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Dolgalev I, Zhou H, Murrell N, Le H, Sakellaropoulos T, Coudray N, Zhu K, Vasudevaraja V, Yeaton A, Goparaju C, Li Y, Sulaiman I, Tsay JCJ, Meyn P, Mohamed H, Sydney I, Shiomi T, Ramaswami S, Narula N, Kulicke R, Davis FP, Stransky N, Smolen GA, Cheng WY, Cai J, Punekar S, Velcheti V, Sterman DH, Poirier JT, Neel B, Wong KK, Chiriboga L, Heguy A, Papagiannakopoulos T, Nadorp B, Snuderl M, Segal LN, Moreira AL, Pass HI, Tsirigos A. Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma. Nat Commun 2023; 14:6764. [PMID: 37938580 PMCID: PMC10632519 DOI: 10.1038/s41467-023-42327-x] [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: 10/28/2022] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Approximately 30% of early-stage lung adenocarcinoma patients present with disease progression after successful surgical resection. Despite efforts of mapping the genetic landscape, there has been limited success in discovering predictive biomarkers of disease outcomes. Here we performed a systematic multi-omic assessment of 143 tumors and matched tumor-adjacent, histologically-normal lung tissue with long-term patient follow-up. Through histologic, mutational, and transcriptomic profiling of tumor and adjacent-normal tissue, we identified an inflammatory gene signature in tumor-adjacent tissue as the strongest clinical predictor of disease progression. Single-cell transcriptomic analysis demonstrated the progression-associated inflammatory signature was expressed in both immune and non-immune cells, and cell type-specific profiling in monocytes further improved outcome predictions. Additional analyses of tumor-adjacent transcriptomic data from The Cancer Genome Atlas validated the association of the inflammatory signature with worse outcomes across cancers. Collectively, our study suggests that molecular profiling of tumor-adjacent tissue can identify patients at high risk for disease progression.
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Affiliation(s)
- Igor Dolgalev
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, USA
| | - Hua Zhou
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, USA
| | - Nina Murrell
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, USA
| | - Hortense Le
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, USA
| | | | - Nicolas Coudray
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, USA
- Department of Cell Biology, NYU Grossman School of Medicine, New York, USA
| | - Kelsey Zhu
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | | | - Anna Yeaton
- The Optical Profiling Platform at The Broad Institute of MIT And Harvard, Cambridge, USA
| | - Chandra Goparaju
- Department of Cardiothoracic Surgery, NYU Grossman School of Medicine, New York, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care and Sleep Medicine, NYU Grossman School of Medicine, New York, USA
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care and Sleep Medicine, NYU Grossman School of Medicine, New York, USA
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care and Sleep Medicine, NYU Grossman School of Medicine, New York, USA
| | - Peter Meyn
- Genome Technology Center, Office of Science and Research, NYU Grossman School of Medicine, New York, USA
| | - Hussein Mohamed
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Iris Sydney
- Center for Biospecimen Research and Development, NYU Grossman School of Medicine, New York, USA
| | - Tomoe Shiomi
- Center for Biospecimen Research and Development, NYU Grossman School of Medicine, New York, USA
| | - Sitharam Ramaswami
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Genome Technology Center, Office of Science and Research, NYU Grossman School of Medicine, New York, USA
| | - Navneet Narula
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Ruth Kulicke
- Celsius Therapeutics, Cambridge, Massachusetts, USA
| | - Fred P Davis
- Celsius Therapeutics, Cambridge, Massachusetts, USA
| | | | | | - Wei-Yi Cheng
- Pharma Research & Early Development Informatics, Roche Innovation Center New York, New Jersey, USA
| | - James Cai
- Pharma Research & Early Development Informatics, Roche Innovation Center New York, New Jersey, USA
| | - Salman Punekar
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Vamsidhar Velcheti
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Daniel H Sterman
- Division of Pulmonary, Critical Care and Sleep Medicine, NYU Grossman School of Medicine, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - J T Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Ben Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Adriana Heguy
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Genome Technology Center, Office of Science and Research, NYU Grossman School of Medicine, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Bettina Nadorp
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, USA
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, NYU Grossman School of Medicine, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, NYU Grossman School of Medicine, New York, USA.
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, USA.
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, USA.
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, USA.
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
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Rashidfarrokhi A, Pillai R, Hao Y, Wu WL, Karadal-Ferrena B, Dimitriadoy SG, Cross M, Yeaton AH, Huang SM, Bhutkar AJ, Herrera A, Rajalingam S, Hayashi M, Huang KL, Bartnicki E, Zavitsanou AM, Wohlhieter CA, Leboeuf SE, Chen T, Loomis C, Mezzano V, Kulicke R, Davis FP, Stransky N, Smolen GA, Rudin CM, Moreira AL, Khanna KM, Pass HI, Wong KK, Koide S, Tsirigos A, Koralov SB, Papagiannakopoulos T. Tumor-intrinsic LKB1-LIF signaling axis establishes a myeloid niche to promote immune evasion and tumor growth. bioRxiv 2023:2023.07.15.549147. [PMID: 37502974 PMCID: PMC10370066 DOI: 10.1101/2023.07.15.549147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tumor mutations can influence the surrounding microenvironment leading to suppression of anti-tumor immune responses and thereby contributing to tumor progression and failure of cancer therapies. Here we use genetically engineered lung cancer mouse models and patient samples to dissect how LKB1 mutations accelerate tumor growth by reshaping the immune microenvironment. Comprehensive immune profiling of LKB1 -mutant vs wildtype tumors revealed dramatic changes in myeloid cells, specifically enrichment of Arg1 + interstitial macrophages and SiglecF Hi neutrophils. We discovered a novel mechanism whereby autocrine LIF signaling in Lkb1 -mutant tumors drives tumorigenesis by reprogramming myeloid cells in the immune microenvironment. Inhibiting LIF signaling in Lkb1 -mutant tumors, via gene targeting or with a neutralizing antibody, resulted in a striking reduction in Arg1 + interstitial macrophages and SiglecF Hi neutrophils, expansion of antigen specific T cells, and inhibition of tumor progression. Thus, targeting LIF signaling provides a new therapeutic approach to reverse the immunosuppressive microenvironment of LKB1 -mutant tumors.
