1
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Metzger VT, Cannon DC, Yang JJ, Mathias SL, Bologa CG, Waller A, Schürer SC, Vidović D, Kelleher KJ, Sheils TK, Jensen LJ, Lambert CG, Oprea TI, Edwards JS. TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets. PeerJ 2024; 12:e17470. [PMID: 38948230 PMCID: PMC11212617 DOI: 10.7717/peerj.17470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 05/06/2024] [Indexed: 07/02/2024] Open
Abstract
TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X's predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user's web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins.
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Affiliation(s)
- Vincent T. Metzger
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | | | - Jeremy J. Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Stephen L. Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Cristian G. Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Anna Waller
- Center for Molecular Discovery, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States
| | - Dušica Vidović
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States
| | - Keith J. Kelleher
- National Center for Advancing Translational Science, Rockville, Maryland, United States
| | - Timothy K. Sheils
- National Center for Advancing Translational Science, Rockville, Maryland, United States
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christophe G. Lambert
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Tudor I. Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Jeremy S. Edwards
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States
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2
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Pirola CJ, Sookoian S. Drug repurposing in MASLD and MASH-cirrhosis: Targets and treatment approaches based on pathways analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:193-206. [PMID: 38942537 DOI: 10.1016/bs.pmbts.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Designing and predicting novel drug targets to accelerate drug discovery for treating metabolic dysfunction-associated steatohepatitis (MASH)-cirrhosis is a challenging task. The presence of superimposed (nested) and co-occurring clinical and histological phenotypes, namely MASH and cirrhosis, may partly explain this. Thus, in this scenario, each sub-phenotype has its own set of pathophysiological mechanisms, triggers, and processes. Here, we used gene/protein and set enrichment analysis to predict druggable pathways for the treatment of MASH-cirrhosis. Our findings indicate that the pathogenesis of MASH-cirrhosis can be explained by perturbations in multiple, simultaneous, and overlapping molecular processes. In this scenario, each sub-phenotype has its own set of pathophysiological mechanisms, triggers, and processes. Therefore, we used systems biology modeling to provide evidence that MASH and cirrhosis paradoxically present unique and distinct as well as common disease mechanisms, including a network of molecular targets. More importantly, pathway analysis revealed straightforward results consistent with modulation of the immune response, cell cycle control, and epigenetic regulation. In conclusion, the selection of potential therapies for MASH-cirrhosis should be guided by a better understanding of the underlying biological processes and molecular perturbations that progressively damage liver tissue and its underlying structure. Therapeutic options for patients with MASH may not necessarily be of choice for MASH cirrhosis. Therefore, the biology of the disease and the processes associated with its natural history must be at the forefront of the decision-making process.
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Affiliation(s)
- Carlos J Pirola
- Systems Biology of Complex Diseases, Centro de Investigación Traslacional en Salud, Universidad Maimónides, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Silvia Sookoian
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Clinical and Molecular Hepatology, Centro de Investigación Traslacional en Salud, Universidad Maimónides, Buenos Aires, Argentina; Facultad de Ciencias de la Salud, Universidad Maimónides, Buenos Aires, Argentina.
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3
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Ren F, Aliper A, Chen J, Zhao H, Rao S, Kuppe C, Ozerov IV, Zhang M, Witte K, Kruse C, Aladinskiy V, Ivanenkov Y, Polykovskiy D, Fu Y, Babin E, Qiao J, Liang X, Mou Z, Wang H, Pun FW, Ayuso PT, Veviorskiy A, Song D, Liu S, Zhang B, Naumov V, Ding X, Kukharenko A, Izumchenko E, Zhavoronkov A. A small-molecule TNIK inhibitor targets fibrosis in preclinical and clinical models. Nat Biotechnol 2024:10.1038/s41587-024-02143-0. [PMID: 38459338 DOI: 10.1038/s41587-024-02143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/16/2024] [Indexed: 03/10/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an aggressive interstitial lung disease with a high mortality rate. Putative drug targets in IPF have failed to translate into effective therapies at the clinical level. We identify TRAF2- and NCK-interacting kinase (TNIK) as an anti-fibrotic target using a predictive artificial intelligence (AI) approach. Using AI-driven methodology, we generated INS018_055, a small-molecule TNIK inhibitor, which exhibits desirable drug-like properties and anti-fibrotic activity across different organs in vivo through oral, inhaled or topical administration. INS018_055 possesses anti-inflammatory effects in addition to its anti-fibrotic profile, validated in multiple in vivo studies. Its safety and tolerability as well as pharmacokinetics were validated in a randomized, double-blinded, placebo-controlled phase I clinical trial (NCT05154240) involving 78 healthy participants. A separate phase I trial in China, CTR20221542, also demonstrated comparable safety and pharmacokinetic profiles. This work was completed in roughly 18 months from target discovery to preclinical candidate nomination and demonstrates the capabilities of our generative AI-driven drug-discovery pipeline.
