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Jeynes JCG, James T, Corney M. Natural Language Processing for Drug Discovery Knowledge Graphs: Promises and Pitfalls. Methods Mol Biol 2024; 2716:223-240. [PMID: 37702942 DOI: 10.1007/978-1-0716-3449-3_10] [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: 09/14/2023]
Abstract
Building and analyzing knowledge graphs (KGs) to aid drug discovery is a topical area of research. A salient feature of KGs is their ability to combine many heterogeneous data sources in a format that facilitates discovering connections. The utility of KGs has been exemplified in areas such as drug repurposing, with insights made through manual exploration and modeling of the data. In this chapter, we discuss promises and pitfalls of using natural language processing (NLP) to mine "unstructured text"- typically from scientific literature- as a data source for KGs. This draws on our experience of initially parsing "structured" data sources-such as ChEMBL-as the basis for data within a KG, and then enriching or expanding upon them using NLP. The fundamental promise of NLP for KGs is the automated extraction of data from millions of documents-a task practically impossible to do via human curation alone. However, there are many potential pitfalls in NLP-KG pipelines, such as incorrect named entity recognition and ontology linking, all of which could ultimately lead to erroneous inferences and conclusions.
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Affiliation(s)
- J Charles G Jeynes
- Evotec (UK) Ltd., in silico Research and Development, Abingdon, Oxfordshire, UK.
| | - Tim James
- Evotec (UK) Ltd., in silico Research and Development, Abingdon, Oxfordshire, UK.
| | - Matthew Corney
- Evotec (UK) Ltd., in silico Research and Development, Abingdon, Oxfordshire, UK
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2
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Endo T. Dominant-negative antagonists of the Ras-ERK pathway: DA-Raf and its related proteins generated by alternative splicing of Raf. Exp Cell Res 2019; 387:111775. [PMID: 31843497 DOI: 10.1016/j.yexcr.2019.111775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras-ERK pathway regulates a variety of cellular and physiological responses, including cell proliferation, differentiation, morphogenesis during animal development, and homeostasis in adults. Deregulated activation of this pathway leads to cellular transformation and tumorigenesis as well as RASopathies. Several negative regulators of this pathway have been documented. Each of these proteins acts at particular points of the pathway, and they exert specific cellular and physiological functions. Among them, DA-Raf1 (DA-Raf), which is a splicing isoform of A-Raf and contains the Ras-binding domain but lacks the kinase domain, antagonizes the Ras-ERK pathway in a dominant-negative manner. DA-Raf induces apoptosis, skeletal myocyte differentiation, lung alveolarization, and fulfills tumor suppressor functions by interfering with the Ras-ERK pathway. After the findings of DA-Raf, several kinase-domain-truncated splicing variants of Raf proteins have also been reported. The family of these truncated proteins represents the concept that alternative splicing can generate antagonistic proteins to their full-length counterparts.
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Affiliation(s)
- Takeshi Endo
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inageku, Chiba, Chiba 263-8522, Japan.
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Kobayashi I, Kobayashi-Sun J, Hirakawa Y, Ouchi M, Yasuda K, Kamei H, Fukuhara S, Yamaguchi M. Dual role of Jam3b in early hematopoietic and vascular development. Development 2019; 147:dev.181040. [DOI: 10.1242/dev.181040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/11/2019] [Indexed: 12/23/2022]
Abstract
In order to efficiently derive hematopoietic stem cells (HSCs) from pluripotent precursors, it is crucial to understand how mesodermal cells acquire hematopoietic and endothelial identities, two divergent, but closely related cell fates. Although Npas4 has been recently identified as a conserved master regulator of hemato-vascular development, the molecular mechanisms underlying cell fate divergence between hematopoietic and vascular endothelial cells are still unclear. Here, we show in zebrafish that mesodermal cell differentiation into hematopoietic and vascular endothelial cells is regulated by Junctional adhesion molecule 3b (Jam3b) via two independent signaling pathways. Mutation of jam3b led to a reduction in npas4l expression in the posterior lateral plate mesoderm and defects in both hematopoietic and vascular development. Mechanistically, we uncover that Jam3b promotes endothelial specification by regulating npas4l expression through repression of the Rap1a-Erk signaling cascade. Jam3b subsequently promotes hematopoietic development, including HSCs, by regulating lrrc15 expression in endothelial precursors through the activation of an integrin-dependent signaling cascade. Our data provide insight into the divergent mechanisms for instructing hematopoietic or vascular fates from mesodermal cells.
