1
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Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021; 600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joshua T Lange
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Celine Chen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria E Valieva
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ivy Tsz-Lo Wong
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor V Duffy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jun Tang
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jordan Friedlein
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Paul S Mischel
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Pierce SE, Granja JM, Corces MR, Brady JJ, Tsai MK, Pierce AB, Tang R, Chu P, Feldser DM, Chang HY, Bassik MC, Greenleaf WJ, Winslow MM. LKB1 inactivation modulates chromatin accessibility to drive metastatic progression. Nat Cell Biol 2021; 23:915-924. [PMID: 34341533 PMCID: PMC8355205 DOI: 10.1038/s41556-021-00728-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/05/2021] [Indexed: 12/11/2022]
Abstract
Metastasis is the leading cause of cancer-related deaths and enables cancer cells to compromise organ function by expanding in secondary sites. Since primary tumours and metastases often share the same constellation of driver mutations, the mechanisms that drive their distinct phenotypes are unclear. Here we show that inactivation of the frequently mutated tumour suppressor gene LKB1 (encoding liver kinase B1) has evolving effects throughout the progression of lung cancer, which leads to the differential epigenetic re-programming of early-stage primary tumours compared with late-stage metastases. By integrating genome-scale CRISPR-Cas9 screening with bulk and single-cell multi-omic analyses, we unexpectedly identify LKB1 as a master regulator of chromatin accessibility in lung adenocarcinoma primary tumours. Using an in vivo model of metastatic progression, we further show that loss of LKB1 activates the early endoderm transcription factor SOX17 in metastases and a metastatic-like sub-population of cancer cells within primary tumours. The expression of SOX17 is necessary and sufficient to drive a second wave of epigenetic changes in LKB1-deficient cells that enhances metastatic ability. Overall, our study demonstrates how the downstream effects of an individual driver mutation can change throughout cancer development, with implications for stage-specific therapeutic resistance mechanisms and the gene regulatory underpinnings of metastatic evolution.
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Affiliation(s)
- Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer J Brady
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aubrey B Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Pauline Chu
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Feldser
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- HHMI, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Pierce SE, Granja JM, Greenleaf WJ. High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer. Nat Commun 2021; 12:2969. [PMID: 34016988 PMCID: PMC8137922 DOI: 10.1038/s41467-021-23213-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/12/2021] [Indexed: 01/07/2023] Open
Abstract
Chromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.
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Affiliation(s)
- Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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4
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Leylek R, Alcántara-Hernández M, Granja JM, Chavez M, Perez K, Diaz OR, Li R, Satpathy AT, Chang HY, Idoyaga J. Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity. Cell Rep 2021; 32:108180. [PMID: 32966789 PMCID: PMC7546547 DOI: 10.1016/j.celrep.2020.108180] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/18/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Human dendritic cells (DCs) comprise subsets with distinct phenotypic and functional characteristics, but the transcriptional programs that dictate their identity remain elusive. Here, we analyze global chromatin accessibility profiles across resting and stimulated human DC subsets by means of the assay for transposase-accessible chromatin using sequencing (ATAC-seq). We uncover specific regions of chromatin accessibility for each subset and transcriptional regulators of DC function. By comparing plasmacytoid DC responses to IFN-I-producing and non-IFN-I-producing conditions, we identify genetic programs related to their function. Finally, by intersecting chromatin accessibility with genome-wide association studies, we recognize DC subset-specific enrichment of heritability in autoimmune diseases. Our results unravel the basis of human DC subset heterogeneity and provide a framework for their analysis in disease pathogenesis. Human dendritic cells (DCs) orchestrate immune responses by a division of labor between functionally specialized subsets; however, the transcriptional basis of this heterogeneity is poorly understood. Using ATAC-seq, Leylek et al. profile the chromatin landscape of human DC subsets, providing insight into the underlying regulatory mechanisms that modulate their function.
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Affiliation(s)
- Rebecca Leylek
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey M Granja
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kimberly Perez
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oscar R Diaz
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
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5
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Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ. Author Correction: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet 2021; 53:935. [PMID: 33790476 PMCID: PMC8187146 DOI: 10.1038/s41588-021-00850-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Program in Biophysics, Stanford University, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Gladstone Institute of Neurological Disease, Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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6
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Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet 2021; 53:403-411. [PMID: 33633365 PMCID: PMC8012210 DOI: 10.1038/s41588-021-00790-6] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/19/2021] [Indexed: 12/26/2022]
Abstract
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells. ArchR is a software suite that enables efficient and end-to-end analysis of single-cell chromatin accessibility data (scATAC-seq).
