1
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Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol 2024; 25:644-658. [PMID: 38503922 DOI: 10.1038/s41590-024-01792-2] [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: 04/02/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7+PD-1+CD8+ T cells, activated CCR7+LAMP3+ dendritic cells and CCL19+ fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10+ macrophages and TCF7-CD8+ T cells as well as between mature regulatory dendritic cells and TCF7+CD4+ and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
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Affiliation(s)
- Jonathan H Chen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Department of Pathology, MGH, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Linda T Nieman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Maxwell Spurrell
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Liad Elmelech
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Peter Richieri
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Katherine H Xu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Roopa Madhu
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA
| | - Milan Parikh
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Izabella Zamora
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Christopher S Nabel
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua D Pirl
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chenyue Lu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Catherine B Meador
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Hematology/Oncology, MGH, HMS, Boston, MA, USA
| | | | | | - Alexander L Tang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Matan Hofree
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Lautenberg Center for Immunology and Cancer Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Angela Shih
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, MGH, Boston, MA, USA
| | - Karin Pelka
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, Gladstone Institutes, San Francisco, CA, USA
| | - Martin J Aryee
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mari Mino-Kenudson
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Center for Thoracic Cancers, MGH, Boston, MA, USA.
| | - Ilya Korsunsky
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA.
| | - Nir Hacohen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N. Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response. bioRxiv 2023:2023.04.04.535379. [PMID: 37066412 PMCID: PMC10104028 DOI: 10.1101/2023.04.04.535379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially-localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens, and found that they were associated with beneficial responses to PD-1-blockade. Immunity hubs were enriched for many interferon-stimulated genes, T cells in multiple differentiation states, and CXCL9/10/11 + macrophages that preferentially interact with CD8 T cells. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcomes, distinct from mature tertiary lymphoid structures, and enriched for stem-like TCF7+PD-1+ CD8 T cells and activated CCR7 + LAMP3 + dendritic cells, as well as chemokines that organize these cells. These results elucidate the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
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3
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Costi S, Morris LS, Collins A, Fernandez NF, Patel M, Xie H, Kim-Schulze S, Stern ER, Collins KA, Cathomas F, Parides MK, Whitton AE, Pizzagalli DA, Russo SJ, Murrough JW. Peripheral immune cell reactivity and neural response to reward in patients with depression and anhedonia. Transl Psychiatry 2021; 11:565. [PMID: 34741019 PMCID: PMC8571388 DOI: 10.1038/s41398-021-01668-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/10/2021] [Accepted: 10/04/2021] [Indexed: 12/20/2022] Open
Abstract
Increased levels of peripheral cytokines have been previously associated with depression in preclinical and clinical research. Although the precise nature of peripheral immune dysfunction in depression remains unclear, evidence from animal studies points towards a dysregulated response of peripheral leukocytes as a risk factor for stress susceptibility. This study examined dynamic release of inflammatory blood factors from peripheral blood mononuclear cells (PBMC) in depressed patients and associations with neural and behavioral measures of reward processing. Thirty unmedicated patients meeting criteria for unipolar depressive disorder and 21 healthy control volunteers were enrolled. PBMCs were isolated from whole blood and stimulated ex vivo with lipopolysaccharide (LPS). Olink multiplex assay was used to analyze a large panel of inflammatory proteins. Participants completed functional magnetic resonance imaging with an incentive flanker task to probe neural responses to reward anticipation, as well as clinical measures of anhedonia and pleasure including the Temporal Experience of Pleasure Scale (TEPS) and the Snaith-Hamilton Pleasure Scale (SHAPS). LPS stimulation revealed larger increases in immune factors in depressed compared to healthy subjects using an aggregate immune score (t49 = 2.83, p = 0.007). Higher peripheral immune score was associated with reduced neural responses to reward anticipation within the ventral striatum (VS) (r = -0.39, p = 0.01), and with reduced anticipation of pleasure as measured with the TEPS anticipatory sub-score (r = -0.318, p = 0.023). Our study provides new evidence suggesting that dynamic hyper-reactivity of peripheral leukocytes in depressed patients is associated with blunted activation of the brain reward system and lower subjective anticipation of pleasure.