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Villarino AV, Laurence ADJ, Davis FP, Nivelo L, Brooks SR, Sun HW, Jiang K, Afzali B, Frasca D, Hennighausen L, Kanno Y, O’Shea JJ. A central role for STAT5 in the transcriptional programing of T helper cell metabolism. Sci Immunol 2022; 7:eabl9467. [PMID: 36427325 PMCID: PMC9844264 DOI: 10.1126/sciimmunol.abl9467] [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: 11/27/2022]
Abstract
Activated lymphocytes adapt their metabolism to meet the energetic and biosynthetic demands imposed by rapid growth and proliferation. Common gamma chain (cγ) family cytokines are central to these processes, but the role of downstream signal transducer and activator of transcription 5 (STAT5) signaling, which is engaged by all cγ members, is poorly understood. Using genome-, transcriptome-, and metabolome-wide analyses, we demonstrate that STAT5 is a master regulator of energy and amino acid metabolism in CD4+ T helper cells. Mechanistically, STAT5 localizes to an array of enhancers and promoters for genes encoding essential enzymes and transporters, where it facilitates p300 recruitment and epigenetic remodeling. We also find that STAT5 licenses the activity of two other key metabolic regulators, the mTOR signaling pathway and the MYC transcription factor. Building on the latter, we present evidence for transcriptome-wide cooperation between STAT5 and MYC in both normal and transformed T cells. Together, our data provide a molecular framework for transcriptional programing of T cell metabolism downstream of cγ cytokines and highlight the JAK-STAT pathway in mediating cellular growth and proliferation.
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Affiliation(s)
- Alejandro V. Villarino
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA,Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA,Corresponding author.
| | - Arian DJ Laurence
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Fred P. Davis
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA,Celsius Therapeutics, Cambridge, MA, USA
| | - Luis Nivelo
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Stephen R. Brooks
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA
| | - Hong-Wei Sun
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA
| | - Kan Jiang
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA
| | - Behdad Afzali
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, USA
| | - Daniela Frasca
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Lothar Hennighausen
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, USA
| | - Yuka Kanno
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA
| | - John J. O’Shea
- National Institute of Arthritis, Musculoskeletal, and Skin Diseases, Bethesda, MD, USA
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Mikami Y, Philips RL, Sciumè G, Petermann F, Meylan F, Nagashima H, Yao C, Davis FP, Brooks SR, Sun HW, Takahashi H, Poholek AC, Shih HY, Afzali B, Muljo SA, Hafner M, Kanno Y, O'Shea JJ. MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23. Immunity 2021; 54:514-525.e6. [PMID: 33657395 DOI: 10.1016/j.immuni.2021.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 07/15/2020] [Revised: 12/08/2020] [Accepted: 02/12/2021] [Indexed: 01/03/2023]
Abstract
MicroRNAs are important regulators of immune responses. Here, we show miR-221 and miR-222 modulate the intestinal Th17 cell response. Expression of miR-221 and miR-222 was induced by proinflammatory cytokines and repressed by the cytokine TGF-β. Molecular targets of miR-221 and miR-222 included Maf and Il23r, and loss of miR-221 and miR-222 expression shifted the transcriptomic spectrum of intestinal Th17 cells to a proinflammatory signature. Although the loss of miR-221 and miR-222 was tolerated for maintaining intestinal Th17 cell homeostasis in healthy mice, Th17 cells lacking miR-221 and miR-222 expanded more efficiently in response to IL-23. Both global and T cell-specific deletion of miR-221 and miR-222 rendered mice prone to mucosal barrier damage. Collectively, these findings demonstrate that miR-221 and miR-222 are an integral part of intestinal Th17 cell response that are induced after IL-23 stimulation to constrain the magnitude of proinflammatory response.
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Affiliation(s)
- Yohei Mikami
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rachael L Philips
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giuseppe Sciumè
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Franziska Petermann
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Françoise Meylan
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiroyuki Nagashima
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen Yao
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred P Davis
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hayato Takahashi
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amanda C Poholek
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Behdad Afzali
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefan A Muljo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus Hafner
- RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Girard F, von Siebenthal M, Davis FP, Celio MR. Gene expression analysis in the mouse brainstem identifies Cart and Nesfatin as neuropeptides coexpressed in the Calbindin-positive neurons of the Nucleus papilio. Sleep 2020; 43:5826369. [PMID: 32343818 PMCID: PMC7658639 DOI: 10.1093/sleep/zsaa085] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/08/2020] [Indexed: 11/17/2022] Open
Abstract
Study Objectives: The brainstem contains several neuronal populations, heterogeneous in terms of neurotransmitter/neuropeptide content, which are important for controlling various aspects of the rapid eye movement (REM) phase of sleep. Among these populations are the Calbindin (Calb)-immunoreactive NPCalb neurons, located in the Nucleus papilio, within the dorsal paragigantocellular nucleus (DPGi), and recently shown to control eye movement during the REM phase of sleep. Methods: We performed in-depth data mining of the in situ hybridization data collected at the Allen Brain Atlas, in order to identify potentially interesting genes expressed in this brainstem nucleus. Our attention focused on genes encoding neuropeptides, including Cart (Cocaine and Amphetamine Regulated Transcripts) and Nesfatin 1. Results: While nesfatin 1 appeared ubiquitously expressed in this Calb-positive neuronal population, Cart was coexpressed in only a subset of these glutamatergic NPCalb neurons. Furthermore, an REM sleep deprivation and rebound assay performed with mice revealed that the Cart-positive neuronal population within the DPGi was activated during REM sleep (as measured by c-fos immunoreactivity), suggesting a role of this neuropeptide in regulating some aspects of REM sleep. Conclusions: The assembled information could afford functional clues to investigators, conducive to further experimental pursuits.
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Affiliation(s)
- Franck Girard
- Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland
| | | | - Fred P Davis
- Janelia-Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Marco R Celio
- Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland
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Davis FP, Nern A, Picard S, Reiser MB, Rubin GM, Eddy SR, Henry GL. A genetic, genomic, and computational resource for exploring neural circuit function. eLife 2020; 9:e50901. [PMID: 31939737 PMCID: PMC7034979 DOI: 10.7554/elife.50901] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [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: 08/06/2019] [Accepted: 01/14/2020] [Indexed: 12/11/2022] Open
Abstract
The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.
