1
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Zhao W, Kepecs B, Mahadevan NR, Segerstolpe A, Weirather JL, Besson NR, Giotti B, Soong BY, Li C, Vigneau S, Slyper M, Wakiro I, Jane-Valbuena J, Ashenberg O, Rotem A, Bueno R, Rozenblatt-Rosen O, Pfaff K, Rodig S, Hata AN, Regev A, Johnson BE, Tsankov AM. A cellular and spatial atlas of TP53 -associated tissue remodeling in lung adenocarcinoma. bioRxiv 2024:2023.06.28.546977. [PMID: 37425718 PMCID: PMC10327017 DOI: 10.1101/2023.06.28.546977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
TP53 is the most frequently mutated gene across many cancers and is associated with shorter survival in lung adenocarcinoma (LUAD). To define how TP53 mutations affect the LUAD tumor microenvironment (TME), we constructed a multi-omic cellular and spatial tumor atlas of 23 treatment-naïve human lung tumors. We found that TP53 -mutant ( TP53 mut ) malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across resectable LUAD patient tumors, genetically engineered mouse models, and cell lines harboring a wide spectrum of TP53 mutations. We further identified a multicellular tumor niche composed of SPP1 + macrophages and collagen-expressing fibroblasts that coincides with hypoxic, pro-metastatic expression programs in TP53 mut tumors. Spatially correlated angiostatic and immune checkpoint interactions, including CD274 - PDCD1 and PVR - TIGIT , are also enriched in TP53 mut LUAD tumors, which may influence response to checkpoint blockade therapy. Our methodology can be further applied to investigate mutation-specific TME changes in other cancers.
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2
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Mzoughi S, Schwarz M, Wang X, Demircioglu D, Ulukaya G, Mohammed K, Tullio FD, Company C, Dramaretska Y, Leushacke M, Giotti B, Lannagan T, Lozano-Ojalvo D, Hasson D, Tsankov AM, Sansom OJ, Marine JC, Barker N, Gargiulo G, Guccione E. A Mutation-driven oncofetal regression fuels phenotypic plasticity in colorectal cancer. bioRxiv 2023:2023.12.10.570854. [PMID: 38106050 PMCID: PMC10723414 DOI: 10.1101/2023.12.10.570854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Targeting cancer stem cells (CSCs) is crucial for effective cancer treatment 1 . However, the molecular mechanisms underlying resistance to LGR5 + CSCs depletion in colorectal cancer (CRC) 2,3 remain largely elusive. Here, we unveil the existence of a primitive cell state dubbed the oncofetal (OnF) state, which works in tandem with the LGR5 + stem cells (SCs) to fuel tumor evolution in CRC. OnF cells emerge early during intestinal tumorigenesis and exhibit features of lineage plasticity. Normally suppressed by the Retinoid X Receptor (RXR) in mature SCs, the OnF program is triggered by genetic deletion of the gatekeeper APC. We demonstrate that diminished RXR activity unlocks an epigenetic circuity governed by the cooperative action of YAP and AP1, leading to OnF reprogramming. This high-plasticity state is inherently resistant to conventional chemotherapies and its adoption by LGR5 + CSCs enables them to enter a drug-tolerant state. Furthermore, through phenotypic tracing and ablation experiments, we uncover a functional redundancy between the OnF and stem cell (SC) states and show that targeting both cellular states is essential for sustained tumor regression in vivo . Collectively, these findings establish a mechanistic foundation for developing effective combination therapies with enduring impact on CRC treatment.
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3
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Chen Z, Giotti B, Kaluzova M, Vallcorba MP, Rawat K, Price G, Herting CJ, Pinero G, Cristea S, Ross JL, Ackley J, Maximov V, Szulzewsky F, Thomason W, Marquez-Ropero M, Angione A, Nichols N, Tsankova NM, Michor F, Shayakhmetov DM, Gutmann DH, Tsankov AM, Hambardzumyan D. A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. J Clin Invest 2023; 133:e163802. [PMID: 37733448 PMCID: PMC10645395 DOI: 10.1172/jci163802] [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: 08/01/2022] [Accepted: 09/19/2023] [Indexed: 09/23/2023] Open
Abstract
Monocytes and monocyte-derived macrophages (MDMs) from blood circulation infiltrate glioblastoma (GBM) and promote growth. Here, we show that PDGFB-driven GBM cells induce the expression of the potent proinflammatory cytokine IL-1β in MDM, which engages IL-1R1 in tumor cells, activates the NF-κB pathway, and subsequently leads to induction of monocyte chemoattractant proteins (MCPs). Thus, a feedforward paracrine circuit of IL-1β/IL-1R1 between tumors and MDM creates an interdependence driving PDGFB-driven GBM progression. Genetic loss or locally antagonizing IL-1β/IL-1R1 leads to reduced MDM infiltration, diminished tumor growth, and reduced exhausted CD8+ T cells and thereby extends the survival of tumor-bearing mice. In contrast to IL-1β, IL-1α exhibits antitumor effects. Genetic deletion of Il1a/b is associated with decreased recruitment of lymphoid cells and loss-of-interferon signaling in various immune populations and subsets of malignant cells and is associated with decreased survival time of PDGFB-driven tumor-bearing mice. In contrast to PDGFB-driven GBM, Nf1-silenced tumors have a constitutively active NF-κB pathway, which drives the expression of MCPs to recruit monocytes into tumors. These results indicate local antagonism of IL-1β could be considered as an effective therapy specifically for proneural GBM.