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Affiliation(s)
- Sara Costi
- grid.59734.3c0000 0001 0670 2351Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Laurel S. Morris
- grid.59734.3c0000 0001 0670 2351Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Abigail Collins
- grid.59734.3c0000 0001 0670 2351Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicolas F. Fernandez
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Manishkumar Patel
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Hui Xie
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Seunghee Kim-Schulze
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Emily R. Stern
- grid.137628.90000 0004 1936 8753Department of Psychiatry, New York University School of Medicine, New York, NY USA ,grid.250263.00000 0001 2189 4777Nathan Kline Institute for Psychiatric Research, Orangeburg, NY USA
| | - Katherine A. Collins
- grid.59734.3c0000 0001 0670 2351Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.250263.00000 0001 2189 4777Nathan Kline Institute for Psychiatric Research, Orangeburg, NY USA
| | - Flurin Cathomas
- grid.59734.3c0000 0001 0670 2351Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Michael K. Parides
- grid.240283.f0000 0001 2152 0791Montefiore Medical Center/Albert Einstein College of Medicine, New York, NY USA
| | - Alexis E. Whitton
- grid.38142.3c000000041936754XDepartment of Psychiatry, McLean Hospital and Harvard Medical School, Belmont, MA USA ,grid.1013.30000 0004 1936 834XSchool of Medical Sciences, The University of Sydney, Sydney, NSW Australia
| | - Diego A. Pizzagalli
- grid.38142.3c000000041936754XDepartment of Psychiatry, McLean Hospital and Harvard Medical School, Belmont, MA USA
| | - Scott J. Russo
- grid.59734.3c0000 0001 0670 2351Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Center for Affective Neuroscience, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - James W. Murrough
- grid.59734.3c0000 0001 0670 2351Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
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4
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Edwards JJ, Rouillard AD, Fernandez NF, Wang Z, Lachmann A, Shankaran SS, Bisgrove BW, Demarest B, Turan N, Srivastava D, Bernstein D, Deanfield J, Giardini A, Porter G, Kim R, Roberts AE, Newburger JW, Goldmuntz E, Brueckner M, Lifton RP, Seidman CE, Chung WK, Tristani-Firouzi M, Yost HJ, Ma'ayan A, Gelb BD. Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. JACC Basic Transl Sci 2020; 5:376-386. [PMID: 32368696 PMCID: PMC7188873 DOI: 10.1016/j.jacbts.2020.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/30/2022]
Abstract
Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes. Mutations affecting genes coding for the WAVE2 protein complex and small GTPase-mediated signaling are associated with LVOTO lesions. WAVE2 complex genes brk1, nckap1, and wasf2 and regulators of small GTPase signaling cul3a and racgap1 are critical to zebrafish heart development.
Genetic variants are the primary driver of congenital heart disease (CHD) pathogenesis. However, our ability to identify causative variants is limited. To identify causal CHD genes that are associated with specific molecular functions, the study used prior knowledge to filter de novo variants from 2,881 probands with sporadic severe CHD. This approach enabled the authors to identify an association between left ventricular outflow tract obstruction lesions and genes associated with the WAVE2 complex and regulation of small GTPase-mediated signal transduction. Using CRISPR zebrafish knockdowns, the study confirmed that WAVE2 complex proteins brk1, nckap1, and wasf2 and the regulators of small GTPase signaling cul3a and racgap1 are critical to cardiac development.
