1
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Altan M, Li QZ, Wang Q, Vokes NI, Sheshadri A, Gao J, Zhu C, Tran HT, Gandhi S, Antonoff MB, Swisher S, Wang J, Byers LA, Abdel-Wahab N, Franco-Vega MC, Wang Y, Lee JJ, Zhang J, Heymach JV. Distinct patterns of auto-reactive antibodies associated with organ-specific immune-related adverse events. Front Immunol 2023; 14:1322818. [PMID: 38152395 PMCID: PMC10751952 DOI: 10.3389/fimmu.2023.1322818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023] Open
Abstract
The roles of preexisting auto-reactive antibodies in immune-related adverse events (irAEs) associated with immune checkpoint inhibitor therapy are not well defined. Here, we analyzed plasma samples longitudinally collected at predefined time points and at the time of irAEs from 58 patients with immunotherapy naïve metastatic non-small cell lung cancer treated on clinical protocol with ipilimumab and nivolumab. We used a proteomic microarray system capable of assaying antibody reactivity for IgG and IgM fractions against 120 antigens for systemically evaluating the correlations between auto-reactive antibodies and certain organ-specific irAEs. We found that distinct patterns of auto-reactive antibodies at baseline were associated with the subsequent development of organ-specific irAEs. Notably, ACHRG IgM was associated with pneumonitis, anti-cytokeratin 19 IgM with dermatitis, and anti-thyroglobulin IgG with hepatitis. These antibodies merit further investigation as potential biomarkers for identifying high-risk populations for irAEs and/or monitoring irAEs during immunotherapy treatment. Trial registration ClinicalTrials.gov identifier: NCT03391869.
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Affiliation(s)
- Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Quan-Zhen Li
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Qi Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natalie I. Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chengsong Zhu
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Hai T. Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Saumil Gandhi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mara B. Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jing Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Lauren A. Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Noha Abdel-Wahab
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Maria C. Franco-Vega
- Department of Hospital Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yinghong Wang
- Department of Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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2
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Katheder NS, Browder KC, Chang D, De Maziere A, Kujala P, van Dijk S, Klumperman J, Lu TC, Li H, Lai Z, Sangaraju D, Jasper H. Nicotinic acetylcholine receptor signaling maintains epithelial barrier integrity. eLife 2023; 12:e86381. [PMID: 38063293 PMCID: PMC10764009 DOI: 10.7554/elife.86381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024] Open
Abstract
Disruption of epithelial barriers is a common disease manifestation in chronic degenerative diseases of the airways, lung, and intestine. Extensive human genetic studies have identified risk loci in such diseases, including in chronic obstructive pulmonary disease (COPD) and inflammatory bowel diseases. The genes associated with these loci have not fully been determined, and functional characterization of such genes requires extensive studies in model organisms. Here, we report the results of a screen in Drosophila melanogaster that allowed for rapid identification, validation, and prioritization of COPD risk genes that were selected based on risk loci identified in human genome-wide association studies (GWAS). Using intestinal barrier dysfunction in flies as a readout, our results validate the impact of candidate gene perturbations on epithelial barrier function in 56% of the cases, resulting in a prioritized target gene list. We further report the functional characterization in flies of one family of these genes, encoding for nicotinic acetylcholine receptor (nAchR) subunits. We find that nAchR signaling in enterocytes of the fly gut promotes epithelial barrier function and epithelial homeostasis by regulating the production of the peritrophic matrix. Our findings identify COPD-associated genes critical for epithelial barrier maintenance, and provide insight into the role of epithelial nAchR signaling for homeostasis.
