1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kamya P, Ozerov IV, Pun FW, Tretina K, Fokina T, Chen S, Naumov V, Long X, Lin S, Korzinkin M, Polykovskiy D, Aliper A, Ren F, Zhavoronkov A. PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery. J Chem Inf Model 2024. [PMID: 38404138 DOI: 10.1021/acs.jcim.3c01619] [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: 02/27/2024]
Abstract
PandaOmics is a cloud-based software platform that applies artificial intelligence and bioinformatics techniques to multimodal omics and biomedical text data for therapeutic target and biomarker discovery. PandaOmics generates novel and repurposed therapeutic target and biomarker hypotheses with the desired properties and is available through licensing or collaboration. Targets and biomarkers generated by the platform were previously validated in both in vitro and in vivo studies. PandaOmics is a core component of Insilico Medicine's Pharma.ai drug discovery suite, which also includes Chemistry42 for the de novo generation of novel small molecules, and inClinico─a data-driven multimodal platform that forecasts a clinical trial's probability of successful transition from phase 2 to phase 3. In this paper, we demonstrate how the PandaOmics platform can efficiently identify novel molecular targets and biomarkers for various diseases.
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Affiliation(s)
- Petrina Kamya
- Insilico Medicine Canada Inc., 3710-1250 René-Lévesque Blvd. W, Montreal, Quebec, Canada H3B 4W8
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Frank W Pun
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Kyle Tretina
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Tatyana Fokina
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Shan Chen
- Insilico Medicine Shanghai Limited, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Xi Long
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Sha Lin
- Insilico Medicine Shanghai Limited, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Mikhail Korzinkin
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
| | - Daniil Polykovskiy
- Insilico Medicine Canada Inc., 3710-1250 René-Lévesque Blvd. W, Montreal, Quebec, Canada H3B 4W8
| | - Alex Aliper
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, P.O. Box 145748, Masdar City, Abu Dhabi, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Limited, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Limited, Hong Kong Science and Technology Park, Hong Kong
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, P.O. Box 145748, Masdar City, Abu Dhabi, United Arab Emirates
- Buck Institute for Research on Aging, Novato, California 94945, United States
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Leung GHD, Wong CW, Pun FW, Aliper A, Ren F, Zhavoronkov A. Leveraging AI to identify dual-purpose aging and disease targets. Expert Opin Ther Targets 2023:1-4. [PMID: 38038952 DOI: 10.1080/14728222.2023.2288270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Affiliation(s)
- Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd, Hong Kong Science and Technology Park, Hong Kong, China
| | - Chun Wai Wong
- Insilico Medicine Hong Kong Ltd, Hong Kong Science and Technology Park, Hong Kong, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd, Hong Kong Science and Technology Park, Hong Kong, China
| | - Alex Aliper
- Insilico Medicine AI Ltd, Abu Dhabi, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd, Shanghai, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd, Hong Kong Science and Technology Park, Hong Kong, China
- Insilico Medicine AI Ltd, Abu Dhabi, United Arab Emirates
- Buck Institute for Research on Aging, Novato, CA, USA
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Pun FW, Leung GHD, Leung HW, Rice J, Schmauck-Medina T, Lautrup S, Long X, Liu BHM, Wong CW, Ozerov IV, Aliper A, Ren F, Rosenberg AJ, Agrawal N, Izumchenko E, Fang EF, Zhavoronkov A. A comprehensive AI-driven analysis of large-scale omic datasets reveals novel dual-purpose targets for the treatment of cancer and aging. Aging Cell 2023; 22:e14017. [PMID: 37888486 PMCID: PMC10726874 DOI: 10.1111/acel.14017] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
As aging and tumorigenesis are tightly interconnected biological processes, targeting their common underlying driving pathways may induce dual-purpose anti-aging and anti-cancer effects. Our transcriptomic analyses of 16,740 healthy samples demonstrated tissue-specific age-associated gene expression, with most tumor suppressor genes downregulated during aging. Furthermore, a large-scale pan-cancer analysis of 11 solid tumor types (11,303 cases and 4431 control samples) revealed that many cellular processes, such as protein localization, DNA replication, DNA repair, cell cycle, and RNA metabolism, were upregulated in cancer but downregulated in healthy aging tissues, whereas pathways regulating cellular senescence were upregulated in both aging and cancer. Common cancer targets were identified by the AI-driven target discovery platform-PandaOmics. Age-associated cancer targets were selected and further classified into four groups based on their reported roles in lifespan. Among the 51 identified age-associated cancer targets with anti-aging experimental evidence, 22 were proposed as dual-purpose targets for anti-aging and anti-cancer treatment with the same therapeutic direction. Among age-associated cancer targets without known lifespan-regulating activity, 23 genes were selected based on predicted dual-purpose properties. Knockdown of histone demethylase KDM1A, one of these unexplored candidates, significantly extended lifespan in Caenorhabditis elegans. Given KDM1A's anti-cancer activities reported in both preclinical and clinical studies, our findings propose KDM1A as a promising dual-purpose target. This is the first study utilizing an innovative AI-driven approach to identify dual-purpose target candidates for anti-aging and anti-cancer treatment, supporting the value of AI-assisted target identification for drug discovery.