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Affiliation(s)
- Fred P Davis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Molecular Immunology and Inflammation BranchNational Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of HealthBethesdaUnited States
| | - Aljoscha Nern
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Serge Picard
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Michael B Reiser
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Sean R Eddy
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Howard Hughes Medical Institute and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - Gilbert L Henry
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
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7
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Nagashima H, Mahlakõiv T, Shih HY, Davis FP, Meylan F, Huang Y, Harrison OJ, Yao C, Mikami Y, Urban JF, Caron KM, Belkaid Y, Kanno Y, Artis D, O'Shea JJ. Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation. Immunity 2019; 51:682-695.e6. [PMID: 31353223 PMCID: PMC6801073 DOI: 10.1016/j.immuni.2019.06.009] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 01/10/2023]
Abstract
Innate lymphocytes maintain tissue homeostasis at mucosal barriers, with group 2 innate lymphoid cells (ILC2s) producing type 2 cytokines and controlling helminth infection. While the molecular understanding of ILC2 responses has advanced, the complexity of microenvironmental factors impacting ILC2s is becoming increasingly apparent. Herein, we used single-cell analysis to explore the diversity of gene expression among lung lymphocytes during helminth infection. Following infection, we identified a subset of ILC2s that preferentially expressed Il5-encoding interleukin (IL)-5, together with Calca-encoding calcitonin gene-related peptide (CGRP) and its cognate receptor components. CGRP in concert with IL-33 and neuromedin U (NMU) supported IL-5 but constrained IL-13 expression and ILC2 proliferation. Without CGRP signaling, ILC2 responses and worm expulsion were enhanced. Collectively, these data point to CGRP as a context-dependent negative regulatory factor that shapes innate lymphocyte responses to alarmins and neuropeptides during type 2 innate immune responses.
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Affiliation(s)
- Hiroyuki Nagashima
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Tanel Mahlakõiv
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Han-Yu Shih
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Fred P Davis
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Francoise Meylan
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Yuefeng Huang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Oliver J Harrison
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Chen Yao
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Yohei Mikami
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Joseph F Urban
- US Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, MD 20705-2350, USA
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
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8
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Schwartz DM, Farley TK, Richoz N, Yao C, Shih HY, Petermann F, Zhang Y, Sun HW, Hayes E, Mikami Y, Jiang K, Davis FP, Kanno Y, Milner JD, Siegel R, Laurence A, Meylan F, O'Shea JJ. Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology. Immunity 2019; 50:106-120.e10. [PMID: 30650370 DOI: 10.1016/j.immuni.2018.12.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022]
Abstract
CD4+ T helper (Th) differentiation is regulated by diverse inputs, including the vitamin A metabolite retinoic acid (RA). RA acts through its receptor RARα to repress transcription of inflammatory cytokines, but is also essential for Th-mediated immunity, indicating complex effects of RA on Th specification and the outcome of the immune response. We examined the impact of RA on the genome-wide transcriptional response during Th differentiation to multiple subsets. RA effects were subset-selective and were most significant in Th9 cells. RA globally antagonized Th9-promoting transcription factors and inhibited Th9 differentiation. RA directly targeted the extended Il9 locus and broadly modified the Th9 epigenome through RARα. RA-RARα activity limited murine Th9-associated pulmonary inflammation, and human allergic inflammation was associated with reduced expression of RA target genes. Thus, repression of the Th9 program is a major function of RA-RARα signaling in Th differentiation, arguing for a role for RA in interleukin 9 (IL-9) related diseases.
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Affiliation(s)
- Daniella M Schwartz
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA; Genenetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases, NIAID, NIH, Rockville, MD 20892, USA.
| | - Taylor K Farley
- Immunoregulation Section, Autoimmunity Branch, NIAMS, NIH, Rockville, MD 20892, USA; Metaorganism Immunity Section, Laboratory of Immune System Biology, NIAID, NIH, Rockville, MD 20892, USA
| | - Nathan Richoz
- Immunoregulation Section, Autoimmunity Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Chen Yao
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Han-Yu Shih
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Franziska Petermann
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Yuan Zhang
- Genenetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases, NIAID, NIH, Rockville, MD 20892, USA
| | - Hong-Wei Sun
- Office of Science and Technology, NIAMS, NIH, Rockville, MD 20892, USA
| | - Erika Hayes
- Immunoregulation Section, Autoimmunity Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Yohei Mikami
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Kan Jiang
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Fred P Davis
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Joshua D Milner
- Genenetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases, NIAID, NIH, Rockville, MD 20892, USA
| | - Richard Siegel
- Immunoregulation Section, Autoimmunity Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - Arian Laurence
- Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, UK
| | - Françoise Meylan
- Immunoregulation Section, Autoimmunity Branch, NIAMS, NIH, Rockville, MD 20892, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Rockville, MD 20892, USA
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9
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Bentzur A, Shmueli A, Omesi L, Ryvkin J, Knapp JM, Parnas M, Davis FP, Shohat-Ophir G. Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila. PLoS Genet 2018; 14:e1007328. [PMID: 29630598 PMCID: PMC5908198 DOI: 10.1371/journal.pgen.1007328] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 08/02/2017] [Revised: 04/19/2018] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
Living in a social environment requires the ability to respond to specific social stimuli and to incorporate information obtained from prior interactions into future ones. One of the mechanisms that facilitates social interaction is pheromone-based communication. In Drosophila melanogaster, the male-specific pheromone cis-vaccenyl acetate (cVA) elicits different responses in male and female flies, and functions to modulate behavior in a context and experience-dependent manner. Although it is the most studied pheromone in flies, the mechanisms that determine the complexity of the response, its intensity and final output with respect to social context, sex and prior interaction, are still not well understood. Here we explored the functional link between social interaction and pheromone-based communication and discovered an odorant binding protein that links social interaction to sex specific changes in cVA related responses. Odorant binding protein 69a (Obp69a) is expressed in auxiliary cells and secreted into the olfactory sensilla. Its expression is inversely regulated in male and female flies by social interactions: cVA exposure reduces its levels in male flies and increases its levels in female flies. Increasing or decreasing Obp69a levels by genetic means establishes a functional link between Obp69a levels and the extent of male aggression and female receptivity. We show that activation of cVA-sensing neurons is sufficeint to regulate Obp69a levels in the absence of cVA, and requires active neurotransmission between the sensory neuron to the second order olfactory neuron. The cross-talk between sensory neurons and non-neuronal auxiliary cells at the olfactory sensilla, represents an additional component in the machinery that promotes behavioral plasticity to the same sensory stimuli in male and female flies. In this work, we used Drosophila melanogaster as a model organism to explore a basic question in neuroscience: why do different individuals experience the same sensory stimuli, such as smell differently, and moreover, why does one individual experience identical stimuli differently on different occasions? Focusing on sex specific behaviors in fruit flies, we identified odorant binding protein 69a (Obp69a) as a new player in the machinery that promotes behavioral plasticity to the same sensory stimuli in male and female flies.