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Affiliation(s)
- Nadja S Katheder
- Regenerative Medicine, Genentech, South San Francisco, United States
| | - Kristen C Browder
- Regenerative Medicine, Genentech, South San Francisco, United States
| | - Diana Chang
- Human Genetics, Genentech, South San Francisco, United States
| | - Ann De Maziere
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Pekka Kujala
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Suzanne van Dijk
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Tzu-Chiao Lu
- Huffington Center on Aging, Baylor College of Medicine, Houston, United States
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Zijuan Lai
- Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, United States
| | - Dewakar Sangaraju
- Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, United States
| | - Heinrich Jasper
- Regenerative Medicine, Genentech, South San Francisco, United States
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3
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Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies. Can Respir J 2022; 2022:3982335. [PMID: 35721789 PMCID: PMC9203202 DOI: 10.1155/2022/3982335] [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: 07/29/2021] [Accepted: 05/26/2022] [Indexed: 12/03/2022] Open
Abstract
Background Last two decades, many association studies on genetic variants and chronic obstructive pulmonary disease (COPD) risk have been published. But results from different studies are inconsistent. Therefore, we performed this article to systematically evaluate results from previous meta-analyses and genome-wide association studies (GWASs). Material and Methods. Firstly, we retrieved meta-analyses in PubMed, Embase, and China National Knowledge Infrastructure and GWASs in PubMed and GWAS catalog on or before April 7th, 2022. Then, data were extracted and screened. Finally, two main methods—Venice criteria and false-positive report probability test—were used to evaluate significant associations. Results As a result, eighty-eight meta-analyses and 5 GWASs were deemed eligible for inclusion. Fifty variants in 26 genes obtained from meta-analyses were significantly associated with COPD risk. Cumulative epidemiological evidence of an association was graded as strong for 10 variants in 8 genes (GSTM1, CHRNA, ADAM33, SP-D, TNF-α, VDBP, HMOX1, and HHIP), moderate for 6 variants in 5 genes (PI, GSTM1, ADAM33, TNF-α, and VDBP), and weak for 40 variants in 23 genes. Five variants in 4 genes showed convincing evidence of no association with COPD risk in meta-analyses. Additionally, 29 SNPs identified in GWASs were proved to be noteworthy based on the FPRP test. Conclusion In summary, more than half (52.38%) of genetic variants reported in previous meta-analyses showed no association with COPD risk. However, 13 variants in 9 genes had moderate to strong evidence for an association. This article can serve as a useful reference for further studies.
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4
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Routhier J, Pons S, Freidja ML, Dalstein V, Cutrona J, Jonquet A, Lalun N, Mérol JC, Lathrop M, Stitzel JA, Kervoaze G, Pichavant M, Gosset P, Tournier JM, Birembaut P, Dormoy V, Maskos U. An innate contribution of human nicotinic receptor polymorphisms to COPD-like lesions. Nat Commun 2021; 12:6384. [PMID: 34737286 PMCID: PMC8568944 DOI: 10.1038/s41467-021-26637-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease is a generally smoking-linked major cause of morbidity and mortality. Genome-wide Association Studies identified a locus including a non-synonymous single nucleotide polymorphism in CHRNA5, rs16969968, encoding the nicotinic acetylcholine receptor α5 subunit, predisposing to both smoking and Chronic Obstructive Pulmonary Disease. Here we report that nasal polyps from rs16969968 non-smoking carriers exhibit airway epithelium remodeling and inflammation. These hallmarks of Chronic Obstructive Pulmonary Disease occur spontaneously in mice expressing human rs16969968. They are significantly amplified after exposure to porcine pancreatic elastase, an emphysema model, and to oxidative stress with a polymorphism-dependent alteration of lung function. Targeted rs16969968 expression in epithelial cells leads to airway remodeling in vivo, increased proliferation and production of pro-inflammatory cytokines through decreased calcium entry and increased adenylyl-cyclase activity. We show that rs16969968 directly contributes to Chronic Obstructive Pulmonary Disease-like lesions, sensitizing the lung to the action of oxidative stress and injury, and represents a therapeutic target. Human polymorphisms in nicotinic acetylcholine receptor genes have been linked to both smoking and lung diseases like Chronic Obstructive Pulmonary Disease (COPD) or lung cancer. Here the authors identify a direct role for a human coding polymorphism in COPD-like lesions independent of smoke or nicotine exposure.