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Affiliation(s)
- Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai, China
- Insilico Medicine AI Limited, Abu Dhabi, UAE
| | - Alex Aliper
- Insilico Medicine AI Limited, Abu Dhabi, UAE
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Jian Chen
- Department of Clinical Pharmacology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Heng Zhao
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Sujata Rao
- Insilico Medicine US Inc., New York, NY, USA
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Department of Nephrology, University Clinic RWTH Aachen, Aachen, Germany
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Klaus Witte
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Chris Kruse
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Yan Ivanenkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Yanyun Fu
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | | | - Junwen Qiao
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Xing Liang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Zhenzhen Mou
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Hui Wang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Pedro Torres Ayuso
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, PA, USA
| | | | - Dandan Song
- Department of Clinical Pharmacology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Sang Liu
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Bei Zhang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Xiaoqiang Ding
- Division of Nephrology, Zhongshan Hospital Shanghai Medical College, Fudan University, Shanghai, China
| | - Andrey Kukharenko
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Evgeny Izumchenko
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Alex Zhavoronkov
- Insilico Medicine AI Limited, Abu Dhabi, UAE.
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China.
- Insilico Medicine US Inc., New York, NY, USA.
- Insilico Medicine Canada Inc, Montreal, Quebec, Canada.
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4
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Oprea TI, Bologa C, Holmes J, Mathias S, Metzger VT, Waller A, Yang JJ, Leach AR, Jensen LJ, Kelleher KJ, Sheils TK, Mathé E, Avram S, Edwards JS. Overview of the Knowledge Management Center for Illuminating the Druggable Genome. Drug Discov Today 2024; 29:103882. [PMID: 38218214 PMCID: PMC10939799 DOI: 10.1016/j.drudis.2024.103882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) project aims to aggregate, update, and articulate protein-centric data knowledge for the entire human proteome, with emphasis on the understudied proteins from the three IDG protein families. KMC collates and analyzes data from over 70 resources to compile the Target Central Resource Database (TCRD), which is the web-based informatics platform (Pharos). These data include experimental, computational, and text-mined information on protein structures, compound interactions, and disease and phenotype associations. Based on this knowledge, proteins are classified into different Target Development Levels (TDLs) for identification of understudied targets. Additional work by the KMC focuses on enriching target knowledge and producing DrugCentral and other data visualization tools for expanding investigation of understudied targets.
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Affiliation(s)
- Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Cristian Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Stephen Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Vincent T Metzger
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Anna Waller
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jeremy J Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Keith J Kelleher
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Timothy K Sheils
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Ewy Mathé
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Sorin Avram
- Coriolan Dragulescu Institute of Chemistry, Timisoara, Romania
| | - Jeremy S Edwards
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA.
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5
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Sharma KR, Colvis CM, Rodgers GP, Sheeley DM. Illuminating the druggable genome: Pathways to progress. Drug Discov Today 2024; 29:103805. [PMID: 37890715 PMCID: PMC10939933 DOI: 10.1016/j.drudis.2023.103805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
There are ∼4500 genes within the 'druggable genome', the subset of the human genome that expresses proteins able to bind drug-like molecules, yet existing drugs only target a few hundred. A substantial subset of druggable proteins are largely uncharacterized or understudied, with many falling within G protein-coupled receptor (GPCR), ion channel, and kinase protein families. To improve scientific understanding of these three understudied protein families, the US National Institutes of Health launched the Illuminating the Druggable Genome Program. Now, as the program draws to a close, this review will lay out resources developed by the program that are intended to equip the scientific community with the tools necessary to explore previously understudied biology with the potential to rapidly impact human health.