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Affiliation(s)
- Assa Bentzur
- The Mina & Everard Goodman Faculty of Life Sciences and Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Anat Shmueli
- The Mina & Everard Goodman Faculty of Life Sciences and Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Liora Omesi
- The Mina & Everard Goodman Faculty of Life Sciences and Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Julia Ryvkin
- The Mina & Everard Goodman Faculty of Life Sciences and Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Moshe Parnas
- Department of Physiology and Pharmacology Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Fred P. Davis
- HHMI Janelia Research Campus, Ashburn, VA, United States of America
| | - Galit Shohat-Ophir
- The Mina & Everard Goodman Faculty of Life Sciences and Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail:
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10
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Xie L, Torigoe SE, Xiao J, Mai DH, Li L, Davis FP, Dong P, Marie-Nelly H, Grimm J, Lavis L, Darzacq X, Cattoglio C, Liu Z, Tjian R. A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency. Genes Dev 2017; 31:1795-1808. [PMID: 28982762 PMCID: PMC5666677 DOI: 10.1101/gad.303321.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 06/12/2017] [Accepted: 08/28/2017] [Indexed: 01/15/2023]
Abstract
Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular "dialog" between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Krüppel-like factor 4 (Klf4) expression in naïve pluripotency. Genome editing by CRISPR/Cas9 revealed that OCT4 and SOX2 safeguard an accessible chromatin neighborhood to assist the binding of other TFs/cofactors to the enhancer. Single-molecule live-cell imaging uncovered that two naïve pluripotency TFs, STAT3 and ESRRB, interrogate chromatin in a highly dynamic manner, in which SOX2 promotes ESRRB target search and chromatin-binding dynamics through a direct protein-tethering mechanism. Together, our results support a highly dynamic yet intrinsically ordered enhanceosome assembly to maintain the finely balanced transcription program underlying naïve pluripotency.
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Affiliation(s)
- Liangqi Xie
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Sharon E Torigoe
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Jifang Xiao
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Daniel H Mai
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Li Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Fred P Davis
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Herve Marie-Nelly
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Jonathan Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Xavier Darzacq
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | | | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
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11
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Villarino AV, Sciumè G, Davis FP, Iwata S, Zitti B, Robinson GW, Hennighausen L, Kanno Y, O'Shea JJ. Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells. J Exp Med 2017; 214:2999-3014. [PMID: 28916644 PMCID: PMC5626390 DOI: 10.1084/jem.20150907] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 05/18/2017] [Accepted: 07/26/2017] [Indexed: 01/06/2023] Open
Abstract
Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect barrier integrity. Using a genetic tuning model, we demonstrate that the signal-dependent transcription factor (TF) STAT5 is critical for accumulation of all known ILC subsets in mice and reveal a hierarchy of STAT5 dependency for populating lymphoid and nonlymphoid tissues. We apply transcriptome and genomic distribution analyses to define a STAT5 gene signature in natural killer (NK) cells, the prototypical ILC subset, and provide a systems-based molecular rationale for its key functions downstream of IL-15. We also uncover surprising features of STAT5 behavior, most notably the wholesale redistribution that occurs when NK cells shift from tonic signaling to acute cytokine-driven signaling, and genome-wide coordination with T-bet, another key TF in ILC biology. Collectively, our data position STAT5 as a central node in the TF network that instructs ILC development, homeostasis, and function and provide mechanistic insights on how it works at cellular and molecular levels.
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Affiliation(s)
- Alejandro V Villarino
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Giuseppe Sciumè
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Fred P Davis
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Shigeru Iwata
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Beatrice Zitti
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Gertraud W Robinson
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
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12
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Afzali B, Grönholm J, Vandrovcova J, O’Brien C, Sun HW, Vanderleyden I, Davis FP, Khoder A, Zhang Y, Hegazy AN, Villarino AV, Palmer IW, Kaufman J, Watts NR, Kazemian M, Kamenyeva O, Keith J, Sayed A, Kasperaviciute D, Mueller M, Hughes JD, Fuss IJ, Sadiyah MF, Montgomery-Recht K, McElwee J, Restifo NP, Strober W, Linterman MA, Wingfield PT, Uhlig HH, Roychoudhuri R, Aitman TJ, Kelleher P, Lenardo MJ, O’Shea JJ, Cooper N, Laurence ADJ. BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency. Nat Immunol 2017; 18:813-823. [PMID: 28530713 PMCID: PMC5593426 DOI: 10.1038/ni.3753] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/25/2017] [Indexed: 02/07/2023]
Abstract
The transcriptional programs that guide lymphocyte differentiation depend on the precise expression and timing of transcription factors (TFs). The TF BACH2 is essential for T and B lymphocytes and is associated with an archetypal super-enhancer (SE). Single-nucleotide variants in the BACH2 locus are associated with several autoimmune diseases, but BACH2 mutations that cause Mendelian monogenic primary immunodeficiency have not previously been identified. Here we describe a syndrome of BACH2-related immunodeficiency and autoimmunity (BRIDA) that results from BACH2 haploinsufficiency. Affected subjects had lymphocyte-maturation defects that caused immunoglobulin deficiency and intestinal inflammation. The mutations disrupted protein stability by interfering with homodimerization or by causing aggregation. We observed analogous lymphocyte defects in Bach2-heterozygous mice. More generally, we observed that genes that cause monogenic haploinsufficient diseases were substantially enriched for TFs and SE architecture. These findings reveal a previously unrecognized feature of SE architecture in Mendelian diseases of immunity: heterozygous mutations in SE-regulated genes identified by whole-exome/genome sequencing may have greater significance than previously recognized.