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Affiliation(s)
- Julie Routhier
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Stéphanie Pons
- Institut Pasteur, Université de Paris, Integrative Neurobiology of Cholinergic Systems, CNRS UMR 3571, Paris, France
| | - Mohamed Lamine Freidja
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria
| | - Véronique Dalstein
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Biopathology, CHU of Reims, Reims, France
| | - Jérôme Cutrona
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Antoine Jonquet
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Nathalie Lalun
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Jean-Claude Mérol
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Otorhinolaryngology, CHU of Reims, Reims, France
| | - Mark Lathrop
- McGill University Genome Center, Montréal, QC, Canada
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Gwenola Kervoaze
- University of Lille, CNRS UMR9017, Inserm U1019, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Muriel Pichavant
- University of Lille, CNRS UMR9017, Inserm U1019, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Philippe Gosset
- University of Lille, CNRS UMR9017, Inserm U1019, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Marie Tournier
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Philippe Birembaut
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Biopathology, CHU of Reims, Reims, France
| | - Valérian Dormoy
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.
| | - Uwe Maskos
- Institut Pasteur, Université de Paris, Integrative Neurobiology of Cholinergic Systems, CNRS UMR 3571, Paris, France.
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5
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Szalontai K, Gémes N, Furák J, Varga T, Neuperger P, Balog JÁ, Puskás LG, Szebeni GJ. Chronic Obstructive Pulmonary Disease: Epidemiology, Biomarkers, and Paving the Way to Lung Cancer. J Clin Med 2021; 10:jcm10132889. [PMID: 34209651 PMCID: PMC8268950 DOI: 10.3390/jcm10132889] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), the frequently fatal pathology of the respiratory tract, accounts for half a billion cases globally. COPD manifests via chronic inflammatory response to irritants, frequently to tobacco smoke. The progression of COPD from early onset to advanced disease leads to the loss of the alveolar wall, pulmonary hypertension, and fibrosis of the respiratory epithelium. Here, we focus on the epidemiology, progression, and biomarkers of COPD with a particular connection to lung cancer. Dissecting the cellular and molecular players in the progression of the disease, we aim to shed light on the role of smoking, which is responsible for the disease, or at least for the more severe symptoms and worse patient outcomes. We summarize the inflammatory conditions, as well as the role of EMT and fibroblasts in establishing a cancer-prone microenvironment, i.e., the soil for ‘COPD-derived’ lung cancer. We highlight that the major health problem of COPD can be alleviated via smoking cessation, early diagnosis, and abandonment of the usage of biomass fuels on a global basis.
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Affiliation(s)
- Klára Szalontai
- Csongrád County Hospital of Chest Diseases, Alkotmány u. 36., H6772 Deszk, Hungary;
| | - Nikolett Gémes
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- PhD School in Biology, University of Szeged, H6726 Szeged, Hungary
| | - József Furák
- Department of Surgery, University of Szeged, Semmelweis u. 8., H6725 Szeged, Hungary;
| | - Tünde Varga
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
| | - Patrícia Neuperger
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- PhD School in Biology, University of Szeged, H6726 Szeged, Hungary
| | - József Á. Balog
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- PhD School in Biology, University of Szeged, H6726 Szeged, Hungary
| | - László G. Puskás
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- Avicor Ltd. Alsó Kikötő sor 11/D, H6726 Szeged, Hungary
| | - Gábor J. Szebeni
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H6726 Szeged, Hungary
- CS-Smartlab Devices Ltd., Ady E. u. 14., H7761 Kozármisleny, Hungary
- Correspondence:
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6
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Diabasana Z, Perotin JM, Belgacemi R, Ancel J, Mulette P, Delepine G, Gosset P, Maskos U, Polette M, Deslée G, Dormoy V. Nicotinic Receptor Subunits Atlas in the Adult Human Lung. Int J Mol Sci 2020; 21:ijms21207446. [PMID: 33050277 PMCID: PMC7588933 DOI: 10.3390/ijms21207446] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels responsible for rapid neural and neuromuscular signal transmission. Although it is well documented that 16 subunits are encoded by the human genome, their presence in airway epithelial cells (AECs) remains poorly understood, and contribution to pathology is mainly discussed in the context of cancer. We analysed nAChR subunit expression in the human lungs of smokers and non-smokers using transcriptomic data for whole-lung tissues, isolated large AECs, and isolated small AECs. We identified differential expressions of nAChRs in terms of detection and repartition in the three modalities. Smoking-associated alterations were also unveiled. Then, we identified an nAChR transcriptomic print at the single-cell level. Finally, we reported the localizations of detectable nAChRs in bronchi and large bronchioles. Thus, we compiled the first complete atlas of pulmonary nAChR subunits to open new avenues to further unravel the involvement of these receptors in lung homeostasis and respiratory diseases.