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Affiliation(s)
- Karlie R Sharma
- National Center for Advancing Translational Sciences, National Institutes of Health, 6701 Democracy Blvd, Bethesda, MD 20892, USA.
| | - Christine M Colvis
- National Center for Advancing Translational Sciences, National Institutes of Health, 6701 Democracy Blvd, Bethesda, MD 20892, USA
| | - Griffin P Rodgers
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Douglas M Sheeley
- Office of Strategic Coordination, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
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6
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Pun FW, Ozerov IV, Zhavoronkov A. AI-powered therapeutic target discovery. Trends Pharmacol Sci 2023; 44:561-572. [PMID: 37479540 DOI: 10.1016/j.tips.2023.06.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/23/2023]
Abstract
Disease modeling and target identification are the most crucial initial steps in drug discovery, and influence the probability of success at every step of drug development. Traditional target identification is a time-consuming process that takes years to decades and usually starts in an academic setting. Given its advantages of analyzing large datasets and intricate biological networks, artificial intelligence (AI) is playing a growing role in modern drug target identification. We review recent advances in target discovery, focusing on breakthroughs in AI-driven therapeutic target exploration. We also discuss the importance of striking a balance between novelty and confidence in target selection. An increasing number of AI-identified targets are being validated through experiments and several AI-derived drugs are entering clinical trials; we highlight current limitations and potential pathways for moving forward.
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Affiliation(s)
- Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong; Insilico Medicine MENA, 6F IRENA Building, Abu Dhabi, United Arab Emirates; Buck Institute for Research on Aging, Novato, CA, USA.
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7
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Pirola CJ, Sookoian S. Editorial: NAFLD, chronic kidney disease, and pleiotropy-Why is PNPLA3 omnipresent? Aliment Pharmacol Ther 2023; 57:1180-1182. [PMID: 37094315 DOI: 10.1111/apt.17491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Affiliation(s)
- Carlos J Pirola
- Systems Biology of Complex Diseases, Centro de Altos Estudios en Ciencias Humanas y de la Salud (CAECIHS), Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Silvia Sookoian
- Clinical and Molecular Hepatology, Centro de Altos Estudios en Ciencias Humanas y de la Salud (CAECIHS), Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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8
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Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger V, Siramshetty V, Nguyen DT, Jensen LJ, Vidović D, Schürer S, Holmes J, Sharma K, Pillai A, Bologa C, Edwards J, Mathé E, Oprea T. Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Res 2022; 51:D1405-D1416. [PMID: 36624666 PMCID: PMC9825581 DOI: 10.1093/nar/gkac1033] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for fusers to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.
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Affiliation(s)
- Keith J Kelleher
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Timothy K Sheils
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Stephen L Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jeremy J Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Vincent T Metzger
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Vishal B Siramshetty
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen 2200, Copenhagen, Denmark
| | - Dušica Vidović
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Stephan C Schürer
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Karlie R Sharma
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ajay Pillai
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Cristian G Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jeremy S Edwards
- Correspondence may also be addressed to Jeremy Edwards. Tel: +1 505 277 6655;
| | - Ewy A Mathé
- To whom correspondence should be addressed. Tel: +1 301 402 8953;
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Xu W, Nelson-Maney NP, Bálint L, Kwon HB, Davis RB, Dy DCM, Dunleavey JM, St. Croix B, Caron KM. Orphan G-Protein Coupled Receptor GPRC5B Is Critical for Lymphatic Development. Int J Mol Sci 2022; 23:ijms23105712. [PMID: 35628521 PMCID: PMC9146384 DOI: 10.3390/ijms23105712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/22/2022] Open
Abstract