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Key Words
- CHD, congenital heart disease
- CORUM, Comprehensive Resource of Mammalian Protein Complexes
- CRISPR, clustered regularly interspaced short palindromic repeats
- CTD, conotruncal defect
- GOBP, Gene Ontology biological processes
- HHE, high heart expression
- HLHS, hypoplastic left heart syndrome
- HTX, heterotaxy
- LVOTO, left ventricular outflow tract obstruction
- MGI, Mouse Genome Informatics
- PCGC, Pediatric Cardiac Genomics Consortium
- PPI, protein-protein interaction
- congenital heart disease
- systems biology
- translational genomics
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Affiliation(s)
- Jonathan J Edwards
- Department of Pediatrics, Division of Pediatric Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew D Rouillard
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas F Fernandez
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sunita S Shankaran
- Department of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee
| | - Brent W Bisgrove
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | - Bradley Demarest
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, California
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - John Deanfield
- Department of Cardiology, Great Ormond Street Hospital, University College London, London, United Kingdom
| | - Alessandro Giardini
- Department of Cardiology, Great Ormond Street Hospital, University College London, London, United Kingdom
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Richard Kim
- Section of Cardiothoracic Surgery, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Amy E Roberts
- Department of Cardiology, Children's Hospital Boston, Boston, Massachusetts
| | - Jane W Newburger
- Department of Cardiology, Children's Hospital Boston, Boston, Massachusetts
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts.,Cardiovascular Division, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Medicine, Columbia University Medical Center, New York, New York
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
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5
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Fernandez D, Fernandez NF, Rahman A, Hill C, Shamailova R, Kim-Schulze S, Mocco J, Faries P, Merad M, Giannarelli C. ZEB2 Regulates Activation and Exhaustion Programming of CD8 T Cells in Atherosclerosis. JVS Vasc Sci 2020. [DOI: 10.1016/j.jvssci.2020.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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6
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Levin-Schwartz Y, Curtin P, Svensson K, Fernandez NF, Kim-Schulze S, Hair GM, Flores D, Pantic I, Tamayo-Ortiz M, Luisa Pizano-Zárate M, Gennings C, Satlin LM, Baccarelli AA, Tellez-Rojo MM, Wright RO, Sanders AP. Length of gestation and birth weight are associated with indices of combined kidney biomarkers in early childhood. PLoS One 2020; 14:e0227219. [PMID: 31891650 PMCID: PMC6938375 DOI: 10.1371/journal.pone.0227219] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/13/2019] [Indexed: 11/19/2022] Open
Abstract
Infants born prematurely or with low birth weights are more susceptible to kidney dysfunction throughout their lives. Multiple proteins measured in urine are noninvasive biomarkers of subclinical kidney damage, but few studies have examined the joint effects of multiple biomarkers. We conducted an exploratory study of 103 children in the Programing Research in Obesity, Growth, Environment, and Social Stressors (PROGRESS) longitudinal birth cohort, and measured nine proteins selected a priori in banked spot urine samples collected at ages 4-6. The goal of our study was to explore the combined effects of kidney damage biomarkers previously associated with birth outcomes. To do this, we generated kidney biomarker indices using weighted quantile sum regression and assessed associations with length of gestation or birth weight. A decile increase in each kidney biomarker index was associated with 2-day shorter gestations (β = -2.0, 95% CI: -3.2, -0.9) and 59-gram lower birth weights (β = -58.5, 95% CI: -98.3, -18.7), respectively. Weights highlighting the contributions showed neutrophil gelatinase-associated lipocalin (NGAL) (60%) and osteopontin (19%) contributed most to the index derived for gestational age. NGAL (66%) and beta-2-microglobulin (10%) contributed most to the index derived for birth weight. Joint analyses of multiple kidney biomarkers can provide integrated measures of kidney dysfunction and improved statistical assessments compared to biomarkers assessed individually. Additionally, shorter gestations and lower birth weights may contribute to subclinical kidney damage measurable in childhood.