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Affiliation(s)
- Behdad Afzali
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- MRC Centre for Transplantation, King’s College London, UK
| | - Juha Grönholm
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, Biological Imaging Section (Research Technologies Branch) and Mucosal Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Jana Vandrovcova
- Molecular Neuroscience, Institute of Neurology, Faculty of Brain Sciences, University College London, UK
- Department of Medicine, Imperial College London, UK
| | | | - Hong-Wei Sun
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ine Vanderleyden
- Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge, UK
| | - Fred P Davis
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ahmad Khoder
- Department of Medicine, Imperial College London, UK
| | - Yu Zhang
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, Biological Imaging Section (Research Technologies Branch) and Mucosal Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Ahmed N Hegazy
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK
| | - Alejandro V Villarino
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ira W Palmer
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Kaufman
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Norman R Watts
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Olena Kamenyeva
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, Biological Imaging Section (Research Technologies Branch) and Mucosal Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Julia Keith
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Anwar Sayed
- Department of Medicine, Imperial College London, UK
| | | | - Michael Mueller
- Imperial BRC Genomics Facility Hammersmith hospital, Du Cane road, London, UK
| | - Jason D. Hughes
- Merck Research Laboratories, Merck & Co. Inc., Boston, MA, USA
| | - Ivan J. Fuss
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, Biological Imaging Section (Research Technologies Branch) and Mucosal Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Mohammed F Sadiyah
- Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge, UK
| | - Kim Montgomery-Recht
- Clinical Research Directorate/CMRP, Leidos Biomedical Research Inc., NCI at Frederick, Frederick, MD, USA
| | - Joshua McElwee
- Merck Research Laboratories, Merck & Co. Inc., Boston, MA, USA
| | - Nicholas P Restifo
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Warren Strober
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, Biological Imaging Section (Research Technologies Branch) and Mucosal Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Michelle A Linterman
- Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge, UK
| | - Paul T Wingfield
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
- Department of Paediatrics, University of Oxford, UK
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge, UK
| | - Timothy J. Aitman
- Department of Medicine, Imperial College London, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | | | - Michael J Lenardo
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, Biological Imaging Section (Research Technologies Branch) and Mucosal Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - John J O’Shea
- Lymphocyte Cell Biology Section (Molecular Immunology and Inflammation Branch), Biodata Mining and Discovery Section and Protein Expression Laboratory, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Arian DJ Laurence
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
- Department of Haematology Northern Centre for Cancer Care, Freeman road, Newcastle upon Tyne, UK
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13
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Iwata S, Mikami Y, Sun HW, Brooks SR, Jankovic D, Hirahara K, Onodera A, Shih HY, Kawabe T, Jiang K, Nakayama T, Sher A, O'Shea JJ, Davis FP, Kanno Y. The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells. Immunity 2017. [PMID: 28623086 DOI: 10.1016/j.immuni.2017.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Host defense requires the specification of CD4+ helper T (Th) cells into distinct fates, including Th1 cells that preferentially produce interferon-γ (IFN-γ). IFN-γ, a member of a large family of anti-pathogenic and anti-tumor IFNs, induces T-bet, a lineage-defining transcription factor for Th1 cells, which in turn supports IFN-γ production in a feed-forward manner. Herein, we show that a cell-intrinsic role of T-bet influences how T cells perceive their secreted product in the environment. In the absence of T-bet, IFN-γ aberrantly induced a type I IFN transcriptomic program. T-bet preferentially repressed genes and pathways ordinarily activated by type I IFNs to ensure that its transcriptional response did not evoke an aberrant amplification of type I IFN signaling circuitry, otherwise triggered by its own product. Thus, in addition to promoting Th1 effector commitment, T-bet acts as a repressor in differentiated Th1 cells to prevent abberant autocrine type I IFN and downstream signaling.
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Affiliation(s)
- Shigeru Iwata
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yohei Mikami
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragana Jankovic
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; Institute for Global Prominent Research, Chiba University, Chiba 260-8670, Japan
| | - Han-Yu Shih
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Takeshi Kawabe
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Cytokine Biology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kan Jiang
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; AMED-CREST, AMED, Chiba 260-8670, Japan
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Fred P Davis
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Preger-Ben Noon E, Davis FP, Stern DL. Evolved Repression Overcomes Enhancer Robustness. Dev Cell 2016; 39:572-584. [PMID: 27840106 DOI: 10.1016/j.devcel.2016.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 03/30/2016] [Revised: 07/26/2016] [Accepted: 10/14/2016] [Indexed: 12/18/2022]
Abstract
Biological systems display extraordinary robustness. Robustness of transcriptional enhancers results mainly from clusters of binding sites for the same transcription factor, and it is not clear how robust enhancers can evolve loss of expression through point mutations. Here, we report the high-resolution functional dissection of a robust enhancer of the shavenbaby gene that has contributed to morphological evolution. We found that robustness is encoded by many binding sites for the transcriptional activator Arrowhead and that, during evolution, some of these activator sites were lost, weakening enhancer activity. Complete silencing of enhancer function, however, required evolution of a binding site for the spatially restricted potent repressor Abrupt. These findings illustrate that recruitment of repressor binding sites can overcome enhancer robustness and may minimize pleiotropic consequences of enhancer evolution. Recruitment of repression may be a general mode of evolution to break robust regulatory linkages.
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Affiliation(s)
- Ella Preger-Ben Noon
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Fred P Davis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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15
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Shih HY, Sciumè G, Mikami Y, Guo L, Sun HW, Brooks SR, Urban JF, Davis FP, Kanno Y, O'Shea JJ. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell 2016; 165:1120-1133. [PMID: 27156451 PMCID: PMC4874839 DOI: 10.1016/j.cell.2016.04.029] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/17/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022]
Abstract
Innate lymphoid cells (ILCs) play key roles in host defense, barrier integrity, and homeostasis and mirror adaptive CD4(+) T helper (Th) cell subtypes in both usage of effector molecules and transcription factors. To better understand the relationship between ILC subsets and their Th cell counterparts, we measured genome-wide chromatin accessibility. We find that chromatin in proximity to effector genes is selectively accessible in ILCs prior to high-level transcription upon activation. Accessibility of these regions is acquired in a stepwise manner during development and changes little after in vitro or in vivo activation. Conversely, dramatic chromatin remodeling occurs in naive CD4(+) T cells during Th cell differentiation using a type-2-infection model. This alteration results in a substantial convergence of Th2 cells toward ILC2 regulomes. Our data indicate extensive sharing of regulatory circuitry across the innate and adaptive compartments of the immune system, in spite of their divergent developing pathways.