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Affiliation(s)
- Zania Diabasana
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
| | - Jeanne-Marie Perotin
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Department of Respiratory Diseases, Centre Hospitalier Universitaire de Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Randa Belgacemi
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
| | - Julien Ancel
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Department of Respiratory Diseases, Centre Hospitalier Universitaire de Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Pauline Mulette
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Department of Respiratory Diseases, Centre Hospitalier Universitaire de Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Gonzague Delepine
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Department of Thoracic Surgery, Centre Hospitalier Universitaire de Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Philippe Gosset
- CNRS UMR9017, Inserm U1019, University of Lille, Centre Hospitalier Régional Universitaire de Lille, Institut Pasteur, CIIL—Center for Infection and Immunity of Lille, 59000 Lille, France;
| | - Uwe Maskos
- Integrative Neurobiology of Cholinergic Systems, Institut Pasteur, CNRS UMR 3571, 75015 Paris, France;
| | - Myriam Polette
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Department of Biopathology, Centre Hospitalier Universitaire de Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Gaëtan Deslée
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Department of Respiratory Diseases, Centre Hospitalier Universitaire de Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Valérian Dormoy
- Inserm UMR-S1250, P3Cell, University of Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (Z.D.); (J.-M.P.); (R.B.); (J.A.); (P.M.); (G.D.); (M.P.); (G.D.)
- Correspondence: ; Tel.: +33-(0)3-10-73-62-28; Fax: +33-(0)3-26-06-58-61
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7
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Sha Q, Wang Z, Zhang X, Zhang S. A clustering linear combination approach to jointly analyze multiple phenotypes for GWAS. Bioinformatics 2020; 35:1373-1379. [PMID: 30239574 DOI: 10.1093/bioinformatics/bty810] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 12/16/2022] Open
Abstract
SUMMARY There is an increasing interest in joint analysis of multiple phenotypes for genome-wide association studies (GWASs) based on the following reasons. First, cohorts usually collect multiple phenotypes and complex diseases are usually measured by multiple correlated intermediate phenotypes. Second, jointly analyzing multiple phenotypes may increase statistical power for detecting genetic variants associated with complex diseases. Third, there is increasing evidence showing that pleiotropy is a widespread phenomenon in complex diseases. In this paper, we develop a clustering linear combination (CLC) method to jointly analyze multiple phenotypes for GWASs. In the CLC method, we first cluster individual statistics into positively correlated clusters and then, combine the individual statistics linearly within each cluster and combine the between-cluster terms in a quadratic form. CLC is not only robust to different signs of the means of individual statistics, but also reduce the degrees of freedom of the test statistic. We also theoretically prove that if we can cluster the individual statistics correctly, CLC is the most powerful test among all tests with certain quadratic forms. Our simulation results show that CLC is either the most powerful test or has similar power to the most powerful test among the tests we compared, and CLC is much more powerful than other tests when effect sizes align with inferred clusters. We also evaluate the performance of CLC through a real case study. AVAILABILITY AND IMPLEMENTATION R code for implementing our method is available at http://www.math.mtu.edu/∼shuzhang/software.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA
| | - Zhenchuan Wang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA
| | - Xiao Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA
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8
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Li X, Zhang S, Sha Q. Joint analysis of multiple phenotypes using a clustering linear combination method based on hierarchical clustering. Genet Epidemiol 2020; 44:67-78. [PMID: 31541490 PMCID: PMC7480017 DOI: 10.1002/gepi.22263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/19/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
Abstract
Emerging evidence suggests that a genetic variant can affect multiple phenotypes, especially in complex human diseases. Therefore, joint analysis of multiple phenotypes may offer new insights into disease etiology. Recently, many statistical methods have been developed for joint analysis of multiple phenotypes, including the clustering linear combination (CLC) method. Due to the unknown number of clusters for a given data, a simulation procedure must be used to evaluate the p-value of the final test statistic of CLC. This makes the CLC method computationally demanding. In this paper, we use a stopping criterion to determine the number of clusters in the CLC method. We have named our method, hierarchical clustering CLC (HCLC). HCLC has an asymptotic distribution, which is very computationally efficient and makes it applicable for genome-wide association studies. Extensive simulations together with the COPDGene data analysis have been used to assess the type I error rates and power of our proposed method. Our simulation results demonstrate that the type I error rates of HCLC are effectively controlled in different realistic settings. HCLC either outperforms all other methods or has statistical power that is very close to the most powerful method with which it has been compared.
