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Mitra S, Malik R, Wong W, Rahman A, Hartemink AJ, Pritykin Y, Dey KK, Leslie CS. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nat Genet 2024; 56:627-636. [PMID: 38514783 PMCID: PMC11018525 DOI: 10.1038/s41588-024-01689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024]
Abstract
We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC-seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene-peak correlations and dependence on peak calling. SCARlink outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across high-coverage multi-ome datasets while giving comparable to improved performance on low-coverage datasets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 11× to 15× and 5× to 12× enriched in fine-mapped eQTLs and fine-mapped genome-wide association study (GWAS) variants, respectively. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.
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Affiliation(s)
- Sneha Mitra
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | | | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York City, NY, USA
| | - Afsana Rahman
- Hunter College, City University of New York, New York City, NY, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kushal K Dey
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
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2
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Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JM, Bassik MC, Reilly SK. Multicenter integrated analysis of noncoding CRISPRi screens. Nat Methods 2024; 21:723-734. [PMID: 38504114 PMCID: PMC11009116 DOI: 10.1038/s41592-024-02216-7] [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: 12/02/2022] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
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Affiliation(s)
- David Yao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - Jin Woo Oh
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lexi R Bounds
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Sager J Gosai
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
| | - Lazaros Lataniotis
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Ava Mackay-Smith
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | | | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Henri Schmidt
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tania Guerrero-Altamirano
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Katherine Guo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alexander D White
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | | | - Kalina Andreeva
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Xingjie Ren
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, 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
| | - Pardis C Sabeti
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuri Pritykin
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A Beer
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Timothy E Reddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jesse M Engreitz
- Department of Genetics, Stanford University, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Steven K Reilly
- Department of Genetics, Yale University, New Haven, CT, USA.
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3
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Nakandakari-Higa S, Walker S, Canesso MCC, van der Heide V, Chudnovskiy A, Kim DY, Jacobsen JT, Parsa R, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Kamphorst AO, Pritykin Y, Victora GD. Universal recording of immune cell interactions in vivo. Nature 2024; 627:399-406. [PMID: 38448581 DOI: 10.1038/s41586-024-07134-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their function1. To study these 'kiss-and-run' interactions directly in vivo, we previously developed LIPSTIC (labelling immune partnerships by SorTagging intercellular contacts)2, an approach that uses enzymatic transfer of a labelled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ T helper cells and antigen-presenting cells, however. Here we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the steady-state cellular partners of regulatory T cells and identify germinal centre-resident T follicular helper cells on the basis of their ability to interact cognately with germinal centre B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalogue of the immune populations that physically interact with intestinal epithelial cells at the steady state and profile the evolution of the interactome of lymphocytic choriomeningitis virus-specific CD8+ T cells in multiple organs following systemic infection. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.
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Affiliation(s)
| | - Sarah Walker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
| | - Maria C C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Verena van der Heide
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Center, 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
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Dong-Yoon Kim
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Institute for Immunology and Transfusion Medicine, Rikshospitalet, University of Oslo, Oslo, Norway
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Giulia Pasqual
- Laboratory of Synthetic Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Alice O Kamphorst
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Center, 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
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
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4
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Alvarez-Breckenridge C, Anderson KG, Correia AL, Demehri S, Dinh HQ, Dixon KO, Dunn GP, Evgin L, Goc J, Good Z, Hacohen N, Han P, Hanč P, Hickey J, Kersten K, Liu BC, Buque A, Miao Y‘P, Milner JJ, Pritykin Y, Pucci F, Scharping NE, Sudmeier L, Wang Y, Wieland A, Williams MM. Lessons for the Next Generation of Scientists from the Second Annual Arthur and Sandra Irving Cancer Immunology Symposium. Cancer Immunol Res 2023; 11:1571-1577. [PMID: 37906619 PMCID: PMC10696930 DOI: 10.1158/2326-6066.cir-23-0522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
Abstract
The Arthur and Sandra Irving Cancer Immunology Symposium has been created as a platform for established cancer immunologists to mentor trainees and young investigators as they launch their research career in the field. By sharing their different paths to success, the senior faculty mentors provide an invaluable resource to support the development of the next generation of leaders in the cancer immunology community. This Commentary describes some of the key topics that were discussed during the 2022 symposium: scientific and career trajectory, leadership, mentoring, collaborations, and publishing. For each of these topics, established investigators discussed the elements that facilitate success in these areas as well as mistakes that can hinder progress. Herein, we outline the critical points raised in these discussions for establishing a successful independent research career. These points are highly relevant for the broader scientific community.
