Timing of Blood Sample Processing Affects the Transcriptomic and Epigenomic Profiles in CD4<sup>+</sup> T-cells of Atopic Subjects
Fahd Alhamdan,
Kristina Laubhahn,
Christine Happle,
Anika Habener,
Adan C. Jirmo,
Clemens Thölken,
Raffaele Conca,
Ho-Ryun Chung,
Gesine Hansen,
Daniel P. Potaczek,
Bianca Schaub,
Ruth Grychtol,
Holger Garn
Affiliations
Fahd Alhamdan
Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, D-35043 Marburg, Germany
Kristina Laubhahn
Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig Maximilian University (LMU) of Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), D-80337 Munich, Germany
Christine Happle
Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany
Anika Habener
Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany
Adan C. Jirmo
Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany
Clemens Thölken
Institute of Medical Bioinformatics and Biostatistics, Medical Faculty, Philipps University of Marburg, D-35032 Marburg, Germany
Raffaele Conca
Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig Maximilian University (LMU) of Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), D-80337 Munich, Germany
Ho-Ryun Chung
Institute of Medical Bioinformatics and Biostatistics, Medical Faculty, Philipps University of Marburg, D-35032 Marburg, Germany
Gesine Hansen
Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany
Daniel P. Potaczek
Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, D-35043 Marburg, Germany
Bianca Schaub
Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig Maximilian University (LMU) of Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), D-80337 Munich, Germany
Ruth Grychtol
Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL) and the Cluster of Excellence RESIST (EXC 2155), D-30625 Hannover, Germany
Holger Garn
Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, D-35043 Marburg, Germany
Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+ T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4+ T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4+ T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4+ T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4+ T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended.
