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Thorne A, Bansal A, Necker-Brown A, Mostafa MM, Gao A, Georgescu A, Kooi C, Leigh R, Newton R. Differential regulation of BIRC2 and BIRC3 expression by inflammatory cytokines and glucocorticoids in pulmonary epithelial cells. PLoS One 2023; 18:e0286783. [PMID: 37289679 PMCID: PMC10249814 DOI: 10.1371/journal.pone.0286783] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Roles for the baculoviral inhibitor of apoptosis repeat-containing (BIRC) genes, BIRC2 and BIRC3, may include signaling to the inflammatory transcription factor, nuclear factor-κB (NF-κB) and protection from cell death. However, distinct functions for each BIRC are not well-delineated. Given roles for the epithelium in barrier function and host defence, BIRC2 and BIRC3 expression was characterized in pulmonary epithelial cell lines and primary human bronchial epithelial cells (pHBECs) grown as undifferentiated cells in submersion culture (SC) or as highly differentiated cells at air-liquid interface (ALI). In A549 cells, interleukin-1β (IL1B) and tumor necrosis factor α (TNF) induced BIRC3 mRNA (~20-50-fold), with maximal protein expression from 6-24 h. Similar effects occurred in BEAS-2B and Calu-3 cells, as well as SC and ALI pHBECs. BIRC2 protein was readily detected in unstimulated cells, but was not markedly modulated by IL1B or TNF. Glucocorticoids (dexamethasone, budesonide) modestly increased BIRC3 mRNA and protein, but showed little effect on BIRC2 expression. In A549 cells, BIRC3 mRNA induced by IL1B was unchanged by glucocorticoids and showed supra-additivity with TNF-plus-glucocorticoid. Supra-additivity was also evident for IL1B-plus-budesonide induced-BIRC3 in SC and ALI pHBECs. Using A549 cells, IL1B- and TNF-induced BIRC3 expression, and to a lesser extent, BIRC2, was prevented by NF-κB inhibition. Glucocorticoid-induced BIRC3 expression was prevented by silencing and antagonism of the glucocorticoid receptor. Whereas TNF, but not IL1B, induced degradation of basal BIRC2 and BIRC3 protein, IL1B- and TNF-induced BIRC3 protein remained stable. Differential regulation by cytokines and glucocorticoids shows BIRC2 protein expression to be consistent with roles in rapid signaling events, whereas cytokine-induced BIRC3 may be more important in later effects. While TNF-induced degradation of both BIRCs may restrict their activity, cytokine-enhanced BIRC3 expression could prime for its function. Finally, shielding from glucocorticoid repression, or further enhancement by glucocorticoid, may indicate a key protective role for BIRC3.
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Affiliation(s)
- Andrew Thorne
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Akanksha Bansal
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Amandah Necker-Brown
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mahmoud M. Mostafa
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Alex Gao
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrei Georgescu
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cora Kooi
- Department of Medicine, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Richard Leigh
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Robert Newton
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Lung Health Research Group, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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2
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Du L, Xu C, Zeng Z, Chen F, Tang K, Liang Y, Guo Y. Exploration of induced sputum BIRC3 levels and clinical implications in asthma. BMC Pulm Med 2022; 22:86. [PMID: 35287655 PMCID: PMC8922789 DOI: 10.1186/s12890-022-01887-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/10/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Baculoviral IAP repeat-containing 3 (BIRC3) which encodes a member of the IAP family of proteins upregulated in the asthma expression profile dataset. However, there was few research on studying the clinical implication of BIRC3 in asthma. OBJECTIVE To validate BIRC3 expression and its clinical implications in induced sputum of asthma. METHODS Based on the GSE76262 (118 asthma cases and 21 healthy controls) dataset, differentially expressed genes were screened using R software. Subsequently, BIRC3 mRNA and protein were clinically verified in induced sputum samples through quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA). Besides, the correlations between BIRC3 expression and asthmatic eosinophilic/allergic inflammation indicators (FeNO, IgE, and EOS%), pulmonary function (FEV1, FEV1% pred, FVC% pred, and FEV1/FVC), and inflammatory cytokines (IL-4, IL-5, IL-13, IL-25, IL-10, IL-33, and TSLP) were analyzed. Finally, BIRC3 mRNA was detected in human primary bronchial epithelial cells stimulated by cytokines (IL-4 or IL-13). RESULTS BIRC3 was screened as a candidate gene in the GSE76262, which was highly expressed in asthma. Highly expressed BIRC3 was positively correlated with eosinophilic and allergic indicators, including FeNO, blood eosinophil, and serum IgE. Moreover, BIRC3 protein was positively associated with inflammation cytokines, like IL-4, IL-5, IL-13, IL-25, IL-10, IL-33, and TSLP, while negatively correlated with FEV1, FEV1%pred, FVC% pred, and FEV1/FVC. Furthermore, the expression of BIRC3 could be induced in primary bronchial epithelial cells treated by cytokines IL-4 or IL-13. CONCLUSIONS BIRC3 significantly increased in induced sputum of asthma and positively correlated with airway eosinophilic and peripheral blood allergic inflammation, type 2 cytokines, and airway obstruction. Increased BIRC3 might be involved in the pathogenesis of asthma by affecting the eosinophilic and allergic inflammation.