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Affiliation(s)
| | - Kristin G. Anderson
- Department of Microbiology, Immunology and Cancer Biology, Carter Center for Immunology Research, University of Virginia, Charlottesville, Virginia
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, Virginia
| | | | - Shadmehr Demehri
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research/Department of Oncology, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Karen Olivia Dixon
- Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Gavin P. Dunn
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Laura Evgin
- Michael Smith Genome Sciences Department, BC Cancer Research Institute, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jeremy Goc
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, New York
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York
| | - Zinaida Good
- Stanford Cancer Institute and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Nir Hacohen
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Patrick Han
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Pavel Hanč
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - John Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kelly Kersten
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Beiyun C. Liu
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Aitziber Buque
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
| | | | - J. Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Department of Computer Science, Princeton University, New Jersey
| | - Ferdinando Pucci
- Department of Otolaryngology and Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Nicole E. Scharping
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California
| | - Lisa Sudmeier
- Department of Radiation Oncology, Winship Cancer Institute and Emory University School of Medicine, Atlanta, Georgia
| | - Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andreas Wieland
- Department of Otolaryngology and Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Michelle M. Williams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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5
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Nakandakari-Higa S, Canesso MCC, Walker S, Chudnovskiy A, Jacobsen JT, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Pritykin Y, Victora GD. Universal recording of cell-cell contacts in vivo for interaction-based transcriptomics. bioRxiv 2023:2023.03.16.533003. [PMID: 36993443 PMCID: PMC10055214 DOI: 10.1101/2023.03.16.533003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and regulate their function. To study these "kiss-and-run" interactions directly in vivo, we previously developed LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts), an approach that uses enzymatic transfer of a labeled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ helper T cells and antigen presenting cells, however. Here, we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the cellular partners of regulatory T cells in steady state, and identify germinal center (GC)-resident T follicular helper (Tfh) cells based on their ability to interact cognately with GC B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalog of the immune populations that physically interact with intestinal epithelial cells (IECs) and find evidence of stepwise acquisition of the ability to interact with IECs as CD4+ T cells adapt to residence in the intestinal tissue. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.
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Affiliation(s)
| | - Maria C C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Sarah Walker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Quantitative and Computational Biology Graduate Program, Princeton University, Princeton, NJ, USA
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Giulia Pasqual
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
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6
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Dolsten GA, Pritykin Y. Genomic Analysis of Foxp3 Function in Regulatory T Cells. J Immunol 2023; 210:880-887. [PMID: 36947819 PMCID: PMC10037560 DOI: 10.4049/jimmunol.2200864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 03/24/2023]
Abstract
Regulatory T (Treg) cells are critical for tolerance to self-antigens and for preventing autoimmunity. Foxp3 has been identified as a Treg cell lineage-defining transcription factor controlling Treg cell differentiation and function. In this article, we review the current mechanistic and systemic understanding of Foxp3 function enabled by experimental and computational advances in high-throughput genomics.
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Affiliation(s)
- Gabriel A Dolsten
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Quantitative and Computational Biology Graduate Program, Princeton University, Princeton, NJ, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
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7
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van der Veeken J, Campbell C, Pritykin Y, Schizas M, Verter J, Hu W, Wang ZM, Matheis F, Mucida D, Charbonnier LM, Chatila TA, Rudensky AY. Genetic tracing reveals transcription factor Foxp3-dependent and Foxp3-independent functionality of peripherally induced Treg cells. Immunity 2022; 55:1173-1184.e7. [PMID: 35700740 PMCID: PMC9885886 DOI: 10.1016/j.immuni.2022.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/19/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023]
Abstract
Regulatory T (Treg) cells expressing the transcription factor Foxp3 are an essential suppressive T cell lineage of dual origin: Foxp3 induction in thymocytes and mature CD4+ T cells gives rise to thymic (tTreg) and peripheral (pTreg) Treg cells, respectively. While tTreg cells suppress autoimmunity, pTreg cells enforce tolerance to food and commensal microbiota. However, the role of Foxp3 in pTreg cells and the mechanisms supporting their differentiation remain poorly understood. Here, we used genetic tracing to identify microbiota-induced pTreg cells and found that many of their distinguishing features were Foxp3 independent. Lineage-committed, microbiota-dependent pTreg-like cells persisted in the colon in the absence of Foxp3. While Foxp3 was critical for the suppression of a Th17 cell program, colitis, and mastocytosis, pTreg cells suppressed colonic effector T cell expansion in a Foxp3-independent manner. Thus, Foxp3 and the tolerogenic signals that precede and promote its expression independently confer distinct facets of pTreg functionality.