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Affiliation(s)
- Han-Yu Shih
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Giuseppe Sciumè
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yohei Mikami
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liying Guo
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph F Urban
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Fred P Davis
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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16
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Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Epigenomic landscapes of retinal rods and cones. eLife 2016; 5:e11613. [PMID: 26949250 PMCID: PMC4798964 DOI: 10.7554/elife.11613] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/18/2016] [Indexed: 12/28/2022] Open
Abstract
Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function. DOI:http://dx.doi.org/10.7554/eLife.11613.001 Vision in humans is made possible by a light-sensing sheet of cells at the back of the eye called the retina. The surface of the retina is populated by specialized sensory cells, known as rods and cones. The rod cells detect very dim light, while the cones are less sensitive to light but are used to detect color. Together, the rods and cones gather the information needed to create a picture that is then transmitted to the brain. Rods and cones have been studied for decades, and genetic analyses have revealed the patterns of gene expression that lead a cell to develop into either a rod or a cone. Researchers have also identified several key regulatory genes that control these patterns, but less is known about the role of other factors that control the expression of genes. Chemical modifications to DNA or modifications to the proteins associated with DNA – which are collectively called epigenetic modifications – can either promote or inhibit the activation of nearby genes. Now, Mo et al. have shown that rods and cones from mice have very different patterns of epigenetic modifications. The experiments also revealed that many sections of DNA that are marked to promote gene activation contain known rod-specific or cone-specific genes; and that rod cells need a known regulatory gene to develop their specific pattern of epigenetic modifications. Finally, Mo et al. showed that epigenetic regulation differed between brain cells and rods and cones. These insights into epigenetic regulation of rod and cone genes may help explain why some people with eye diseases caused by the same genetic mutation may develop symptoms at different ages or lose vision at different rates. The new information about gene regulation may also help scientists to reprogram stem cells to become healthy rods or cones that could be transplanted into people with eye disease to restore their vision. DOI:http://dx.doi.org/10.7554/eLife.11613.002
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Affiliation(s)
- Alisa Mo
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
| | - Fred P Davis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, United States
| | - Gilbert L Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Mark A Urich
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Serge Picard
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ryan Lister
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Australia
| | - Sean R Eddy
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Michael A Beer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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17
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Striedter GF, Belgard TG, Chen CC, Davis FP, Finlay BL, Güntürkün O, Hale ME, Harris JA, Hecht EE, Hof PR, Hofmann HA, Holland LZ, Iwaniuk AN, Jarvis ED, Karten HJ, Katz PS, Kristan WB, Macagno ER, Mitra PP, Moroz LL, Preuss TM, Ragsdale CW, Sherwood CC, Stevens CF, Stüttgen MC, Tsumoto T, Wilczynski W. NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species. J Comp Neurol 2014; 522:1445-53. [PMID: 24596113 DOI: 10.1002/cne.23568] [Citation(s) in RCA: 33] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 02/18/2014] [Indexed: 01/23/2023]
Abstract
Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute to this effort by leading to the discovery of general principles of neural circuit design, information processing, and gene-structure-function relationships that are not apparent from studies on single species. We here propose to extend the comparative approach to nervous system 'maps' comprising molecular, anatomical, and physiological data. This research will identify which neural features are likely to generalize across species, and which are unlikely to be broadly conserved. It will also suggest causal relationships between genes, development, adult anatomy, physiology, and, ultimately, behavior. These causal hypotheses can then be tested experimentally. Finally, insights from comparative research can inspire and guide technological development. To promote this research agenda, we recommend that teams of investigators coalesce around specific research questions and select a set of 'reference species' to anchor their comparative analyses. These reference species should be chosen not just for practical advantages, but also with regard for their phylogenetic position, behavioral repertoire, well-annotated genome, or other strategic reasons. We envision that the nervous systems of these reference species will be mapped in more detail than those of other species. The collected data may range from the molecular to the behavioral, depending on the research question. To integrate across levels of analysis and across species, standards for data collection, annotation, archiving, and distribution must be developed and respected. To that end, it will help to form networks or consortia of researchers and centers for science, technology, and education that focus on organized data collection, distribution, and training. These activities could be supported, at least in part, through existing mechanisms at NSF, NIH, and other agencies. It will also be important to develop new integrated software and database systems for cross-species data analyses. Multidisciplinary efforts to develop such analytical tools should be supported financially. Finally, training opportunities should be created to stimulate multidisciplinary, integrative research into brain structure, function, and evolution.
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Affiliation(s)
- Georg F Striedter
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California
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18
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Striedter GF, Belgard TG, Chen CC, Davis FP, Finlay BL, Güntürkün O, Hale ME, Harris JA, Hecht EE, Hof PR, Hofmann HA, Holland LZ, Iwaniuk AN, Jarvis ED, Karten HJ, Katz PS, Kristan WB, Macagno ER, Mitra PP, Moroz LL, Preuss TM, Ragsdale CW, Sherwood CC, Stevens CF, Stüttgen MC, Tsumoto T, Wilczynski W. NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species. Brain Behav Evol 2014; 83:1-8. [PMID: 24603302 DOI: 10.1159/000360152] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute to this effort by leading to the discovery of general principles of neural circuit design, information processing, and gene-structure-function relationships that are not apparent from studies on single species. We here propose to extend the comparative approach to nervous system 'maps' comprising molecular, anatomical, and physiological data. This research will identify which neural features are likely to generalize across species, and which are unlikely to be broadly conserved. It will also suggest causal relationships between genes, development, adult anatomy, physiology, and, ultimately, behavior. These causal hypotheses can then be tested experimentally. Finally, insights from comparative research can inspire and guide technological development. To promote this research agenda, we recommend that teams of investigators coalesce around specific research questions and select a set of 'reference species' to anchor their comparative analyses. These reference species should be chosen not just for practical advantages, but also with regard for their phylogenetic position, behavioral repertoire, well-annotated genome, or other strategic reasons. We envision that the nervous systems of these reference species will be mapped in more detail than those of other species. The collected data may range from the molecular to the behavioral, depending on the research question. To integrate across levels of analysis and across species, standards for data collection, annotation, archiving, and distribution must be developed and respected. To that end, it will help to form networks or consortia of researchers and centers for science, technology, and education that focus on organized data collection, distribution, and training. These activities could be supported, at least in part, through existing mechanisms at NSF, NIH, and other agencies. It will also be important to develop new integrated software and database systems for cross-species data analyses. Multidisciplinary efforts to develop such analytical tools should be supported financially. Finally, training opportunities should be created to stimulate multidisciplinary, integrative research into brain structure, function, and evolution.
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Affiliation(s)
- Georg F Striedter
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, Calif., USA
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19
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Davis FP, Eddy SR. Transcription factors that convert adult cell identity are differentially polycomb repressed. PLoS One 2013; 8:e63407. [PMID: 23650565 PMCID: PMC3641127 DOI: 10.1371/journal.pone.0063407] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/30/2013] [Indexed: 01/25/2023] Open
Abstract
Transcription factors that can convert adult cells of one type to another are usually discovered empirically by testing factors with a known developmental role in the target cell. Here we show that standard genomic methods (RNA-seq and ChIP-seq) can help identify these factors, as most are more strongly Polycomb repressed in the source cell and more highly expressed in the target cell. This criterion is an effective genome-wide screen that significantly enriches for factors that can transdifferentiate several mammalian cell types including neural stem cells, neurons, pancreatic islets, and hepatocytes. These results suggest that barriers between adult cell types, as depicted in Waddington's "epigenetic landscape", consist in part of differentially Polycomb-repressed transcription factors. This genomic model of cell identity helps rationalize a growing number of transdifferentiation protocols and may help facilitate the engineering of cell identity for regenerative medicine.
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Affiliation(s)
- Fred P. Davis
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia United States of America
- * E-mail:
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20
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Abstract
Many tools are available to analyse genomes but are often challenging to use in a cell type–specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell, 18, 1030–1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. and Henikoff,S. (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res., doi:10.1101/gr.131748.111], first developed in plants, for use in Drosophila neurons. We profile gene expression and histone modifications in Kenyon cells and octopaminergic neurons in the adult brain. In addition to recovering known gene expression differences, we also observe significant cell type–specific chromatin modifications. In particular, a small subset of differentially expressed genes exhibits a striking anti-correlation between repressive and activating histone modifications. These genes are enriched for transcription factors, recovering those known to regulate mushroom body identity and predicting analogous regulators of octopaminergic neurons. Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity.
