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Green JR, Mahalingaiah PKS, Gopalakrishnan SM, Liguori MJ, Mittelstadt SW, Blomme EAG, Van Vleet TR. Off-target pharmacological activity at various kinases: Potential functional and pathological side effects. J Pharmacol Toxicol Methods 2023; 123:107468. [PMID: 37553032 DOI: 10.1016/j.vascn.2023.107468] [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: 03/23/2023] [Revised: 06/16/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
In drug discovery, during the lead optimization and candidate characterization stages, novel small molecules are frequently evaluated in a battery of in vitro pharmacology assays to identify potential unintended, off-target interactions with various receptors, transporters, ion channels, and enzymes, including kinases. Furthermore, these screening panels may also provide utility at later stages of development to provide a mechanistic understanding of unexpected safety findings. Here, we present a compendium of the most likely functional and pathological outcomes associated with interaction(s) to a panel of 95 kinases based on an extensive curation of the scientific literature. This panel of kinases was designed by AbbVie based on safety-related data extracted from the literature, as well as from over 20 years of institutional knowledge generated from discovery efforts. For each kinase, the scientific literature was reviewed using online databases and the most often reported functional and pathological effects were summarized. This work should serve as a practical guide for small molecule drug discovery scientists and clinical investigators to predict and/or interpret adverse effects related to pharmacological interactions with these kinases.
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Affiliation(s)
- Jonathon R Green
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
| | | | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Michael J Liguori
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Scott W Mittelstadt
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Eric A G Blomme
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Terry R Van Vleet
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
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Yin BW, Li B, Mehmood A, Yuan C, Song S, Guo RY, Zhang L, Ma T, Guo L. BLK polymorphisms and expression level in neuromyelitis optica spectrum disorder. CNS Neurosci Ther 2021; 27:1549-1560. [PMID: 34637583 PMCID: PMC8611770 DOI: 10.1111/cns.13738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/04/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/18/2022] Open
Abstract
Aim This study aimed to determine the correlation between B‐lymphoid tyrosine kinase (BLK) polymorphism, mRNA gene expression of BLK, and NMOSD in a Chinese Han population. Background B‐lymphoid tyrosine kinase gene expressed mainly in B cells plays a key role in various autoimmune disorders. However, no studies have investigated the association of BLK polymorphisms with neuromyelitis optica spectrum disorder (NMOSD). Methods Han Chinese population of 310 subjects were recruited to analyze three single nucleotide polymorphisms (rs13277113, rs4840568, and rs2248932) under allele, genotype, and haplotype frequencies, followed by clinical characteristics stratified analysis. Real‐time PCR was used to analyze mRNA expression levels of BLK in the peripheral blood mononuclear cells of 64 subjects. Results Patients with NMOSD showed lower frequencies of the minor allele G of rs2248932 than healthy controls (odds ratio (OR) =0.57, 95% confidence intervals (CI) 0.39–0.83, p = 0.003). The association between minor allele G of rs2248932 and reduced NMOSD susceptibility was found by applying genetic models of inheritance (codominant, dominant, and recessive) and haplotypes analysis. Subsequently, by stratification analysis for AQP4‐positivity, the minor allele G frequencies of rs2248932 in AQP4‐positive subgroup were significantly lower than in the healthy controls (OR =0.46, 95% CI 0.30–0.72, p = 0.001). Notably, the genotype GG of rs2248932 was more frequent in AQP4‐negative subgroup (n = 14) than in AQP4‐positive subgroup (n = 93) (p = 0.003, OR =0.05, 95% CI =0.01–0.57). BLK mRNA expression levels in the NMOSD patients (n = 36) were lower than in healthy controls (n = 28) (p < 0.05). However, the acute non‐treatment (n = 7), who were untreated patients in the acute phase from the NMOSD group, showed BLK mRNA expression levels 1.8‐fold higher than healthy controls (n = 8) (p < 0.05). Conclusion This study evaluated that the minor allele G of rs2248932 in BLK is associated with reduced susceptibility to NMOSD and protected the risk of AQP4‐positive. BLK mRNA expression in NMOSD was lower as compared to healthy controls while significantly increased in acute‐untreated patients.