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Affiliation(s)
- Joris van der Veeken
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
| | - Clarissa Campbell
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA,CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Computer Science Department, Princeton University, Princeton, NJ, USA
| | - Michail Schizas
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob Verter
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Hu
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA,Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanny Matheis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Talal A Chatila
- Division of Immunology, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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8
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Zhong Y, Walker SK, Pritykin Y, Leslie CS, Rudensky AY, van der Veeken J. Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families. Nat Immunol 2021; 23:122-134. [PMID: 34937932 PMCID: PMC8712421 DOI: 10.1038/s41590-021-01086-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022]
Abstract
T cell activation, a key early event in the adaptive immune response, is subject to elaborate transcriptional control. Here, we examined how the activities of eight major transcription factor (TF) families are integrated to shape the epigenome of naïve and activated CD4 and CD8 T cells. By leveraging extensive polymorphisms in evolutionarily divergent mice, we identified the “heavy lifters” positively influencing chromatin accessibility. Members of Ets, Runx, and TCF/Lef TF families occupied the vast majority of accessible chromatin regions, acting as “housekeepers”, “universal amplifiers”, and “placeholders”, respectively, at sites that maintained or gained accessibility upon T cell activation. Additionally, a small subset of strongly induced immune response genes displayed a non-canonical TF recruitment pattern. Our study provides a key resource and foundation for the understanding of transcriptional and epigenetic regulation in T cells and offers a new perspective on the hierarchical interactions between critical TFs.
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9
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Zhang M, Zhao Z, Pritykin Y, Hannum M, Scott AC, Kuo F, Sanghvi V, Chan TA, Seshan V, Wendel HG, Schietinger A, Sadelain M, Huse M. Ectopic activation of the miR-200c-EpCAM axis enhances antitumor T cell responses in models of adoptive cell therapy. Sci Transl Med 2021; 13:eabg4328. [PMID: 34524864 PMCID: PMC9374309 DOI: 10.1126/scitranslmed.abg4328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Indexed: 11/02/2022]
Abstract
Adoptive T cell therapy (ACT) is a promising strategy for treating cancer, but it often fails because of cell intrinsic regulatory programs that limit the degree or duration of T cell function. In this study, we found that ectopic expression of microRNA-200c (miR-200c) markedly enhanced the antitumor activity of CD8+ cytotoxic T lymphocytes (CTLs) during ACT in multiple mouse models. CTLs transduced with miR-200c exhibited reduced apoptosis during engraftment and enhanced in vivo persistence, accompanied by up-regulation of the transcriptional regulator T cell factor 1 (TCF1) and the inflammatory cytokine tumor necrosis factor (TNF). miR-200c elicited these changes by suppressing the transcription factor Zeb1 and thereby inducing genes characteristic of epithelial cells. Overexpression of one of these genes, Epcam, was sufficient to augment therapeutic T cell responses against both solid and liquid tumors. These results identify the miR-200c–EpCAM axis as an avenue for improving ACT and demonstrate that select genetic perturbations can produce phenotypically distinct T cells with advantageous therapeutic properties.
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Affiliation(s)
- Minggang Zhang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zeguo Zhao
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Computer Science Department, Princeton University, Princeton, NJ 08540, USA
| | - Margaret Hannum
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Viraj Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michel Sadelain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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10
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Pritykin Y, van der Veeken J, Pine AR, Zhong Y, Sahin M, Mazutis L, Pe'er D, Rudensky AY, Leslie CS. A unified atlas of CD8 T cell dysfunctional states in cancer and infection. Mol Cell 2021; 81:2477-2493.e10. [PMID: 33891860 PMCID: PMC8454502 DOI: 10.1016/j.molcel.2021.03.045] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [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: 08/04/2020] [Revised: 02/02/2021] [Accepted: 03/29/2021] [Indexed: 12/16/2022]
Abstract
CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across experimental and clinical settings. By carrying out a unified analysis of over 300 assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) experiments from 12 studies of CD8 T cells in cancer and infection, we defined a shared differentiation trajectory toward dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T cell states across models. Experimental dissection of acute and chronic viral infection using single-cell ATAC (scATAC)-seq and allele-specific single-cell RNA (scRNA)-seq identified state-specific drivers and captured the emergence of similar TCF1+ progenitor-like populations at an early branch point, at which functional and dysfunctional T cells diverge. Our atlas of CD8 T cell states will facilitate mechanistic studies of T cell immunity and translational efforts.