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Affiliation(s)
- Zhihong Chen
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Milota Kaluzova
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
- Department of Neurology, Rutgers University, New Brunswick, New Jersey, USA
| | - Montse Puigdelloses Vallcorba
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Kavita Rawat
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Gabrielle Price
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Cameron J. Herting
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
| | - Gonzalo Pinero
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - James L. Ross
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
- Emory University Department of Microbiology and Immunology, Emory Vaccine Center, Atlanta, Georgia, USA
| | - James Ackley
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
| | - Victor Maximov
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
| | - Frank Szulzewsky
- Department of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Wes Thomason
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Mar Marquez-Ropero
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Angelo Angione
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | | | - Nadejda M. Tsankova
- Department of Pathology and Molecular and Cell-Based Medicine, Mount Sinai Icahn School of Medicine, New York, New York, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- The Ludwig Center at Harvard, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dmitry M. Shayakhmetov
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology and Emory Vaccine Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David H. Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alexander M. Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, New York, USA
- Department of Pediatrics, AFLAC Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Winship Cancer Institute, and
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurosurgery and
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4
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Sattiraju A, Kang S, Giotti B, Chen Z, Marallano VJ, Brusco C, Ramakrishnan A, Shen L, Tsankov AM, Hambardzumyan D, Friedel RH, Zou H. Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression. Immunity 2023; 56:1825-1843.e6. [PMID: 37451265 PMCID: PMC10527169 DOI: 10.1016/j.immuni.2023.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 03/01/2022] [Revised: 02/24/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Glioblastoma (GBM), a highly lethal brain cancer, is notorious for immunosuppression, but the mechanisms remain unclear. Here, we documented a temporospatial patterning of tumor-associated myeloid cells (TAMs) corresponding to vascular changes during GBM progression. As tumor vessels transitioned from the initial dense regular network to later scant and engorged vasculature, TAMs shifted away from perivascular regions and trafficked to vascular-poor areas. This process was heavily influenced by the immunocompetence state of the host. Utilizing a sensitive fluorescent UnaG reporter to track tumor hypoxia, coupled with single-cell transcriptomics, we revealed that hypoxic niches attracted and sequestered TAMs and cytotoxic T lymphocytes (CTLs), where they were reprogrammed toward an immunosuppressive state. Mechanistically, we identified chemokine CCL8 and cytokine IL-1β as two hypoxic-niche factors critical for TAM trafficking and co-evolution of hypoxic zones into pseudopalisading patterns. Therefore, perturbation of TAM patterning in hypoxic zones may improve tumor control.
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Affiliation(s)
- Anirudh Sattiraju
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sangjo Kang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhihong Chen
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valerie J Marallano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Concetta Brusco
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dolores Hambardzumyan
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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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Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Intratumoral dendritic cell-CD4 + T helper cell niches enable CD8 + T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 2023; 29:1389-1399. [PMID: 37322116 PMCID: PMC11027932 DOI: 10.1038/s41591-023-02345-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [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: 06/09/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Despite no apparent defects in T cell priming and recruitment to tumors, a large subset of T cell rich tumors fail to respond to immune checkpoint blockade (ICB). We leveraged a neoadjuvant anti-PD-1 trial in patients with hepatocellular carcinoma (HCC), as well as additional samples collected from patients treated off-label, to explore correlates of response to ICB within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+CH25H+IL-21+PD-1+CD4+ T helper cells ("CXCL13+ TH") and Granzyme K+ PD-1+ effector-like CD8+ T cells, whereas terminally exhausted CD39hiTOXhiPD-1hiCD8+ T cells dominated in nonresponders. CD4+ and CD8+ T cell clones that expanded post-treatment were found in pretreatment biopsies. Notably, PD-1+TCF-1+ (Progenitor-exhausted) CD8+ T cells shared clones mainly with effector-like cells in responders or terminally exhausted cells in nonresponders, suggesting that local CD8+ T cell differentiation occurs upon ICB. We found that these Progenitor CD8+ T cells interact with CXCL13+ TH within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ TH control the differentiation of tumor-specific Progenitor exhasuted CD8+ T cells following ICB.