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Affiliation(s)
- Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong, China
| | | | | | - Jared Rice
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Tomas Schmauck-Medina
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Xi Long
- Insilico Medicine Hong Kong Ltd., Hong Kong, China
| | | | | | | | - Alex Aliper
- Insilico Medicine AI Ltd., Masdar City, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Ari J Rosenberg
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, Illinois, USA
| | - Nishant Agrawal
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, Illinois, USA
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
- The Norwegian Centre On Healthy Ageing (NO-Age), Oslo, Norway
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong, China
- Insilico Medicine AI Ltd., Masdar City, United Arab Emirates
- Buck Institute for Research on Aging, Novato, California, USA
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Liu HM, Rayner A, Mendelsohn AR, Shneyderman A, Chen M, Pun FW. Applying Artificial Intelligence to Identify Common Targets for Treatment of Asthma, Eczema, and Food Allergy. Int Arch Allergy Immunol 2023; 185:99-110. [PMID: 37989115 DOI: 10.1159/000534827] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023] Open
Abstract
INTRODUCTION Allergic disorders are common diseases marked by the abnormal immune response toward foreign antigens that are not pathogens. Often patients with food allergy also suffer from asthma and eczema. Given the similarities of these diseases and a shortage of effective treatments, developing novel therapeutics against common targets of multiple allergies would offer an efficient and cost-effective treatment for patients. METHODS We employed the artificial intelligence-driven target discovery platform, PandaOmics, to identify common targets for treating asthma, eczema, and food allergy. Thirty-two case-control comparisons were generated from 15, 11, and 6 transcriptomics datasets related to asthma (558 cases, 315 controls), eczema (441 cases, 371 controls), and food allergy (208 cases, 106 controls), respectively, and allocated into three meta-analyses for target identification. Top-100 high-confidence targets and Top-100 novel targets were prioritized by PandaOmics for each allergic disease. RESULTS Six common high-confidence targets (i.e., IL4R, IL5, JAK1, JAK2, JAK3, and NR3C1) across all three allergic diseases have approved drugs for treating asthma and eczema. Based on the targets' dysregulated expression profiles and their mechanism of action in allergic diseases, three potential therapeutic targets were proposed. IL5 was selected as a high-confidence target due to its strong involvement in allergies. PTAFR was identified for drug repurposing, while RNF19B was selected as a novel target for therapeutic innovation. Analysis of the dysregulated pathways commonly identified across asthma, eczema, and food allergy revealed the well-characterized disease signature and novel biological processes that may underlie the pathophysiology of allergies. CONCLUSION Altogether, our study dissects the shared pathophysiology of allergic disorders and reveals the power of artificial intelligence in the exploration of novel therapeutic targets.
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Affiliation(s)
- Hei Man Liu
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong, China,
| | - Andre Rayner
- Henry M. Gunn High School, Palo Alto, California, USA
- Regenerative Sciences Institute, Sunnyvale, California, USA
| | | | - Anastasia Shneyderman
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong, China
| | - Michelle Chen
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong, China
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6
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Lim CM, González Díaz A, Fuxreiter M, Pun FW, Zhavoronkov A, Vendruscolo M. Multiomic prediction of therapeutic targets for human diseases associated with protein phase separation. Proc Natl Acad Sci U S A 2023; 120:e2300215120. [PMID: 37774095 PMCID: PMC10556643 DOI: 10.1073/pnas.2300215120] [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: 01/05/2023] [Accepted: 08/02/2023] [Indexed: 10/01/2023] Open
Abstract
The phenomenon of protein phase separation (PPS) underlies a wide range of cellular functions. Correspondingly, the dysregulation of the PPS process has been associated with numerous human diseases. To enable therapeutic interventions based on the regulation of this association, possible targets should be identified. For this purpose, we present an approach that combines the multiomic PandaOmics platform with the FuzDrop method to identify PPS-prone disease-associated proteins. Using this approach, we prioritize candidates with high PandaOmics and FuzDrop scores using a profiling method that accounts for a wide range of parameters relevant for disease mechanism and pharmacological intervention. We validate the differential phase separation behaviors of three predicted Alzheimer's disease targets (MARCKS, CAMKK2, and p62) in two cell models of this disease. Overall, the approach that we present generates a list of possible therapeutic targets for human diseases associated with the dysregulation of the PPS process.
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Affiliation(s)
- Christine M. Lim
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Alicia González Díaz
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova35131, Italy
| | - Frank W. Pun
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Alex Zhavoronkov
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
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Zagirova D, Pushkov S, Leung GHD, Liu BHM, Urban A, Sidorenko D, Kalashnikov A, Kozlova E, Naumov V, Pun FW, Ozerov IV, Aliper A, Zhavoronkov A. Biomedical generative pre-trained based transformer language model for age-related disease target discovery. Aging (Albany NY) 2023; 15:9293-9309. [PMID: 37742294 PMCID: PMC10564439 DOI: 10.18632/aging.205055] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/20/2023] [Indexed: 09/26/2023]
Abstract
Target discovery is crucial for the development of innovative therapeutics and diagnostics. However, current approaches often face limitations in efficiency, specificity, and scalability, necessitating the exploration of novel strategies for identifying and validating disease-relevant targets. Advances in natural language processing have provided new avenues for predicting potential therapeutic targets for various diseases. Here, we present a novel approach for predicting therapeutic targets using a large language model (LLM). We trained a domain-specific BioGPT model on a large corpus of biomedical literature consisting of grant text and developed a pipeline for generating target prediction. Our study demonstrates that pre-training of the LLM model with task-specific texts improves its performance. Applying the developed pipeline, we retrieved prospective aging and age-related disease targets and showed that these proteins are in correspondence with the database data. Moreover, we propose CCR5 and PTH as potential novel dual-purpose anti-aging and disease targets which were not previously identified as age-related but were highly ranked in our approach. Overall, our work highlights the high potential of transformer models in novel target prediction and provides a roadmap for future integration of AI approaches for addressing the intricate challenges presented in the biomedical field.
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Affiliation(s)
- Diana Zagirova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Stefan Pushkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Bonnie Hei Man Liu
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Anatoly Urban
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Denis Sidorenko
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Aleksandr Kalashnikov
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Ekaterina Kozlova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Frank W. Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Ivan V. Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, Abu Dhabi, UAE
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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: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Urban A, Sidorenko D, Zagirova D, Kozlova E, Kalashnikov A, Pushkov S, Naumov V, Sarkisova V, Leung GHD, Leung HW, Pun FW, Ozerov IV, Aliper A, Ren F, Zhavoronkov A. Precious1GPT: multimodal transformer-based transfer learning for aging clock development and feature importance analysis for aging and age-related disease target discovery. Aging (Albany NY) 2023; 15:4649-4666. [PMID: 37315204 PMCID: PMC10292881 DOI: 10.18632/aging.204788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023]
Abstract
Aging is a complex and multifactorial process that increases the risk of various age-related diseases and there are many aging clocks that can accurately predict chronological age, mortality, and health status. These clocks are disconnected and are rarely fit for therapeutic target discovery. In this study, we propose a novel approach to multimodal aging clock we call Precious1GPT utilizing methylation and transcriptomic data for interpretable age prediction and target discovery developed using a transformer-based model and transfer learning for case-control classification. While the accuracy of the multimodal transformer is lower within each individual data type compared to the state of art specialized aging clocks based on methylation or transcriptomic data separately it may have higher practical utility for target discovery. This method provides the ability to discover novel therapeutic targets that hypothetically may be able to reverse or accelerate biological age providing a pathway for therapeutic drug discovery and validation using the aging clock. In addition, we provide a list of promising targets annotated using the PandaOmics industrial target discovery platform.