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Affiliation(s)
- Isao Kobayashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
| | - Jingjing Kobayashi-Sun
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Yuto Hirakawa
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Madoka Ouchi
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Koyuki Yasuda
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
| | - Hiroyasu Kamei
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Kanagawa, Japan
| | - Masaaki Yamaguchi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
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Wang Y, Han Y, Xu P, Ding S, Li G, Jin H, Meng Y, Meng A, Jia S. prpf4 is essential for cell survival and posterior lateral line primordium migration in zebrafish. J Genet Genomics 2018; 45:443-453. [DOI: 10.1016/j.jgg.2018.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/20/2018] [Accepted: 05/17/2018] [Indexed: 11/16/2022]
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5
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Hwang HW, Saito Y, Park CY, Blachère NE, Tajima Y, Fak JJ, Zucker-Scharff I, Darnell RB. cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation. Neuron 2017; 95:1334-1349.e5. [PMID: 28910620 DOI: 10.1016/j.neuron.2017.08.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/07/2017] [Accepted: 08/11/2017] [Indexed: 12/23/2022]
Abstract
Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell types and cellular states within the brain.
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Affiliation(s)
- Hun-Way Hwang
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA; Department of Pathology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15213, USA.
| | - Yuhki Saito
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Christopher Y Park
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA; New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Nathalie E Blachère
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Yoko Tajima
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Ilana Zucker-Scharff
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA; New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA.
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Ying HZ, Chen Q, Zhang WY, Zhang HH, Ma Y, Zhang SZ, Fang J, Yu CH. PDGF signaling pathway in hepatic fibrosis pathogenesis and therapeutics (Review). Mol Med Rep 2017; 16:7879-7889. [PMID: 28983598 PMCID: PMC5779870 DOI: 10.3892/mmr.2017.7641] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 07/20/2017] [Indexed: 02/06/2023] Open
Abstract
The platelet‑derived growth factor (PDFG) signaling pathway exerts persistent activation in response to a variety of stimuli and facilitates the progression of hepatic fibrosis. Since this pathway modulates a broad spectrum of cellular processes, including cell growth, differentiation, inflammation and carcinogenesis, it has emerged as a therapeutic target for hepatic fibrosis and liver‑associated disorders. The present review exhibits the current knowledge of the role of the PDGF signaling pathway and its pathological profiles in hepatic fibrosis, and assesses the potential of inhibitors which have been investigated in the experimental hepatic fibrosis model, in addition to the clinical challenges associated with these inhibitors.
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Affiliation(s)
- Hua-Zhong Ying
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, P.R. China
| | - Qin Chen
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Wen-You Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, P.R. China
| | - Huan-Huan Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, P.R. China
| | - Yue Ma
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, P.R. China
| | - Song-Zhao Zhang
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jie Fang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, P.R. China
| | - Chen-Huan Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, P.R. China
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Liu J, Hemphill J, Samanta S, Tsang M, Deiters A. Genetic Code Expansion in Zebrafish Embryos and Its Application to Optical Control of Cell Signaling. J Am Chem Soc 2017; 139:9100-9103. [PMID: 28657738 DOI: 10.1021/jacs.7b02145] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Site-specific incorporation of unnatural amino acids into proteins provides a powerful tool to study protein function. Here we report genetic code expansion in zebrafish embryos and its application to the optogenetic control of cell signaling. We genetically encoded four unnatural amino acids with a diverse set of functional groups, which included a photocaged lysine that was applied to the light-activation of luciferase and kinase activity. This approach enables versatile manipulation of protein function in live zebrafish embryos, a transparent and commonly used model organism to study embryonic development.
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Affiliation(s)
- Jihe Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - James Hemphill
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Subhas Samanta
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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