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Affiliation(s)
- Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Joris van der Veeken
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Allison R Pine
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Yi Zhong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Merve Sahin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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11
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Campbell C, Marchildon F, Michaels AJ, Takemoto N, van der Veeken J, Schizas M, Pritykin Y, Leslie CS, Intlekofer AM, Cohen P, Rudensky AY. FXR mediates T cell-intrinsic responses to reduced feeding during infection. Proc Natl Acad Sci U S A 2020; 117:33446-33454. [PMID: 33318189 PMCID: PMC7776647 DOI: 10.1073/pnas.2020619117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reduced nutrient intake is a widely conserved manifestation of sickness behavior with poorly characterized effects on adaptive immune responses. During infectious challenges, naive T cells encountering their cognate antigen become activated and differentiate into highly proliferative effector T cells. Despite their evident metabolic shift upon activation, it remains unclear how effector T cells respond to changes in nutrient availability in vivo. Here, we show that spontaneous or imposed feeding reduction during infection decreases the numbers of splenic lymphocytes. Effector T cells showed cell-intrinsic responses dependent on the nuclear receptor Farnesoid X Receptor (FXR). Deletion of FXR in T cells prevented starvation-induced loss of lymphocytes and increased effector T cell fitness in nutrient-limiting conditions, but imparted greater weight loss to the host. FXR deficiency increased the contribution of glutamine and fatty acids toward respiration and enhanced cell survival under low-glucose conditions. Provision of glucose during anorexia of infection rescued effector T cells, suggesting that this sugar is a limiting nutrient for activated lymphocytes and that alternative fuel usage may affect cell survival in starved animals. Altogether, we identified a mechanism by which the host scales immune responses according to food intake, featuring FXR as a T cell-intrinsic sensor.
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Affiliation(s)
- Clarissa Campbell
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
| | - Francois Marchildon
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065
| | - Anthony J Michaels
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021
| | - Naofumi Takemoto
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Joris van der Veeken
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Michail Schizas
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Andrew M Intlekofer
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065
| | - Alexander Y Rudensky
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021
- Howard Hughes Medical Institute, Sloan Kettering Institute, New York, NY 10065
- Immunology Program, Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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12
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Li X, Pritykin Y, Concepcion CP, Lu Y, La Rocca G, Zhang M, King B, Cook PJ, Au YW, Popow O, Paulo JA, Otis HG, Mastroleo C, Ogrodowski P, Schreiner R, Haigis KM, Betel D, Leslie CS, Ventura A. High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. Mol Cell 2020; 79:167-179.e11. [PMID: 32497496 DOI: 10.1016/j.molcel.2020.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 10/08/2019] [Revised: 03/18/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022]
Abstract
The identification of microRNA (miRNA) targets by Ago2 crosslinking-immunoprecipitation (CLIP) methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily applicable to an in vivo setting. To overcome these limitations and facilitate the investigation of miRNA functions in vivo, we have developed a method based on a genetically engineered mouse harboring a conditional Halo-Ago2 allele expressed from the endogenous Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be purified from cells and tissues expressing the endogenous Halo-Ago2 allele. We demonstrate the reproducibility and sensitivity of this method in mouse embryonic stem cells, developing embryos, adult tissues, and autochthonous mouse models of human brain and lung cancers. This method and the datasets we have generated will facilitate the characterization of miRNA-mRNA networks in vivo under physiological and pathological conditions.