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Affiliation(s)
- Assaf Magen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Fiaschi
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Brian Y Soong
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphaël Mattiuz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Etienne Humblin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanna Troncoso
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Darwin D'souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Kim
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Hamel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hara Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nausicaa Malissen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonit Lavin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandra Soares-Schanoski
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Zhao
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen C Ward
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Isabel Fiel
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Baijun Kou
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Michael Dobosz
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Lianjie Li
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Christina Adler
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Min Ni
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Yi Wei
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Wei Wang
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Gurinder S Atwal
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kunal Kundu
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kamil J Cygan
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Namita T Gupta
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raquel P Deering
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Myron Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Thomas U Marron
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gavin Thurston
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA.
| | - Alice O Kamphorst
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Institute for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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7
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Chen Z, Soni N, Pinero G, Giotti B, Eddins DJ, Lindblad KE, Ross JL, Puigdelloses Vallcorba M, Joshi T, Angione A, Thomason W, Keane A, Tsankova NM, Gutmann DH, Lira SA, Lujambio A, Ghosn EEB, Tsankov AM, Hambardzumyan D. Monocyte depletion enhances neutrophil influx and proneural to mesenchymal transition in glioblastoma. Nat Commun 2023; 14:1839. [PMID: 37012245 PMCID: PMC10070461 DOI: 10.1038/s41467-023-37361-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 01/06/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Myeloid cells comprise the majority of immune cells in tumors, contributing to tumor growth and therapeutic resistance. Incomplete understanding of myeloid cells response to tumor driver mutation and therapeutic intervention impedes effective therapeutic design. Here, by leveraging CRISPR/Cas9-based genome editing, we generate a mouse model that is deficient of all monocyte chemoattractant proteins. Using this strain, we effectively abolish monocyte infiltration in genetically engineered murine models of de novo glioblastoma (GBM) and hepatocellular carcinoma (HCC), which show differential enrichment patterns for monocytes and neutrophils. Eliminating monocyte chemoattraction in monocyte enriched PDGFB-driven GBM invokes a compensatory neutrophil influx, while having no effect on Nf1-silenced GBM model. Single-cell RNA sequencing reveals that intratumoral neutrophils promote proneural-to-mesenchymal transition and increase hypoxia in PDGFB-driven GBM. We further demonstrate neutrophil-derived TNF-a directly drives mesenchymal transition in PDGFB-driven primary GBM cells. Genetic or pharmacological inhibiting neutrophils in HCC or monocyte-deficient PDGFB-driven and Nf1-silenced GBM models extend the survival of tumor-bearing mice. Our findings demonstrate tumor-type and genotype dependent infiltration and function of monocytes and neutrophils and highlight the importance of targeting them simultaneously for cancer treatments.
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Affiliation(s)
- Zhihong Chen
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Nishant Soni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gonzalo Pinero
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Devon J Eddins
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Medicine, Lowance Center for Human Immunology and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Katherine E Lindblad
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James L Ross
- Emory University Department of Microbiology and Immunology, Emory Vaccine Center, Atlanta, GA, 30322, USA
| | | | - Tanvi Joshi
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Angelo Angione
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wes Thomason
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aislinn Keane
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nadejda M Tsankova
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sergio A Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eliver E B Ghosn
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Medicine, Lowance Center for Human Immunology and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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8
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Martin-Serrano MA, Kepecs B, Torres-Martin M, Bramel ER, Haber PK, Merritt E, Rialdi A, Param NJ, Maeda M, Lindblad KE, Carter JK, Barcena-Varela M, Mazzaferro V, Schwartz M, Affo S, Schwabe RF, Villanueva A, Guccione E, Friedman SL, Lujambio A, Tocheva A, Llovet JM, Thung SN, Tsankov AM, Sia D. Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications. Gut 2023; 72:736-748. [PMID: 35584893 PMCID: PMC10388405 DOI: 10.1136/gutjnl-2021-326514] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The diversity of the tumour microenvironment (TME) of intrahepatic cholangiocarcinoma (iCCA) has not been comprehensively assessed. We aimed to generate a novel molecular iCCA classifier that incorporates elements of the stroma, tumour and immune microenvironment ('STIM' classification). DESIGN We applied virtual deconvolution to transcriptomic data from ~900 iCCAs, enabling us to devise a novel classification by selecting for the most relevant TME components. Murine models were generated through hydrodynamic tail vein injection and compared with the human disease. RESULTS iCCA is composed of five robust STIM classes encompassing both inflamed (35%) and non-inflamed profiles (65%). The inflamed classes, named immune classical (~10%) and inflammatory stroma (~25%), differ in oncogenic pathways and extent of desmoplasia, with the inflammatory stroma showing T cell exhaustion, abundant stroma and KRAS mutations (p<0.001). Analysis of cell-cell interactions highlights cancer-associated fibroblast subtypes as potential mediators of immune evasion. Among the non-inflamed classes, the desert-like class (~20%) harbours the lowest immune infiltration with abundant regulatory T cells (p<0.001), whereas the hepatic stem-like class (~35%) is enriched in 'M2-like' macrophages, mutations in IDH1/2 and BAP1, and FGFR2 fusions. The remaining class (tumour classical: ~10%) is defined by cell cycle pathways and poor prognosis. Comparative analysis unveils high similarity between a KRAS/p19 murine model and the inflammatory stroma class (p=0.02). The KRAS-SOS inhibitor, BI3406, sensitises a KRAS-mutant iCCA murine model to anti-PD1 therapy. CONCLUSIONS We describe a comprehensive TME-based stratification of iCCA. Cross-species analysis establishes murine models that align closely to human iCCA for the preclinical testing of combination strategies.