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Affiliation(s)
- Yuri Levin-Schwartz
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Paul Curtin
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Katherine Svensson
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Nicolas F. Fernandez
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gleicy M. Hair
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Daniel Flores
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ivan Pantic
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, Mexico
- Department of Developmental Neurobiology, National Institute of Perinatology, Mexico City, Mexico
| | - Marcela Tamayo-Ortiz
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, Mexico
- National Council of Science and Technology, Mexico City, Mexico
| | - María Luisa Pizano-Zárate
- Division of Community Interventions Research, National Institute of Perinatology, Mexico City, Mexico
| | - Chris Gennings
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Lisa M. Satlin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University, New York, NY, United States of America
| | - Martha M. Tellez-Rojo
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - Robert O. Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alison P. Sanders
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- * E-mail:
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7
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Fernandez DM, Rahman AH, Fernandez NF, Chudnovskiy A, Amir EAD, Amadori L, Khan NS, Wong CK, Shamailova R, Hill CA, Wang Z, Remark R, Li JR, Pina C, Faries C, Awad AJ, Moss N, Bjorkegren JLM, Kim-Schulze S, Gnjatic S, Ma'ayan A, Mocco J, Faries P, Merad M, Giannarelli C. Single-cell immune landscape of human atherosclerotic plaques. Nat Med 2019; 25:1576-1588. [PMID: 31591603 PMCID: PMC7318784 DOI: 10.1038/s41591-019-0590-4] [Citation(s) in RCA: 478] [Impact Index Per Article: 95.6] [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: 10/23/2018] [Accepted: 08/16/2019] [Indexed: 12/29/2022]
Abstract
Atherosclerosis is driven by multifaceted contributions of the immune system within the circulation and at vascular focal sites. However, specific characteristics of dysregulated immune cells within atherosclerotic lesions that lead to clinical events such as ischemic stroke or myocardial infarction are poorly understood. Here, using single-cell proteomic and transcriptomic analyses, we uncovered distinct features of both T cells and macrophages in carotid artery plaques of patients with clinically symptomatic disease (recent stroke or transient ischemic attack) compared to asymptomatic disease (no recent stroke). Plaques from symptomatic patients were characterized by a distinct subset of CD4+ T cells and by T cells that were activated and differentiated. Moreover, some T cell subsets in these plaques presented markers of T cell exhaustion. Additionally, macrophages from these plaques contained alternatively activated phenotypes, including subsets associated with plaque vulnerability. In plaques from asymptomatic patients, T cells and macrophages were activated and displayed evidence of interleukin-1β signaling. The identification of specific features of innate and adaptive immune cells in plaques that are associated with cerebrovascular events may enable the design of more precisely tailored cardiovascular immunotherapies.
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Affiliation(s)
- Dawn M Fernandez
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb H Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas F Fernandez
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksey Chudnovskiy
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - El-Ad David Amir
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nayaab S Khan
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christine K Wong
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roza Shamailova
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher A Hill
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zichen Wang
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romain Remark
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Innate Pharma, Marseille, France
| | - Jennifer R Li
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian Pina
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ahmed J Awad
- Cerebrovascular Center, Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Noah Moss
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan L M Bjorkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Integrated Cardio MetabolicCentre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hematology and Medical Oncology Division, The Tish Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avi Ma'ayan
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Mocco
- Cerebrovascular Center, Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Giannarelli
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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8
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Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma’ayan A. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci Data 2017; 4:170151. [PMID: 28994825 PMCID: PMC5634325 DOI: 10.1038/sdata.2017.151] [Citation(s) in RCA: 114] [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: 06/19/2017] [Accepted: 09/06/2017] [Indexed: 01/11/2023] Open
Abstract
Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data.