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Affiliation(s)
- Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Program in Biophysics, Stanford University, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Gladstone Institute of Neurological Disease, Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, Montgomery SB, Chang HY, Montine TJ. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet 2020; 52:1158-1168. [PMID: 33106633 PMCID: PMC7606627 DOI: 10.1038/s41588-020-00721-x] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 12/27/2019] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies of neurological diseases have identified thousands of variants associated with disease phenotypes. However, most of these variants do not alter coding sequences, making it difficult to assign their function. Here, we present a multi-omic epigenetic atlas of the adult human brain through profiling of single-cell chromatin accessibility landscapes and three-dimensional chromatin interactions of diverse adult brain regions across a cohort of cognitively healthy individuals. We developed a machine-learning classifier to integrate this multi-omic framework and predict dozens of functional SNPs for Alzheimer's and Parkinson's diseases, nominating target genes and cell types for previously orphaned loci from genome-wide association studies. Moreover, we dissected the complex inverted haplotype of the MAPT (encoding tau) Parkinson's disease risk locus, identifying putative ectopic regulatory interactions in neurons that may mediate this disease association. This work expands understanding of inherited variation and provides a roadmap for the epigenomic dissection of causal regulatory variation in disease.
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Affiliation(s)
- M Ryan Corces
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Michael J Gloudemans
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Laure Frésard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Bryan H Louie
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Tiffany Eulalio
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Shadi Shams
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - S Tansu Bagdatli
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Boxiang Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Baidu Research, Sunnyvale, CA, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 2019; 575:699-703. [PMID: 31748743 PMCID: PMC7094777 DOI: 10.1038/s41586-019-1763-5] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 09/26/2019] [Indexed: 01/01/2023]
Abstract
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.
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Affiliation(s)
- Sihan Wu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Nam Nguyen
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Ramya Raviram
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Marcella Erb
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jennifer Santini
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Yarui Diao
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cell Biology, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Wenjing Zhang
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Nathan Jameson
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Jack Houston
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California at San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California at San Diego, La Jolla, CA, USA.
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9
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Durai V, Bagadia P, Granja JM, Satpathy AT, Kulkarni DH, Davidson JT, Wu R, Patel SJ, Iwata A, Liu TT, Huang X, Briseño CG, Grajales-Reyes GE, Wöhner M, Tagoh H, Kee BL, Newberry RD, Busslinger M, Chang HY, Murphy TL, Murphy KM. Cryptic activation of an Irf8 enhancer governs cDC1 fate specification. Nat Immunol 2019; 20:1161-1173. [PMID: 31406378 PMCID: PMC6707878 DOI: 10.1038/s41590-019-0450-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/17/2019] [Indexed: 01/25/2023]
Abstract
Induction of the transcription factor Irf8 in the common dendritic cell progenitor (CDP) is required for classical type 1 dendritic cell (cDC1) fate specification, but the mechanisms controlling this induction are unclear. In the present study Irf8 enhancers were identified via chromatin profiling of dendritic cells and CRISPR/Cas9 genome editing was used to assess their roles in Irf8 regulation. An enhancer 32 kilobases (kb) downstream of the Irf8 transcriptional start site (+32-kb Irf8) that was active in mature cDC1s was required for the development of this lineage, but not for its specification. Instead, a +41-kb Irf8 enhancer, previously thought to be active only in plasmacytoid dendritic cells, was found to also be transiently accessible in cDC1 progenitors, and deleting this enhancer prevented the induction of Irf8 in CDPs and abolished cDC1 specification. Thus, cryptic activation of the +41-kb Irf8 enhancer in dendritic cell progenitors is responsible for cDC1 fate specification.
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Affiliation(s)
- Vivek Durai
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Deparment of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Devesha H Kulkarni
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Jesse T Davidson
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Swapneel J Patel
- Division of Rheumatology, John T. Milliken Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Arifumi Iwata
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
- Howard Hughes Medical Institute, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Xiao Huang
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Carlos G Briseño
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Gary E Grajales-Reyes
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Miriam Wöhner
- Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Barbara L Kee
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Rodney D Newberry
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, MO, USA.