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Affiliation(s)
- Xueling Li
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
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9
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Joint Analysis of Multiple Phenotypes in Association Studies based on Cross-Validation Prediction Error. Sci Rep 2019; 9:1073. [PMID: 30705317 PMCID: PMC6355816 DOI: 10.1038/s41598-018-37538-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 11/19/2018] [Indexed: 01/28/2023] Open
Abstract
In genome-wide association studies (GWAS), joint analysis of multiple phenotypes could have increased statistical power over analyzing each phenotype individually to identify genetic variants that are associated with complex diseases. With this motivation, several statistical methods that jointly analyze multiple phenotypes have been developed, such as O’Brien’s method, Trait-based Association Test that uses Extended Simes procedure (TATES), multivariate analysis of variance (MANOVA), and joint model of multiple phenotypes (MultiPhen). However, the performance of these methods under a wide range of scenarios is not consistent: one test may be powerful in some situations, but not in the others. Thus, one challenge in joint analysis of multiple phenotypes is to construct a test that could maintain good performance across different scenarios. In this article, we develop a novel statistical method to test associations between a genetic variant and Multiple Phenotypes based on cross-validation Prediction Error (MultP-PE). Extensive simulations are conducted to evaluate the type I error rates and to compare the power performance of MultP-PE with various existing methods. The simulation studies show that MultP-PE controls type I error rates very well and has consistently higher power than the tests we compared in all simulation scenarios. We conclude with the recommendation for the use of MultP-PE for its good performance in association studies with multiple phenotypes.
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Nedeljkovic I, Carnero-Montoro E, Lahousse L, van der Plaat DA, de Jong K, Vonk JM, van Diemen CC, Faiz A, van den Berge M, Obeidat M, Bossé Y, Nickle DC, Consortium B, Uitterlinden AG, van Meurs JJB, Stricker BCH, Brusselle GG, Postma DS, Boezen HM, van Duijn CM, Amin N. Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics. Eur J Hum Genet 2018; 26:709-722. [PMID: 29422661 PMCID: PMC5945654 DOI: 10.1038/s41431-017-0089-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 11/06/2017] [Accepted: 12/19/2017] [Indexed: 12/25/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a major health burden in adults and cigarette smoking is considered the most important environmental risk factor of COPD. Chromosome 15q25.1 locus is associated with both COPD and smoking. Our study aims at understanding the mechanism underlying the association of chromosome 15q25.1 with COPD through epigenetic and transcriptional variation in a population-based setting. To assess if COPD-associated variants in 15q25.1 are methylation quantitative trait loci, epigenome-wide association analysis of four genetic variants, previously associated with COPD (P < 5 × 10-8) in the 15q25.1 locus (rs12914385:C>T-CHRNA3, rs8034191:T>C-HYKK, rs13180:C>T-IREB2 and rs8042238:C>T-IREB2), was performed in the Rotterdam study (n = 1489). All four variants were significantly associated (P < 1.4 × 10-6) with blood DNA methylation of IREB2, CHRNA3 and PSMA4, of which two, including IREB2 and PSMA4, were also differentially methylated in COPD cases and controls (P < 0.04). Further additive and multiplicative effects of smoking were evaluated and no significant effect was observed. To evaluate if these four genetic variants are expression quantitative trait loci, transcriptome-wide association analysis was performed in 1087 lung samples. All four variants were also significantly associated with differential expression of the IREB2 3'UTR in lung tissues (P < 5.4 × 10-95). We conclude that regulatory mechanisms affecting the expression of IREB2 gene, such as DNA methylation, may explain the association between genetic variants in chromosome 15q25.1 and COPD, largely independent of smoking.