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Affiliation(s)
- Nicolas F. Fernandez
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center (DCIC), Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gregory W. Gundersen
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center (DCIC), Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Adeeb Rahman
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Mark L. Grimes
- Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana 59812, USA
| | - Klarisa Rikova
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923, USA
| | - Peter Hornbeck
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923, USA
| | - Avi Ma’ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center (DCIC), Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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9
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Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma'ayan A, Frenette PS. Differential cytokine contributions of perivascular haematopoietic stem cell niches. Nat Cell Biol 2017; 19:214-223. [PMID: 28218906 PMCID: PMC5467892 DOI: 10.1038/ncb3475] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [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: 06/08/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022]
Abstract
Arterioles and sinusoids of the bone marrow (BM) are accompanied by stromal cells that express nerve/glial antigen 2 (NG2) and leptin receptor (LepR), and constitute specialized niches that regulate quiescence and proliferation of haematopoietic stem cells (HSCs). However, how niche cells differentially regulate HSC functions remains unknown. Here, we show that the effects of cytokines regulating HSC functions are dependent on the producing cell sources. Deletion of chemokine C-X-C motif ligand 12 (Cxcl12) or stem cell factor (Scf) from all perivascular cells marked by nestin-GFP dramatically depleted BM HSCs. Selective Cxcl12 deletion from arteriolar NG2+ cells, but not from sinusoidal LepR+ cells, caused HSC reductions and altered HSC localization in BM. By contrast, deletion of Scf in LepR+ cells, but not NG2+ cells, led to reductions in BM HSC numbers. These results uncover distinct contributions of cytokines derived from perivascular cells in separate vascular niches to HSC maintenance.
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Affiliation(s)
- Noboru Asada
- Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yuya Kunisaki
- Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Halley Pierce
- Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Nicolas F Fernandez
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Alexander Birbrair
- Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Paul S Frenette
- Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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10
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Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat Commun 2016; 7:12846. [PMID: 27667448 PMCID: PMC5052684 DOI: 10.1038/ncomms12846] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/05/2016] [Indexed: 12/14/2022] Open
Abstract
Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO). Through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbation signatures. All these signatures are unique and are manually validated for quality. Global analysis of these signatures confirms known associations and identifies novel associations between genes, diseases and drugs. The manually curated signatures are used as a training set to develop classifiers for extracting similar signatures from the entire GEO repository. We develop a web portal to serve these signatures for query, download and visualization.
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Affiliation(s)
- Zichen Wang
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Caroline D. Monteiro
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
- Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd, Cleveland, Ohio 44135, USA
- Center for Space Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
| | - Nicolas F. Fernandez
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Gregory W. Gundersen
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Andrew D. Rouillard
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Axel S. Feldmann
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Kevin S. Hu
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Michael G. McDermott
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Qiaonan Duan
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Neil R. Clark
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Matthew R. Jones
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Yan Kou
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Troy Goff
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | | | - Fabio M R. Amaral
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Gregory L. Szeto
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Oliver Fuchs