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Affiliation(s)
- Gilbert L Henry
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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21
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Abstract
Proteomic studies have identified thousands of eukaryotic phosphorylation sites (phosphosites), but few are functionally characterized. Nishi et al., in this issue of Structure, characterize phosphosites at protein-protein interfaces and estimate the effect of their phosphorylation on interaction affinity, by combining proteomics data with protein structures.
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Affiliation(s)
- Fred P Davis
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr., Ashburn, VA 20147, USA.
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22
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Abstract
Small molecules that modulate protein-protein interactions are of great interest for chemical biology and therapeutics. Here I present a structure-based approach to predict 'bi-functional' sites able to bind both small molecule ligands and proteins, in proteins of unknown structure. First, I develop a homology-based annotation method that transfers binding sites of known three-dimensional structure onto protein sequences, predicting residues in ligand and protein binding sites with estimated true positive rates of 98% and 88%, respectively, at 1% false positive rates. Applying this method to the human proteome predicts 8463 proteins with bi-functional residues and correctly recovers the targets of known interaction modulators. Proteins with significantly (p < 0.01) more bi-functional residues than expected were found to be enriched in regulatory and depleted in metabolism functions. Finally, I demonstrate the utility of the method by describing examples of predicted overlap and evidence of their biological and therapeutic relevance. The results suggest that combining the structures of known binding sites with established fold detection algorithms can predict regions of protein-protein interfaces that are amenable to small molecule modulation. Open-source software and the results for several complete proteomes are available at http://pibase.janelia.org/homolobind.
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Affiliation(s)
- Fred P Davis
- Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA.
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23
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Abstract
Protein–protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250–1000 Da), and 197 exhibit a statistically significant (p<0.01) overlap between ligand and protein binding positions. These “bi-functional positions”, which bind both ligands and proteins, are particularly enriched in tyrosine and tryptophan residues, similar to “energetic hotspots” described previously, and are significantly less conserved than mono-functional and solvent exposed positions. Homology transfer identifies ligands whose binding sites overlap at least 20% of the protein interface for 35% of domain–domain and 45% of domain–peptide mediated interactions. The analysis recovered known small-molecule modulators of protein interactions as well as predicted new interaction targets based on the sequence similarity of ligand binding sites. We illustrate the predictive utility of the method by suggesting structural mechanisms for the effects of sanglifehrin A on HIV virion production, bepridil on the cellular entry of anthrax edema factor, and fusicoccin on vertebrate developmental pathways. The results, available at http://pibase.janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators. Proteins function through their interactions with other biological molecules, including other proteins. Often times, these interactions underlie cellular processes that go awry in disease. Therefore, modulating these interactions with small molecules is an active area of research for new drugs to treat diseases and new chemical tools to dissect cellular interaction networks. However, targeting protein–protein interactions has proven to be more challenging than the typical drug targets found on individual proteins. Here, we present a computational approach that aims to help in this challenge by identifying regions of protein–protein interfaces that may be amenable to targeting by small molecules. Through a comprehensive analysis of all known protein structures, we identify closely related proteins that in one case bind a protein and in another case bind a small molecule. We find that a significant number of protein–protein interactions occur through surface regions that bind small molecules in related proteins. These “bi-functional” positions, which can bind both proteins and ligands, will serve as an additional piece of structural information that can aid experimentalists in developing small molecules that modulate protein interactions.
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Affiliation(s)
- Fred P. Davis
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
- * E-mail: (FPD); (AS)
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (FPD); (AS)
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24
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Abstract
MOTIVATION Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest. RESULTS Regionally enriched genes identified by ALLENMINER accurately reflect the in situ data (95-99% concordance with manual curation) and compare with regional microarray studies as expected from previous comparisons (61-80% concordance). We demonstrate the utility of ALLENMINER by identifying genes that exhibit patterned expression in the caudoputamen and neocortex. We discuss general characteristics of gene expression in the mouse brain and the potential application of ALLENMINER to design strategies for specific genetic access to brain regions and cell types. AVAILABILITY ALLENMINER is freely available on the Internet at http://research.janelia.org/davis/allenminer.
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Affiliation(s)
- Fred P Davis
- HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
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25
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Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2009; 37:D347-54. [PMID: 18948282 PMCID: PMC2686492 DOI: 10.1093/nar/gkn791] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [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: 09/15/2008] [Accepted: 10/08/2008] [Indexed: 11/14/2022] Open
Abstract
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).
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Affiliation(s)
- Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Narayanan Eswar
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Ben M. Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David Eramian
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Libusha Kelly
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David T. Barkan
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Hannah Carter
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Parminder Mankoo
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Rachel Karchin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Marc A. Marti-Renom
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Fred P. Davis
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, Graduate Group in Biophysics, Graduate Group in Bioinformatics, University of California at San Francisco, CA, Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
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26
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Abstract
Pathogens have evolved numerous strategies to infect their hosts, while hosts have evolved immune responses and other defenses to these foreign challenges. The vast majority of host-pathogen interactions involve protein-protein recognition, yet our current understanding of these interactions is limited. Here, we present and apply a computational whole-genome protocol that generates testable predictions of host-pathogen protein interactions. The protocol first scans the host and pathogen genomes for proteins with similarity to known protein complexes, then assesses these putative interactions, using structure if available, and, finally, filters the remaining interactions using biological context, such as the stage-specific expression of pathogen proteins and tissue expression of host proteins. The technique was applied to 10 pathogens, including species of Mycobacterium, apicomplexa, and kinetoplastida, responsible for "neglected" human diseases. The method was assessed by (1) comparison to a set of known host-pathogen interactions, (2) comparison to gene expression and essentiality data describing host and pathogen genes involved in infection, and (3) analysis of the functional properties of the human proteins predicted to interact with pathogen proteins, demonstrating an enrichment for functionally relevant host-pathogen interactions. We present several specific predictions that warrant experimental follow-up, including interactions from previously characterized mechanisms, such as cytoadhesion and protease inhibition, as well as suspected interactions in hypothesized networks, such as apoptotic pathways. Our computational method provides a means to mine whole-genome data and is complementary to experimental efforts in elucidating networks of host-pathogen protein interactions.
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Affiliation(s)
- Fred P Davis
- Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, California 94158, USA.
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Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics 2007; 8 Suppl 4:S4. [PMID: 17570147 PMCID: PMC1892083 DOI: 10.1186/1471-2105-8-s4-s4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [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] [Indexed: 11/10/2022] Open
Abstract
Background Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database. Description AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of ~90% and average precision of ~80%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of ~70% and average precision of ~30%, correctly localizing binding sites for small molecules in ~95% of its predictions. Conclusion The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at .
