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Ding L, Liu Y, Meng X, Jiang Y, Lin J, Cheng S, Xu Z, Zhao X, Li H, Wang Y, Li Z. Biomarker and genomic analyses reveal molecular signatures of non-cardioembolic ischemic stroke. Signal Transduct Target Ther 2023; 8:222. [PMID: 37248226 DOI: 10.1038/s41392-023-01465-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Acute ischemic stroke (AIS) is a major cause of disability and mortality worldwide. Non-cardioembolic ischemic stroke (NCIS), which constitutes the majority of AIS cases, is highly heterogeneous, thus requiring precision medicine treatments. This study aimed to investigate the molecular mechanisms underlying NCIS heterogeneity. We integrated data from the Third China National Stroke Registry, including clinical phenotypes, biomarkers, and whole-genome sequencing data for 7695 patients with NCIS. We identified 30 molecular clusters based on 63 biomarkers and explored the comprehensive landscape of biological heterogeneity and subpopulations in NCIS. Dimensionality reduction revealed fine-scale subpopulation structures associated with specific biomarkers. The subpopulations with biomarkers for inflammation, abnormal liver and kidney function, homocysteine metabolism, lipid metabolism, and gut microbiota metabolism were associated with a high risk of unfavorable clinical outcomes, including stroke recurrence, disability, and mortality. Several genes encoding potential drug targets were identified as putative causal genes that drive the clusters, such as CDK10, ERCC3, and CHEK2. We comprehensively characterized the genetic architecture of these subpopulations, identified their molecular signatures, and revealed the potential of the polybiomarkers and polygenic prediction for assessing clinical outcomes. Our study demonstrates the power of large-scale molecular biomarkers and genomics to understand the underlying biological mechanisms of and advance precision medicine for NCIS.
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Affiliation(s)
- Lingling Ding
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Research Unit of Artificial Intelligence in Cerebrovascular Disease, Chinese Academy of Medical Sciences, Beijing, 100070, China
| | - Yu Liu
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Xia Meng
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Yong Jiang
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Research Unit of Artificial Intelligence in Cerebrovascular Disease, Chinese Academy of Medical Sciences, Beijing, 100070, China
| | - Jinxi Lin
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Si Cheng
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Zhe Xu
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Xingquan Zhao
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Research Unit of Artificial Intelligence in Cerebrovascular Disease, Chinese Academy of Medical Sciences, Beijing, 100070, China
| | - Hao Li
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Yongjun Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Research Unit of Artificial Intelligence in Cerebrovascular Disease, Chinese Academy of Medical Sciences, Beijing, 100070, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100070, China
- Clinical Center for Precision Medicine in Stroke, Capital Medical University, Beijing, 100070, China
| | - Zixiao Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China.
- Research Unit of Artificial Intelligence in Cerebrovascular Disease, Chinese Academy of Medical Sciences, Beijing, 100070, China.
- Chinese Institute for Brain Research, Beijing, China.
- Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, 100070, China.
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Yeh CH, Chou YJ, Tsai TH, Hsu PWC, Li CH, Chan YH, Tsai SF, Ng SC, Chou KM, Lin YC, Juan YH, Fu TC, Lai CC, Sytwu HK, Tsai TF. Artificial-Intelligence-Assisted Discovery of Genetic Factors for Precision Medicine of Antiplatelet Therapy in Diabetic Peripheral Artery Disease. Biomedicines 2022; 10:biomedicines10010116. [PMID: 35052795 PMCID: PMC8773099 DOI: 10.3390/biomedicines10010116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 12/15/2022] Open
Abstract
An increased risk of cardiovascular events was identified in patients with peripheral artery disease (PAD). Clopidogrel is one of the most widely used antiplatelet medications. However, there are heterogeneous outcomes when clopidogrel is used to prevent cardiovascular events in PAD patients. Here, we use an artificial intelligence (AI)-assisted methodology to identify genetic factors potentially involved in the clopidogrel-resistant mechanism, which is currently unclear. Several discoveries can be pinpointed. Firstly, a high proportion (>50%) of clopidogrel resistance was found among diabetic PAD patients in Taiwan. Interestingly, our result suggests that platelet function test-guided antiplatelet therapy appears to reduce the post-interventional occurrence of major adverse cerebrovascular and cardiac events in diabetic PAD patients. Secondly, AI-assisted genome-wide association study of a single-nucleotide polymorphism (SNP) database identified a SNP signature composed of 20 SNPs, which are mapped into 9 protein-coding genes (SLC37A2, IQSEC1, WASHC3, PSD3, BTBD7, GLIS3, PRDM11, LRBA1, and CNR1). Finally, analysis of the protein connectivity map revealed that LRBA, GLIS3, BTBD7, IQSEC1, and PSD3 appear to form a protein interaction network. Intriguingly, the genetic factors seem to pinpoint a pathway related to endocytosis and recycling of P2Y12 receptor, which is the drug target of clopidogrel. Our findings reveal that a combination of AI-assisted discovery of SNP signatures and clinical parameters has the potential to develop an ethnic-specific precision medicine for antiplatelet therapy in diabetic PAD patients.