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Affiliation(s)
- Xiaoyi Li
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carla P Concepcion
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuheng Lu
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peter J Cook
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Yu Wah Au
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Internal Medicine (Nephrology), Leiden University Medical Center, Zuid-Holland, 2333 ZA, the Netherlands
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah G Otis
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ryan Schreiner
- Margaret Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Doron Betel
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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13
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Geary CD, Krishna C, Lau CM, Adams NM, Gearty SV, Pritykin Y, Thomsen AR, Leslie CS, Sun JC. Non-redundant ISGF3 Components Promote NK Cell Survival in an Auto-regulatory Manner during Viral Infection. Cell Rep 2020; 24:1949-1957.e6. [PMID: 30134157 PMCID: PMC6153266 DOI: 10.1016/j.celrep.2018.07.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 02/16/2018] [Revised: 06/05/2018] [Accepted: 07/17/2018] [Indexed: 01/14/2023] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that possess adaptive features, including antigen-specific clonal expansion and long-lived memory responses. Although previous work demonstrated that type I interferon (IFN) signaling is crucial for NK cell expansion and memory cell formation following mouse cytomegalovirus (MCMV) infection, the global transcriptional mechanisms underlying type I IFN-mediated responses remained to be determined. Here, we demonstrate that among the suite of transcripts induced in activated NK cells, IFN-α is necessary and sufficient to promote expression of its downstream transcription factors STAT1, STAT2, and IRF9, via an auto-regulatory, feedforward loop. Similar to STAT1 deficiency, we show that STAT2- or IRF9-deficient NK cells are defective in their ability to expand following MCMV infection, in part because of diminished survival rather than an inability to proliferate. Thus, our findings demonstrate that individual ISGF3 components are crucial cell-autonomous and non-redundant regulators of the NK cell response to viral infection. Using RNA-seq and ChIP-seq, Geary et al. investigate the impacts of type I interferon on NK cells during MCMV infection and demonstrate crucial and non-redundant roles for STAT1, STAT2, and IRF9 in promoting cytotoxicity and survival of antiviral NK cells.
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Affiliation(s)
- Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sofia V Gearty
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Allan R Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
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14
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Brown CC, Gudjonson H, Pritykin Y, Deep D, Lavallée VP, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe'er D, Rudensky AY. Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Cell 2019; 179:846-863.e24. [PMID: 31668803 PMCID: PMC6838684 DOI: 10.1016/j.cell.2019.09.035] [Citation(s) in RCA: 298] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/12/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
Abstract
Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to initiate T cell responses and direct their differentiation into effector lineages. Classical DCs have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells. While the transcriptional regulation of the cDC1 subset has been well characterized, cDC2 development and function remain poorly understood. By combining transcriptional and chromatin analyses with genetic reporter expression, we identified two principal cDC2 lineages defined by distinct developmental pathways and transcriptional regulators, including T-bet and RORγt, two key transcription factors known to define innate and adaptive lymphocyte subsets. These novel cDC2 lineages were characterized by distinct metabolic and functional programs. Extending our findings to humans revealed conserved DC heterogeneity and the presence of the newly defined cDC2 subsets in human cancer. Single-cell analyses reveal novel dendritic cell subsets Major cDC2 subsets differentially express T-bet and RORγt Distinct pro- and anti-inflammatory potential of T-bet+ and Tbet– cDC2s Transcriptional basis for cDC2 heterogeneity conserved across mouse and human
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Affiliation(s)
- Chrysothemis C Brown
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Infection, Inflammation and Rheumatology Section, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
| | - Herman Gudjonson
- Infection, Inflammation and Rheumatology Section, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Yuri Pritykin
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Deeksha Deep
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vincent-Philippe Lavallée
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alejandra Mendoza
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rachel Fromme
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charlotte Ariyan
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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15
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Pritykin Y, Leslie C. Abstract 3384: Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent studies in mouse models of cancer and chronic viral infection applied genomic assays to profile various states of impaired T cell function and demonstrated that T cell dysfunction is epigenetically imprinted. However, comprehensive characterization of T cell dysfunction across models based on their epigenetic and transcriptional profiles is lacking. We reanalyzed a large collection of recently published chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data sets. After batch effect correction, we observed that epigenetic profiles of dysfunctional tumor-infiltrating T cells and exhausted T cells in chronic viral infection were surprisingly extremely similar. Furthermore, we observed that temporal progression towards dysfunction in chronic infection resembles that in tumorigenesis, and found that T cells committed to becoming dysfunctional early after activation. Motif analysis using generalized linear modeling allowed us to find candidate transcription factors associated with development of dysfunction in both immune settings. This analysis provides a better systematic understanding of cell-intrinsic mechanisms driving different functional states of CD8 T cells and demonstrates the power of systems biology approaches in cancer immunology.