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Affiliation(s)
- Anatoly Urban
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
| | | | - Diana Zagirova
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
| | | | | | - Stefan Pushkov
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
| | | | | | | | - Hoi Wing Leung
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
| | - Frank W. Pun
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
| | - Ivan V. Ozerov
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
| | - Alex Aliper
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
- Insilico Medicine, Masdar City, United Arab Emirates
| | - Feng Ren
- Insilico Medicine, Shanghai, China
| | - Alex Zhavoronkov
- Insilico Medicine, Pak Shek Kok, New Territories, Hong Kong
- Insilico Medicine, Masdar City, United Arab Emirates
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10
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Olsen A, Harpaz Z, Ren C, Shneyderman A, Veviorskiy A, Dralkina M, Konnov S, Shcheglova O, Pun FW, Leung GHD, Leung HW, Ozerov IV, Aliper A, Korzinkin M, Zhavoronkov A. Identification of dual-purpose therapeutic targets implicated in aging and glioblastoma multiforme using PandaOmics - an AI-enabled biological target discovery platform. Aging (Albany NY) 2023; 15:2863-2876. [PMID: 37100462 DOI: 10.18632/aging.204678] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023]
Abstract
Glioblastoma Multiforme (GBM) is the most aggressive and most common primary malignant brain tumor. The age of GBM patients is considered as one of the disease's negative prognostic factors and the mean age of diagnosis is 62 years. A promising approach to preventing both GBM and aging is to identify new potential therapeutic targets that are associated with both conditions as concurrent drivers. In this work, we present a multi-angled approach of identifying targets, which takes into account not only the disease-related genes but also the ones important in aging. For this purpose, we developed three strategies of target identification using the results of correlation analysis augmented with survival data, differences in expression levels and previously published information of aging-related genes. Several studies have recently validated the robustness and applicability of AI-driven computational methods for target identification in both cancer and aging-related diseases. Therefore, we leveraged the AI predictive power of the PandaOmics TargetID engine in order to rank the resulting target hypotheses and prioritize the most promising therapeutic gene targets. We propose cyclic nucleotide gated channel subunit alpha 3 (CNGA3), glutamate dehydrogenase 1 (GLUD1) and sirtuin 1 (SIRT1) as potential novel dual-purpose therapeutic targets to treat aging and GBM.
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Affiliation(s)
- Andrea Olsen
- The Youth Longevity Association, Sevenoaks, NA, United Kingdom
| | - Zachary Harpaz
- The Youth Longevity Association, Sevenoaks, NA, United Kingdom
- Pine Crest School Science Research Department, Fort Lauderdale, Florida 33334, USA
| | - Christopher Ren
- Shanghai High School International Division, Shanghai 200231, China
| | - Anastasia Shneyderman
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alexander Veviorskiy
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Maria Dralkina
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Simon Konnov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Olga Shcheglova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Hoi Wing Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Mikhail Korzinkin
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
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11
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Ren F, Ding X, Zheng M, Korzinkin M, Cai X, Zhu W, Mantsyzov A, Aliper A, Aladinskiy V, Cao Z, Kong S, Long X, Man Liu BH, Liu Y, Naumov V, Shneyderman A, Ozerov IV, Wang J, Pun FW, Polykovskiy DA, Sun C, Levitt M, Aspuru-Guzik A, Zhavoronkov A. AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor. Chem Sci 2023; 14:1443-1452. [PMID: 36794205 PMCID: PMC9906638 DOI: 10.1039/d2sc05709c] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The application of artificial intelligence (AI) has been considered a revolutionary change in drug discovery and development. In 2020, the AlphaFold computer program predicted protein structures for the whole human genome, which has been considered a remarkable breakthrough in both AI applications and structural biology. Despite the varying confidence levels, these predicted structures could still significantly contribute to structure-based drug design of novel targets, especially the ones with no or limited structural information. In this work, we successfully applied AlphaFold to our end-to-end AI-powered drug discovery engines, including a biocomputational platform PandaOmics and a generative chemistry platform Chemistry42. A novel hit molecule against a novel target without an experimental structure was identified, starting from target selection towards hit identification, in a cost- and time-efficient manner. PandaOmics provided the protein of interest for the treatment of hepatocellular carcinoma (HCC) and Chemistry42 generated the molecules based on the structure predicted by AlphaFold, and the selected molecules were synthesized and tested in biological assays. Through this approach, we identified a small molecule hit compound for cyclin-dependent kinase 20 (CDK20) with a binding constant Kd value of 9.2 ± 0.5 μM (n = 3) within 30 days from target selection and after only synthesizing 7 compounds. Based on the available data, a second round of AI-powered compound generation was conducted and through this, a more potent hit molecule, ISM042-2-048, was discovered with an average Kd value of 566.7 ± 256.2 nM (n = 3). Compound ISM042-2-048 also showed good CDK20 inhibitory activity with an IC50 value of 33.4 ± 22.6 nM (n = 3). In addition, ISM042-2-048 demonstrated selective anti-proliferation activity in an HCC cell line with CDK20 overexpression, Huh7, with an IC50 of 208.7 ± 3.3 nM, compared to a counter screen cell line HEK293 (IC50 = 1706.7 ± 670.0 nM). This work is the first demonstration of applying AlphaFold to the hit identification process in drug discovery.
