue. Further, our studies establish a facile in vitro organoid model for human distal lung infectious diseases including COVID-19-associated pneumonia.
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Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K, Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R, Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT, Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L, Henning SJ, Wong MH, Kuo CJ. Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell 2017; 21:78-90.e6. [PMID: 28686870 PMCID: PMC5642297 DOI: 10.1016/j.stem.2017.06.014] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [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: 09/07/2016] [Revised: 04/17/2017] [Accepted: 06/20/2017] [Indexed: 12/22/2022]
Abstract
Several cell populations have been reported to possess intestinal stem cell (ISC) activity during homeostasis and injury-induced regeneration. Here, we explored inter-relationships between putative mouse ISC populations by comparative RNA-sequencing (RNA-seq). The transcriptomes of multiple cycling ISC populations closely resembled Lgr5+ ISCs, the most well-defined ISC pool, but Bmi1-GFP+ cells were distinct and enriched for enteroendocrine (EE) markers, including Prox1. Prox1-GFP+ cells exhibited sustained clonogenic growth in vitro, and lineage-tracing of Prox1+ cells revealed long-lived clones during homeostasis and after radiation-induced injury in vivo. Single-cell mRNA-seq revealed two subsets of Prox1-GFP+ cells, one of which resembled mature EE cells while the other displayed low-level EE gene expression but co-expressed tuft cell markers, Lgr5 and Ascl2, reminiscent of label-retaining secretory progenitors. Our data suggest that the EE lineage, including mature EE cells, comprises a reservoir of homeostatic and injury-inducible ISCs, extending our understanding of cellular plasticity and stemness.
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Affiliation(s)
- Kelley S Yan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Olivier Gevaert
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Benedict Anchang
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher S Probert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn A Larkin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paige S Davies
- Oregon Health & Science University, Department of Cell, Developmental and Cancer Biology, Portland, OR 97239, USA
| | - Zhuan-Fen Cheng
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Arnold Han
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Columbia Center for Translational Immunology, Department of Medicine, Division of Digestive and Liver Diseases, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Kelly Roelf
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruben I Calderon
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Esther Cynn
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiaoyi Hu
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Komal Mandleywala
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Department of Medicine, Division of Digestive and Liver Diseases, Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Julie Wilhelmy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sue M Grimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David C Corney
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | | | | | - Fengchao Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Nicholas R Smith
- Oregon Health & Science University, Department of Cell, Developmental and Cancer Biology, Portland, OR 97239, USA
| | - Parthasarathy Chandrakesan
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Randal May
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Mary Ann S Chrissy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajan Jain
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Joyce C Niland
- Department of Diabetes and Cancer Discovery Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Young-Kwon Hong
- Departments of Surgery and of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jill Carrington
- National Institutes of Health, Division of Digestive Diseases and Nutrition, NIDDK, Bethesda, MD 20892, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jonathan Epstein
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Courtney W Houchen
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - John P Lynch
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin G Martin
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Mattel Children's Hospital and the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvia K Plevritis
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Curtis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hanlee P Ji
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Susan J Henning
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa H Wong
- Oregon Health & Science University, Department of Cell, Developmental and Cancer Biology, Portland, OR 97239, USA
| | - Calvin J Kuo
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH. Massively parallel digital transcriptional profiling of single cells. Nat Commun 2017; 8:14049. [PMID: 28091601 PMCID: PMC5241818 DOI: 10.1038/ncomms14049] [Citation(s) in RCA: 3238] [Impact Index Per Article: 462.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/23/2016] [Indexed: 02/07/2023] Open
Abstract
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.
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Affiliation(s)
| | | | | | - Paul Ryvkin
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Ryan Wilson
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Junjie Zhu
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Joe Shuga
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Jason G Underwood
- 10x Genomics Inc., Pleasanton, California, 94566, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | - Paul W Wyatt
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Kevin D Ness
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Lan W Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Christopher McFarland
- Seattle Cancer Care Alliance Clinical Immunogenetics Laboratory, Seattle, Washington 98109, USA
| | - Keith R Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emily A Stevens
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | | | | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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