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Affiliation(s)
- Marc A Marti-Renom
- Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Andrea Rossi
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Fátima Al-Shahrour
- Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Fred P Davis
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Ursula Pieper
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Joaquín Dopazo
- Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Andrej Sali
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143, USA
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Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Res 2007; 35:W393-7. [PMID: 17478513 PMCID: PMC1933139 DOI: 10.1093/nar/gkm236] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions.
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Affiliation(s)
- Marc A Marti-Renom
- Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158-2330, USA.
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Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Comput Biol 2006; 2:e153. [PMID: 17096593 PMCID: PMC1635541 DOI: 10.1371/journal.pcbi.0020153] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [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: 06/08/2006] [Accepted: 10/04/2006] [Indexed: 11/18/2022] Open
Abstract
We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of comparative modeling based on a template complex and protein docking, with a greater applicability than comparative modeling and a higher accuracy than docking. It relies on structurally defined interactions of each of the complex components, or their homologs, with any other protein, irrespective of its fold. For each component, its known binding modes with other proteins of any fold are collected and expanded by the known binding modes of its homologs. These modes are then used to restrain conventional molecular docking, resulting in a set of binary domain complexes that are subsequently ranked by geometric complementarity and a statistical potential. The method is evaluated by predicting 20 binary complexes of known structure. It is able to correctly identify the binding mode in 70% of the benchmark complexes compared with 30% for protein docking. We applied comparative patch analysis to model the complex of the third PSD-95, DLG, and ZO-1 (PDZ) domain and the SH3-GK domains in the PSD-95 protein, whose structure is unknown. In the first predicted configuration of the domains, PDZ interacts with SH3, leaving both the GMP-binding site of guanylate kinase (GK) and the C-terminus binding cleft of PDZ accessible, while in the second configuration PDZ interacts with GK, burying both binding sites. We suggest that the two alternate configurations correspond to the different functional forms of PSD-95 and provide a possible structural description for the experimentally observed cooperative folding transitions in PSD-95 and its homologs. More generally, we expect that comparative patch analysis will provide useful spatial restraints for the structural characterization of an increasing number of binary and higher-order protein complexes.
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Affiliation(s)
- Dmitry Korkin
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
| | - Fred P Davis
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
| | - Frank Alber
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
| | - Tinh Luong
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Min-Yi Shen
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
| | - Vladan Lucic
- Department of Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mary B Kennedy
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Andrej Sali
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Abstract
Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain—porcine α–amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE ().
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Affiliation(s)
- Fred P. Davis
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
| | - Hannes Braberg
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
| | - Min-Yi Shen
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
| | - Ursula Pieper
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
| | - Andrej Sali
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Correspondence may also be addressed to A. Sali. Tel: +1 415 514 4227; Fax: +1 415 514 4231;
| | - M.S. Madhusudhan
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of CaliforniaSan Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143-2552, USA
- To whom correspondence should be addressed. Tel: + 1 415 514 4232; Fax: +1 415 514 4231;
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Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2006; 34:D291-5. [PMID: 16381869 PMCID: PMC1347422 DOI: 10.1093/nar/gkj059] [Citation(s) in RCA: 229] [Impact Index Per Article: 12.7] [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] [Indexed: 11/24/2022] Open
Abstract
MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, ), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, ) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, ).
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Affiliation(s)
- Ursula Pieper
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Narayanan Eswar
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Fred P. Davis
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Hannes Braberg
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - M. S. Madhusudhan
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Andrea Rossi
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Marc Marti-Renom
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Rachel Karchin
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Ben M. Webb
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - David Eramian
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Graduate Group in Biophysics, University of CaliforniaSan Francisco, CA, USA
| | - Min-Yi Shen
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
| | - Libusha Kelly
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Graduate Group in Biological and Medical Informatics, University of CaliforniaSan Francisco, CA, USA
| | - Francisco Melo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileAlameda 340, Santiago, Chile
| | - Andrej Sali
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical ResearchQB3 at Mission Bay, Office 503BUniversity of California at San Francisco1700 4th Street, San Francisco, CA 94158, USA
- To whom correspondence should be addressed. Tel: +1 415 514 4227; Fax: +1 415 514 4231;
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Abstract
We address the question of whether or not the positions of protein-binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein-binding sites are extracted from our comprehensive database of structurally defined binary domain interactions (PIBASE). Second, the binding sites within each family are superposed using a structural alignment of its members. Finally, the degree of localization of binding sites within each family is quantified by comparing it with localization expected by chance. We found that 72% of the 1847 SCOP domain families in PIBASE have binding sites with localization values greater than expected by chance. Moreover, 554 (30%) of these families have localizations that are statistically significant (i.e., more than four standard deviations away from the mean expected by chance). In contrast, only 144 (8%) families have significantly low localization. The absence of a significant correlation of the binding site localization with the average sequence and structural conservations in a family suggests that localization can be helpful for describing the functional diversity of protein-protein interactions, complementing measures of sequence and structural conservation. Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures.
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Affiliation(s)
- Dmitry Korkin
- Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143-2552, USA
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Abstract
MOTIVATION In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize the utility of the high resolution protein-protein interaction data stored in the PDB, we have developed PIBASE, a comprehensive relational database of structurally defined interfaces between pairs of protein domains. It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems. RESULTS PIBASE currently contains 158,915 interacting domain pairs between 105,061 domains from 2125 SCOP families. A diverse set of geometric, physiochemical and topologic properties are calculated for each complex, its domains, interfaces and binding sites. A subset of the interface properties are used to remove interface redundancy within PDB entries, resulting in 20,912 distinct domain-domain interfaces. The complexes are grouped into 989 topological classes based on their patterns of domain-domain contacts. The binary interfaces and their corresponding binding sites are categorized into 18,755 and 30,975 topological classes, respectively, based on the topology of secondary structure elements. The utility of the database is illustrated by outlining several current applications. AVAILABILITY The database is accessible via the world wide web at http://salilab.org/pibase SUPPLEMENTARY INFORMATION http://salilab.org/pibase/suppinfo.html.
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Affiliation(s)
- Fred P Davis
- Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, 94143, USA
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Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004; 14:313-24. [PMID: 15193311 DOI: 10.1016/j.sbi.2004.04.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structures of macromolecular complexes are necessary for a mechanistic description of biochemical and cellular processes. They can be solved by experimental methods, such as X-ray crystallography, NMR spectroscopy and electron microscopy, as well as by computational protein structure prediction, docking and bioinformatics. Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness.
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Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2004; 32:D217-22. [PMID: 14681398 PMCID: PMC308829 DOI: 10.1093/nar/gkh095] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [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] [Indexed: 11/12/2022] Open
Abstract
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).
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Affiliation(s)
- Ursula Pieper
- Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143-2240, USA
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