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Duan Z, Yang M, Yang J, Wu Z, Zhu Y, Jia Q, Ma X, Yin Y, Zheng J, Yang J, Jiang S, Hu L, Zhang J, Liu D, Huo Y, Yao L, Sun Y. AGFG1 increases cholesterol biosynthesis by disrupting intracellular cholesterol homeostasis to promote PDAC progression. Cancer Lett 2024; 598:217130. [PMID: 39089666 DOI: 10.1016/j.canlet.2024.217130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/01/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
PURPOSE Cholesterol metabolism reprograming has been acknowledged as a novel feature of cancers. Pancreatic ductal adenocarcinoma (PDAC) is a cancer with a high demand of cholesterol for rapid growth. The underlying mechanism of how cholesterol metabolism homestasis are disturbed in PDAC is explored. EXPERIMENTAL DESIGN The relevance between PDAC and cholesterol was confirmed in TCGA database. The expression and clinical association were discovered in TCGA and GEO datasets. Knockdown and overexpression of AGFG1 was adopted to perform function studies. RNA sequencing, cholesterol detection, transmission electron microscope, co-immunoprecipitation, and immunofluorescence et al. were utilized to reveal the underlying mechanism. RESULTS AGFG1 was identified as one gene positively correlated with cholesterol metabolism in PDAC as revealed by bioinformatics analysis. AGFG1 expression was then found associated with poor prognosis in PDAC. AGFG1 knockdown led to decreased proliferation of tumor cells both in vitro and in vivo. By RNA sequencing, we found AGFG1 upregulated expression leads to enhanced intracellular cholesterol biosynthesis. AGFG1 knockdown suppressed cholesterol biosynthesis and an accumulation of cholesterol in the ER. Mechanistically, we confirmed that AGFG1 interacted with CAV1 to relocate cholesterol for the proceeding of cholesterol biosynthesis, therefore causing disorders in intracellular cholesterol metabolism. CONCLUSIONS Our study demonstrates the tumor-promoting role of AGFG1 by disturbing cholesterol metabolism homestasis in PDAC. Our study has present a new perspective on cancer therapeutic approach based on cholerstrol metabolism in PDAC.
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Affiliation(s)
- Zonghao Duan
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Minwei Yang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Jian Yang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Department of General Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, PR China; Department of Hepatobiliary Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100029, PR China
| | - Zheng Wu
- Department of Radiation Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Yuheng Zhu
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Qinyuan Jia
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xueshiyu Ma
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Yifan Yin
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Jiahao Zheng
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Jianyu Yang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Shuheng Jiang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Lipeng Hu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Junfeng Zhang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, 201800, PR China
| | - Dejun Liu
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
| | - Yanmiao Huo
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
| | - Linli Yao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
| | - Yongwei Sun
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
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Crucial Genes in Aortic Dissection Identified by Weighted Gene Coexpression Network Analysis. J Immunol Res 2022; 2022:7585149. [PMID: 35178459 PMCID: PMC8844153 DOI: 10.1155/2022/7585149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 12/07/2021] [Accepted: 12/31/2021] [Indexed: 01/01/2023] Open
Abstract
Background Aortic dissection (AD) is a lethal vascular disease with high mortality and morbidity. Though AD clinical pathology is well understood, its molecular mechanisms remain unclear. Specifically, gene expression profiling helps illustrate the potential mechanism of aortic dissection in terms of gene regulation and its modification by risk factors. This study was aimed at identifying the genes and molecular mechanisms in aortic dissection through bioinformatics analysis. Method Nine patients with AD and 10 healthy controls were enrolled. The gene expression in peripheral mononuclear cells was profiled through next-generation RNA sequencing. Analyses including differential expressed gene (DEG) via DEGseq, weighted gene coexpression network (WGCNA), and VisANT were performed to identify crucial genes associated with AD. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was also utilized to analyze Gene Ontology (GO). Results DEG analysis revealed that 1,113 genes were associated with AD. Of these, 812 genes were markedly reduced, whereas 301 genes were highly expressed, in AD patients. DEGs were rich in certain categories such as MHC class II receptor activity, MHC class II protein complex, and immune response genes. Gene coexpression networks via WGCNA identified 3 gene hub modules, with one positively and 2 negatively correlated with AD, respectively. Specifically, module 37 was the most strongly positively correlated with AD with a correlation coefficient of 0.72. Within module 37, five hub genes (AGFG1, MCEMP1, IRAK3, KCNE1, and CLEC4D) displayed high connectivity and may have clinical significance in the pathogenesis of AD. Conclusion Our analysis provides the possible association of specific genes and gene modules for the involvement of the immune system in aortic dissection. AGFG1, MCEMP1, IRAK3, KCNE1, and CLEC4D in module M37 were highly connected and strongly linked with AD, suggesting that these genes may help understand the pathogenesis of aortic dissection.