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Affiliation(s)
- Feng Ren
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Min Zheng
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Mikhail Korzinkin
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Xin Cai
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Wei Zhu
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Alexey Mantsyzov
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Alex Aliper
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Vladimir Aladinskiy
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Zhongying Cao
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Shanshan Kong
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Xi Long
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Bonnie Hei Man Liu
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Yingtao Liu
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Vladimir Naumov
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Anastasia Shneyderman
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Ivan V Ozerov
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Ju Wang
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
| | - Frank W Pun
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Daniil A Polykovskiy
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
| | - Chong Sun
- Department of Chemistry, Department of Computer Science, University of Toronto, Vector Institute for Artificial Intelligence, Canadian Institute for Advanced Research Toronto Ontario Canada
| | - Michael Levitt
- Department of Structural Biology, Stanford University Palo Alto CA USA
| | - Alán Aspuru-Guzik
- Department of Chemistry, Department of Computer Science, University of Toronto, Vector Institute for Artificial Intelligence, Canadian Institute for Advanced Research Toronto Ontario Canada
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road. Pudong New District Shanghai 201203 China
- Insilico Medicine Kong Kong Ltd Unit 310, 3/F, Building 8W, Phase 2, Hong Kong Science Park, Pak Shek Kok Hong Kong China
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12
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Mkrtchyan GV, Veviorskiy A, Izumchenko E, Shneyderman A, Pun FW, Ozerov IV, Aliper A, Zhavoronkov A, Scheibye-Knudsen M. High-confidence cancer patient stratification through multiomics investigation of DNA repair disorders. Cell Death Dis 2022; 13:999. [PMID: 36435816 PMCID: PMC9701218 DOI: 10.1038/s41419-022-05437-w] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
Multiple cancer types have limited targeted therapeutic options, in part due to incomplete understanding of the molecular processes underlying tumorigenesis and significant intra- and inter-tumor heterogeneity. Identification of novel molecular biomarkers stratifying cancer patients with different survival outcomes may provide new opportunities for target discovery and subsequent development of tailored therapies. Here, we applied the artificial intelligence-driven PandaOmics platform ( https://pandaomics.com/ ) to explore gene expression changes in rare DNA repair-deficient disorders and identify novel cancer targets. Our analysis revealed that CEP135, a scaffolding protein associated with early centriole biogenesis, is commonly downregulated in DNA repair diseases with high cancer predisposition. Further screening of survival data in 33 cancers available at TCGA database identified sarcoma as a cancer type where lower survival was significantly associated with high CEP135 expression. Stratification of cancer patients based on CEP135 expression enabled us to examine therapeutic targets that could be used for the improvement of existing therapies against sarcoma. The latter was based on application of the PandaOmics target-ID algorithm coupled with in vitro studies that revealed polo-like kinase 1 (PLK1) as a potential therapeutic candidate in sarcoma patients with high CEP135 levels and poor survival. While further target validation is required, this study demonstrated the potential of in silico-based studies for a rapid biomarker discovery and target characterization.
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Affiliation(s)
- Garik V. Mkrtchyan
- grid.5254.60000 0001 0674 042XCenter for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Evgeny Izumchenko
- grid.170205.10000 0004 1936 7822Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL USA
| | | | | | | | | | | | - Morten Scheibye-Knudsen
- grid.5254.60000 0001 0674 042XCenter for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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13
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Pun FW, Liu BHM, Long X, Leung HW, Leung GHD, Mewborne QT, Gao J, Shneyderman A, Ozerov IV, Wang J, Ren F, Aliper A, Bischof E, Izumchenko E, Guan X, Zhang K, Lu B, Rothstein JD, Cudkowicz ME, Zhavoronkov A. Identification of Therapeutic Targets for Amyotrophic Lateral Sclerosis Using PandaOmics – An AI-Enabled Biological Target Discovery Platform. Front Aging Neurosci 2022; 14:914017. [PMID: 35837482 PMCID: PMC9273868 DOI: 10.3389/fnagi.2022.914017] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 04/06/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease with ill-defined pathogenesis, calling for urgent developments of new therapeutic regimens. Herein, we applied PandaOmics, an AI-driven target discovery platform, to analyze the expression profiles of central nervous system (CNS) samples (237 cases; 91 controls) from public datasets, and direct iPSC-derived motor neurons (diMNs) (135 cases; 31 controls) from Answer ALS. Seventeen high-confidence and eleven novel therapeutic targets were identified and will be released onto ALS.AI (http://als.ai/). Among the proposed targets screened in the c9ALS Drosophila model, we verified 8 unreported genes (KCNB2, KCNS3, ADRA2B, NR3C1, P2RY14, PPP3CB, PTPRC, and RARA) whose suppression strongly rescues eye neurodegeneration. Dysregulated pathways identified from CNS and diMN data characterize different stages of disease development. Altogether, our study provides new insights into ALS pathophysiology and demonstrates how AI speeds up the target discovery process, and opens up new opportunities for therapeutic interventions.
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Affiliation(s)
- Frank W. Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Bonnie Hei Man Liu
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Xi Long
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Hoi Wing Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Quinlan T. Mewborne
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Junli Gao
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Anastasia Shneyderman
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Ivan V. Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Ju Wang
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Feng Ren
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Alexander Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Evelyne Bischof
- College of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
- International Center for Multimorbidity and Complexity in Medicine (ICMC), Universität Zürich, Zurich, Switzerland
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, United States
| | - Xiaoming Guan
- 4B Technologies Limited, Suzhou BioBay, Suzhou, China
| | - Ke Zhang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, United States
| | - Bai Lu
- School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Merit E. Cudkowicz
- Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- *Correspondence: Merit E. Cudkowicz,
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
- Buck Institute for Research on Aging, Novato, CA, United States
- Alex Zhavoronkov,
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14
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Pun FW, Leung GHD, Leung HW, Liu BHM, Long X, Ozerov IV, Wang J, Ren F, Aliper A, Izumchenko E, Moskalev A, de Magalhães JP, Zhavoronkov A. Hallmarks of aging-based dual-purpose disease and age-associated targets predicted using PandaOmics AI-powered discovery engine. Aging (Albany NY) 2022; 14:2475-2506. [PMID: 35347083 PMCID: PMC9004567 DOI: 10.18632/aging.203960] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 01/21/2022] [Accepted: 03/06/2022] [Indexed: 11/25/2022]
Abstract
Aging biology is a promising and burgeoning research area that can yield dual-purpose pathways and protein targets that may impact multiple diseases, while retarding or possibly even reversing age-associated processes. One widely used approach to classify a multiplicity of mechanisms driving the aging process is the hallmarks of aging. In addition to the classic nine hallmarks of aging, processes such as extracellular matrix stiffness, chronic inflammation and activation of retrotransposons are also often considered, given their strong association with aging. In this study, we used a variety of target identification and prioritization techniques offered by the AI-powered PandaOmics platform, to propose a list of promising novel aging-associated targets that may be used for drug discovery. We also propose a list of more classical targets that may be used for drug repurposing within each hallmark of aging. Most of the top targets generated by this comprehensive analysis play a role in inflammation and extracellular matrix stiffness, highlighting the relevance of these processes as therapeutic targets in aging and age-related diseases. Overall, our study reveals both high confidence and novel targets associated with multiple hallmarks of aging and demonstrates application of the PandaOmics platform to target discovery across multiple disease areas.