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Affiliation(s)
- Lijuan Du
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Changyi Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Zhimin Zeng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Fengjia Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Kun Tang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Yuxia Liang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China. .,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
| | - Yubiao Guo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China. .,Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
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3
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Multiomics Analysis Identifies BIRC3 as a Novel Glucocorticoid Response-Associated Gene. J Allergy Clin Immunol 2021; 149:1981-1991. [PMID: 34971648 DOI: 10.1016/j.jaci.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Inhaled corticosteroid (ICS) response among patients with asthma is influenced by genetics, but biologically actionable insights based on associations have not been found. Various glucocorticoid response omics datasets are available to interrogate their biological effects. OBJECTIVE We sought to identify functionally relevant ICS response genetic associations by integrating complementary multiomics datasets. METHODS Variants with p-values<10-4 from a previous ICS response genome-wide association study were re-ranked based on integrative scores determined from: i) glucocorticoid receptor (GR)- and ii) RNA polymerase II (RNAP II)-binding regions inferred from ChIP-Seq data for three airway cell types, iii) glucocorticoid response element (GRE) motifs, iv) differentially expressed genes in response to glucocorticoid exposure according to 20 transcriptomic datasets, and v) expression quantitative trait loci (eQTLs) from GTEx. Candidate variants were tested for association with ICS response and asthma in six independent studies. RESULTS Four variants had significant (q-value<0.05) multiomics integrative scores. These variants were in a locus consisting of 52 variants in high LD (r2≥0.8) near GR-binding sites by the gene BIRC3. Variants were also BIRC3 eQTLs in lung, and two were within/near putative GRE motifs. BIRC3 had increased RNAP II occupancy and gene expression with glucocorticoid exposure in two ChIP-Seq and 13 transcriptomic datasets. Some BIRC3 variants in the 52-variant locus were associated (p-value<0.05) with ICS response in three independent studies and others with asthma in one study. CONCLUSION BIRC3 should be prioritized for further functional studies of ICS response. CLINICAL IMPLICATION Genetic variation near BIRC3 may influence ICS response in people with asthma.
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Zhang S, Li N, Sheng Y, Chen W, Ma Q, Yu X, Lian J, Zeng J, Yang Y, Yan J. Hepatitis B virus induces sorafenib resistance in liver cancer via upregulation of cIAP2 expression. Infect Agent Cancer 2021; 16:20. [PMID: 33757557 PMCID: PMC7988944 DOI: 10.1186/s13027-021-00359-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND HBV promotes cell survival by upregulating the expression of the cellular inhibitor of apoptosis protein 2 (cIAP2), however whether it is involved in HBV-induced sorafenib resistance in liver cancer remains unclear. METHODS cIAP2 overexpression and knockdown was adopted to assess the involvement of cIAP2 in HBV-induced sorafenib resistance. Anti-HBV drug lamivudine and Akt inhibitor were used to investigate the impact of HBV replication on cIAP2 expression and sorafenib resistance. Xenotransplantation mouse model was used to confirm the data on cell lines in vitro. RESULTS Liver cancer cell line HepG2.215 showed increased cIAP2 expression and enhanced resistance to sorafenib. Upon sorafenib treatment, overexpression of cIAP2 in HepG2 lead to decreased cleaved caspase 3 level and increased cell viability, while knockdown of cIAP2 in HepG2.215 resulted in increased level of cleaved caspase 3 and decreased cell viability, suggesting the involvement of cIAP2 in HBV-induced sorafenib resistance. Furthermore, anti-HBV treatment reduced cIAP2 expression and partially restored sorafenib sensitivity in HepG2.215 cells. Xenotransplantation mouse model further confirmed that co-treatment with lamivudine and sorafenib could reduce sorafenib-resistant HepG2.215 tumor cell growth. CONCLUSION cIAP2 is involved in HBV-induced sorafenib resistance in liver cancer and anti-HBV treatments reduce cIAP2 expression and partially restore sorafenib sensibility.