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Affiliation(s)
- Bo-Wen Yin
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China.,Department of Neurology, The First Hospital of Qinhuangdao, Qinhuangdao, Hebei, China
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Arshad Mehmood
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Congcong Yuan
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Shuang Song
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Ruo-Yi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Lu Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Tianzhao Ma
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
| | - Li Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, City Shijiazhuang, Province Hebei, China.,Key Laboratory of Neurology of Hebei Province, City Shijiazhuang, Province Hebei, China
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Jiang Z, Shi Y, Zhao W, Zhou L, Zhang B, Xie Y, Zhang Y, Tan G, Wang Z. Association between chronic periodontitis and the risk of Alzheimer's disease: combination of text mining and GEO dataset. BMC Oral Health 2021; 21:466. [PMID: 34556089 PMCID: PMC8461934 DOI: 10.1186/s12903-021-01827-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Although chronic periodontitis has previously been reported to be linked with Alzheimer's disease (AD), the pathogenesis between the two is unclear. The purpose of this study is to analyze and screen the relevant and promising molecular markers between chronic periodontitis and Alzheimer's disease (AD). METHODS In this paper, we analyzed three AD expression datasets and extracted differentially expressed genes (DEGs), then intersected them with chronic periodontitis genes obtained from text mining, and finally obtained integrated DEGs. We followed that by enriching the matching the matching cell signal cascade through DAVID analysis. Moreover, the MCODE of Cytoscape software was employed to uncover the protein-protein interaction (PPI) network and the matching hub gene. Finally, we verified our data using a different independent AD cohort. RESULTS The chronic periodontitis gene set acquired from text abstracting was intersected with the previously obtained three AD groups, and 12 common genes were obtained. Functional enrichment assessment uncovered 12 cross-genes, which were mainly linked to cell morphogenesis involved in neuron differentiation, leading edge membrane, and receptor ligand activity. After PPI network creation, the ten hub genes linked to AD were retrieved, consisting of SPP1, THY1, CD44, ITGB1, HSPB3, CREB1, SST, UCHL1, CCL5 and BMP7. Finally, the function terms in the new independent dataset were used to verify the previous dataset, and we found 22 GO terms and one pathway, "ECM-receptor interaction pathways", in the overlapping functional terms. CONCLUSIONS The establishment of the above-mentioned candidate key genes, as well as the enriched signaling cascades, provides promising molecular markers for chronic periodontitis-related AD, which may help the diagnosis and treatment of AD patients in the future.
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Affiliation(s)
- Zhengye Jiang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Yanxi Shi
- Department of Cardiology, Jiaxing Second Hospital, Jiaxing, China
| | - Wenpeng Zhao
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Liwei Zhou
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Bingchang Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Yuanyuan Xie
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Yaya Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Guowei Tan
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China
| | - Zhanxiang Wang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.
- The Department of Neuroscience, Institute of Neurosurgery, School of Medicine, Xiamen University, Xiamen, China.
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Cheng CW, Fang WF, Tang KT, Lin JD. Serum interferon levels associated with the disease activity in women with overt Graves' disease. Cytokine 2021; 138:155353. [PMID: 33121876 DOI: 10.1016/j.cyto.2020.155353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/16/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/24/2023]
Abstract
BACKGROUND Inflammatory cytokines participate in immune reactions and the pathogenesis of autoimmunity. Herein, we quantified four groups of inflammatory cytokines, including interferons (IFNs), the tumor necrosis factor (TNF) superfamily (TNFSF), interleukin (IL)-related cytokines, and bone and extracellular matrix remodeling-related cytokines to determine their contributions in women with overt Graves' disease (GD). METHODS Forty-three women with GD were enrolled in this cross-sectional study. Thirty-seven cytokines, thyroid-stimulating hormone (TSH), free thyroxine, and TSH receptor antibody (TSHRAb) were quantified. GD patients with a low TSH level at the time of sample collection were defined as having active GD. RESULTS Patients with active GD had higher IFN-α2, IFN-γ, IFN-λ1, and IFN-λ2 levels than those with inactive GD. In addition, certain TNFSF cytokines, including soluble cluster of differentiation 30 (sCD30), TNFSF member 14 (TNFSF14), pentraxin (PTX)-3, soluble TNF receptor 2 (sTNF-R2), and thymic stromal lymphopoietin (TSLP) were higher in active GD than in inactive GD. Moreover, active GD patients had higher IL-2, IL-12(p40), osteocalcin (OCN), and matrix metalloproteinase (MMP)-3 than inactive GD patients. All IFNs except IFN-λ1 were correlated with TSHRAb titers. Moreover, TNFSF cytokines, consisting of B-cell-activating factor, sCD30, TNFSF14, PTX-3, sTNF-R2, and TSLP, were associated with TSHRAb levels. CONCLUSIONS Serum IFNs could be the most remarkable cytokines in modulating the disease severity and TSHRAb titers in women with full-blown GD. Further molecular-based research to clarify the actual role of IFNs in the disease progression of GD is needed.