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Affiliation(s)
- Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Hoi Wing Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Bonnie Hei Man Liu
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Xi Long
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Ju Wang
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Feng Ren
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alexander Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Alexey Moskalev
- School of Systems Biology, George Mason University (GMU), Fairfax, VA 22030, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China.,Buck Institute for Research on Aging, Novato, CA 94945, USA
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15
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Kumar Y, Yang J, Hu T, Chen L, Xu Z, Xu L, Hu XX, Tang G, Wang JM, Li Y, Poon WS, Wan W, Zhang L, Mat WK, Pun FW, Lee P, Cheong THY, Ding X, Ng SK, Tsang SY, Chen JF, Zhang P, Li S, Wang HY, Xue H. Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response. BMC Med Genomics 2015. [PMID: 26208496 PMCID: PMC4515014 DOI: 10.1186/s12920-015-0104-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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] [Indexed: 02/08/2023] Open
Abstract
Background The presence of loss-of-heterozygosity (LOH) mutations in cancer cell genomes is commonly encountered. Moreover, the occurrences of LOHs in tumor suppressor genes play important roles in oncogenesis. However, because the causative mechanisms underlying LOH mutations in cancer cells yet remain to be elucidated, enquiry into the nature of these mechanisms based on a comprehensive examination of the characteristics of LOHs in multiple types of cancers has become a necessity. Methods We performed next-generation sequencing on inter-Alu sequences of five different types of solid tumors and acute myeloid leukemias, employing the AluScan platform which entailed amplification of such sequences using multiple PCR primers based on the consensus sequences of Alu elements; as well as the whole genome sequences of a lung-to-liver metastatic cancer and a primary liver cancer. Paired-end sequencing reads were aligned to the reference human genome to identify major and minor alleles so that the partition of LOH products between homozygous-major vs. homozygous-minor alleles could be determined at single-base resolution. Strict filtering conditions were employed to avoid false positives. Measurements of LOH occurrences in copy number variation (CNV)-neutral regions were obtained through removal of CNV-associated LOHs. Results We found: (a) average occurrence of copy-neutral LOHs amounting to 6.9 % of heterologous loci in the various cancers; (b) the mainly interstitial nature of the LOHs; and (c) preference for formation of homozygous-major over homozygous-minor, and transitional over transversional, LOHs. Conclusions The characteristics of the cancer LOHs, observed in both AluScan and whole genome sequencings, point to the formation of LOHs through repair of double-strand breaks by interhomolog recombination, or gene conversion, as the consequence of a defective DNA-damage response, leading to a unified mechanism for generating the mutations required for oncogenesis as well as the progression of cancer cells. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0104-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yogesh Kumar
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Jianfeng Yang
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Taobo Hu
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Lei Chen
- Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China.
| | - Zhi Xu
- Department of Oncology, Nanjing First Hospital, and Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Lin Xu
- Jiangsu Key Laboratory of Cancer Molecular Biology and Translational Medicine, Jiangsu Cancer Hospital, Nanjing, China.
| | - Xiao-Xia Hu
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China.
| | - Gusheng Tang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China.
| | - Jian-Min Wang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China.
| | - Yi Li
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China.
| | - Wai-Sang Poon
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China.
| | - Weiqing Wan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.
| | - Wai-Kin Mat
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Frank W Pun
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Peggy Lee
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Timothy H Y Cheong
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Xiaofan Ding
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Siu-Kin Ng
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Shui-Ying Tsang
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Jin-Fei Chen
- Department of Oncology, Nanjing First Hospital, and Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Peng Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Shao Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Hong-Yang Wang
- Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China.
| | - Hong Xue
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
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16
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Tsang SY, Mei L, Wan W, Li J, Li Y, Zhao C, Ding X, Pun FW, Hu X, Wang J, Zhang J, Luo R, Cheung ST, Leung GKK, Poon WS, Ng HK, Zhang L, Xue H. Glioma Association and Balancing Selection of ZFPM2. PLoS One 2015. [PMID: 26207917 PMCID: PMC4514883 DOI: 10.1371/journal.pone.0133003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
ZFPM2, encoding a zinc finger protein and abundantly expressed in the brain, uterus and smooth muscles, plays important roles in cardiac and gonadal development. Abnormal expression of ZFPM2 in ovarian tumors and neuroblastoma has been reported but hitherto its genetic association with cancer and effects on gliomas have not been studied. In the present study, the hexamer insertion-deletion polymorphism rs71305152, located within a large haplotype block spanning intron 1 to intron 3 of ZFPM2, was genotyped in Chinese cohorts of glioma (n = 350), non-glioma cancer (n = 354) and healthy control (n = 463) by direct sequencing and length polymorphism in gel electrophoresis, and ZFPM2 expression in glioma tissues (n = 69) of different grades was quantified by real-time RT-PCR. Moreover, potential natural selection pressure acting on the gene was investigated. Disease-association analysis showed that the overall genotype of rs71305152 was significantly associated with gliomas (P = 0.016), and the heterozygous genotype compared to the combined homozygous genotypes was less frequent in gliomas than in controls (P = 0.005) or non-glioma cancers (P = 0.020). ZFPM2 mRNA expression was negatively correlated with the grades of gliomas (P = 0.002), with higher expression levels in the low-grade gliomas. In the astrocytoma subtype, higher ZFPM2 expression was also correlated with the rs71305152 heterozygous genotype (P = 0.028). In addition, summary statistics tests gave highly positive values, demonstrating that the gene is under the influence of balancing selection. These findings suggest that ZFPM2 is a glioma susceptibility gene, its genotype and expression showing associations with incidence and severity, respectively. Moreover, the balancing selection acting on ZFPM2 may be related to the important roles it has to play in multiple organ development or associated disease etiology.