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Affiliation(s)
- Shouhua Zhang
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, China
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Nuoya Li
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, China
| | - Yanling Sheng
- Department of Ultrasound, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Wen Chen
- Department of Surgery, Jiangxi Provincial Cancer Hospital, Nanchang, China
| | - Qiangliang Ma
- Department of dermatology, Ili Kazakh Autonomous State Chinese Medicine Hospital, Xinjiang, Uygur Autonomous Region, China
| | - Xin Yu
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, China
| | - Jianping Lian
- Department of Oncology, The Affiliated Hospital of Jinggangshan University, Ji'an, China
| | - Junquan Zeng
- Department of Oncology, The Affiliated Hospital of Jinggangshan University, Ji'an, China
| | - Yipeng Yang
- Department of General Surgery, Xinhua Hospital of Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Rd, Shanghai, China.
| | - Jinlong Yan
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, China.
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5
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Islam T, Rahman MR, Aydin B, Beklen H, Arga KY, Shahjaman M. Integrative transcriptomics analysis of lung epithelial cells and identification of repurposable drug candidates for COVID-19. Eur J Pharmacol 2020; 887:173594. [PMID: 32971089 PMCID: PMC7505772 DOI: 10.1016/j.ejphar.2020.173594] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease, more commonly COVID-19 has emerged as a world health pandemic. There are couples of treatment methods for COVID-19, however, well-established drugs and vaccines are urgently needed to treat the COVID-19. The new drug discovery is a tremendous challenge; repurposing of existing drugs could shorten the time and expense compared with de novo drug development. In this study, we aimed to decode molecular signatures and pathways of the host cells in response to SARS-CoV-2 and the rapid identification of repurposable drugs using bioinformatics and network biology strategies. We have analyzed available transcriptomic RNA-seq COVID-19 data to identify differentially expressed genes (DEGs). We detected 177 DEGs specific for COVID-19 where 122 were upregulated and 55 were downregulated compared to control (FDR<0.05 and logFC ≥ 1). The DEGs were significantly involved in the immune and inflammatory response. The pathway analysis revealed the DEGs were found in influenza A, measles, cytokine signaling in the immune system, interleukin-4, interleukin -13, interleukin -17 signaling, and TNF signaling pathways. Protein-protein interaction analysis showed 10 hub genes (BIRC3, ICAM1, IRAK2, MAP3K8, S100A8, SOCS3, STAT5A, TNF, TNFAIP3, TNIP1). The regulatory network analysis showed significant transcription factors (TFs) that target DEGs, namely FOXC1, GATA2, YY1, FOXL1, NFKB1. Finally, drug repositioning analysis was performed with these 10 hub genes and showed that in silico validated three drugs with molecular docking. The transcriptomics signatures, molecular pathways, and regulatory biomolecules shed light on candidate biomarkers and drug targets which have potential roles to manage COVID-19. ICAM1 and TNFAIP3 were the key hubs that have demonstrated good binding affinities with repurposed drug candidates. Dabrafenib, radicicol, and AT-7519 were the top-scored repurposed drugs that showed efficient docking results when they tested with hub genes. The identified drugs should be further evaluated in molecular level wet-lab experiments in prior to clinical studies in the treatment of COVID-19.