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Affiliation(s)
- Chi-Hsiao Yeh
- Department of Thoracic and Cardiovascular Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (Y.-C.L.); (Y.-H.J.); (T.-C.F.)
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung 204, Taiwan
| | - Yi-Ju Chou
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan; (Y.-J.C.); (P.W.-C.H.); (S.-F.T.)
| | - Tsung-Hsien Tsai
- Advanced Tech BU, Acer Inc., New Taipei City 221, Taiwan; (T.-H.T.); (C.-H.L.); (Y.-H.C.)
| | - Paul Wei-Che Hsu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan; (Y.-J.C.); (P.W.-C.H.); (S.-F.T.)
| | - Chun-Hsien Li
- Advanced Tech BU, Acer Inc., New Taipei City 221, Taiwan; (T.-H.T.); (C.-H.L.); (Y.-H.C.)
| | - Yun-Hsuan Chan
- Advanced Tech BU, Acer Inc., New Taipei City 221, Taiwan; (T.-H.T.); (C.-H.L.); (Y.-H.C.)
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan; (Y.-J.C.); (P.W.-C.H.); (S.-F.T.)
| | - Soh-Ching Ng
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Chang Gung Memorial Hospital, Keelung 204, Taiwan; (S.-C.N.); (K.-M.C.)
| | - Kuei-Mei Chou
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Chang Gung Memorial Hospital, Keelung 204, Taiwan; (S.-C.N.); (K.-M.C.)
| | - Yu-Ching Lin
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (Y.-C.L.); (Y.-H.J.); (T.-C.F.)
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Keelung 204, Taiwan
| | - Yu-Hsiang Juan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (Y.-C.L.); (Y.-H.J.); (T.-C.F.)
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Keelung 204, Taiwan
| | - Tieh-Cheng Fu
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (Y.-C.L.); (Y.-H.J.); (T.-C.F.)
- Department of Physical Medicine and Rehabilitation, Chang Gung Memorial Hospital, Keelung 204, Taiwan
| | - Chi-Chun Lai
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (Y.-C.L.); (Y.-H.J.); (T.-C.F.)
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung 204, Taiwan
- Department of Ophthalmology, Chang Gung Memorial Hospital, Keelung 204, Taiwan
- Correspondence: (C.-C.L.); (H.-K.S.); (T.-F.T.); Tel.: +886-2-24313131 (ext. 6101) (C.-C.L.); +886-37-206166 (ext. 31010) (H.-K.S.); +886-2-28267293 (T.-F.T.)
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan
- National Defense Medical Center, Department & Graduate Institute of Microbiology and Immunology, Taipei 114, Taiwan
- Correspondence: (C.-C.L.); (H.-K.S.); (T.-F.T.); Tel.: +886-2-24313131 (ext. 6101) (C.-C.L.); +886-37-206166 (ext. 31010) (H.-K.S.); +886-2-28267293 (T.-F.T.)
| | - Ting-Fen Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan; (Y.-J.C.); (P.W.-C.H.); (S.-F.T.)
- Departments of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Center for Healthy Longevity and Aging Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Correspondence: (C.-C.L.); (H.-K.S.); (T.-F.T.); Tel.: +886-2-24313131 (ext. 6101) (C.-C.L.); +886-37-206166 (ext. 31010) (H.-K.S.); +886-2-28267293 (T.-F.T.)