- Paediatric Allergology and Pulmonology, Dr von Hauner University Children's Hospital, Ludwig-Maximilians-University of Munich, Member of the German Centre for Lung Research (DZL), Lindwurmstrasse 4, Munich 80337, Germany
| | - Sophia M. Schüssler-Fiorenza Rose
- Spinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
- Department of Neurosurgery, Stanford School of Medicine, Stanford, California 94304, USA
| | - Shvetank Sharma
- Department of Research, Institute of Liver & Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India
| | - Uwe Schwartz
- Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Xabier Bengoetxea Bausela
- Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain
| | - Maciej Szymkiewicz
- Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01–447, Poland
| | | | - Anton Salykin
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Carolina M. Barra
- IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain
| | | | - Nicholas J. Bongio
- Department of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA
| | | | | | - Udi E. Rubin
- Department of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA
| | - Apostolos Malatras
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France
| | - Carl T. Fulp
- 13-1, Higashi 4-chome Shibuya-ku, Tokyo 150-0011, Japan
| | - John A. Galindo
- Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia
| | - Ruta Motiejunaite
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Christoph Jüschke
- Department of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany
| | | | - Katharina Lahl
- Technical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark
| | - Mohieddin Jafari
- Protein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, No. 358, 12th Farwardin Ave, Jomhhoori St, Tehran 13164, Iran
- School of Biological Sciences, Institute for Researches in Fundamental Sciences, Niavaran Square, P.O.Box, Tehran 19395-5746, Iran
| | - Sara Aibar
- University of Salamanca, Salamanca, Madrid 37008, Spain
| | - Apostolos Zaravinos
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, level 7, Stockholm SE141 86, Sweden
- Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenes Str. Engomi, P.O.Box 22006, Nicosia 1516, Cyprus
| | | | | | | | - Fernando de Andres Segura
- CICAB, Clinical Research Centre, Extremadura University Hospital, Elvas Av., s/n. 06006 Badajoz 06006, Spain
| | | | - Vicente Pérez-García
- Consejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología, Department of Immunology and Oncology, c/Darwin, 3 Madrid 28049, Spain
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
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11
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Duan Q, Reid SP, Clark NR, Wang Z, Fernandez NF, Rouillard AD, Readhead B, Tritsch SR, Hodos R, Hafner M, Niepel M, Sorger PK, Dudley JT, Bavari S, Panchal RG, Ma'ayan A. L1000CDS 2: LINCS L1000 characteristic direction signatures search engine. NPJ Syst Biol Appl 2016; 2. [PMID: 28413689 PMCID: PMC5389891 DOI: 10.1038/npjsba.2016.15] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The library of integrated network-based cellular signatures (LINCS) L1000 data set currently comprises of over a million gene expression profiles of chemically perturbed human cell lines. Through unique several intrinsic and extrinsic benchmarking schemes, we demonstrate that processing the L1000 data with the characteristic direction (CD) method significantly improves signal to noise compared with the MODZ method currently used to compute L1000 signatures. The CD processed L1000 signatures are served through a state-of-the-art web-based search engine application called L1000CDS2. The L1000CDS2 search engine provides prioritization of thousands of small-molecule signatures, and their pairwise combinations, predicted to either mimic or reverse an input gene expression signature using two methods. The L1000CDS2 search engine also predicts drug targets for all the small molecules profiled by the L1000 assay that we processed. Targets are predicted by computing the cosine similarity between the L1000 small-molecule signatures and a large collection of signatures extracted from the gene expression omnibus (GEO) for single-gene perturbations in mammalian cells. We applied L1000CDS2 to prioritize small molecules that are predicted to reverse expression in 670 disease signatures also extracted from GEO, and prioritized small molecules that can mimic expression of 22 endogenous ligand signatures profiled by the L1000 assay. As a case study, to further demonstrate the utility of L1000CDS2, we collected expression signatures from human cells infected with Ebola virus at 30, 60 and 120 min. Querying these signatures with L1000CDS2 we identified kenpaullone, a GSK3B/CDK2 inhibitor that we show, in subsequent experiments, has a dose-dependent efficacy in inhibiting Ebola infection in vitro without causing cellular toxicity in human cell lines. In summary, the L1000CDS2 tool can be applied in many biological and biomedical settings, while improving the extraction of knowledge from the LINCS L1000 resource.