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Portas L, Pereira M, Shaheen SO, Wyss AB, London SJ, Burney PGJ, Hind M, Dean CH, Minelli C. Lung Development Genes and Adult Lung Function. Am J Respir Crit Care Med 2020; 202:853-865. [PMID: 32392078 PMCID: PMC7491406 DOI: 10.1164/rccm.201912-2338oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rationale: Poor lung health in adult life may occur partly through
suboptimal growth and development, as suggested by epidemiological evidence
pointing to early life risk factors. Objectives: To systematically investigate the effects of lung
development genes on adult lung function. Methods: Using UK Biobank data, we tested the association of 391
genes known to influence lung development with FVC and FEV1/FVC. We
split the dataset into two random subsets of 207,616 and 138,411 individuals,
using the larger subset to select the most promising signals and the smaller
subset for replication. Measurements and Main Results: We identified 55 genes, of which 36
(16 for FVC, 19 for FEV1/FVC, and one for both) had not been
identified in the largest, most recent genome-wide study of lung function. Most
of these 36 signals were intronic variants; expression data from blood and lung
tissue showed that the majority affect the expression of the genes they lie
within. Further testing of 34 of these 36 signals in the CHARGE and SpiroMeta
consortia showed that 16 replicated after Bonferroni correction and another 12
replicated at nominal significance level. Of the 55 genes, 53 fell into four
biological categories whose function is to regulate organ size and cell
integrity (growth factors; transcriptional regulators; cell-to-cell adhesion;
extracellular matrix), suggesting that these specific processes are important
for adult lung health. Conclusions: Our study demonstrates the importance of lung
development genes in regulating adult lung function and influencing both
restrictive and obstructive patterns. Further investigation of these
developmental pathways could lead to druggable targets.
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Affiliation(s)
- Laura Portas
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Miguel Pereira
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Congenica Ltd., Wellcome Genome Campus, Cambridge, United Kingdom
| | - Seif O Shaheen
- Institute of Population Health Sciences, Queen Mary University of London, London, United Kingdom
| | - Annah B Wyss
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Peter G J Burney
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Matthew Hind
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Respiratory Medicine, Royal Brompton & Harefield NHS Foundation Trust, London, United Kingdom; and
| | - Charlotte H Dean
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,MRC Harwell Institute, Oxfordshire, United Kingdom
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Thompson EE, Dang Q, Mitchell-Handley B, Rajendran K, Ram-Mohan S, Solway J, Ober C, Krishnan R. Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma. Genome Med 2020; 12:64. [PMID: 32690065 PMCID: PMC7370514 DOI: 10.1186/s13073-020-00759-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A challenge in the post-GWAS era is to assign function to disease-associated variants. However, available resources do not include all tissues or environmental exposures that are relevant to all diseases. For example, exaggerated bronchoconstriction of airway smooth muscle cells (ASMCs) defines airway hyperresponsiveness (AHR), a cardinal feature of asthma. However, the contribution of ASMC to genetic and genomic studies has largely been overlooked. Our study aimed to address the gap in data availability from a critical tissue in genomic studies of asthma. METHODS We developed a cell model of AHR to discover variants associated with transcriptional, epigenetic, and cellular responses to two AHR promoting cytokines, IL-13 and IL-17A, and performed a GWAS of bronchial responsiveness (BRI) in humans. RESULTS Our study revealed significant response differences between ASMCs from asthma cases and controls, including genes implicated in asthma susceptibility. We defined molecular quantitative trait loci (QTLs) for expression (eQTLs) and methylation (meQTLs), and cellular QTLs for contractility (coQTLs) and performed a GWAS of BRI in human subjects. Variants in asthma GWAS were significantly enriched for ASM QTLs and BRI-associated SNPs, and near genes enriched for ASM function, many with small P values that did not reach stringent thresholds of significance in GWAS. CONCLUSIONS Our study identified significant differences between ASMCs from asthma cases and controls, potentially reflecting trained tolerance in these cells, as well as a set of variants, overlooked in previous GWAS, which reflect the AHR component of asthma.