Citation Format: Yuri Pritykin, Christina Leslie. Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3384.
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Affiliation(s)
- Yuri Pritykin
- Memorial Sloan Kettering Cancer Center, New York, NY
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16
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Pritykin Y, Leslie C. Abstract B038: A unified genome-wide analysis of dysfunctional T-cell states in cancer and chronic viral infection. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-b038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tumor-specific T-cells that have differentiated into a terminal dysfunctional state exist in the tumor microenvironment. A systematic understanding of the requirements of immunotherapeutic rescue of these cells is critically needed to improve clinical results in patients. Mouse models of chronic infection and cancer have been studied to elucidate biologic mechanisms of persistent antigen stimulation resulting in T-cell dysfunction, or “exhaustion.” Recently, chromatin accessibility imprinting has been associated with T-cells falling back into the dysfunctional state after temporary rescue by checkpoint blockade, suggesting epigenetic mechanisms in control of T-cell dysfunction. However, comprehensive characterization of T-cell dysfunction across models based on their epigenetic and transcriptional profiles is lacking.We collected 106 chromatin accessibility (ATAC-seq) samples and 87 gene expression (RNA-seq) samples from seven recent publications. We analyzed these data by first applying batch effect correction using generalized linear modeling. This enabled mapping profiles of chromatin accessibility peaks in gene promoters and enhancers from different studies into the same space. We observed that epigenetic profiles of dysfunctional tumor-infiltrating T-cells and dysfunctional T-cells in chronic viral infection were, surprisingly, extremely similar. Furthermore, a recently characterized discrete distinction between epigenetic profiles of early (day 7-8) and late (day 28-35) dysfunction in the tumor was recapitulated in the model of chronic infection. Overall we observed across mouse models that T-cells committed to becoming dysfunctional early after an immune challenge, rather than first mounting and then loosing an effector response. These observations were also largely recapitulated in gene expression analysis. Differentially expressed genes with massive differential accessibility of their promoter and enhancer peaks during development of dysfunction, observed consistently across models, including transcription factors (TF) well studied in immunity such as Tcf7, Lef1, Satb1, Ikzf2, Tox, are good candidates for further targeted analysis.We then turned to TF binding analysis. We associated absolute levels of chromatin accessibility in peaks of each sample with TF binding (predicted by motif analysis) using regularized negative binomial regression with cross-validation. We estimated the effect of each TF in each sample, which allowed us to map chromatin accessibility profiles into the TF activity space of much lower dimensionality. This mapping largely preserved the hierarchy of relative similarities between samples. We identified key TFs whose binding was associated with open or closed chromatin in functional and dysfunctional cell states. For example, not surprisingly, binding of well known effector factors Eomes and Batf was associated with closed chromatin in naive cells and open chromatin in effector cells. Strikingly, the strongest association with closing chromatin in dysfunction, consistently across mouse models, was observed for Tcf7/Lef1 binding, further suggesting the role of these TFs in establishing the terminal CD8 T-cell dysfunctional state. Notably, we found two large groups of TFs anti-correlated to each other whose predicted binding sites had higher accessibility in either functional or dysfunctional cells. This suggested that coordinated activity of a broad range of TFs (not necessarily binding at the same sites) might be responsible for establishing and maintaining T-cell functional states, and focusing on one or a handful of TFs is not sufficient to explain them. This analysis provides a better systematic understanding of cell-intrinsic mechanisms driving different functional states of CD8 T-cells, and the developed computational methods are broadly applicable in other experimental setups where diverse cell states are profiled by high-throughput genomic assays.
Citation Format: Yuri Pritykin, Christina Leslie. A unified genome-wide analysis of dysfunctional T-cell states in cancer and chronic viral infection [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B038.