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Affiliation(s)
- Qiaonan Duan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - St Patrick Reid
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Neil R Clark
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas F Fernandez
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew D Rouillard
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ben Readhead
- Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah R Tritsch
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rachel Hodos
- Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Mario Niepel
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Joel T Dudley
- Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sina Bavari
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rekha G Panchal
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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12
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Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res 2016; 44. [PMID: 27141961 PMCID: PMC4987924 DOI: 10.1093/nar%2fgkw377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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Affiliation(s)
- Maxim V. Kuleshov
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Matthew R. Jones
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Andrew D. Rouillard
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Nicolas F. Fernandez
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Qiaonan Duan
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Simon Koplev
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Kathleen M. Jagodnik
- Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd., Cleveland, OH 44135, USA
| | - Alexander Lachmann
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Michael G. McDermott
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Caroline D. Monteiro
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Gregory W. Gundersen
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA,To whom correspondence should be addressed. Tel: +1 212 241 1153; Fax: +1 212 996 7214;
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Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res 2016. [PMID: 27141961 DOI: 10.1093/nar/gkw377)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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Affiliation(s)
- Maxim V Kuleshov
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Matthew R Jones
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Andrew D Rouillard
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Nicolas F Fernandez
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Qiaonan Duan
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Simon Koplev
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Sherry L Jenkins
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd., Cleveland, OH 44135, USA
| | - Alexander Lachmann
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Michael G McDermott
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Caroline D Monteiro
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Gregory W Gundersen
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
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Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford) 2016; 2016:baw100. [PMID: 27374120 PMCID: PMC4930834 DOI: 10.1093/database/baw100] [Citation(s) in RCA: 841] [Impact Index Per Article: 105.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly generate a plethora of data on the activity and levels of biomolecules within mammalian cells. At the same time, curation projects that organize knowledge from the biomedical literature into online databases are expanding. Hence, there is a wealth of information about genes, proteins and their associations, with an urgent need for data integration to achieve better knowledge extraction and data reuse. For this purpose, we developed the Harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from over 70 major online resources. We extracted, abstracted and organized data into ∼72 million functional associations between genes/proteins and their attributes. Such attributes could be physical relationships with other biomolecules, expression in cell lines and tissues, genetic associations with knockout mouse or human phenotypes, or changes in expression after drug treatment. We stored these associations in a relational database along with rich metadata for the genes/proteins, their attributes and the original resources. The freely available Harmonizome web portal provides a graphical user interface, a web service and a mobile app for querying, browsing and downloading all of the collected data. To demonstrate the utility of the Harmonizome, we computed and visualized gene–gene and attribute–attribute similarity networks, and through unsupervised clustering, identified many unexpected relationships by combining pairs of datasets such as the association between kinase perturbations and disease signatures. We also applied supervised machine learning methods to predict novel substrates for kinases, endogenous ligands for G-protein coupled receptors, mouse phenotypes for knockout genes, and classified unannotated transmembrane proteins for likelihood of being ion channels. The Harmonizome is a comprehensive resource of knowledge about genes and proteins, and as such, it enables researchers to discover novel relationships between biological entities, as well as form novel data-driven hypotheses for experimental validation. Database URL: http://amp.pharm.mssm.edu/Harmonizome.
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Affiliation(s)
- Andrew D Rouillard
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory W Gundersen
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas F Fernandez
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline D Monteiro
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael G McDermott
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai's Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res 2016; 44:W90-7. [PMID: 27141961 PMCID: PMC4987924 DOI: 10.1093/nar/gkw377] [Citation(s) in RCA: 5411] [Impact Index Per Article: 676.4] [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: 01/29/2016] [Accepted: 04/25/2016] [Indexed: 12/11/2022] Open
Abstract
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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Affiliation(s)
- Maxim V Kuleshov
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Matthew R Jones
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Andrew D Rouillard
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Nicolas F Fernandez
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Qiaonan Duan
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Simon Koplev
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Sherry L Jenkins
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd., Cleveland, OH 44135, USA
| | - Alexander Lachmann
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Michael G McDermott
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Caroline D Monteiro
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Gregory W Gundersen
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
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Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma'ayan A. Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. ACTA ACUST UNITED AC 2014; 30:3289-90. [PMID: 25100688 DOI: 10.1093/bioinformatics/btu526] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. AVAILABILITY AND IMPLEMENTATION DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB CONTACT: avi.maayan@mssm.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiaonan Duan
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicolas F Fernandez
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Andrew D Rouillard
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Christopher M Tan
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Cyril H Benes
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029 and Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
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Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res 2014; 42:W449-60. [PMID: 24906883 PMCID: PMC4086130 DOI: 10.1093/nar/gku476] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites.
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Affiliation(s)
- Qiaonan Duan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA
| | - Corey Flynn
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Mario Niepel
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Marc Hafner
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Jeremy L Muhlich
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Nicolas F Fernandez
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA
| | - Andrew D Rouillard
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA
| | - Christopher M Tan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA
| | - Edward Y Chen
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA
| | - Todd R Golub
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | | | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA
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