Numerous studies have focused on the molecular signaling pathways that govern the development and growth of lymphatics in the hopes of elucidating promising druggable targets. G protein-coupled receptors (GPCRs) are currently the largest family of membrane receptors targeted by FDA-approved drugs, but there remain many unexplored receptors, including orphan GPCRs with no known biological ligand or physiological function. Thus, we sought to illuminate the cadre of GPCRs expressed at high levels in lymphatic endothelial cells and identified four orphan receptors: GPRC5B, AGDRF5/GPR116, FZD8 and GPR61. Compared to blood endothelial cells, GPRC5B is the most abundant GPCR expressed in cultured human lymphatic endothelial cells (LECs), and in situ RNAscope shows high mRNA levels in lymphatics of mice. Using genetic engineering approaches in both zebrafish and mice, we characterized the function of GPRC5B in lymphatic development. Morphant gprc5b zebrafish exhibited failure of thoracic duct formation, and Gprc5b-/- mice suffered from embryonic hydrops fetalis and hemorrhage associated with subcutaneous edema and blood-filled lymphatic vessels. Compared to Gprc5+/+ littermate controls, Gprc5b-/- embryos exhibited attenuated developmental lymphangiogenesis. During the postnatal period, ~30% of Gprc5b-/- mice were growth-restricted or died prior to weaning, with associated attenuation of postnatal cardiac lymphatic growth. In cultured human primary LECs, expression of GPRC5B is required to maintain cell proliferation and viability. Collectively, we identify a novel role for the lymphatic-enriched orphan GPRC5B receptor in lymphangiogenesis of fish, mice and human cells. Elucidating the roles of orphan GPCRs in lymphatics provides new avenues for discovery of druggable targets to treat lymphatic-related conditions such as lymphedema and cancer.
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Affiliation(s)
- Wenjing Xu
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
| | - Nathan P. Nelson-Maney
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
| | - László Bálint
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
| | - Hyouk-Bum Kwon
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
| | - Reema B. Davis
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
| | - Danielle C. M. Dy
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
| | - James M. Dunleavey
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program, National Cancer Institute–Frederick, NIH, Frederick, MD 21702, USA; (J.M.D.); (B.S.C.)
| | - Brad St. Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program, National Cancer Institute–Frederick, NIH, Frederick, MD 21702, USA; (J.M.D.); (B.S.C.)
| | - Kathleen M. Caron
- Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC 27599, USA; (W.X.); (N.P.N.-M.); (L.B.); (H.-B.K.); (R.B.D.); (D.C.M.D.)
- Correspondence:
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10
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Grissa D, Junge A, Oprea TI, Jensen LJ. Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration. Database (Oxford) 2022; 2022:6554833. [PMID: 35348648 PMCID: PMC9216524 DOI: 10.1093/database/baac019] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 03/11/2022] [Indexed: 12/04/2022]
Abstract
The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by systematically integrating and assigning confidence scores to evidence for disease–gene associations from curated databases, genome-wide association studies (GWAS) and automatic text mining of the biomedical literature. Here, we present a major update to this resource, which greatly increases the number of associations from all these sources. This is especially true for the text-mined associations, which have increased by at least 9-fold at all confidence cutoffs. We show that this dramatic increase is primarily due to adding full-text articles to the text corpus, secondarily due to improvements to both the disease and gene dictionaries used for named entity recognition, and only to a very small extent due to the growth in number of PubMed abstracts. DISEASES now also makes use of a new GWAS database, Target Illumination by GWAS Analytics, which considerably increased the number of GWAS-derived disease–gene associations. DISEASES itself is also integrated into several other databases and resources, including GeneCards/MalaCards, Pharos/Target Central Resource Database and the Cytoscape stringApp. All data in DISEASES are updated on a weekly basis and is available via a web interface at https://diseases.jensenlab.org, from where it can also be downloaded under open licenses. Database URL: https://diseases.jensenlab.org
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Affiliation(s)
- Dhouha Grissa
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Tudor I Oprea
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Internal Medicine, Division of Translational Informatics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
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11