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Affiliation(s)
- Yuri Pritykin
- Memorial Sloan Kettering Cancer Center, New York, NY
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17
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Konopacki C, Pritykin Y, Rubtsov Y, Leslie CS, Rudensky AY. Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function. Nat Immunol 2019; 20:232-242. [PMID: 30643266 DOI: 10.1038/s41590-018-0291-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/25/2018] [Indexed: 12/22/2022]
Abstract
Regulatory T cells (Treg cells), whose differentiation and function are controlled by transcription factor Foxp3, express the closely related family member Foxp1. Here we explored Foxp1 function in Treg cells. We found that a large number of Foxp3-bound genomic sites in Treg cells were occupied by Foxp1 in both Treg cells and conventional T cells (Tconv cells). In Treg cells, Foxp1 markedly increased Foxp3 binding to these sites. Foxp1 deficiency in Treg cells resulted in their impaired function and competitive fitness, associated with markedly reduced CD25 expression and interleukin-2 (IL-2) responsiveness, diminished CTLA-4 expression and increased SATB1 expression. The characteristic expression patterns of CD25, Foxp3 and CTLA-4 in Treg cells were fully or partially rescued by strong IL-2 signaling. Our studies suggest that Foxp1 serves an essential non-redundant function in Treg cells by enforcing Foxp3-mediated regulation of gene expression and enabling efficient IL-2 signaling in these cells.
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Affiliation(s)
- Catherine Konopacki
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yury Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Weizman OE, Adams NM, Schuster IS, Krishna C, Pritykin Y, Lau C, Degli-Esposti MA, Leslie CS, Sun JC, O'Sullivan TE. ILC1 Confer Early Host Protection at Initial Sites of Viral Infection. Cell 2017; 171:795-808.e12. [PMID: 29056343 DOI: 10.1016/j.cell.2017.09.052] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/11/2017] [Accepted: 08/16/2017] [Indexed: 10/18/2022]
Abstract
Infection is restrained by the concerted activation of tissue-resident and circulating immune cells. Whether tissue-resident lymphocytes confer early antiviral immunity at local sites of primary infection prior to the initiation of circulating responses is not well understood. Furthermore, the kinetics of initial antiviral responses at sites of infection remain unclear. Here, we show that tissue-resident type 1 innate lymphoid cells (ILC1) serve an essential early role in host immunity through rapid production of interferon (IFN)-γ following viral infection. Ablation of Zfp683-dependent liver ILC1 lead to increased viral load in the presence of intact adaptive and innate immune cells critical for mouse cytomegalovirus (MCMV) clearance. Swift production of interleukin (IL)-12 by tissue-resident XCR1+ conventional dendritic cells (cDC1) promoted ILC1 production of IFN-γ in a STAT4-dependent manner to limit early viral burden. Thus, ILC1 contribute an essential role in viral immunosurveillance at sites of initial infection in response to local cDC1-derived proinflammatory cytokines.
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Affiliation(s)
- Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Timothy E O'Sullivan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Pritykin Y, Brito T, Schupbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA 2017; 23:1097-1109. [PMID: 28420675 PMCID: PMC5473144 DOI: 10.1261/rna.058594.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 04/03/2017] [Indexed: 06/01/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock, and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila ovaries and analyzing these data together with other publicly available data sets. In agreement with previous studies, we confirm that Cutoff is involved in the transcriptional regulation of piRNA clusters and in the repression of transposable elements in germ cells. Surprisingly, however, we find that Cutoff is enriched at and affects the expression of other noncoding RNAs, including spliceosomal RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). At least in some instances, Cutoff appears to act at a transcriptional level in concert with Rhino and perhaps Deadlock. Finally, we show that mutations in Cutoff result in the deregulation of hundreds of protein-coding genes in germ cells. Our study uncovers a broader function for the RDC complex in the Drosophila germline development.
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Affiliation(s)
- Yuri Pritykin
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tarcisio Brito
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-902, Brazil
| | - Trudi Schupbach
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Mona Singh
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, USA
| | - Attilio Pane
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21949-902, Brazil
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Perez AR, Pritykin Y, Vidigal JA, Chhangawala S, Zamparo L, Leslie CS, Ventura A. GuideScan software for improved single and paired CRISPR guide RNA design. Nat Biotechnol 2017; 35:347-349. [PMID: 28263296 PMCID: PMC5607865 DOI: 10.1038/nbt.3804] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [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: 08/22/2016] [Accepted: 01/27/2017] [Indexed: 12/26/2022]
Abstract
We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We also show that the trie data structure of GuideScan enables the design of gRNAs that are more specific than those designed by existing tools.