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Affiliation(s)
- Emma E Thompson
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
| | - Quynh Dang
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Kavitha Rajendran
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sumati Ram-Mohan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Julian Solway
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ramaswamy Krishnan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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Al-Eitan LN, Alghamdi MA, Tarkhan AH, Al-Qarqaz FA. Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection. Int J Mol Sci 2019; 20:E4822. [PMID: 31569353 PMCID: PMC6801420 DOI: 10.3390/ijms20194822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
HPV infection is one of the most commonly transmitted diseases among the global population. While it can be asymptomatic, non-genital HPV infection often gives rise to cutaneous warts, which are benign growths arising from the epidermal layer of the skin. This study aimed to produce a global analysis of the ways in which cutaneous wart formation affected the CpG island methylome. The Infinium MethylationEPIC BeadChip microarray was utilized in order to quantitatively interrogate CpG island methylation in genomic DNA extracted from 24 paired wart and normal skin samples. Differential methylation analysis was carried out by means of assigning a combined rank score using RnBeads. The 1000 top-ranking CpG islands were then subject to Locus Overlap Analysis (LOLA) for enrichment of genomic ranges, while signaling pathway analysis was carried out on the top 100 differentially methylated CpG islands. Differential methylation analysis illustrated that the most differentially methylated CpG islands in warts lay within the ITGB5, DTNB, RBFOX3, SLC6A9, and C2orf27A genes. In addition, the most enriched genomic region sets in warts were Sheffield's tissue-clustered DNase hypersensitive sites, ENCODE's segmentation and transcription factor binding sites, codex sites, and the epigenome sites from cistrome. Lastly, signaling pathway analysis showed that the GRB2, GNB1, NTRK1, AXIN1, and SKI genes were the most common regulators of the genes associated with the top 100 most differentially methylated CpG islands in warts. Our study shows that HPV-induced cutaneous warts have a clear CpG island methylation profile that sets them apart from normal skin. Such a finding could account for the temporary nature of warts and the capacity for individuals to undergo clinical remission.
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Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Mansour A Alghamdi
- Department of Human Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia.
| | - Amneh H Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Firas A Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan.
- Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid 22110, Jordan.
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Kim KW, Ober C. Lessons Learned From GWAS of Asthma. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:170-187. [PMID: 30661310 PMCID: PMC6340805 DOI: 10.4168/aair.2019.11.2.170] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/05/2018] [Indexed: 02/05/2023]
Abstract
Asthma is a common complex disease of the airways. Genome-wide association studies (GWASs) of asthma have identified many risk alleles and loci that have been replicated in worldwide populations. Although the risk alleles identified by GWAS have small effects and explain only a small portion of prevalence, the discovery of asthma loci can provide an understanding of its genetic architecture and the molecular pathways involved in disease pathogenesis. These discoveries can translate into advances in clinical care by identifying therapeutic targets, preventive strategies and ultimately approaches for personalized medicine. In this review, we summarize results from GWAS of asthma from the past 10 years and the insights gleaned from these discoveries.
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Affiliation(s)
- Kyung Won Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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Willis-Owen SAG, Thompson A, Kemp PR, Polkey MI, Cookson WOCM, Moffatt MF, Natanek SA. COPD is accompanied by co-ordinated transcriptional perturbation in the quadriceps affecting the mitochondria and extracellular matrix. Sci Rep 2018; 8:12165. [PMID: 30111857 PMCID: PMC6093887 DOI: 10.1038/s41598-018-29789-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/16/2018] [Indexed: 12/04/2022] Open
Abstract
Skeletal muscle dysfunction is a frequent extra-pulmonary manifestation of Chronic Obstructive Pulmonary Disease (COPD) with implications for both quality of life and survival. The underlying biology nevertheless remains poorly understood. We measured global gene transcription in the quadriceps using Affymetrix HuGene1.1ST arrays in an unselected cohort of 79 stable COPD patients in secondary care and 16 healthy age- and gender-matched controls. We detected 1,826 transcripts showing COPD-related variation. Eighteen exhibited ≥2fold changes (SLC22A3, FAM184B, CDKN1A, FST, LINC01405, MUSK, PANX1, ANKRD1, C12orf75, MYH1, POSTN, FRZB, TNC, ACTC1, LINC00310, MYH3, MYBPH and AREG). Thirty-one transcripts possessed previous reported evidence of involvement in COPD through genome-wide association, including FAM13A. Network analysis revealed a substructure comprising 6 modules of co-expressed genes. We identified modules with mitochondrial and extracellular matrix features, of which IDH2, a central component of the mitochondrial antioxidant pathway, and ABI3BP, a proposed switch between proliferation and differentiation, represent hubs respectively. COPD is accompanied by coordinated patterns of transcription in the quadriceps involving the mitochondria and extracellular matrix and including genes previously implicated in primary disease processes.