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Affiliation(s)
- Miguel A Martin-Serrano
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Kepecs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miguel Torres-Martin
- Translational Research in Hepatic Oncology, Liver Unit, IDIBAPS, Hospital Clinic, University of Barcelona, Barcelona, Catalunya, Spain
| | - Emily R Bramel
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philipp K Haber
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Elliot Merritt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Precision Immunology Institute (PrIISM), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Rialdi
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nesteene Joy Param
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miho Maeda
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Katherine E Lindblad
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Precision Immunology Institute (PrIISM), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James K Carter
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina Barcena-Varela
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Precision Immunology Institute (PrIISM), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Vincenzo Mazzaferro
- General Surgery and Liver Transplantation Unit, Department of Oncology and Hemato-Oncology, University of Milan and Istituto Nazionale Tumori, IRCCS Foundation, Milano, Lombardia, Italy
| | - Myron Schwartz
- Department of Surgery, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Silvia Affo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalunya, Spain
| | - Robert F Schwabe
- Department of Medicine, Columbia University, New York, New York, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ernesto Guccione
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amaia Lujambio
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Precision Immunology Institute (PrIISM), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anna Tocheva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Precision Immunology Institute (PrIISM), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Josep M Llovet
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Translational Research in Hepatic Oncology, Liver Unit, IDIBAPS, Hospital Clinic, University of Barcelona, Barcelona, Catalunya, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Swan N Thung
- Department of Pathology, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daniela Sia
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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9
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Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Slyper M, Wang J, Van Wittenberghe N, Rouhana JM, Waldman J, Ashenberg O, Lek M, Dionne D, Win TS, Cuoco MS, Kuksenko O, Tsankov AM, Branton PA, Marshall JL, Greka A, Getz G, Segrè AV, Aguet F, Rozenblatt-Rosen O, Ardlie KG, Regev A. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science 2022; 376:eabl4290. [PMID: 35549429 PMCID: PMC9383269 DOI: 10.1126/science.abl4290] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [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: 12/12/2022]
Abstract
Understanding gene function and regulation in homeostasis and disease requires knowledge of the cellular and tissue contexts in which genes are expressed. Here, we applied four single-nucleus RNA sequencing methods to eight diverse, archived, frozen tissue types from 16 donors and 25 samples, generating a cross-tissue atlas of 209,126 nuclei profiles, which we integrated across tissues, donors, and laboratory methods with a conditional variational autoencoder. Using the resulting cross-tissue atlas, we highlight shared and tissue-specific features of tissue-resident cell populations; identify cell types that might contribute to neuromuscular, metabolic, and immune components of monogenic diseases and the biological processes involved in their pathology; and determine cell types and gene modules that might underlie disease mechanisms for complex traits analyzed by genome-wide association studies.
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Affiliation(s)
- Gökcen Eraslan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shankara Anand
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Evgenij Fiskin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiali Wang
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - John M. Rouhana
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thet Su Win
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Michael S. Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Olena Kuksenko
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Philip A. Branton
- The Joint Pathology Center Gynecologic/Breast Pathology, Silver Spring, MD 20910, USA
| | | | - Anna Greka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020; 26:1307. [PMID: 32587393 PMCID: PMC7417328 DOI: 10.1038/s41591-020-0976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Isaac Wakiro
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jingyi Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sébastien Vigneau
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara Napolitano
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Asa Karlstrom
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon Gritsch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Nomura
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Satyen H Gohil
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ofir Cohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bo Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.,Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Ludwig Center for Cancer Research at Harvard, Boston, MA, USA.,Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Rizwan Haq
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth H Stover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael R Clay
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Natalie B Collins
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikhil Wagle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020; 26:792-802. [PMID: 32405060 PMCID: PMC7220853 DOI: 10.1038/s41591-020-0844-1] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/20/2020] [Indexed: 01/20/2023]
Abstract
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.