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Affiliation(s)
- Tania Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Rezanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh; Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Enayetpur, Sirajganj, Bangladesh.
| | - Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur, Bangladesh
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6
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Nelson RK, Brickner H, Panwar B, Ramírez-Suástegui C, Herrera-de la Mata S, Liu N, Diaz D, Alexander LEC, Ay F, Vijayanand P, Seumois G, Akuthota P. Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared with Common β-Chain Cytokines IL-5 and GM-CSF. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:329-337. [PMID: 31175163 PMCID: PMC6616007 DOI: 10.4049/jimmunol.1801668] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/15/2019] [Indexed: 12/31/2022]
Abstract
Despite recent advances in asthma management with anti-IL-5 therapies, many patients have eosinophilic asthma that remains poorly controlled. IL-3 shares a common β subunit receptor with both IL-5 and GM-CSF but, through α-subunit-specific properties, uniquely influences eosinophil biology and may serve as a potential therapeutic target. We aimed to globally characterize the transcriptomic profiles of GM-CSF, IL-3, and IL-5 stimulation on human circulating eosinophils and identify differences in gene expression using advanced statistical modeling. Human eosinophils were isolated from the peripheral blood of healthy volunteers and stimulated with either GM-CSF, IL-3, or IL-5 for 48 h. RNA was then extracted and bulk sequencing performed. DESeq analysis identified differentially expressed genes and weighted gene coexpression network analysis independently defined modules of genes that are highly coexpressed. GM-CSF, IL-3, and IL-5 commonly upregulated 252 genes and downregulated 553 genes, producing a proinflammatory and survival phenotype that was predominantly mediated through TWEAK signaling. IL-3 stimulation yielded the most numbers of differentially expressed genes that were also highly coexpressed (n = 119). These genes were enriched in pathways involving JAK/STAT signaling. GM-CSF and IL-5 stimulation demonstrated redundancy in eosinophil gene expression. In conclusion, IL-3 produces a distinct eosinophil gene expression program among the β-chain receptor cytokines. IL-3-upregulated genes may provide a foundation for research into therapeutics for patients with eosinophilic asthma who do not respond to anti-IL-5 therapies.
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Affiliation(s)
- Ryan K Nelson
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA 92037
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Howard Brickner
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA 92037
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Bharat Panwar
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | | | | | - Neiman Liu
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA 92037
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Damaris Diaz
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA 92037
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Laura E Crotty Alexander
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA 92037
- Veterans Affairs San Diego Healthcare System, La Jolla, CA 92161; and
| | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA 92037
- University of California San Diego School of Medicine, La Jolla, CA 92093
| | | | | | - Praveen Akuthota
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA 92037;
- La Jolla Institute for Immunology, La Jolla, CA 92037
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7
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James G, Reisberg S, Lepik K, Galwey N, Avillach P, Kolberg L, Mägi R, Esko T, Alexander M, Waterworth D, Loomis AK, Vilo J. An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank. PLoS One 2019; 14:e0215026. [PMID: 30978214 PMCID: PMC6461350 DOI: 10.1371/journal.pone.0215026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
The Estonian Biobank, governed by the Institute of Genomics at the University of Tartu (Biobank), has stored genetic material/DNA and continuously collected data since 2002 on a total of 52,274 individuals representing ~5% of the Estonian adult population and is increasing. To explore the utility of data available in the Biobank, we conducted a phenome-wide association study (PheWAS) in two areas of interest to healthcare researchers; asthma and liver disease. We used 11 asthma and 13 liver disease-associated single nucleotide polymorphisms (SNPs), identified from published genome-wide association studies, to test our ability to detect established associations. We confirmed 2 asthma and 5 liver disease associated variants at nominal significance and directionally consistent with published results. We found 2 associations that were opposite to what was published before (rs4374383:AA increases risk of NASH/NAFLD, rs11597086 increases ALT level). Three SNP-diagnosis pairs passed the phenome-wide significance threshold: rs9273349 and E06 (thyroiditis, p = 5.50x10-8); rs9273349 and E10 (type-1 diabetes, p = 2.60x10-7); and rs2281135 and K76 (non-alcoholic liver diseases, including NAFLD, p = 4.10x10-7). We have validated our approach and confirmed the quality of the data for these conditions. Importantly, we demonstrate that the extensive amount of genetic and medical information from the Estonian Biobank can be successfully utilized for scientific research.
