Diagnostic potential of genomic blood biomarkers of pulmonary fibrosis in a prospective cohort

Abstract

Fibrotic interstitial lung diseases (ILDs) result from excessive deposition of extracellular matrix (ECM) proteins in the lung, causing irreversible damage to the lung architecture. Clinical management of ILDs differs depending on the diagnosis, but differentiation between subtypes can be difficult and better clinical biomarkers are needed. In this study, we use a 166-gene NanoString assay to investigate whether there are ILD subtype-specific transcripts in whole blood. We identified one transcript, killer cell lectin like receptor 1 (KLRF1), as differentially expressed between idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated ILD (SSc-ILD), and identified two transcripts (VCAN, LTK) associated with IPF expression against other ILD subtypes. These findings were validated by examining their expression in ILD lung, with KLRF1 expression significantly higher in SSc-ILD compared to IPF and hypersensitivity pneumonitis (HP) samples. Taken together, this pilot study provides support for the use of the peripheral transcriptome in identifying diagnostic biomarkers of ILD with biological relevance.

Fig 1. Expression of KLRF1, LTK, VCAN in whole blood (log₂ RNA expression) or lung tissue microarray sections (H-Score) containing samples from patients with idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis (HP), and systemic sclerosis-associated interstitial lung disease (SSc-ILD).

Statistical significance of blood RNA expression was determined using differential expression analysis via ‘limma’ and corrected using false discovery rate (FDR), with statistical significance indicated by FDR<0.05 (***). To determine statistical significance of H-scores, a linear mixed-effects model was fitted and pairwise comparisons between diagnoses were performed and corrected for using Tukey’s post-hoc adjustment (* denotes p<0.05).

Fig 2. Histological staining of tissue microarray cores taken from donor lungs of patients with idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis (HP), and systemic sclerosis-associated interstitial lung disease (SSc-ILD).

Arrows indicate areas of positive staining.