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Affiliation(s)
- Shui-Ying Tsang
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Lingling Mei
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Weiqing Wan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jun Li
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yi Li
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Cunyou Zhao
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiaofan Ding
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiaoxia Hu
- Department of Hematology, Institute of Hematology, PLA, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianmin Wang
- Department of Hematology, Institute of Hematology, PLA, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Junyi Zhang
- Cancer Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rongcheng Luo
- Cancer Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siu-Tim Cheung
- Division of Neurosurgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Gilberto K. K. Leung
- Division of Neurosurgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Wai-Sang Poon
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- * E-mail: (HX); (LZ)
| | - Hong Xue
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- * E-mail: (HX); (LZ)
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Tsang SY, Zhong S, Mei L, Chen J, Ng SK, Pun FW, Zhao C, Jing B, Chark R, Guo J, Tan Y, Li L, Wang C, Chew SH, Xue H. Social cognitive role of schizophrenia candidate gene GABRB2. PLoS One 2013; 8:e62322. [PMID: 23638040 PMCID: PMC3634734 DOI: 10.1371/journal.pone.0062322] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 03/20/2013] [Indexed: 11/18/2022] Open
Abstract
The occurrence of positive selection in schizophrenia-associated GABRB2 suggests a broader impact of the gene product on population fitness. The present study considered the possibility of cognition-related GABRB2 involvement by examining the association of GABRB2 with psychosis and altruism, respectively representing psychiatric and psychological facets of social cognition. Four single nucleotide polymorphisms (SNPs) were genotyped for quantitative trait analyses and population-based association studies. Psychosis was measured by either the Positive and Negative Syndrome Scale (PANSS) or antipsychotics dosage, and altruism was based on a self-report altruism scale. The minor alleles of SNPs rs6556547, rs1816071 and rs187269 in GABRB2 were correlated with high PANSS score for positive symptoms in a Han Chinese schizophrenic cohort, whereas those of rs1816071 and rs1816072 were associated with high antipsychotics dosage in a US Caucasian schizophrenic cohort. Moreover, strongly significant GABRB2-disease associations were found among schizophrenics with severe psychosis based on high PANSS positive score, but no significant association was observed for schizophrenics with only mild psychosis. Interestingly, in addition to association with psychosis in schizophrenics, rs187269 was also associated with altruism in healthy Han Chinese. Furthermore, parallel to correlation with severe psychosis, its minor allele was correlated with high altruism scores. These findings revealed that GABRB2 is associated with psychosis, the core symptom and an endophenotype of schizophrenia. Importantly, the association was found across the breadth of the psychiatric (psychosis) to psychological (altruism) spectrum of social cognition suggesting GABRB2 involvement in human cognition.
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Affiliation(s)
- Shui Ying Tsang
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Songfa Zhong
- Department of Economics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Department of Economics, National University of Singapore, Singapore, Rep. of Singapore
| | - Lingling Mei
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianhuan Chen
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Siu-Kin Ng
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cunyou Zhao
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Bingyi Jing
- Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Robin Chark
- Department of Marketing, National University of Singapore, Singapore, Rep. of Singapore
| | - Jianhua Guo
- School of Mathematics and Statistics, Northeast Normal University, Changchun, China
| | - Yunlong Tan
- Beijing Huilongguan Hospital, Beijing, China
| | - Lijun Li
- Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Chuanyue Wang
- Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Soo Hong Chew
- Department of Economics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Department of Economics, National University of Singapore, Singapore, Rep. of Singapore
| | - Hong Xue
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- * E-mail:
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Zhao C, Wang F, Pun FW, Mei L, Ren L, Yu Z, Ng SK, Chen J, Tsang SY, Xue H. Epigenetic regulation on GABRB2 isoforms expression: developmental variations and disruptions in psychotic disorders. Schizophr Res 2012; 134:260-6. [PMID: 22206711 DOI: 10.1016/j.schres.2011.11.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/28/2022]
Abstract
INTRODUCTION To improve the understanding of psychotic abnormalities and their non-Mendelian inheritance patterns, the epigenetic regulation of the psychotic disorder-associated GABRB2, gene for the type A γ-aminobutyric acid receptor β(2)-subunit, was investigated. METHODS Expression of GABRB2, and the epigenetic regulatory enzymes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) in mouse and postmortem human brains was analyzed using real-time PCR. RESULTS Results showed that expression of GABRB2 isoforms significantly increased over time in both mouse and human, especially for the long splicing isoform. In the brains of non-psychiatric controls (CON), a significant positive correlation of GABRB2 expression with age was observed in individuals with MM genotypes of the single nucleotide polymorphisms (SNPs) rs187269 and rs1816072. This was reversed to a significant negative correlation in schizophrenics (SCZ). A similar reversal was also displayed by bipolar disorder (BPD) patients. In parallel, a significant co-variation of HDAC1 with GABRB2 expression observed in CON remained significant in BPD but not in SCZ; comparably, a significant co-variation of HDAC2 with GABRB2 expression observed in CON became non-significant in both SCZ and BPD. Moreover, co-variations of DNMT1 and DNMT3B with GABRB2, not observable in CON, became significant in BPD. CONCLUSION These findings demonstrated that GABRB2 expression was under epigenetic regulation that varied with development, genotype and disease status, and these regulatory mechanisms were observably disrupted in SCZ and BPD. This study provided insight into the complex inheritance patterns of psychiatric disorders, and pointed to the involvement of epigenetic dysregulation in the disease process of major psychotic disorders.