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Yang JJ, Gessner CR, Duerksen JL, Biber D, Binder JL, Ozturk M, Foote B, McEntire R, Stirling K, Ding Y, Wild DJ. Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination. BMC Bioinformatics 2022; 23:37. [PMID: 35021991 PMCID: PMC8756622 DOI: 10.1186/s12859-021-04530-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
Background LINCS, "Library of Integrated Network-based Cellular Signatures", and IDG, "Illuminating the Druggable Genome", are both NIH projects and consortia that have generated rich datasets for the study of the molecular basis of human health and disease. LINCS L1000 expression signatures provide unbiased systems/omics experimental evidence. IDG provides compiled and curated knowledge for illumination and prioritization of novel drug target hypotheses. Together, these resources can support a powerful new approach to identifying novel drug targets for complex diseases, such as Parkinson's disease (PD), which continues to inflict severe harm on human health, and resist traditional research approaches. Results Integrating LINCS and IDG, we built the Knowledge Graph Analytics Platform (KGAP) to support an important use case: identification and prioritization of drug target hypotheses for associated diseases. The KGAP approach includes strong semantics interpretable by domain scientists and a robust, high performance implementation of a graph database and related analytical methods. Illustrating the value of our approach, we investigated results from queries relevant to PD. Approved PD drug indications from IDG’s resource DrugCentral were used as starting points for evidence paths exploring chemogenomic space via LINCS expression signatures for associated genes, evaluated as target hypotheses by integration with IDG. The KG-analytic scoring function was validated against a gold standard dataset of genes associated with PD as elucidated, published mechanism-of-action drug targets, also from DrugCentral. IDG's resource TIN-X was used to rank and filter KGAP results for novel PD targets, and one, SYNGR3 (Synaptogyrin-3), was manually investigated further as a case study and plausible new drug target for PD. Conclusions The synergy of LINCS and IDG, via KG methods, empowers graph analytics methods for the investigation of the molecular basis of complex diseases, and specifically for identification and prioritization of novel drug targets. The KGAP approach enables downstream applications via integration with resources similarly aligned with modern KG methodology. The generality of the approach indicates that KGAP is applicable to many disease areas, in addition to PD, the focus of this paper. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04530-9.
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12
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Kropiwnicki E, Binder J, Yang J, Holmes J, Lachmann A, Clarke DJB, Sheils T, Kelleher K, Metzger V, Bologa CG, Oprea TI, Ma’ayan A. Getting Started with the IDG KMC Datasets and Tools. Curr Protoc 2022; 2:e355. [PMID: 35085427 PMCID: PMC10789444 DOI: 10.1002/cpz1.355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Illuminating the Druggable Genome (IDG) consortium is a National Institutes of Health (NIH) Common Fund program designed to enhance our knowledge of under-studied proteins, more specifically, proteins unannotated within the three most commonly drug-targeted protein families: G-protein coupled receptors, ion channels, and protein kinases. Since 2014, the IDG Knowledge Management Center (IDG-KMC) has generated several open-access datasets and resources that jointly serve as a highly translational machine-learning-ready knowledgebase focused on human protein-coding genes and their products. The goal of the IDG-KMC is to develop comprehensive integrated knowledge for the druggable genome to illuminate the uncharacterized or poorly annotated portion of the druggable genome. The tools derived from the IDG-KMC provide either user-friendly visualizations or ways to impute the knowledge about potential targets using machine learning strategies. In the following protocols, we describe how to use each web-based tool to accelerate illumination in under-studied proteins. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Interacting with the Pharos user interface Basic Protocol 2: Accessing the data in Harmonizome Basic Protocol 3: The ARCHS4 resource Basic Protocol 4: Making predictions about gene function with PrismExp Basic Protocol 5: Using Geneshot to illuminate knowledge about under-studied targets Basic Protocol 6: Exploring under-studied targets with TIN-X Basic Protocol 7: Interacting with the DrugCentral user interface Basic Protocol 8: Estimating Anti-SARS-CoV-2 activities with DrugCentral REDIAL-2020 Basic Protocol 9: Drug Set Enrichment Analysis using Drugmonizome Basic Protocol 10: The Drugmonizome-ML Appyter Basic Protocol 11: The Harmonizome-ML Appyter Basic Protocol 12: GWAS target illumination with TIGA Basic Protocol 13: Prioritizing kinases for lists of proteins and phosphoproteins with KEA3 Basic Protocol 14: Converting PubMed searches to drug sets with the DrugShot Appyter.
