Novel Type 2-high gene clusters associated with corticosteroid sensitivity in COPD

Faiz, A.; Pavlidis, S.; Kuo, C.-H. S.; Rowe, A.; Hiemstra, P. S.; Timens, W.; Berg, M.; Wisman, M.; Guo, Y.; Djukanovic, R.; Sterk, P. J.; Nawijn, M. C.; Adcock, I. M.; Chung, K. F.; van den Berge, M.

doi:10.1101/2020.01.22.912022

bioRxiv · 10.1101/2020.01.22.912022

Novel Type 2-high gene clusters associated with corticosteroid sensitivity in COPD

Faiz, A.·Pavlidis, S.·Kuo, C.-H. S.·Rowe, A.·Hiemstra, P. S.·Timens, W.·Berg, M.·Wisman, M.·Guo, Y.·Djukanovic, R.·Sterk, P. J.·Nawijn, M. C.·Adcock, I. M.·Chung, K. F.·van den Berge, M.

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Abstract

RationaleSevere asthma and COPD share common pathophysiologic traits such as relative corticosteroid insensitivity. We recently published three transcriptome-associated clusters (TACs) using hierarchical analysis of the sputum transcriptome in asthmatics from the U-BIOPRED cohort with one Type 2-high signature (TAC1) and 2 Type 2-low signatures. ObjectiveWe examined whether gene-expression signatures obtained in asthma can be used to identify the subgroup of COPD patients with steroid sensitivity. MethodsUsing gene set variation analysis (GSVA), we examined the distribution and enrichment scores (ES) of the 3 TACs in the transcriptome of bronchial biopsies from 46 patients who participated in the GLUCOLD COPD study that received 30 months of treatment with inhaled corticosteroids (ICS) with and without an added long-acting {beta}-agonist (LABA). The identified signatures were then associated with longitudinal clinical variables after treatment. Measurements and main resultsBronchial biopsies in COPD patients at baseline showed a wide range of expression of the 3 TACs. After ICS{+/-}LABA treatment, the ES of TAC1 was significantly reduced at 30 months, but those of TAC2 and TAC3 were unaffected. A corticosteroid-sensitive TAC1 (sub)signature was developed from the TAC1 ICS-responsive genes. This signature consisted of mast cell-specific genes identified by single-cell RNA-seq and positively correlated with bronchial biopsy mast cell numbers following ICS{+/-}LABA. Baseline levels of gene transcription predicted change in FEV1 %predicted following 30-month ICS{+/-}LABA. ConclusionsSputum-derived transcriptomic signatures from an asthma cohort can be recapitulated in bronchial biopsies of COPD patients and identified airway wall mast cells as a predictor of those COPD patients who will benefit from inhaled corticosteroids.

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Faiz, A., Pavlidis, S., Kuo, C.-H. S., Rowe, A., Hiemstra, P. S., Timens, W., Berg, M., Wisman, M., Guo, Y., Djukanovic, R., Sterk, P. J., Nawijn, M. C., Adcock, I. M., Chung, K. F., van den Berge, M.. 2020-01-23. Novel Type 2-high gene clusters associated with corticosteroid sensitivity in COPD. https://doi.org/10.1101/2020.01.22.912022

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