Identification and validation of transcripts by RNA-sequencing lung tissue from patients with Idiopathics Pulmonary Fibrosis

Short Communication - Research and Reports in Pulmonology (2021) Volume 2, Issue 2

Transcriptomic profiling in IPF has largely been performed by microarrays using RNA obtained from

whole lung lysates obtained from fresh frozen tissues. These studies have provided significant mechanistic

insights regarding IPF pathogenesis, and have largely impacted the field of lung fibrosis. However, these

studies are limited because acquisition of fresh frozen tissues is only available in highly specialized

academic centers with tissue banking facilities. Thus, the majority of studies contain mostly tissues

explanted from patients with IPF at the time of biopsy, and studies containing tissues obtained from

diagnostic biopsies are limited. Additionally, it is nearly impossible to assess the lung morphology on

frozen tissue, thus the studies utilizing fresh frozen samples depend on histological assessment of adjacent

tissue which may or may not contain the exact same pathology. While transcriptomic data generated

from different dissections within a single lobe of the lung are highly correlated, and that transcriptomic

data correlates well with UIP pattern itself the lack of visual confirmation of the histology of the region

profiled is still considered a limitation RNA isolated from Formalin-Fixed Paraffin Embedded FFPE

tissues is partially degraded, thus transcriptomic analysis of FFPE tissues was considered challenging.

Several recent studies demonstrated that transcriptomic analysis of FFPE tissues using microarrays was

possible, was nearly comparable to fresh frozen tissues but still had significant limitations. In contrast to

microarrays, next generation RNA Sequencing (RNA-Seq) allows for relatively unbiased measurements

of expression levels across the entire length of a transcript and its level of expression, and therefore may

be more suitable for sequencing of partially degraded FFPE RNA. Transcriptomic analysis of FFPE

tissues by RNA-Seq demonstrates high concordance to RNA-Seq data produced from matching fresh

frozen tissues. Because formalin fixation and paraffin embedding are routinely done on all samples from

clinically indicated lung biopsies, optimization of a method to perform genome scale transcript profiling

of archived FFPE tissues will greatly enhance the access to IPF lungs. In this study, we sought to determine

whether whole transcriptomic analysis of RNA isolated from FFPE biopsies by RNA-Seq was feasible

in IPF, and whether the results are comparable to those obtained from gene expression microarrays. To

test our hypothesis, we isolated RNA from FFPE lung biopsies of IPF individuals and controls, generated

RNA-Seq expression data and compared it to publically available microarray array data previously

generated by us from fresh frozen IPF lung tissues Our study demonstrates high concordance in IPF

relevant genes and pathways between RNA-Seq and microarrays of un-paired tissues from patients

evaluated in different cohorts, suggesting that RNA-Seq from FFPE tissues could be considered an

acceptable technique for transcriptomic profiling in IPF.

Author(s): Muhammed Amir Essibayi,