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Affiliation(s)
- Saffron A G Willis-Owen
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom.
| | - Anna Thompson
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom
| | - Paul R Kemp
- Respiratory Sciences, National Heart and Lung Institute, Imperial College London, SW3 6NP, London, United Kingdom
| | - Michael I Polkey
- Respiratory Sciences, National Heart and Lung Institute, Imperial College London, SW3 6NP, London, United Kingdom
| | - William O C M Cookson
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom
| | - Miriam F Moffatt
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom
| | - Samantha A Natanek
- Respiratory Sciences, National Heart and Lung Institute, Imperial College London, SW3 6NP, London, United Kingdom.
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Tarasenko NV, Goncharova IA, Markov AV, Kondrat’eva EI. Association of genes of different functional classes with type 1 diabetes. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417070110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nieuwenhuis MAE, Vonk JM, Himes BE, Sarnowski C, Minelli C, Jarvis D, Bouzigon E, Nickle DC, Laviolette M, Sin D, Weiss ST, van den Berge M, Koppelman GH, Postma DS. PTTG1IP and MAML3, novel genomewide association study genes for severity of hyperresponsiveness in adult asthma. Allergy 2017; 72:792-801. [PMID: 27709636 DOI: 10.1111/all.13062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2016] [Indexed: 01/15/2023]
Abstract
BACKGROUND The severity of bronchial hyperresponsiveness (BHR) is a fundamental feature of asthma. The severity of BHR varies between asthmatics and is associated with lack of asthma control. The mechanisms underlying this trait are still unclear. This study aimed to identify genes associated with BHR severity, using a genomewide association study (GWAS) on the slope of BHR in adult asthmatics. METHODS We performed a GWAS on BHR severity in adult asthmatics from the Dutch Asthma GWAS cohort (n = 650), adjusting for smoking and inhaled corticosteroid use, and verified results in three other cohorts. Furthermore, we performed eQTL and co-expression analyses in lung tissue. RESULTS In the discovery cohort, one genomewide significant hit located in phosphodiesterase 4D, cAMP-specif (PDE4D) and 26 SNPs with P-values < 1*10-5 were found. None of our findings replicated in adult and childhood replication cohorts jointly. In adult cohorts separately, rs1344110 in pituitary tumour-transforming 1 interacting protein (PTTG1IP) and rs345983 in Mastermind-like 3 (MAML3) replicated nominally; minor alleles of rs345983 and rs1344110 were associated with less severe BHR and higher lung tissue gene expression. PTTG1IP showed significant co-expression with pituitary tumour-transforming 1, the binding factor of PTTG1lP, and with vimentin and E-cadherin1. MAML3 co-expressed significantly with Mastermind-like 2 (MAML2), both involved in Notch signalling. CONCLUSIONS PTTG1IP and MAML3 are associated with BHR severity in adult asthma. The relevance of these genes is supported by the eQTL analyses and co-expression of PTTG1lP with vimentin and E-cadherin1, and MAML3 with MAML2.