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Affiliation(s)
- Eryk Kropiwnicki
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Jessica Binder
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jeremy Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Daniel J. B. Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Timothy Sheils
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Keith Kelleher
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Vincent Metzger
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Cristian G. Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Tudor I. Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Avi Ma’ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
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13
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Prabahar A. Integration of Transcriptomics Data and Metabolomic Data Using Biomedical Literature Mining and Pathway Analysis. Methods Mol Biol 2022; 2496:301-316. [PMID: 35713871 DOI: 10.1007/978-1-0716-2305-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent progress in omics technologies such as transcriptomics and metabolomics offers an unprecedented opportunity to understand the disease mechanisms and determines the associated biomedical entities using biomedical literature mining. Tremendous data available in the biomedical literature helps in addressing complex biomedical problems. Advancements in genomics and transcriptomics helps in decoding the genetic information obtained from various high throughput techniques for its use in personalized medicine and therapeutics. Integration of data from biomedical literature and data from large-scale genomic studies aids in the determination of the etiology of a disease and drug targets. This chapter addresses the perspectives of transcriptomics and metabolomics in biomedical literature mining and gives an overview of state-of-the-art techniques in this field.
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Affiliation(s)
- Archana Prabahar
- R&D Division, Eriks-Precision Components India Pvt Ltd, Mohali, Punjab, India.
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14
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Yang JJ, Grissa D, Lambert CG, Bologa CG, Mathias SL, Waller A, Wild DJ, Jensen LJ, Oprea TI. TIGA: target illumination GWAS analytics. Bioinformatics 2021; 37:3865-3873. [PMID: 34086846 PMCID: PMC11025677 DOI: 10.1093/bioinformatics/btab427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Genome-wide association studies can reveal important genotype-phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study. RESULTS Here, we describe rational ranking, filtering and interpretation of inferred gene-trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene-trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene-trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists. AVAILABILITY AND IMPLEMENTATION Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeremy J Yang
- Division of Translational Informatics, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Integrative Data Science Laboratory, School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN 47408, USA
| | - Dhouha Grissa
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Christophe G Lambert
- Division of Translational Informatics, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Cristian G Bologa
- Division of Translational Informatics, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Stephen L Mathias
- Division of Translational Informatics, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Anna Waller
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - David J Wild
- Integrative Data Science Laboratory, School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN 47408, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Tudor I Oprea
- Division of Translational Informatics, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
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15
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Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI. How to Illuminate the Druggable Genome Using Pharos. ACTA ACUST UNITED AC 2021; 69:e92. [PMID: 31898878 DOI: 10.1002/cpbi.92] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pharos is an integrated web-based informatics platform for the analysis of data aggregated by the Illuminating the Druggable Genome (IDG) Knowledge Management Center, an NIH Common Fund initiative. The current version of Pharos (as of October 2019) spans 20,244 proteins in the human proteome, 19,880 disease and phenotype associations, and 226,829 ChEMBL compounds. This resource not only collates and analyzes data from over 60 high-quality resources to generate these types, but also uses text indexing to find less apparent connections between targets, and has recently begun to collaborate with institutions that generate data and resources. Proteins are ranked according to a knowledge-based classification system, which can help researchers to identify less studied "dark" targets that could be potentially further illuminated. This is an important process for both drug discovery and target validation, as more knowledge can accelerate target identification, and previously understudied proteins can serve as novel targets in drug discovery. Two basic protocols illustrate the levels of detail available for targets and several methods of finding targets of interest. An Alternate Protocol illustrates the difference in available knowledge between less and more studied targets. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Search for a target and view details Alternate Protocol: Search for dark target and view details Basic Protocol 2: Filter a target list to get refined results.