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Affiliation(s)
- Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Elena Carnero-Montoro
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Pfizer University of Granada, GENYO Centre for Genomics and Oncological Research, Andalusian Region Government, Granada, Spain
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Bioanalysis Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
| | - Diana A van der Plaat
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Kim de Jong
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec, QC, Canada
| | - David C Nickle
- Genetics and Pharmacogenomics (GpGx), Merck Research Laboratories, Seattle, WA, USA
| | | | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Joyce J B van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Bruno C H Stricker
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Bioanalysis Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
- Department of Pulmonology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands.
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11
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Liang X, Sha Q, Rho Y, Zhang S. A hierarchical clustering method for dimension reduction in joint analysis of multiple phenotypes. Genet Epidemiol 2018; 42:344-353. [PMID: 29682782 DOI: 10.1002/gepi.22124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/01/2018] [Accepted: 02/19/2018] [Indexed: 12/25/2022]
Abstract
Genome-wide association studies (GWAS) have become a very effective research tool to identify genetic variants of underlying various complex diseases. In spite of the success of GWAS in identifying thousands of reproducible associations between genetic variants and complex disease, in general, the association between genetic variants and a single phenotype is usually weak. It is increasingly recognized that joint analysis of multiple phenotypes can be potentially more powerful than the univariate analysis, and can shed new light on underlying biological mechanisms of complex diseases. In this paper, we develop a novel variable reduction method using hierarchical clustering method (HCM) for joint analysis of multiple phenotypes in association studies. The proposed method involves two steps. The first step applies a dimension reduction technique by using a representative phenotype for each cluster of phenotypes. Then, existing methods are used in the second step to test the association between genetic variants and the representative phenotypes rather than the individual phenotypes. We perform extensive simulation studies to compare the powers of multivariate analysis of variance (MANOVA), joint model of multiple phenotypes (MultiPhen), and trait-based association test that uses extended simes procedure (TATES) using HCM with those of without using HCM. Our simulation studies show that using HCM is more powerful than without using HCM in most scenarios. We also illustrate the usefulness of using HCM by analyzing a whole-genome genotyping data from a lung function study.
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Affiliation(s)
- Xiaoyu Liang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Yeonwoo Rho
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
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12
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Zhu H, Zhang S, Sha Q. A novel method to test associations between a weighted combination of phenotypes and genetic variants. PLoS One 2018; 13:e0190788. [PMID: 29329304 PMCID: PMC5766098 DOI: 10.1371/journal.pone.0190788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
Many complex diseases like diabetes, hypertension, metabolic syndrome, et cetera, are measured by multiple correlated phenotypes. However, most genome-wide association studies (GWAS) focus on one phenotype of interest or study multiple phenotypes separately for identifying genetic variants associated with complex diseases. Analyzing one phenotype or the related phenotypes separately may lose power due to ignoring the information obtained by combining phenotypes, such as the correlation between phenotypes. In order to increase statistical power to detect genetic variants associated with complex diseases, we develop a novel method to test a weighted combination of multiple phenotypes (WCmulP). We perform extensive simulation studies as well as real data (COPDGene) analysis to evaluate the performance of the proposed method. Our simulation results show that WCmulP has correct type I error rates and is either the most powerful test or comparable to the most powerful test among the methods we compared. WCmulP also has an outstanding performance for identifying single-nucleotide polymorphisms (SNPs) associated with COPD-related phenotypes.