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Affiliation(s)
- M. A. E. Nieuwenhuis
- Department of Pulmonary Diseases; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC); University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - J. M. Vonk
- Groningen Research Institute for Asthma and COPD (GRIAC); University Medical Center Groningen; University of Groningen; Groningen The Netherlands
- Department of Epidemiology; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - B. E. Himes
- Department of Biostatistics and Epidemiology; University of Pennsylvania; Philadelphia PA USA
| | - C. Sarnowski
- Genetic Variation and Human Diseases Unit; U946; INSERM; Paris France
- Institut Universitaire d'Hématologie; Université Paris Diderot, Sorbonne Paris Cité; Paris France
| | - C. Minelli
- Respiratory Epidemiology, Occupational Medicine and Public Health; National Heart and Lung Institute; Imperial College; London UK
| | - D. Jarvis
- Respiratory Epidemiology, Occupational Medicine and Public Health; National Heart and Lung Institute; Imperial College; London UK
- MRC-PHE Centre for Environment & Health; London UK
| | - E. Bouzigon
- Genetic Variation and Human Diseases Unit; U946; INSERM; Paris France
- Institut Universitaire d'Hématologie; Université Paris Diderot, Sorbonne Paris Cité; Paris France
| | | | - M. Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec; Laval University; Québec City QC Canada
| | - D. Sin
- The University of British Columbia James Hogg Research Laboratory; St Paul's Hospital; Vancouver BC Canada
- 7 Respiratory Division; Department of Medicine; University of British Columbia; Vancouver BC Canada
| | - S. T. Weiss
- Channing Division of Network Medicine; Department of Medicine; Brigham & Women's Hospital and Harvard Medical School; Boston MA USA
| | - M. van den Berge
- Department of Pulmonary Diseases; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC); University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - G. H. Koppelman
- Groningen Research Institute for Asthma and COPD (GRIAC); University Medical Center Groningen; University of Groningen; Groningen The Netherlands
- Department of Pediatric Pulmonology and Pediatric Allergology; Beatrix Children's Hospital; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - D. S. Postma
- Department of Pulmonary Diseases; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC); University Medical Center Groningen; University of Groningen; Groningen The Netherlands
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Hansel NN, Paré PD, Rafaels N, Sin DD, Sandford A, Daley D, Vergara C, Huang L, Elliott WM, Pascoe CD, Arsenault BA, Postma DS, Boezen HM, Bossé Y, van den Berge M, Hiemstra PS, Cho MH, Litonjua AA, Sparrow D, Ober C, Wise RA, Connett J, Neptune ER, Beaty TH, Ruczinski I, Mathias RA, Barnes KC. Genome-Wide Association Study Identification of Novel Loci Associated with Airway Responsiveness in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2015; 53:226-34. [PMID: 25514360 DOI: 10.1165/rcmb.2014-0198oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Increased airway responsiveness is linked to lung function decline and mortality in subjects with chronic obstructive pulmonary disease (COPD); however, the genetic contribution to airway responsiveness remains largely unknown. A genome-wide association study (GWAS) was performed using the Illumina (San Diego, CA) Human660W-Quad BeadChip on European Americans with COPD from the Lung Health Study. Linear regression models with correlated meta-analyses, including data from baseline (n = 2,814) and Year 5 (n = 2,657), were used to test for common genetic variants associated with airway responsiveness. Genotypic imputation was performed using reference 1000 Genomes Project data. Expression quantitative trait loci (eQTL) analyses in lung tissues were assessed for the top 10 markers identified, and immunohistochemistry assays assessed protein staining for SGCD and MYH15. Four genes were identified within the top 10 associations with airway responsiveness. Markers on chromosome 9p21.2 flanked by LINGO2 met a predetermined threshold of genome-wide significance (P < 9.57 × 10(-8)). Markers on chromosomes 3q13.1 (flanked by MYH15), 5q33 (SGCD), and 6q21 (PDSS2) yielded suggestive evidence of association (9.57 × 10(-8) < P ≤ 4.6 × 10(-6)). Gene expression studies in lung tissue showed single nucleotide polymorphisms on chromosomes 5 and 3 to act as eQTL for SGCD (P = 2.57 × 10(-9)) and MYH15 (P = 1.62 × 10(-6)), respectively. Immunohistochemistry confirmed localization of SGCD protein to airway smooth muscle and vessels and MYH15 to airway epithelium, vascular endothelium, and inflammatory cells. We identified novel loci associated with airway responsiveness in a GWAS among smokers with COPD. Risk alleles on chromosomes 5 and 3 acted as eQTLs for SGCD and MYH15 messenger RNA, and these proteins were expressed in lung cells relevant to the development of airway responsiveness.
