Kenneth Wysocki1, Yvette Conley2, Sally Wenzel3. 1. School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA ken.wysocki@me.com. 2. School of Nursing and Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA. 3. School of Medicine and Director of Asthma Institute, University of Pittsburgh, Pittsburgh, PA, USA.
Abstract
BACKGROUND: Asthma is a complex heterogeneous disease process with mild, moderate, and severe classifications. Although the science of genomics has opened our understanding of the molecular underpinnings of asthma, epigenetics is emerging as a mechanism whereby the expression of disease-risk genes may be influenced by environmental exposure. OBJECTIVES: The purpose of this article is to discuss the methodology of data collection and evaluation involved in genome-wide methylation profiling (epigenomic) through presentation of data generated for a population presenting with severe asthma. METHOD: Over 14,000 gene promoter sites were analyzed for methylation status among six subjects with severe asthma and four normal controls in this pilot study. Two duplicate samples were used as technical replicates. Nonsmoking case/control subjects were chosen based on similar gender and age. Blood samples were used for DNA extraction, and methylation data were collected utilizing the Illumina Infinium HumanMethylation27BeadChip platform. RESULTS: Technical replicates were highly concordant, and statistically significant differences were found in methylation profiles between subjects with severe asthma and normal controls (p < 10(-8)), some previously reported with pulmonary function and others never before reported. After correction for multiple testing, three gene promoter regions remained statistically different: FAM181A, ZNF718, and MRI1. DISCUSSION: This research supports the internal validity of the Illumina platform in methylation analysis of DNA from stored blood samples. Although significant differences in methylation were noted between subjects with severe asthma and controls, the small sample size warrants further investigation into these results.
BACKGROUND:Asthma is a complex heterogeneous disease process with mild, moderate, and severe classifications. Although the science of genomics has opened our understanding of the molecular underpinnings of asthma, epigenetics is emerging as a mechanism whereby the expression of disease-risk genes may be influenced by environmental exposure. OBJECTIVES: The purpose of this article is to discuss the methodology of data collection and evaluation involved in genome-wide methylation profiling (epigenomic) through presentation of data generated for a population presenting with severe asthma. METHOD: Over 14,000 gene promoter sites were analyzed for methylation status among six subjects with severe asthma and four normal controls in this pilot study. Two duplicate samples were used as technical replicates. Nonsmoking case/control subjects were chosen based on similar gender and age. Blood samples were used for DNA extraction, and methylation data were collected utilizing the Illumina Infinium HumanMethylation27BeadChip platform. RESULTS: Technical replicates were highly concordant, and statistically significant differences were found in methylation profiles between subjects with severe asthma and normal controls (p < 10(-8)), some previously reported with pulmonary function and others never before reported. After correction for multiple testing, three gene promoter regions remained statistically different: FAM181A, ZNF718, and MRI1. DISCUSSION: This research supports the internal validity of the Illumina platform in methylation analysis of DNA from stored blood samples. Although significant differences in methylation were noted between subjects with severe asthma and controls, the small sample size warrants further investigation into these results.
Authors: Kim D Pruitt; Jennifer Harrow; Rachel A Harte; Craig Wallin; Mark Diekhans; Donna R Maglott; Steve Searle; Catherine M Farrell; Jane E Loveland; Barbara J Ruef; Elizabeth Hart; Marie-Marthe Suner; Melissa J Landrum; Bronwen Aken; Sarah Ayling; Robert Baertsch; Julio Fernandez-Banet; Joshua L Cherry; Val Curwen; Michael Dicuccio; Manolis Kellis; Jennifer Lee; Michael F Lin; Michael Schuster; Andrew Shkeda; Clara Amid; Garth Brown; Oksana Dukhanina; Adam Frankish; Jennifer Hart; Bonnie L Maidak; Jonathan Mudge; Michael R Murphy; Terence Murphy; Jeena Rajan; Bhanu Rajput; Lillian D Riddick; Catherine Snow; Charles Steward; David Webb; Janet A Weber; Laurens Wilming; Wenyu Wu; Ewan Birney; David Haussler; Tim Hubbard; James Ostell; Richard Durbin; David Lipman Journal: Genome Res Date: 2009-06-04 Impact factor: 9.043
Authors: Gergely Tölgyesi; Viktor Molnár; Agnes F Semsei; Petra Kiszel; Ildikó Ungvári; Péter Pócza; Zoltán Wiener; Zsolt I Komlósi; László Kunos; Gabriella Gálffy; György Losonczy; Ildikó Seres; András Falus; Csaba Szalai Journal: Int Immunol Date: 2009-06-25 Impact factor: 4.823
Authors: David Gibeon; Kannangara Batuwita; Michelle Osmond; Liam G Heaney; Chris E Brightling; Rob Niven; Adel Mansur; Rekha Chaudhuri; Christine E Bucknall; Anthony Rowe; Yike Guo; Pankaj K Bhavsar; Kian Fan Chung; Andrew Menzies-Gow Journal: Chest Date: 2013-02-01 Impact factor: 9.410
Authors: Olena Gruzieva; Cheng-Jian Xu; Paul Yousefi; Caroline Relton; Simon Kebede Merid; Carrie V Breton; Lu Gao; Heather E Volk; Jason I Feinberg; Christine Ladd-Acosta; Kelly Bakulski; Charles Auffray; Nathanaël Lemonnier; Michelle Plusquin; Akram Ghantous; Zdenko Herceg; Tim S Nawrot; Costanza Pizzi; Lorenzo Richiardi; Franca Rusconi; Paolo Vineis; Manolis Kogevinas; Janine F Felix; Liesbeth Duijts; Herman T den Dekker; Vincent W V Jaddoe; José L Ruiz; Mariona Bustamante; Josep Maria Antó; Jordi Sunyer; Martine Vrijheid; Kristine B Gutzkow; Regina Grazuleviciene; Carles Hernandez-Ferrer; Isabella Annesi-Maesano; Johanna Lepeule; Jean Bousquet; Anna Bergström; Inger Kull; Cilla Söderhäll; Juha Kere; Ulrike Gehring; Bert Brunekreef; Allan C Just; Rosalind J Wright; Cheng Peng; Diane R Gold; Itai Kloog; Dawn L DeMeo; Göran Pershagen; Gerard H Koppelman; Stephanie J London; Andrea A Baccarelli; Erik Melén Journal: Environ Health Perspect Date: 2019-05-31 Impact factor: 9.031
Authors: Stéphanie Grégoire; David Cheishvili; Mali Salmon-Divon; Sergiy Dymov; Lucas Topham; Virginie Calderon; Yoram Shir; Moshe Szyf; Laura S Stone Journal: Pain Rep Date: 2021-11-03
Authors: Mahmoud I Abdel-Aziz; Anne H Neerincx; Susanne J H Vijverberg; Simone Hashimoto; Paul Brinkman; Mario Gorenjak; Antoaneta A Toncheva; Susanne Harner; Susanne Brandstetter; Christine Wolff; Javier Perez-Garcia; Anna M Hedman; Catarina Almqvist; Paula Corcuera-Elosegui; Javier Korta-Murua; Olaia Sardón-Prado; Maria Pino-Yanes; Uroš Potočnik; Michael Kabesch; Aletta D Kraneveld; Anke H Maitland-van der Zee Journal: J Pers Med Date: 2021-05-28