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Affiliation(s)
- Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Isaac Wakiro
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jingyi Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sébastien Vigneau
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara Napolitano
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Asa Karlstrom
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon Gritsch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Nomura
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Satyen H Gohil
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ofir Cohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bo Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA, USA
- Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Rizwan Haq
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth H Stover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael R Clay
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Natalie B Collins
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikhil Wagle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Tsankov AM, Wadsworth MH, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Development 2019; 146:dev174722. [PMID: 31515224 PMCID: PMC6803377 DOI: 10.1242/dev.174722] [Citation(s) in RCA: 5] [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: 12/07/2018] [Accepted: 08/12/2019] [Indexed: 01/23/2023]
Abstract
Maintenance of pluripotency and specification towards a new cell fate are both dependent on precise interactions between extrinsic signals and transcriptional and epigenetic regulators. Directed methylation of cytosines by the de novo methyltransferases DNMT3A and DNMT3B plays an important role in facilitating proper differentiation, whereas DNMT1 is essential for maintaining global methylation levels in all cell types. Here, we generated single-cell mRNA expression data from wild-type, DNMT3A, DNMT3A/3B and DNMT1 knockout human embryonic stem cells and observed a widespread increase in cellular and transcriptional variability, even with limited changes in global methylation levels in the de novo knockouts. Furthermore, we found unexpected transcriptional repression upon either loss of the de novo methyltransferase DNMT3A or the double knockout of DNMT3A/3B that is further propagated upon differentiation to mesoderm and ectoderm. Taken together, our single-cell RNA-sequencing data provide a high-resolution view into the consequences of depleting the three catalytically active DNMTs in human pluripotent stem cells.
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Affiliation(s)
- Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Samuel J Allon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Aleksandra Arczewska
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin E Mead
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Riley S Drake
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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13
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Tome-Garcia J, Erfani P, Nudelman G, Tsankov AM, Katsyv I, Tejero R, Bin Zhang, Walsh M, Friedel RH, Zaslavsky E, Tsankova NM. Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma. Nat Commun 2018; 9:4020. [PMID: 30275445 PMCID: PMC6167382 DOI: 10.1038/s41467-018-06258-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 09/13/2017] [Accepted: 08/21/2018] [Indexed: 12/17/2022] Open
Abstract
The intrinsic drivers of migration in glioblastoma (GBM) are poorly understood. To better capture the native molecular imprint of GBM and its developmental context, here we isolate human stem cell populations from GBM (GSC) and germinal matrix tissues and map their chromatin accessibility via ATAC-seq. We uncover two distinct regulatory GSC signatures, a developmentally shared/proliferative and a tumor-specific/migratory one in which TEAD1/4 motifs are uniquely overrepresented. Using ChIP-PCR, we validate TEAD1 trans occupancy at accessibility sites within AQP4, EGFR, and CDH4. To further characterize TEAD’s functional role in GBM, we knockout TEAD1 or TEAD4 in patient-derived GBM lines using CRISPR-Cas9. TEAD1 ablation robustly diminishes migration, both in vitro and in vivo, and alters migratory and EMT transcriptome signatures with consistent downregulation of its target AQP4. TEAD1 overexpression restores AQP4 expression, and both TEAD1 and AQP4 overexpression rescue migratory deficits in TEAD1-knockout cells, implicating a direct regulatory role for TEAD1–AQP4 in GBM migration. The intrinsic drivers of glioblastoma (GBM) migration are still poorly understood. Here the authors purify GBM stem cells (GSCs) from patients and profile chromatin accessibility in these cells, identifying TEAD1 as a regulator of migration in human glioblastoma.
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Affiliation(s)
- Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Parsa Erfani
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Igor Katsyv
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rut Tejero
- Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Martin Walsh
- Department of Pharmacological Sciences, Center for RNA Biology and Medicine, New York, NY, 10029, USA
| | - Roland H Friedel
- Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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14
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Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 2018; 560:319-324. [PMID: 30069044 PMCID: PMC6295155 DOI: 10.1038/s41586-018-0393-7] [Citation(s) in RCA: 684] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 06/21/2018] [Indexed: 12/16/2022]
Abstract
The airways of the lung are the primary sites of disease in asthma and cystic fibrosis. Here we study the cellular composition and hierarchy of the mouse tracheal epithelium by single-cell RNA-sequencing (scRNA-seq) and in vivo lineage tracing. We identify a rare cell type, the Foxi1+ pulmonary ionocyte; functional variations in club cells based on their location; a distinct cell type in high turnover squamous epithelial structures that we term 'hillocks'; and disease-relevant subsets of tuft and goblet cells. We developed 'pulse-seq', combining scRNA-seq and lineage tracing, to show that tuft, neuroendocrine and ionocyte cells are continually and directly replenished by basal progenitor cells. Ionocytes are the major source of transcripts of the cystic fibrosis transmembrane conductance regulator in both mouse (Cftr) and human (CFTR). Knockout of Foxi1 in mouse ionocytes causes loss of Cftr expression and disrupts airway fluid and mucus physiology, phenotypes that are characteristic of cystic fibrosis. By associating cell-type-specific expression programs with key disease genes, we establish a new cellular narrative for airways disease.