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Affiliation(s)
- Glen James
- AstraZeneca, Global Medical Affairs, Cambridge, United Kingdom
| | - Sulev Reisberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- STACC, Tartu, Estonia
- Quretec, Tartu, Estonia
| | - Kaido Lepik
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Nicholas Galwey
- GlaxoSmithKline, Research and Development, Stevenage, United Kingdom
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, United States of America
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Liis Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Myriam Alexander
- GlaxoSmithKline, Research and Development, Stevenage, United Kingdom
| | - Dawn Waterworth
- GlaxoSmithKline, Genetics, Collegeville, PA, United States of America
| | - A. Katrina Loomis
- Pfizer Worldwide Research and Development, Groton, CT, United States of America
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
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8
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Reisberg S, Galwey N, Avillach P, Sahlqvist AS, Kolberg L, Mägi R, Esko T, Vilo J, James G. Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations. Int J Immunogenet 2019; 46:49-58. [PMID: 30659741 DOI: 10.1111/iji.12413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/04/2018] [Indexed: 11/28/2022]
Abstract
Allele-specific analyses to understand frequency differences across populations, particularly populations not well studied, are important to help identify variants that may have a functional effect on disease mechanisms and phenotypic predisposition, facilitating new Genome-Wide Association Studies (GWAS). We aimed to compare the allele frequency of 11 asthma-associated and 16 liver disease-associated single nucleotide polymorphisms (SNPs) between the Estonian, HapMap and 1000 genome project populations. When comparing EGCUT with HapMap populations, the largest difference in allele frequencies was observed with the Maasai population in Kinyawa, Kenya, with 12 SNP variants reporting statistical significance. Similarly, when comparing EGCUT with 1000 genomes project populations, the largest difference in allele frequencies was observed with pooled African populations with 22 SNP variants reporting statistical significance. For 11 asthma-associated and 16 liver disease-associated SNPs, Estonians are genetically similar to other European populations but significantly different from African populations. Understanding differences in genetic architecture between ethnic populations is important to facilitate new GWAS targeted at underserved ethnic groups to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality.
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Affiliation(s)
- Sulev Reisberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia.,Software Technology and Applications Competence Center, Tartu, Estonia.,Quretec Ltd, Tartu, Estonia
| | | | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA.,Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Liis Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Glen James
- Research and Development, GlaxoSmithKline, Stevenage, UK
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9
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IAPs protect host target tissues from graft-versus-host disease in mice. Blood Adv 2017; 1:1517-1532. [PMID: 29296793 DOI: 10.1182/bloodadvances.2017004242] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/01/2017] [Indexed: 12/13/2022] Open
Abstract
Inhibitors of apoptosis proteins (IAPs) regulate apoptosis, but little is known about the role of IAPs in the regulation of immunity. Development of IAP inhibition by second mitochondria-derived activator of caspase (SMAC) mimetics is emerging as a novel therapeutic strategy to treat malignancies. We explored the role of IAPs in allogeneic immunity with 2 distinct yet complementary strategies, namely, chemical and genetic approaches, in clinically relevant models of experimental bone marrow transplantation (BMT). The small-molecule pan-IAP inhibitor SMAC mimetic AT-406 aggravated gastrointestinal graft-versus-host disease (GVHD) in multiple models. The role of specific IAPs in various host and donor cellular compartments was explored by utilizing X-linked IAP (XIAP)- and cellular IAP (cIAP)-deficient animals as donors or recipients. Donor T cells from C57BL/6 cIAP1-/- or XIAP-/- animals demonstrated equivalent GVHD severity and allogeneic responses, both in vivo and in vitro, when compared with B6 wild-type (B6-WT) T cells. By contrast, when used as recipient animals, both XIAP-/- and cIAP1-/- animals demonstrated increased mortality from GVHD when compared with B6-WT animals. BM chimera studies revealed that cIAP and XIAP deficiency in host nonhematopoietic target cells, but not in host hematopoietic-derived cells, is critical for exacerbation of GVHD. Intestinal epithelial cells from IAP-deficient animals showed reduced levels of antiapoptotic proteins as well as autophagy-related protein LC3 after allogeneic BMT. Collectively, our data highlight a novel immune cell-independent but target tissue-intrinsic role for IAPs in the regulation of gastrointestinal damage from GVHD.
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