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Affiliation(s)
- Huanhuan Zhu
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
- * E-mail:
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Sun Y, Li J, Zheng C, Zhou B. Study on polymorphisms in CHRNA5/CHRNA3/CHRNB4 gene cluster and the associated with the risk of non-small cell lung cancer. Oncotarget 2018; 9:2435-2444. [PMID: 29416783 PMCID: PMC5788651 DOI: 10.18632/oncotarget.23459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 12/11/2017] [Indexed: 01/26/2023] Open
Abstract
CHRNA5/CHRNA3/CHRNB4 gene cluster is located on chromosome 15q25.1 and was reported to be associated with risk of lung cancer. So far, the effect of three single nucleotide polymorphisms rs6495309, rs8040868, rs1948 in this gene cluster was unclear about lung cancer risk. The aim of the present study was to evaluate the associations of rs6495309, rs8040868, rs1948 polymorphism, smoking exposure and the interaction with non-small cell lung cancer risk in Chinese population. In this hospital-based case-control study, 306 lung cancer patients and 306 cancer-free controls were interviewed to collect demographic data and exposure status of smoking, and then donate 2ml venous blood which was used to be genotyped by Taqman allelic discrimination method. Our study found that subjects carrying rs1948 CT genotype stated to be a risk factor in Chinese Han population (adjusted OR = 1.594, 95% CI = 1.066-2.383, P = 0.023) and in non-smoking population (adjusted OR = 1.896, 95%CI = 1.069-3.362, P = 0.029). rs8040868 CC genotype indicated a higher risk for lung cancer in non-smokers in a recessive model (adjusted OR = 2.496, 95%CI = 1.044-5.965, P = 0.040) and in age-based stratified analysis (age <= 60, adjusted OR = 4.213, 95%CI = 1.062-16.708, P = 0.041). All smoking interaction were positive in the multiplicative interaction of the SNPs and smoking status (-/+) compared with recessive model. Overall, these finding suggested that rs1948(C > T) and rs8040868(T > C) could be meaningful as genetic markers for lung cancer risk in Chinese Han population.
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Affiliation(s)
- Yiting Sun
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China
- First Clinical College, China Medical University, Shenyang, China
| | - Jiaye Li
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China
- First Clinical College, China Medical University, Shenyang, China
| | - Chang Zheng
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Baosen Zhou
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
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Simchovitz A, Heneka MT, Soreq H. Personalized genetics of the cholinergic blockade of neuroinflammation. J Neurochem 2017; 142 Suppl 2:178-187. [PMID: 28326544 PMCID: PMC5600134 DOI: 10.1111/jnc.13928] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/27/2016] [Accepted: 12/05/2016] [Indexed: 01/09/2023]
Abstract
Acetylcholine signaling is essential for cognitive functioning and blocks inflammation. To maintain homeostasis, cholinergic signaling is subjected to multi‐leveled and bidirectional regulation by both proteins and non‐coding microRNAs (‘CholinomiRs’). CholinomiRs coordinate the cognitive and inflammatory aspects of cholinergic signaling by targeting major cholinergic transcripts including the acetylcholine hydrolyzing enzyme acetylcholinesterase (AChE). Notably, AChE inhibitors are the only currently approved line of treatment for Alzheimer's disease patients. Since cholinergic signaling blocks neuroinflammation which is inherent to Alzheimer's disease, genomic changes modifying AChE's properties and its susceptibility to inhibitors and/or to CholinomiRs regulation may affect the levels and properties of inflammasome components such as NLRP3. This calls for genomic‐based medicine approaches based on genotyping of both coding and non‐coding single nucleotide polymorphisms (SNPs) in the genes involved in cholinergic signaling. An example is a SNP in a recognition element for the primate‐specific microRNA‐608 within the 3′ untranslated region of the AChE transcript. Carriers of the minor allele of that SNP present massively elevated brain AChE levels, increased trait anxiety and inflammation, accompanied by perturbed CholinomiR‐608 regulatory networks and elevated prefrontal activity under exposure to stressful insults. Several additional SNPs in the AChE and other cholinergic genes await further studies, and might likewise involve different CholinomiRs and pathways including those modulating the initiation and progression of neurodegenerative diseases. CholinomiRs regulation of the cholinergic system thus merits in‐depth interrogation and is likely to lead to personalized medicine approaches for achieving better homeostasis in health and disease. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms. ![]()
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Affiliation(s)
- Alon Simchovitz
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | | | - Hermona Soreq
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
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15
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Genetic susceptibility variants for lung cancer: replication study and assessment as expression quantitative trait loci. Sci Rep 2017; 7:42185. [PMID: 28181565 PMCID: PMC5299838 DOI: 10.1038/srep42185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival. Five of these SNPs acted as cis-eQTLs, being associated with the transcription of IREB2 (rs2568494, rs16969968, rs11634351, rs6495309), PSMA4 (rs6495309) and ERCC1 (rs735482), out of 10,821 genes analyzed in lung. For these three genes, we obtained experimental evidence of differential allelic expression in lung tissue, pointing to the existence of in-cis genomic variants that regulate their transcription. These results suggest that these SNPs exert their effects on cancer risk/outcome through the modulation of mRNA levels of their target genes.