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Affiliation(s)
- Chao-Wen Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Traditional Herb Medicine Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Wen-Fang Fang
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Kam-Tsun Tang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Jiunn-Diann Lin
- Division of Endocrinology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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Shi TT, Xin Z, Hua L, Wang H, Zhao RX, Yang YL, Xie RR, Liu HY, Yang JK. Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy. J Endocrinol Invest 2021; 44:297-310. [PMID: 32449092 DOI: 10.1007/s40618-020-01298-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND A previous study indicated that gut microbiota changed notably in Graves' orbitopathy (GO) patients as compared to controls. However, the characteristics of intestinal bacteria in Graves' disease (GD) and GO are unclear. OBJECTIVE The present study aimed to identify specific intestinal bacteria of GD and GO, respectively. METHODS The gut microbial communities of the fecal samples of 30 GD patients without GO, 33 GO subjects, and 32 healthy subjects were analyzed and compared by 16S rRNA gene sequencing. RESULTS At the phylum level, the proportion of Deinococcus-Thermus and Chloroflexi was decreased significantly in GO patients as compared to GD. At the genus level, the proportion of Subdoligranulum and Bilophila was increased while that of Blautia, Anaerostipes, Dorea, Butyricicoccus, Romboutsia, Fusicatenibacter, unidentified_ Lachnospiraceae, unidentified_Clostridiales, Collineslla, Intestinibacter, and Phascolarctobacterium was decreased in the GO group as compared to the GD group. Random forest analysis was used for the identification of specific intestinal microbiota, and Deinococcus-Thermus, Cyanobacteria and Chloroflexi were ranked in the top ten according to their contributions to sample classification. Moreover, compared to the control, there were multiple gut bacterial enrichment metabolic pathways in GO and GD patients, including nucleotide metabolism, enzyme family, and energy metabolism. Compared to GO, the only enrichment metabolic pathway found in GD was the viral protein family. CONCLUSIONS This study highlighted the significant differences in the intestinal microbiota and predictive functions of GD with GO, thereby providing new insights into the role of the gut bacteria that might contribute to the development of GO in GD patients.
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Affiliation(s)
- T-T Shi
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China
| | - Z Xin
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China.
| | - L Hua
- Department of Mathematics, School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China.
| | - H Wang
- Department of Emergency, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - R-X Zhao
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China
| | - Y-L Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China
| | - R-R Xie
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China
| | - H-Y Liu
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China
| | - J-K Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Beijing, 100730, China
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Zhang Y, Garofano F, Wu X, Schmid M, Krawitz P, Essler M, Schmidt-Wolf IGH. Integrative analysis of key candidate genes and signaling pathways in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy by bioinformatics. Invest New Drugs 2020; 38:1717-1729. [PMID: 32500465 PMCID: PMC7575511 DOI: 10.1007/s10637-020-00952-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 03/31/2020] [Accepted: 05/14/2020] [Indexed: 11/26/2022]
Abstract
Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), the first immune checkpoint to be targeted clinically, has provided an effective treatment option for various malignancies. However, the clinical advantages associated with CTLA-4 inhibitors can be offset by the potentially severe immune-related adverse events (IRAEs), including autoimmune thyroid dysfunction. To investigate the candidate genes and signaling pathways involving in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy, integrated differentially expressed genes (DEGs) were extracted from the intersection of genes from Gene Expression Omnibus (GEO) datasets and text mining. The functional enrichment was performed by gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Protein-protein interaction (PPI) network, module enrichment, and hub gene identification were constructed and visualized by the online Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. A total of 22 and 17 integrated human DEGs in hypothyroidism and hyperthyroidism group related to anti-CTLA-4 therapy were identified, respectively. Functional enrichment analysis revealed 24 GO terms and 1 KEGG pathways in the hypothyroid group and 21 GO terms and 2 KEGG pathways in the hyperthyroid group. After PPI network construction, the top five hub genes associated with hypothyroidism were extracted, including ALB, MAPK1, SPP1, PPARG, and MIF, whereas those associated with hyperthyroidism were ALB, FCGR2B, CD44, LCN2, and CD74. The identification of the candidate key genes and enriched signaling pathways provides potential biomarkers for autoimmune thyroid dysfunction related to anti-CTLA-4 therapy and might contribute to the future diagnosis and management of IRAEs for cancer patients.
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Affiliation(s)
- Ying Zhang
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Francesca Garofano
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Xiaolong Wu
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Matthias Schmid
- Institute for Medical Biometry, Computer Science and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics of Medical School University Bonn, Bonn, Germany
| | - Markus Essler
- Department of Nuclear Medicine, University Hospital Bonn, Bonn, Germany
| | - Ingo G H Schmidt-Wolf
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany.
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