- Howard Hughes Medical Institute, Washington University in St Louis, School of Medicine, St Louis, MO, USA.
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10
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Bagadia P, Huang X, Liu TT, Durai V, Grajales-Reyes GE, Nitschké M, Modrusan Z, Granja JM, Satpathy AT, Briseño CG, Gargaro M, Iwata A, Kim S, Chang HY, Shaw AS, Murphy TL, Murphy KM. An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development. Nat Immunol 2019; 20:1174-1185. [PMID: 31406377 PMCID: PMC6707889 DOI: 10.1038/s41590-019-0449-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [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: 12/03/2018] [Accepted: 06/17/2019] [Indexed: 01/25/2023]
Abstract
Classical type 1 dendritic cells (cDC1s) are required for antiviral and antitumor immunity, which necessitates an understanding of their development. Development of the cDC1 progenitor requires an E-protein-dependent enhancer located 41 kilobases downstream of the transcription start site of the transcription factor Irf8 (+41-kb Irf8 enhancer), but its maturation instead requires the Batf3-dependent +32-kb Irf8 enhancer. To understand this switch, we performed single-cell RNA sequencing of the common dendritic cell progenitor (CDP) and identified a cluster of cells that expressed transcription factors that influence cDC1 development, such as Nfil3, Id2 and Zeb2. Genetic epistasis among these factors revealed that Nfil3 expression is required for the transition from Zeb2hi and Id2lo CDPs to Zeb2lo and Id2hi CDPs, which represent the earliest committed cDC1 progenitors. This genetic circuit blocks E-protein activity to exclude plasmacytoid dendritic cell potential and explains the switch in Irf8 enhancer usage during cDC1 development.
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Affiliation(s)
- Prachi Bagadia
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Xiao Huang
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
- Howard Hughes Medical Institute, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Gary E Grajales-Reyes
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | | | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos G Briseño
- Department of Oncology, Amgen Inc., South San Francisco, CA, USA
| | - Marco Gargaro
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Sunkyung Kim
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrey S Shaw
- Research Biology, Genentech, South San Francisco, CA, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
- Howard Hughes Medical Institute, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
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11
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Yost KE, Satpathy AT, Wells DK, Qi Y, Wang C, Kageyama R, McNamara KL, Granja JM, Sarin KY, Brown RA, Gupta RK, Curtis C, Bucktrout SL, Davis MM, Chang ALS, Chang HY. Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat Med 2019; 25:1251-1259. [PMID: 31359002 PMCID: PMC6689255 DOI: 10.1038/s41591-019-0522-3] [Citation(s) in RCA: 807] [Impact Index Per Article: 161.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of patients with cancer1. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear2-4. Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Tracking T cell receptor clones and transcriptional phenotypes revealed coupling of tumor recognition, clonal expansion and T cell dysfunction marked by clonal expansion of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, the expansion of T cell clones did not derive from pre-existing tumor-infiltrating T lymphocytes; instead, the expanded clones consisted of novel clonotypes that had not previously been observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells and evident in patients with basal or squamous cell carcinoma. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.
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Affiliation(s)
- Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Robin Kageyama
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Katherine L McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Ryanne A Brown
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Rohit K Gupta
- Stanford Biobank, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mark M Davis
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, Wang L, Yin Y, Giresi PG, Chang ALS, Zheng GXY, Greenleaf WJ, Chang HY. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 2019; 37:925-936. [PMID: 31375813 PMCID: PMC7299161 DOI: 10.1038/s41587-019-0206-z] [Citation(s) in RCA: 457] [Impact Index Per Article: 91.4] [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: 01/21/2019] [Accepted: 07/01/2019] [Indexed: 02/08/2023]
Abstract
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | | | - Jean Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | - Li Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | | | | | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY. HiChIRP reveals RNA-associated chromosome conformation. Nat Methods 2019; 16:489-492. [PMID: 31133759 DOI: 10.1038/s41592-019-0407-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/05/2019] [Indexed: 12/25/2022]
Abstract
Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. HiChIRP of three nuclear RNAs reveals insights into promoter interactions (7SK), telomere biology (telomerase RNA component) and inflammatory gene regulation (lincRNA-EPS).
