COPD is accompanied by coordinated transcriptional perturbation in the quadriceps affecting the mitochondria and ECM

In this experiment we catalogue transcriptional changes accompanying COPD in the quadriceps. We measure global gene transcription in the quadriceps using Affymetrix HuGene 1.1 ST arrays in an unselected cohort of 79 stable COPD patients in secondary care and 16 healthy age-and gender-matched controls. We identified 1,826 differentially expressed transcript clusters, comprising 6 modules of co-expressed genes, which differentially associate with clinical and immunological features of COPD. RNA samples derived from 95 quadriceps biopsy specimens were analysed as part of this study (79 COPD, 16 healthy). Differential expression between healthy and COPD samples was estimated using Limma (3.22.7). P-values were adjusted for multiple testing using the Benjamini & Hochberg method to control the False Discovery Rate below 5%. Patterns of transcriptional co-ordination were sought amongst differentially expressed genes through Weighted Gene Co-expression Network Analysis (WGCNA).