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16
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An Adaptive Fisher's Combination Method for Joint Analysis of Multiple Phenotypes in Association Studies. Sci Rep 2016; 6:34323. [PMID: 27694844 PMCID: PMC5046106 DOI: 10.1038/srep34323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022] Open
Abstract
Currently, the analyses of most genome-wide association studies (GWAS) have been performed on a single phenotype. There is increasing evidence showing that pleiotropy is a widespread phenomenon in complex diseases. Therefore, using only one single phenotype may lose statistical power to identify the underlying genetic mechanism. There is an increasing need to develop and apply powerful statistical tests to detect association between multiple phenotypes and a genetic variant. In this paper, we develop an Adaptive Fisher’s Combination (AFC) method for joint analysis of multiple phenotypes in association studies. The AFC method combines p-values obtained in standard univariate GWAS by using the optimal number of p-values which is determined by the data. We perform extensive simulations to evaluate the performance of the AFC method and compare the power of our method with the powers of TATES, Tippett’s method, Fisher’s combination test, MANOVA, MultiPhen, and SUMSCORE. Our simulation studies show that the proposed method has correct type I error rates and is either the most powerful test or comparable with the most powerful test. Finally, we illustrate our proposed methodology by analyzing whole-genome genotyping data from a lung function study.
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Zhao Z, Peng F, Zhou Y, Hu G, He H, He F, Zou W, Zhao Z, Li B, Ran P. Exon sequencing identifies a novelCHRNA3-CHRNA5-CHRNB4variant that increases the risk for chronic obstructive pulmonary disease. Respirology 2015; 20:790-8. [PMID: 25891420 DOI: 10.1111/resp.12539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/28/2015] [Accepted: 02/16/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Zhuxiang Zhao
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
- First Affiliated Municipal Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Fang Peng
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Yumin Zhou
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Guoping Hu
- Third Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Hua He
- First Affiliated Municipal Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Fang He
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Weifeng Zou
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Ziwen Zhao
- First Affiliated Municipal Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Bing Li
- Research Center of Experiment Medicine; Guangzhou Medical University; Guangzhou Guangdong China
| | - Pixin Ran
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
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Adelian R, Jamali J, Zare N, Ayatollahi SMT, Pooladfar GR, Roustaei N. Comparison of Cox's Regression Model and Parametric Models in Evaluating the Prognostic Factors for Survival after Liver Transplantation in Shiraz during 2000-2012. Int J Organ Transplant Med 2015; 6:119-25. [PMID: 26306158 PMCID: PMC4545306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Identification of the prognostic factors for survival in patients with liver transplantation is challengeable. Various methods of survival analysis have provided different, sometimes contradictory, results from the same data. OBJECTIVE To compare Cox's regression model with parametric models for determining the independent factors for predicting adults' and pediatrics' survival after liver transplantation. METHOD This study was conducted on 183 pediatric patients and 346 adults underwent liver transplantation in Namazi Hospital, Shiraz, southern Iran. The study population included all patients undergoing liver transplantation from 2000 to 2012. The prognostic factors sex, age, Child class, initial diagnosis of the liver disease, PELD/MELD score, and pre-operative laboratory markers were selected for survival analysis. RESULT Among 529 patients, 346 (64.5%) were adult and 183 (34.6%) were pediatric cases. Overall, the lognormal distribution was the best-fitting model for adult and pediatric patients. Age in adults (HR=1.16, p<0.05) and weight (HR=2.68, p<0.01) and Child class B (HR=2.12, p<0.05) in pediatric patients were the most important factors for prediction of survival after liver transplantation. Adult patients younger than the mean age and pediatric patients weighing above the mean and Child class A (compared to those with classes B or C) had better survival. CONCLUSION Parametric regression model is a good alternative for the Cox's regression model.
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Affiliation(s)
- R. Adelian
- Department of Pediatrics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - J. Jamali
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - N. Zare
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - S. M. T. Ayatollahi
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - G. R. Pooladfar
- Department of Pediatrics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - N. Roustaei
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran,Correspondence: Narges Roustaei, Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Zand Blvd, Shiraz, Iran ,E-mail:
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