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Affiliation(s)
- Daniel T Montoro
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam L Haber
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Vladimir Vinarsky
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Susan E Birket
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL, USA
| | - Feng Yuan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sijia Chen
- Department of Experimental Immunology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - Hui Min Leung
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jorge Villoria
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Burgin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Purushothama Rao Tata
- Department of Cell Biology, Duke University, Durham, NC, USA
- Duke Cancer Institute, Duke University, Durham, NC, USA
- Division of Pulmonary Critical Care, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Regeneration Next, Duke University, Durham, NC, USA
| | - Hongmei Mou
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Manjunatha Shivaraju
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Hermann Bihler
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Martin Mense
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Guillermo J Tearney
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, AL, USA
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Global delay in nascent strand DNA methylation. Nat Struct Mol Biol 2018; 25:327-332. [PMID: 29531288 PMCID: PMC5889353 DOI: 10.1038/s41594-018-0046-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [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: 10/18/2017] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitotically propagated over many generations with extraordinarily high fidelity. Here, we combine BrdU labeling and immunoprecipitation with genome-wide bisulfite sequencing to explore the inheritance of cytosine methylation onto newly replicated DNA in human cells. Globally, we observe a pronounced lag between the copying of genetic and epigenetic information in embryonic stem cells that is reconsolidated within hours to accomplish faithful mitotic transmission. Populations of arrested cells show a global reduction of lag-induced intermediate CpG methylation when compared to proliferating cells, whereas sites of transcription factor engagement appear cell-cycle invariant. Alternatively, the cancer cell line HCT116 preserves global epigenetic heterogeneity independently of cell-cycle arrest. Taken together, our data suggest that heterogeneous methylation largely reflects asynchronous proliferation, but is intrinsic to actively engaged cis-regulatory elements and cancer.
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Affiliation(s)
- Jocelyn Charlton
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Timothy L Downing
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering, University of California-Irvine, Irvine, CA, USA
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramona Pop
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sven Klages
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David P Santos
- The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexander M Tsankov
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernd Timmermann
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael J Ziller
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Warren CR, O'Sullivan JF, Friesen M, Becker CE, Zhang X, Liu P, Wakabayashi Y, Morningstar JE, Shi X, Choi J, Xia F, Peters DT, Florido MHC, Tsankov AM, Duberow E, Comisar L, Shay J, Jiang X, Meissner A, Musunuru K, Kathiresan S, Daheron L, Zhu J, Gerszten RE, Deo RC, Vasan RS, O'Donnell CJ, Cowan CA. Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease. Cell Stem Cell 2017; 20:547-557.e7. [PMID: 28388431 DOI: 10.1016/j.stem.2017.01.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 10/10/2016] [Accepted: 01/27/2017] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) have highlighted a large number of genetic variants with potential disease association, but functional analysis remains a challenge. Here we describe an approach to functionally validate identified variants through differentiation of induced pluripotent stem cells (iPSCs) to study cellular pathophysiology. We collected peripheral blood cells from Framingham Heart Study participants and reprogrammed them to iPSCs. We then differentiated 68 iPSC lines into hepatocytes and adipocytes to investigate the effect of the 1p13 rs12740374 variant on cardiometabolic disease phenotypes via transcriptomics and metabolomic signatures. We observed a clear association between rs12740374 and lipid accumulation and gene expression in differentiated hepatocytes, in particular, expression of SORT1, CELSR2, and PSRC1, consistent with previous analyses of this variant using other approaches. Initial investigation of additional SNPs also highlighted correlations with gene expression. These findings suggest that iPSC-based population studies hold promise as tools for the functional validation of GWAS variants.
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Affiliation(s)
- Curtis R Warren
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - John F O'Sullivan
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Max Friesen
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Caroline E Becker
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Xiaoling Zhang
- School of Medicine, Boston University, Boston, MA 02118, USA; The Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 01702, USA
| | - Poching Liu
- DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Yoshiyuki Wakabayashi
- DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Jordan E Morningstar
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Xu Shi
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jihoon Choi
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Fang Xia
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Derek T Peters
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Mary H C Florido
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Alexander M Tsankov
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eilene Duberow
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Lauren Comisar
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jennifer Shay
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Xin Jiang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiran Musunuru
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Sekar Kathiresan
- Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, CPZN 5.252, Boston, MA 02114, USA
| | - Laurence Daheron
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Robert E Gerszten
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Rahul C Deo
- Cardiovascular Research Institute, Department of Medicine and Institute for Human Genetics, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94143, USA
| | - Ramachandran S Vasan
- The Framingham Heart Study, Sections of Preventive Medicine and Epidemiology and Cardiology, Framingham, MA 01702, USA; School of Medicine, Boston University, Boston, MA 02118, USA; School of Public Health, Boston University, Boston, MA 02118, USA
| | - Christopher J O'Donnell
- The Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 01702, USA; Cardiology Section, Department of Medicine, Boston Veterans Administration Healthcare and Brigham and Women's Hospital, Boston, MA 02114, USA
| | - Chad A Cowan
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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17
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Chetty S, Engquist EN, Mehanna E, Lui KO, Tsankov AM, Melton DA. A Src inhibitor regulates the cell cycle of human pluripotent stem cells and improves directed differentiation. J Cell Biol 2015; 210:1257-68. [PMID: 26416968 PMCID: PMC4586752 DOI: 10.1083/jcb.201502035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Driving human pluripotent stem cells (hPSCs) into specific lineages is an inefficient and challenging process. We show that a potent Src inhibitor, PP1, regulates expression of genes involved in the G1 to S phase transition of the cell cycle, activates proteins in the retinoblastoma family, and subsequently increases the differentiation propensities of hPSCs into all three germ layers. We further demonstrate that genetic suppression of Src regulates the activity of the retinoblastoma protein and enhances the differentiation potential of hPSCs across all germ layers. These positive effects extend beyond the initial germ layer specification and enable efficient differentiation at subsequent stages of differentiation.