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Affiliation(s)
- Nadia N Hansel
- 1 Department of Medicine, School of Medicine; and.,Departments of 2 Environmental Health Sciences
| | - Peter D Paré
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | | | - Don D Sin
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Andrew Sandford
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Denise Daley
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | | | - Lili Huang
- 1 Department of Medicine, School of Medicine; and
| | - W Mark Elliott
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Chris D Pascoe
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Bryna A Arsenault
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Dirkje S Postma
- Departments of 4 Pulmonary Diseases and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - H Marike Boezen
- 6 Epidemiology, and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - Yohan Bossé
- 7 Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Québec, Canada
| | - Maarten van den Berge
- Departments of 4 Pulmonary Diseases and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - Pieter S Hiemstra
- 8 Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Michael H Cho
- 9 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Augusto A Litonjua
- 9 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 10 VA Normative Aging Study and Boston University School of Medicine, Boston, Massachusetts
| | - Carole Ober
- 11 Department of Human Genetics, University of Chicago, Chicago, Illinois
| | | | - John Connett
- 12 Division of Biostatistics, School of Public Health, University of Minnesota, St. Paul, Minnesota
| | | | | | - Ingo Ruczinski
- 14 Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Kathleen C Barnes
- 1 Department of Medicine, School of Medicine; and.,13 Epidemiology, and
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11
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Kurakula K, Vos M, Logiantara A, Roelofs JJ, Nieuwenhuis MA, Koppelman GH, Postma DS, van Rijt LS, de Vries CJM. Nuclear Receptor Nur77 Attenuates Airway Inflammation in Mice by Suppressing NF-κB Activity in Lung Epithelial Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:1388-98. [PMID: 26170382 DOI: 10.4049/jimmunol.1401714] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 06/17/2015] [Indexed: 12/13/2022]
Abstract
Allergic asthma is characterized by persistent chronic airway inflammation, which leads to mucus hypersecretion and airway hyperresponsiveness. Nuclear receptor Nur77 plays a pivotal role in distinct immune and inflammatory cells and is expressed in eosinophils and lung epithelium. However, the role of Nur77 in allergic airway inflammation has not been studied so far. In the present study, we determined the role of Nur77 in airway inflammation using a murine model of OVA-induced allergic airway inflammation. We found that OVA-challenged Nur77 knockout (KO) mice show significantly enhanced infiltration of inflammatory cells, including eosinophils and lymphocytes, and aggravated mucus production. The infiltration of macrophages is limited in this model and was similar in wild-type and Nur77 KO mice. Higher levels of Th2 cytokines were found in bronchoalveolar lavage fluid and draining lymph node cells of Nur77-KO mice, as well as increased serum IgG1 and IgG2a levels. Knockdown of Nur77 in human lung epithelial cells resulted in a marked increase in IκBα phosphorylation, corresponding with elevated NF-κB activity, whereas Nur77 overexpression decreased NF-κB activity. Consistently, Nur77 significantly decreased mRNA levels of inflammatory cytokines and Muc5ac expression and also attenuated mucus production in lung epithelial cells. To further corroborate these findings, we searched for association of single nucleotide polymorphisms in Nur77 gene with asthma and with the severity of bronchial hyperresponsiveness. We identified three Nur77 single nucleotide polymorphisms showing association with severity of bronchial hyperresponsiveness in asthma patients. Collectively, these findings support a protective role of Nur77 in OVA-induced airway inflammation and identify Nur77 as a novel therapeutic target for airway inflammation.
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Affiliation(s)
- Kondababu Kurakula
- Department of Medical Biochemistry, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Mariska Vos
- Department of Medical Biochemistry, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Adrian Logiantara
- Department of Experimental Immunology, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Joris J Roelofs
- Department of Pathology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Maartje A Nieuwenhuis
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, and Groningen Research Institute for Asthma and COPD, 9700 RB Groningen, the Netherlands; and
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology, University Medical Center Groningen, University of Groningen, and Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, 9700 RB Groningen, the Netherlands
| | - Dirkje S Postma
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, and Groningen Research Institute for Asthma and COPD, 9700 RB Groningen, the Netherlands; and
| | - Leonie S van Rijt
- Department of Experimental Immunology, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Carlie J M de Vries
- Department of Medical Biochemistry, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands;
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12
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Pilecki B, Schlosser A, Wulf-Johansson H, Trian T, Moeller JB, Marcussen N, Aguilar-Pimentel JA, de Angelis MH, Vestbo J, Berger P, Holmskov U, Sorensen GL. Microfibrillar-associated protein 4 modulates airway smooth muscle cell phenotype in experimental asthma. Thorax 2015; 70:862-72. [PMID: 26038533 DOI: 10.1136/thoraxjnl-2014-206609] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/20/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND Recently, several proteins of the extracellular matrix have been characterised as active contributors to allergic airway disease. Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix protein abundant in the lung, whose biological functions remain poorly understood. In the current study we investigated the role of MFAP4 in experimental allergic asthma. METHODS MFAP4-deficient mice were subjected to alum/ovalbumin and house dust mite induced models of allergic airway disease. In addition, human healthy and asthmatic primary bronchial smooth muscle cell cultures were used to evaluate MFAP4-dependent airway smooth muscle responses. RESULTS MFAP4 deficiency attenuated classical hallmarks of asthma, such as eosinophilic inflammation, eotaxin production, airway remodelling and hyperresponsiveness. In wild-type mice, serum MFAP4 was increased after disease development and correlated with local eotaxin levels. MFAP4 was expressed in human bronchial smooth muscle cells and its expression was upregulated in asthmatic cells. Regarding the underlying mechanism, we showed that MFAP4 interacted with integrin αvβ5 and promoted asthmatic bronchial smooth muscle cell proliferation and CCL11 release dependent on phosphatidyloinositol-3-kinase but not extracellular signal-regulated kinase pathway. CONCLUSIONS MFAP4 promoted the development of asthmatic airway disease in vivo and pro-asthmatic functions of bronchial smooth muscle cells in vitro. Collectively, our results identify MFAP4 as a novel contributor to experimental asthma, acting through modulation of airway smooth muscle cells.
