Comparison of genome-wide gene expression profiling by RNA Sequencing versus microarray in bronchial biopsies of COPD patients before and after inhaled corticosteroid treatment: does it provide new insights?

Benedikt Ditz; Jeunard G Boekhoudt; Hananeh Aliee; Fabian J Theis; Martijn Nawijn; Corry-Anke Brandsma; Pieter S Hiemstra; Wim Timens; Gaik W Tew; Michele A Grimbaldeston; Margaret Neighbors; Victor Guryev; Maarten van den Berge; Alen Faiz

doi:10.1183/23120541.00104-2021

Comparison of genome-wide gene expression profiling by RNA Sequencing versus microarray in bronchial biopsies of COPD patients before and after inhaled corticosteroid treatment: does it provide new insights?

ERJ Open Res. 2021 Jun 21;7(2):00104-2021. doi: 10.1183/23120541.00104-2021. eCollection 2021 Apr.

Authors

Benedikt Ditz^{1

2

3}, Jeunard G Boekhoudt^{2

4

3}, Hananeh Aliee⁵, Fabian J Theis^{5

6}, Martijn Nawijn^{2

4}, Corry-Anke Brandsma^{2

4}, Pieter S Hiemstra⁷, Wim Timens^{2

4}, Gaik W Tew⁸, Michele A Grimbaldeston⁸, Margaret Neighbors⁸, Victor Guryev⁹, Maarten van den Berge^{1

2

10}, Alen Faiz^{1

2

11

10}

Affiliations

¹ Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
² University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands.
³ Co-first authors.
⁴ Dept of Pathology and Medical Biology, section Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
⁵ Institute of Computational Biology, Helmholtz Centre, Munich, Germany.
⁶ Dept of Mathematics, Technical University of Munich, Munich, Germany.
⁷ Dept of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands.
⁸ OMNI Biomarker Development, Genentech Inc, San Francisco, CA, USA.
⁹ European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
¹⁰ Co-senior authors.
¹¹ Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia.

Abstract

More DEGs are detected by RNA-Seq than microarrays in COPD lung biopsies and are associated with immunological pathways. Performing bulk tissue cell-type deconvolution in microarray lung samples, using the SVR method, reflects RNA-Seq results. https://bit.ly/2N8sY3s.