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Affiliation(s)
- Sundari Chetty
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Elise N Engquist
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Elie Mehanna
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Kathy O Lui
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Alexander M Tsankov
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138 Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Douglas A Melton
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138 Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
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18
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Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet 2015; 47:469-78. [PMID: 25822089 PMCID: PMC4414868 DOI: 10.1038/ng.3258] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [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: 08/01/2014] [Accepted: 03/06/2015] [Indexed: 12/14/2022]
Abstract
DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Here we inactivated all three catalytically active DNA methyltransferases (DNMTs) in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing to further investigate the roles and genomic targets of these enzymes. Disruption of DNMT3A or DNMT3B individually as well as of both enzymes in tandem results in viable, pluripotent cell lines with distinct effects on the DNA methylation landscape, as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to findings in mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome this immediate lethality, we generated a doxycycline-responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1-mutant lines. However, doxycycline-mediated repression of exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death. Our data provide a comprehensive characterization of DNMT-mutant ESCs, including single-base genome-wide maps of the targets of these enzymes.
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Affiliation(s)
- Jing Liao
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rahul Karnik
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael J. Ziller
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Alexander M. Tsankov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Veronika Akopian
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Casey A. Gifford
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Julie Donaghey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Christina Galonska
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ramona Pop
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Deepak Reyon
- Department of Pathology, Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Shengdar Q. Tsai
- Department of Pathology, Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - William Mallard
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - J. Keith Joung
- Department of Pathology, Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - John L. Rinn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
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19
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Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A. Transcription factor binding dynamics during human ES cell differentiation. Nature 2015; 518:344-9. [PMID: 25693565 PMCID: PMC4499331 DOI: 10.1038/nature14233] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/14/2015] [Indexed: 12/24/2022]
Abstract
Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage-specific behaviour of selected factors. In addition to the orchestrated remodelling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer, and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signalling effectors, and the epigenome during human embryonic stem cell differentiation.
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Affiliation(s)
- Alexander M Tsankov
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Veronika Akopian
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Michael J Ziller
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Julie Donaghey
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ido Amit
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Immunology, Weizmann Institute, Rehovot, 76100 Israel
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alexander Meissner
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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20
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Schlaeger TM, Daheron L, Brickler TR, Entwisle S, Chan K, Cianci A, DeVine A, Ettenger A, Fitzgerald K, Godfrey M, Gupta D, McPherson J, Malwadkar P, Gupta M, Bell B, Doi A, Jung N, Li X, Lynes MS, Brookes E, Cherry ABC, Demirbas D, Tsankov AM, Zon LI, Rubin LL, Feinberg AP, Meissner A, Cowan CA, Daley GQ. A comparison of non-integrating reprogramming methods. Nat Biotechnol 2014; 33:58-63. [PMID: 25437882 DOI: 10.1038/nbt.3070] [Citation(s) in RCA: 346] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/14/2014] [Indexed: 01/06/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) are useful in disease modeling and drug discovery, and they promise to provide a new generation of cell-based therapeutics. To date there has been no systematic evaluation of the most widely used techniques for generating integration-free hiPSCs. Here we compare Sendai-viral (SeV), episomal (Epi) and mRNA transfection mRNA methods using a number of criteria. All methods generated high-quality hiPSCs, but significant differences existed in aneuploidy rates, reprogramming efficiency, reliability and workload. We discuss the advantages and shortcomings of each approach, and present and review the results of a survey of a large number of human reprogramming laboratories on their independent experiences and preferences. Our analysis provides a valuable resource to inform the use of specific reprogramming methods for different laboratories and different applications, including clinical translation.
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Affiliation(s)
- Thorsten M Schlaeger
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | | | | | | | - Karrie Chan
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amelia Cianci
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander DeVine
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Andrew Ettenger
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kelly Fitzgerald
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michelle Godfrey
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Dipti Gupta
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jade McPherson
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Prerana Malwadkar
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Manav Gupta
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Blair Bell
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Akiko Doi
- 1] Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Namyoung Jung
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xin Li
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Emily Brookes
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anne B C Cherry
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Didem Demirbas
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alexander M Tsankov
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - Leonard I Zon
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Lee L Rubin
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Andrew P Feinberg
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander Meissner
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - Chad A Cowan
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA. [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [4] Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - George Q Daley
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [3] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts, USA
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21
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Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol 2012; 13:R27. [PMID: 22531001 PMCID: PMC3446301 DOI: 10.1186/gb-2012-13-4-r27] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 03/27/2012] [Accepted: 04/24/2012] [Indexed: 01/13/2023] Open
Abstract
Background DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood. Results We have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions. Conclusions The sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.
