RNA-Sequencing of Transplant Stage Idiopathic Pulmonary Fibrosis Lung Reveals Unique Pathway Regulation

We report an RNA-seq based transcriptomic fingerprint of severe IPF enriched in pathways of T-cell infiltration/activation, tumor development and cholesterol homeostasis. We highlight novel splice variants, candidate targets and biomarkers in advanced IPF. All human subject sample acquisitions and experiments were conducted with the appropriate approval from the Institutional Review Board (IRB 806468, IRB 813685). Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (cat. No RS-122-2203) was used to generate sequencing libraries per manufacturer’s recommendation. Gene expression was determined via RNA-Seq libraries run on an Illumina HiSeq 2500 platform producing 75bp paired-end reads. We generated on average 40 million PE read for each sample. Reads were aligned to the Human genome (GRCh38) with the Omicsoft Sequence Aligner. Gene and transcript abundance was determined using Ensembl release 90 human gene models using RSEM. All RNA-Seq data were processed in R with Bioconductor packages. RNA-Seq samples were TMM normalized with the edgeR package. Raw data not provided due to patient privacy concerns