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Affiliation(s)
- Alexendar R. Perez
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA
| | - Yuri Pritykin
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Joana A. Vidigal
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sagar Chhangawala
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA
| | - Lee Zamparo
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina S. Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Dadi S, Chhangawala S, Whitlock BM, Franklin RA, Luo C, Oh SA, Toure A, Pritykin Y, Huse M, Leslie CS, Li MO. Cancer Immunosurveillance by Tissue-resident Innate Lymphoid Cells and Innate-like T Cells. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.74.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Malignancy can be suppressed by the immune system in a process termed immunosurveillance. However, to what extent immunosurveillance occurs in spontaneous cancers and the composition of participating cell types remain obscure. Here we show that cell transformation triggers a tissue-resident lymphocyte response in oncogene-induced murine cancer models. Non-circulating cytotoxic lymphocytes, derived from innate, TCRαβ and TCRγδ lineages, expand in early tumors. Characterized by high expression of NK1.1, CD49a and CD103, these cells share a gene expression signature distinct from those of conventional NK cells, T cells and invariant NKT cells. Generation of these lymphocytes is dependent on the cytokine IL-15, but not the transcription factor Nfil3 that is required for the differentiation of tumor-infiltrating NK cells, and IL-15, but not Nfil3, deficiency results in accelerated tumor growth. These findings reveal a tumor-elicited immunosurveillance mechanism that engages unconventional type 1-like innate lymphoid cells and type 1 innate-like T cells.
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Dadi S, Chhangawala S, Whitlock BM, Franklin RA, Luo CT, Oh SA, Toure A, Pritykin Y, Huse M, Leslie CS, Li MO. Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells. Cell 2016; 164:365-77. [PMID: 26806130 DOI: 10.1016/j.cell.2016.01.002] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/22/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023]
Abstract
Malignancy can be suppressed by the immune system in a process termed immunosurveillance. However, to what extent immunosurveillance occurs in spontaneous cancers and the composition of participating cell types remains obscure. Here, we show that cell transformation triggers a tissue-resident lymphocyte response in oncogene-induced murine cancer models. Non-circulating cytotoxic lymphocytes, derived from innate, T cell receptor (TCR)αβ, and TCRγδ lineages, expand in early tumors. Characterized by high expression of NK1.1, CD49a, and CD103, these cells share a gene-expression signature distinct from those of conventional NK cells, T cells, and invariant NKT cells. Generation of these lymphocytes is dependent on the cytokine IL-15, but not the transcription factor Nfil3 that is required for the differentiation of tumor-infiltrating NK cells, and IL-15 deficiency, but not Nfil3 deficiency, results in accelerated tumor growth. These findings reveal a tumor-elicited immunosurveillance mechanism that engages unconventional type-1-like innate lymphoid cells and type 1 innate-like T cells.
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Affiliation(s)
- Saïda Dadi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sagar Chhangawala
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Physiology Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Benjamin M Whitlock
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Ruth A Franklin
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Chong T Luo
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Soyoung A Oh
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmed Toure
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Abstract
Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, D. melanogaster, and S. cerevisiae—and show that, as compared to other annotated genes, genes involved in multiple biological processes possess distinct physicochemical properties, are more broadly expressed, tend to be more central in protein interaction networks, tend to be more evolutionarily conserved, and are more likely to be essential. We also find that multifunctional genes are significantly more likely to be involved in human disorders. These same features also hold when multifunctionality is defined with respect to molecular functions instead of biological processes. Our analysis uncovers key features about multifunctional genes, and is a step towards a better genome-wide understanding of gene multifunctionality. Almost every aspect of cellular function depends on protein activity. In spite of being fine-tuned to carry out highly specific functions, proteins can also multitask. Experimental studies have identified genes and proteins endowed with more than one molecular function, or participating in very different biological processes. These studies suggest that the degree of functional plasticity exhibited by proteins might go well beyond a simple “one protein—one function” relationship. However, systematic studies of the properties of multifunctional genes (and their encoded proteins) have been limited. Here we present a computational framework to identify putative multifunctional genes, and compare their properties with those of other genes. We find that multifunctional genes are significantly different from other genes with respect to their physicochemical properties, expression profiles, and interaction properties. We also observe that multifunctional genes tend to be more conserved, and that a greater fraction of them are associated with human disorders. Taken together, these results represent a step towards a more complete understanding of the role multifunctional genes play in the functional organization of the cell.
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Affiliation(s)
- Yuri Pritykin
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis–Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Dario Ghersi
- Lewis–Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
- * E-mail: (DG); (MS)
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis–Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (DG); (MS)
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