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Affiliation(s)
- Cunyou Zhao
- Division of Life Science, Applied Genomics Center and Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
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Mei L, Ding X, Tsang SY, Pun FW, Ng SK, Yang J, Zhao C, Li D, Wan W, Yu CH, Tan TC, Poon WS, Leung GKK, Ng HK, Zhang L, Xue H. AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome. BMC Genomics 2011; 12:564. [PMID: 22087792 PMCID: PMC3228862 DOI: 10.1186/1471-2164-12-564] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [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: 08/22/2011] [Accepted: 11/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. RESULTS Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA. CONCLUSIONS AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.
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Affiliation(s)
- Lingling Mei
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, 1 University Road, Clear Water Bay, Kowloon, Hong Kong, China.
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Pun FW, Zhao C, Lo WS, Ng SK, Tsang SY, Nimgaonkar V, Chung WS, Ungvari GS, Xue H. Imprinting in the schizophrenia candidate gene GABRB2 encoding GABA(A) receptor β(2) subunit. Mol Psychiatry 2011; 16:557-68. [PMID: 20404824 DOI: 10.1038/mp.2010.47] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Schizophrenia is a complex genetic disorder, the inheritance pattern of which is likely complicated by epigenetic factors yet to be elucidated. In this study, transmission disequilibrium tests with family trios yielded significant differences between paternal and maternal transmissions of the disease-associated single-nucleotide polymorphism (SNP) rs6556547 and its haplotypes. The minor allele (T) of rs6556547 was paternally undertransmitted to male schizophrenic offsprings, and this parent-of-origin effect strongly suggested that GABRB2 is imprinted. 'Flipping' of allelic expression in heterozygotes of SNP rs2229944 (C/T) in GABRB2 or rs2290732 (G/A) in the neighboring GABRA1 was compatible with imprinting effects on gene expression. Clustering analysis of GABRB2 mRNA expressions suggested that imprinting brought about the observed two-tiered distribution of expression levels in controls with heterozygous genotype at the disease-associated SNP rs1816071 (A/G). The deficit of upper-tiered expressions accounted for the lowered expression levels in the schizophrenic heterozygotes. The occurrence of a two-tiered distribution furnished support for imprinting, and also pointed to the necessity of differentiating between two kinds of heterozygotes of different parental origins in disease association studies on GABRB2. Bisulfite sequencing revealed hypermethylation in the neighborhood of SNP rs1816071, and methylation differences between controls and schizophrenia patients. Notably, the two schizophrenia-associated SNPs rs6556547 and rs1816071 overlapped with a CpG dinucleotide, thereby opening the possibility that CpG methylation status of these sites could have an impact on the risk of schizophrenia. Thus multiple lines of evidence pointed to the occurrence of imprinting in the GABRB2 gene and its possible role in the development of schizophrenia.
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Affiliation(s)
- F W Pun
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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Zhao C, Xu Z, Wang F, Chen J, Ng SK, Wong PW, Yu Z, Pun FW, Ren L, Lo WS, Tsang SY, Xue H. Alternative-splicing in the exon-10 region of GABA(A) receptor beta(2) subunit gene: relationships between novel isoforms and psychotic disorders. PLoS One 2009; 4:e6977. [PMID: 19763268 PMCID: PMC2741204 DOI: 10.1371/journal.pone.0006977] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 08/06/2009] [Indexed: 11/18/2022] Open
Abstract
Background Non-coding single nucleotide polymorphisms (SNPs) in GABRB2, the gene for β2-subunit of gamma-aminobutyric acid type A (GABAA) receptor, have been associated with schizophrenia (SCZ) and quantitatively correlated to mRNA expression and alternative splicing. Methods and Findings Expression of the Exon 10 region of GABRB2 from minigene constructs revealed this region to be an “alternative splicing hotspot” that readily gave rise to differently spliced isoforms depending on intron sequences. This led to a search in human brain cDNA libraries, and the discovery of two novel isoforms, β2S1 and β2S2, bearing variations in the neighborhood of Exon-10. Quantitative real-time PCR analysis of postmortem brain samples showed increased β2S1 expression and decreased β2S2 expression in both SCZ and bipolar disorder (BPD) compared to controls. Disease-control differences were significantly correlated with SNP rs187269 in BPD males for both β2S1 and β2S2 expressions, and significantly correlated with SNPs rs2546620 and rs187269 in SCZ males for β2S2 expression. Moreover, site-directed mutagenesis indicated that Thr365, a potential phosphorylation site in Exon-10, played a key role in determining the time profile of the ATP-dependent electrophysiological current run-down. Conclusion This study therefore provided experimental evidence for the importance of non-coding sequences in the Exon-10 region in GABRB2 with respect to β2-subunit splicing diversity and the etiologies of SCZ and BPD.