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Affiliation(s)
- Bartosz Pilecki
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Anders Schlosser
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Helle Wulf-Johansson
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Thomas Trian
- Department of Pharmacology, Bordeaux University, Cardio-thoracic Research Centre, U1045, Bordeaux, France
| | - Jesper B Moeller
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Niels Marcussen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Juan A Aguilar-Pimentel
- German Research Center for Environmental Health, German Mouse Clinic and Institute of Experimental Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany Department of Dermatology and Allergology am Biederstein, University Hospital Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Martin Hrabe de Angelis
- German Research Center for Environmental Health, German Mouse Clinic and Institute of Experimental Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technical University Munich, Freising-Weihenstephan, Germany
| | - Jorgen Vestbo
- Department of Respiratory Medicine, Gentofte Hospital, Hellerup, Denmark Manchester Academic Health Science Centre, University Hospital South Manchester NHS Foundation Trust, Manchester, UK
| | - Patrick Berger
- Department of Pharmacology, Bordeaux University, Cardio-thoracic Research Centre, U1045, Bordeaux, France Department of Lung Function Testing, Department of Thoracic Chirurgy, Department of Anatomy and Pathology, CHU Bordeaux Teaching Hospital, Pessac, France
| | - Uffe Holmskov
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Grith L Sorensen
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
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13
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Abstract
Genome-wide association studies (GWAS) have been employed in the field of allergic disease, and significant associations have been published for nearly 100 asthma genes/loci. An outcome of GWAS in allergic disease has been the formation of national and international collaborations leading to consortia meta-analyses, and an appreciation for the specificity of genetic associations to sub-phenotypes of allergic disease. Molecular genetics has undergone a technological revolution, leading to next-generation sequencing strategies that are increasingly employed to hone in on the causal variants associated with allergic diseases. Unmet needs include the inclusion of diverse cohorts and strategies for managing big data.
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Affiliation(s)
- Romina A Ortiz
- Department of Medicine, The Johns Hopkins Asthma and Allergy Center, 5501 Hopkins Bayview Circle, Room 3A.62, Baltimore, MD 21224, USA
| | - Kathleen C Barnes
- Department of Medicine, The Johns Hopkins Asthma and Allergy Center, 5501 Hopkins Bayview Circle, Room 3A.62, Baltimore, MD 21224, USA.
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14
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Integrins: therapeutic targets in airway hyperresponsiveness and remodelling? Trends Pharmacol Sci 2014; 35:567-74. [PMID: 25441775 DOI: 10.1016/j.tips.2014.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/25/2014] [Accepted: 09/15/2014] [Indexed: 12/28/2022]
Abstract
Integrins are a group of transmembrane heterodimeric proteins that mediate cell-cell and cell-extracellular matrix (ECM) interactions. Integrins have been under intense investigation for their role in inflammation in asthma. Clinical trials investigating integrin antagonists, however, have shown that these compounds are relatively ineffective. Airway remodelling is another pathological feature of asthma that is thought to make an important contribution to airway hyperresponsiveness (AHR) and lung function decline. Recent studies have identified integrins as important players in this process, with a particular role for β1 and αv integrins. Here we review the role of these integrins in airway remodelling and hyperresponsiveness in obstructive airway disease and their potential as pharmacological targets for future treatment.
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