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Affiliation(s)
- Jia Xu
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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22
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Akopian V, Chan MM, Clement K, Galonska C, Gifford CA, Lehtola E, Liao J, Samavarchi-Tehrani P, Sindhu C, Smith ZD, Tsankov AM, Webster J, Zhang Y, Ziller MJ, Meissner A. Epigenomics and chromatin dynamics. Genome Biol 2012; 13:313. [PMID: 22364154 PMCID: PMC3334565 DOI: 10.1186/gb-2012-13-2-313] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 02/22/2012] [Indexed: 11/10/2022] Open
Abstract
A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest Keystone meetings to date, reflecting the excitement and many developments in this area. Richard Young opened the meeting by giving a historic overview before sharing more detailed insights from his recent work in describing the role of the lysine demethylase Lsd1 in mouse embryonic stem (ES) cell differentiation. He also set the broader stage and highlighted the excitement concerning recent advances in epigenetic drugs such as the new bromodomain inhibitors.
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Affiliation(s)
- Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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23
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Akopian V, Chan MM, Clement K, Galonska C, Gifford CA, Lehtola E, Liao J, Samavarchi-Tehrani P, Sindhu C, Smith ZD, Tsankov AM, Webster J, Zhang Y, Ziller MJ, Meissner A. Epigenomics and chromatin dynamics. Genome Biol 2012. [DOI: 10.1186/1465-6906-13-] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010; 8:e1000414. [PMID: 20625544 PMCID: PMC2897762 DOI: 10.1371/journal.pbio.1000414] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 05/27/2010] [Indexed: 11/18/2022] Open
Abstract
Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs. However, it can be difficult to decipher the basis of changes in chromatin organization and their functional effect on gene expression. Here, we present a large-scale comparative genomic analysis of the relationship between chromatin organization and gene expression, by measuring mRNA abundance and nucleosome positions genome-wide in 12 Hemiascomycota yeast species. We found substantial conservation of global and functional chromatin organization in all species, including prominent nucleosome-free regions (NFRs) at gene promoters, and distinct chromatin architecture in growth and stress genes. Chromatin organization has also substantially diverged in both global quantitative features, such as spacing between adjacent nucleosomes, and in functional groups of genes. Expression levels, intrinsic anti-nucleosomal sequences, and trans-acting chromatin modifiers all play important, complementary, and evolvable roles in determining NFRs. We identify five mechanisms that couple chromatin organization to evolution of gene regulation and have contributed to the evolution of respiro-fermentation and other key systems, including (1) compensatory evolution of alternative modifiers associated with conserved chromatin organization, (2) a gradual transition from constitutive to trans-regulated NFRs, (3) a loss of intrinsic anti-nucleosomal sequences accompanying changes in chromatin organization and gene expression, (4) re-positioning of motifs from NFRs to nucleosome-occluded regions, and (5) the expanded use of NFRs by paralogous activator-repressor pairs. Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation.
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Affiliation(s)
- Alexander M. Tsankov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dawn Anne Thompson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Amanda Socha
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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25
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Tsankov AM, Brown CR, Yu MC, Win MZ, Silver PA, Casolari JM. Communication between levels of transcriptional control improves robustness and adaptivity. Mol Syst Biol 2006; 2:65. [PMID: 17130867 PMCID: PMC1682026 DOI: 10.1038/msb4100106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 09/18/2006] [Indexed: 12/19/2022] Open
Abstract
Regulation of eukaryotic gene expression depends on groups of related proteins acting at the levels of chromatin organization, transcriptional initiation, RNA processing, and nuclear transport. However, a unified understanding of how these different levels of transcriptional control interact has been lacking. Here, we combine genome-wide protein–DNA binding data from multiple sources to infer the connections between functional groups of regulators in Saccharomyces cerevisiae. Our resulting transcriptional network uncovers novel biological relationships; supporting experiments confirm new associations between actively transcribed genes and Sir2 and Esc1, two proteins normally linked to silencing chromatin. Analysis of the regulatory network also reveals an elegant architecture for transcriptional control. Using communication theory, we show that most protein regulators prefer to form modules within their functional class, whereas essential proteins maintain the sparse connections between different classes. Moreover, we provide evidence that communication between different regulatory groups improves the robustness and adaptivity of the cell.
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Affiliation(s)
- Alexander M Tsankov
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Laboratory of Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Michael C Yu
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Moe Z Win
- Laboratory of Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., WAB 536 Boston, MA 02115, USA. Tel: +1 617 432 6401; Fax: +1 617 432 5012; E-mail:
| | - Jason M Casolari
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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