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Affiliation(s)
- Timothy Sheils
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Stephen L Mathias
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | | | - Giovanni Bocci
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Cristian G Bologa
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Jeremy J Yang
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Anna Waller
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Noel Southall
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Tudor I Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,UNM Comprehensive Cancer Center, Albuquerque, New Mexico.,Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Pirola CJ, Sookoian S. The lipidome in nonalcoholic fatty liver disease: actionable targets. J Lipid Res 2021; 62:100073. [PMID: 33845089 PMCID: PMC8121699 DOI: 10.1016/j.jlr.2021.100073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become the most prevalent chronic liver disease. Recent technological advances, combined with OMICs experiments and explorations involving different biological samples, have uncovered vital aspects of NAFLD biology. In this review, we summarize recent work by our group and others that expands what is known about the role of lipidome in NAFLD pathogenesis. We discuss how pathway and enrichment analyses were performed by integrating a list of query metabolites derived from text-mining existing NAFLD-lipidomics studies, resulting in the identification of nine Kyoto Encyclopedia of Genes and Genomes dysregulated pathways, including biosynthesis of unsaturated fatty acids, butanoate metabolism, synthesis and degradation of ketone bodies, sphingolipid, arachidonic acid and pyruvate metabolism, and numerous nonsteroidal antiinflammatory drug pathways predicted from The Small Molecule Pathway Database. We also summarize an integrated pathway-level analysis of genes and lipid-related metabolites associated with NAFLD, which shows overrepresentation of signal transduction, selenium micronutrient network, Class A/1Rhodopsin-like receptors and G protein-coupled receptor ligand binding, and G protein-coupled receptor downstream signaling. Generated gene-metabolite-disease interaction networks indicate that NAFLD and arterial hypertension are interlinked by molecular signatures. Finally, we discuss how mining pathways and associations among metabolites, lipids, genes, and proteins can be exploited to infer networks and potential pharmacological targets and how lipidomic studies may provide insight into the interrelationships among metabolite clusters that modify NAFLD biology, genetic susceptibility, diet, and the gut microbiome.
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Affiliation(s)
- Carlos J Pirola
- Instituto de Investigaciones Médicas A Lanari, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina; Departamento de Genética y Biología Molecular de Enfermedades Complejas, Instituto of Investigaciones Médicas (IDIM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Silvia Sookoian
- Instituto de Investigaciones Médicas A Lanari, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina; Departamento de Hepatología Clínica y Molecular, Instituto of Investigaciones Médicas (IDIM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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17
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Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A, Oprea TI. TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Res 2021; 49:D1334-D1346. [PMID: 33156327 PMCID: PMC7778974 DOI: 10.1093/nar/gkaa993] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.
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Affiliation(s)
- Timothy K Sheils
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Stephen L Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Keith J Kelleher
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Vishal B Siramshetty
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Cristian G Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Dušica Vidović
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Amar Koleti
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
| | - Stephan C Schürer
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anna Waller
- UNM Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jeremy J Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Giovanni Bocci
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Noel Southall
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Poorva Dharkar
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ewy Mathé
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- UNM Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, 40530 Gothenburg, Sweden
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18
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Paananen J, Fortino V. An omics perspective on drug target discovery platforms. Brief Bioinform 2019; 21:1937-1953. [PMID: 31774113 PMCID: PMC7711264 DOI: 10.1093/bib/bbz122] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 01/28/2023] Open
Abstract
The drug discovery process starts with identification of a disease-modifying target. This critical step traditionally begins with manual investigation of scientific literature and biomedical databases to gather evidence linking molecular target to disease, and to evaluate the efficacy, safety and commercial potential of the target. The high-throughput and affordability of current omics technologies, allowing quantitative measurements of many putative targets (e.g. DNA, RNA, protein, metabolite), has exponentially increased the volume of scientific data available for this arduous task. Therefore, computational platforms identifying and ranking disease-relevant targets from existing biomedical data sources, including omics databases, are needed. To date, more than 30 drug target discovery (DTD) platforms exist. They provide information-rich databases and graphical user interfaces to help scientists identify putative targets and pre-evaluate their therapeutic efficacy and potential side effects. Here we survey and compare a set of popular DTD platforms that utilize multiple data sources and omics-driven knowledge bases (either directly or indirectly) for identifying drug targets. We also provide a description of omics technologies and related data repositories which are important for DTD tasks.