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Caitlin M Roake
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhaozhao Jiang
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shadi Shams
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan H Louie
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maninjay K Atianand
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Jeng MY, Mumbach MR, Granja JM, Satpathy AT, Chang HY, Chang ALS. Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders. J Invest Dermatol 2019; 139:605-614. [DOI: 10.1016/j.jid.2018.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/24/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022]
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15
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Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 2018; 362:362/6413/eaav1898. [PMID: 30361341 DOI: 10.1126/science.aav1898] [Citation(s) in RCA: 593] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.
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16
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Yang D, Denny SK, Greenside PG, Chaikovsky AC, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kwok S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, Preusser M, Kundaje A, Greenleaf WJ, Sage J, Winslow MM. Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. Cancer Discov 2018; 8:1316-1331. [PMID: 30228179 DOI: 10.1158/2159-8290.cd-17-0987] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 05/14/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
The extent to which early events shape tumor evolution is largely uncharacterized, even though a better understanding of these early events may help identify key vulnerabilities in advanced tumors. Here, using genetically defined mouse models of small cell lung cancer (SCLC), we uncovered distinct metastatic programs attributable to the cell type of origin. In one model, tumors gain metastatic ability through amplification of the transcription factor NFIB and a widespread increase in chromatin accessibility, whereas in the other model, tumors become metastatic in the absence of NFIB-driven chromatin alterations. Gene-expression and chromatin accessibility analyses identify distinct mechanisms as well as markers predictive of metastatic progression in both groups. Underlying the difference between the two programs was the cell type of origin of the tumors, with NFIB-independent metastases arising from mature neuroendocrine cells. Our findings underscore the importance of the identity of cell type of origin in influencing tumor evolution and metastatic mechanisms.Significance: We show that SCLC can arise from different cell types of origin, which profoundly influences the eventual genetic and epigenetic changes that enable metastatic progression. Understanding intertumoral heterogeneity in SCLC, and across cancer types, may illuminate mechanisms of tumor progression and uncover how the cell type of origin affects tumor evolution. Cancer Discov; 8(10); 1316-31. ©2018 AACR. See related commentary by Pozo et al., p. 1216 This article is highlighted in the In This Issue feature, p. 1195.
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Affiliation(s)
- Dian Yang
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Sarah K Denny
- Department of Genetics, Stanford University, Stanford, California.,Biophysics Program, Stanford University, Stanford, California
| | - Peyton G Greenside
- Program in Biomedical Informatics, Stanford University, Stanford, California
| | - Andrea C Chaikovsky
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Jennifer J Brady
- Department of Genetics, Stanford University, Stanford, California
| | - Youcef Ouadah
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Biochemistry, Stanford University, Stanford, California
| | - Jeffrey M Granja
- Department of Genetics, Stanford University, Stanford, California.,Biophysics Program, Stanford University, Stanford, California
| | - Nadine S Jahchan
- Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Jing Shan Lim
- Cancer Biology Program, Stanford University, Stanford, California.,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Shirley Kwok
- Department of Pathology, Stanford University, Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University, Stanford, California
| | - Anna S Berghoff
- Institute of Neurology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center CNS Tumors Unit, Medical University of Vienna, Vienna, Austria
| | - Anna Schmitt
- Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany
| | - H Christian Reinhardt
- Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Matthias Preusser
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center CNS Tumors Unit, Medical University of Vienna, Vienna, Austria
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California.,Department of Computer Science, Stanford University, Stanford, California
| | | | - Julien Sage
- Cancer Biology Program, Stanford University, Stanford, California. .,Department of Genetics, Stanford University, Stanford, California.,Department of Pediatrics, Stanford University, Stanford, California
| | - Monte M Winslow
- Cancer Biology Program, Stanford University, Stanford, California. .,Department of Genetics, Stanford University, Stanford, California.,Department of Pathology, Stanford University, Stanford, California
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17
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Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med 2018; 24:580-590. [PMID: 29686426 PMCID: PMC5948148 DOI: 10.1038/s41591-018-0008-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [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: 06/08/2017] [Accepted: 02/07/2018] [Indexed: 02/04/2023]
Abstract
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naresha Saligrama
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Caleb A Lareau
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William S Serratelli
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alicia N Schep
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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18
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Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet 2017; 49:1602-1612. [PMID: 28945252 DOI: 10.1038/ng.3963] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Evan A Boyle
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Nabeela Suliman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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