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Affiliation(s)
- Cunyou Zhao
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Zhiwen Xu
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Feng Wang
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Jianhuan Chen
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Siu-Kin Ng
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Pak-Wing Wong
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Zhiliang Yu
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Lihuan Ren
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Wing-Sze Lo
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Shui-Ying Tsang
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Hong Xue
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
- * E-mail:
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Lo WS, Xu Z, Yu Z, Pun FW, Ng SK, Chen J, Tong KL, Zhao C, Xu X, Tsang SY, Harano M, Stöber G, Nimgaonkar VL, Xue H. Positive selection within the Schizophrenia-associated GABA(A) receptor beta(2) gene. PLoS One 2007; 2:e462. [PMID: 17520021 PMCID: PMC1866178 DOI: 10.1371/journal.pone.0000462] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 04/24/2007] [Indexed: 01/08/2023] Open
Abstract
The gamma-aminobutyric acid type-A (GABAA) receptor plays a major role in inhibitory neurotransmissions. Intronic SNPs and haplotypes in GABRB2, the gene for GABAA receptor β2 subunit, are associated with schizophrenia and correlated with the expression of two alternatively spliced β2 isoforms. In the present study, using chimpanzee as an ancestral reference, high frequencies were observed for the derived (D) alleles of the four SNPs rs6556547, rs187269, rs1816071 and rs1816072 in GABRB2, suggesting the occurrence of positive selection for these derived alleles. Coalescence-based simulation showed that the population frequency spectra and the frequencies of H56, the haplotype having all four D alleles, significantly deviated from neutral-evolution expectation in various demographic models. Haplotypes containing the derived allele of rs1816072 displayed significantly less diversity compared to haplotypes containing its ancestral allele, further supporting positive selection. The variations in DD-genotype frequencies in five human populations provided a snapshot of the evolutionary history, which suggested that the positive selections of the D alleles are recent and likely ongoing. The divergence between the DD-genotype profiles of schizophrenic and control samples pointed to the schizophrenia-relevance of positive selections, with the schizophrenic samples showing weakened selections compared to the controls. These DD-genotypes were previously found to increase the expression of β2, especially its long isoform. Electrophysiological analysis showed that this long β2 isoform favored by the positive selections is more sensitive than the short isoform to the inhibition of GABAA receptor function by energy depletion. These findings represent the first demonstration of positive selection in a schizophrenia-associated gene.
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Affiliation(s)
- Wing-Sze Lo
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zhiwen Xu
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zhiliang Yu
- Graduate program of Atmospheric, Marine, and Coastal Environment, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Siu-Kin Ng
- Graduate Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianhuan Chen
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ka-Lok Tong
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cunyou Zhao
- Graduate Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiaojing Xu
- Graduate Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shui-Ying Tsang
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Mutsuo Harano
- Department of Neuropsychiatry, Kurume University School of Medicine, Fukuka, Japan
| | - Gerald Stöber
- Department of Psychiatry and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Vishwajit L. Nimgaonkar
- Departments of Psychiatry and Human Genetics, University of Pittsburgh School of Medicine, and Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Hong Xue
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- * To whom correspondence should be addressed. E-mail:
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Lo WS, Harano M, Gawlik M, Yu Z, Chen J, Pun FW, Tong KL, Zhao C, Ng SK, Tsang SY, Uchimura N, Stober G, Xue H. GABRB2 association with schizophrenia: commonalities and differences between ethnic groups and clinical subtypes. Biol Psychiatry 2007; 61:653-60. [PMID: 16950232 DOI: 10.1016/j.biopsych.2006.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/03/2006] [Accepted: 05/09/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) and haplotypes in intron 8 of type A gamma-aminobutyric acid (GABA(A)) receptor beta2 subunit gene (GABRB2) were initially found to be associated with schizophrenia in Chinese. This finding was subjected to cross-validation in this study with Japanese (JP) and German Caucasian (GE) subjects. METHODS Single nucleotide polymorphisms discovery and genotyping were carried out through resequencing of a 1839 base pair (bp) region in GABRB2. Tagging SNPs (tSNPs) were selected based on linkage disequilibrium (LD), combinations of which were analyzed with Bonferroni correction and permutation for disease association. Random resampling was applied to generate size- and gender-balanced cases and control subjects. RESULTS Out of the 17 SNPs (9.2/kilobase [kb]) revealed, 6 were population-specific. Population variations in LD were observable, and at least two low LD points were identified in both populations. Although disease association at single SNP level was only shown in GE, strong association was demonstrated in both JP (p = .0002 - .0191) and GE (p = .0033 - .0410) subjects, centering on haplotypes containing rs1816072 and rs1816071. Among different clinical subtypes, the most significant association was exhibited by systematic schizophrenia. CONCLUSIONS Cross-population validation of GABRB2 association with schizophrenia has been obtained with JP and GE subjects, with the genotype-disease correlations being strongest in systematic schizophrenia, the most severe subtype of the disease.
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Affiliation(s)
- Wing-Sze Lo
- Department of Biochemistry and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Hong Kong, China
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Zhao C, Xu Z, Chen J, Yu Z, Tong KL, Lo WS, Pun FW, Ng SK, Tsang SY, Xue H. Two isoforms of GABA(A) receptor beta2 subunit with different electrophysiological properties: Differential expression and genotypical correlations in schizophrenia. Mol Psychiatry 2006; 11:1092-105. [PMID: 16983389 DOI: 10.1038/sj.mp.4001899] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Single nucleotide polymorphisms in type A gamma-aminobutyric acid (GABA(A)) receptor beta2 subunit gene (GABRB2) were found to be associated with schizophrenia in Chinese, German, Japanese and Portuguese. To explore potential functional consequences of these DNA sequence polymorphisms, this study examined the expression and electrophysiological properties of two alternatively spliced products of GABRB2 along with genotypical disease association analysis. Real-time quantitative polymerase chain reaction, performed with a cohort of 31 schizophrenics and 31 controls of US population, showed 21.7% reduction in the expression of the long isoform beta(2L), 13.4% in the short isoform beta(2S) and 15.8% in the sum of the two isoforms beta(2T) in postmortem schizophrenic brain. Furthermore, two independent mRNA quantitation methods showed that the relative expression of the long over the short isoforms was significantly decreased, suggesting the occurrence of altered splicing, in schizophrenia. In male schizophrenics, the heterozygous genotypes of rs1876071 (T/C) and rs1876072 (A/G) were correlated with reduced expression of beta(2L), beta(2S) and beta(2T), and the heterozygous of rs2546620 (A/G) and homozygous-minor of rs1876071 (C/C) and rs1876072 (G/G) were correlated with reduced expression of beta(2T). Significant correlations of expression levels with different alleles and haplotypes were also indicated by quantitative trait analysis. Recombinant GABA(A) receptors expressed in HEK293 human cells containing beta(2L) underwent a steeper current rundown upon repetitive GABA activation than receptors containing beta(2S). The results thus revealed genotype-dependent expression of the alternatively spliced isoforms of GABA(A) receptor beta2 subunit, giving rise to electrophysiological consequences that could play an important role in the pathogenesis mechanism of schizophrenia.
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Affiliation(s)
- C Zhao
- Bioengineering Graduate Program, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
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