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Cacciari B, Crepaldi P, Cheng CY, Bossi E, Spalluto G, Federico S, Jacobson KA, Cattaneo M. Structure Activity Relationship of 4-Amino-2-thiopyrimidine Derivatives as Platelet Aggregation Inhibitors. Med Chem 2019; 15:863-872. [PMID: 30734681 DOI: 10.2174/1573406415666190208124534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Platelet aggregation plays a pathogenic role in the development of arterial thrombi, which are responsible for common diseases caused by thrombotic arterial occlusion, such as myocardial infarction and stroke. Much efforts are directed toward developing platelet aggregation inhibitors that act through several mechanisms: The main antiplatelet family of COXinhibitors, phosphodiesterase inhibitors, and thrombin inhibitors. Recently, the important role in the platelet aggregation of adenosine diphosphate (ADP)-activated P2Y12 and P2Y1 receptors, Gprotein coupled receptors of the P2 purinergic family, has emerged, and their inhibitors are explored as potential therapeutic antithrombotics. P2Y12 inhibitors, i.e. clopidogrel, prasugrel, ticagrelor, and cangrelor, are already used clinically to reduce coronary artery thrombosis risk and prevent acute coronary syndromes. The search for new P2Y12 inhibitors, with better risk-to-benefit profiles is still ongoing. METHODS Several years ago, our group prepared a series of 6-amino-2-thio-3H-pyrimidin-4-one derivatives that displayed an interesting platelet aggregation inhibiting activity. In order to probe the structure-activity relationships and improve their inhibitory effects of these compounds, we synthesized variously substituted 6-amino-2-thio-3H-pyrimidin-4-one derivatives and substituted 4-amino-2-thiopyrimidine-5-carboxylic acid analogues. All the synthesized compounds were tested by light trasmission aggregometry (LTA) as inducers or inhibitors of platelet aggregation in citrated platelet-rich plasma (PRP). RESULTS Among the 6-amino-2-thio-3H-pyrimidin-4-one derivatives, compounds 2c and 2h displayed marked inhibitory activity, with a capability to inhibit the ADP(10-6M)-induced platelet aggregation by 91% and 87% at 10-4M concentration, respectively. Selected 4-amino-2- thiopyrimidine-5-carboxylic acid derivatives were tested as P2Y12 and P2Y1 antagonists and found to display negligible activity. CONCLUSION These negative findings demonstrated that this heterocyclic nucleus is not a useful common pharmacophore for developing P2Y-dependent inhibitors of platelet aggregation. Nevertheless, compounds 2c and 2h could represent a new chemotype to further develop inhibitors of platelet aggregation.
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Affiliation(s)
- Barbara Cacciari
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17/19, I-44121 Ferrara, Italy
| | - Pamela Crepaldi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17/19, I-44121 Ferrara, Italy
| | - Chun Yan Cheng
- Unità di Medicina III, Azienda Ospedaliera San Paolo, Dipartimento di Scienze della Salute, Università di Milano, Via di Rudinì 8, I-20142 Milano, Italy
| | - Elena Bossi
- Unità di Medicina III, Azienda Ospedaliera San Paolo, Dipartimento di Scienze della Salute, Università di Milano, Via di Rudinì 8, I-20142 Milano, Italy
| | - Giampiero Spalluto
- Dipartimento di Scienze Cimiche e Farmaceutiche, Università di Trieste, Piazzale europa 1, I-34127 Trieste, Italy
| | - Stephanie Federico
- Dipartimento di Scienze Cimiche e Farmaceutiche, Università di Trieste, Piazzale europa 1, I-34127 Trieste, Italy
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Marco Cattaneo
- Unità di Medicina III, Azienda Ospedaliera San Paolo, Dipartimento di Scienze della Salute, Università di Milano, Via di Rudinì 8, I-20142 Milano, Italy
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Melo JB. Genetics and myocardial infarction. Rev Port Cardiol 2018; 37:737-738. [PMID: 30197191 DOI: 10.1016/j.repc.2018.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Joana Barbosa Melo
- Laboratório de Citogenética e Genómica, CNC.IBILI, CIMAGO, Faculdade de Medicina da Universidade de Coimbra, Coimbra, Portugal.
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Genetics and myocardial infarction. REVISTA PORTUGUESA DE CARDIOLOGIA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.repce.2018.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kamiyama M, Naguro I, Ichijo H. mASKing cancer cells in a tumor microenvironment. Cell Cycle 2017; 17:139-140. [PMID: 29157105 DOI: 10.1080/15384101.2017.1407402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Miki Kamiyama
- a Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Isao Naguro
- a Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hidenori Ichijo
- a Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 , Japan
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Affiliation(s)
- Aylin C Hanyaloglu
- Institute of Reproductive and Developmental Biology, Dept. Surgery and Cancer, Imperial College London, UK.
| | - Dimitris K Grammatopoulos
- Translational Medicine, Warwick Medical School & Clinical Biochemistry, Coventry and Warwickshire Pathology Service, UK.
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