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Affiliation(s)
- Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Finland.,Blueprint Genetics Ltd, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Finland
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19
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Oprea TI. Exploring the dark genome: implications for precision medicine. Mamm Genome 2019; 30:192-200. [PMID: 31270560 DOI: 10.1007/s00335-019-09809-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/15/2019] [Indexed: 01/08/2023]
Abstract
The increase in the number of both patients and healthcare practitioners who grew up using the Internet and computers (so-called "digital natives") is likely to impact the practice of precision medicine, and requires novel platforms for data integration and mining, as well as contextualized information retrieval. The "Illuminating the Druggable Genome Knowledge Management Center" (IDG KMC) quantifies data availability from a wide range of chemical, biological, and clinical resources, and has developed platforms that can be used to navigate understudied proteins (the "dark genome"), and their potential contribution to specific pathologies. Using the "Target Importance and Novelty Explorer" (TIN-X) highlights the role of LRRC10 (a dark gene) in dilated cardiomyopathy. Combining mouse and human phenotype data leads to increased strength of evidence, which is discussed for four additional dark genes: SLX4IP and its role in glucose metabolism, the role of HSF2BP in coronary artery disease, the involvement of ELFN1 in attention-deficit hyperactivity disorder and the role of VPS13D in mouse neural tube development and its confirmed role in childhood onset movement disorders. The workflow and tools described here are aimed at guiding further experimental research, particularly within the context of precision medicine.
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Affiliation(s)
- Tudor I Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA. .,UNM Comprehensive Cancer Center, Albuquerque, NM, USA. .,Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden. .,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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20
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Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC. Drug target ontology to classify and integrate drug discovery data. J Biomed Semantics 2017; 8:50. [PMID: 29122012 PMCID: PMC5679337 DOI: 10.1186/s13326-017-0161-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/17/2017] [Indexed: 11/12/2022] Open
Abstract
Background One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome. Results As part of that effort, we have developed a framework to integrate, navigate, and analyze drug discovery data based on formalized and standardized classifications and annotations of druggable protein targets, the Drug Target Ontology (DTO). DTO was constructed by extensive curation and consolidation of various resources. DTO classifies the four major drug target protein families, GPCRs, kinases, ion channels and nuclear receptors, based on phylogenecity, function, target development level, disease association, tissue expression, chemical ligand and substrate characteristics, and target-family specific characteristics. The formal ontology was built using a new software tool to auto-generate most axioms from a database while supporting manual knowledge acquisition. A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem of biomedical ontologies. As a formal OWL-DL ontology, DTO contains asserted and inferred axioms. Modeling data from the Library of Integrated Network-based Cellular Signatures (LINCS) program illustrates the potential of DTO for contextual data integration and nuanced definition of important drug target characteristics. DTO has been implemented in the IDG user interface Portal, Pharos and the TIN-X explorer of protein target disease relationships. Conclusions DTO was built based on the need for a formal semantic model for druggable targets including various related information such as protein, gene, protein domain, protein structure, binding site, small molecule drug, mechanism of action, protein tissue localization, disease association, and many other types of information. DTO will further facilitate the otherwise challenging integration and formal linking to biological assays, phenotypes, disease models, drug poly-pharmacology, binding kinetics and many other processes, functions and qualities that are at the core of drug discovery. The first version of DTO is publically available via the website http://drugtargetontology.org/, Github (http://github.com/DrugTargetOntology/DTO), and the NCBO Bioportal (http://bioportal.bioontology.org/ontologies/DTO). The long-term goal of DTO is to provide such an integrative framework and to populate the ontology with this information as a community resource. Electronic supplementary material The online version of this article (10.1186/s13326-017-0161-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Lin
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Saurabh Mehta
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Applied Chemistry, Delhi Technological University, Delhi, India
| | - Hande Küçük-McGinty
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - John Paul Turner
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Dusica Vidovic
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Michele Forlin
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Amar Koleti
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajarshi Guha
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Stephen L Mathias
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Oleg Ursu
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jianbin Duan
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - Nooshin Nabizadeh
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Caty Chung
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Christopher Mader
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Ubbo Visser
- Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - Jeremy J Yang
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Cristian G Bologa
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Tudor I Oprea
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA.
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, Coral Gables, FL, USA. .,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA.
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