Abstract Rationale Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease of older adults that carries a high mortality rate. Around 50,000 new cases are diagnosed each year, and the average age of survival after diagnosis is three to five years. Three FDA-approved drugs, nintedanib, pirfenidone, and nerandomilast, are available, but these do not prevent decline in lung function or convincingly improve survival. Thus, there is an urgent need to better understand the disease’s pathophysiology to target therapeutic interventions. Specialized ribosomes, ribosomes altered to have specific functions such as the translation of certain mRNAs, are a previously unexplored area of fibroblast biology that may elucidate new therapeutic approaches. Methods We performed single cell RNA sequencing (scRNA-sequencing) on explanted lungs from patients with IPF (n = 10) and donor controls (n = 8). Analysis was performed with the R package Seurat to identify cell types, fibroblast subpopulations, differentially expressed genes, and ribosomal gene expression profiles. We quantified the differential and average expression of the components of large (RPL) and small (RPS) ribosomal subunits across fibroblast populations in both IPF and donor lungs. Results After filtering for high-quality cells, 65,179 cells were analyzed by scRNA-seq, including 6,149 mesenchymal cells (Figure 1). Three primary populations of fibroblasts (alveolar, adventitial, myofibroblast), and one minor (CXCL3hi) were defined, including myofibroblasts marked by upregulation of CTHRC1, POSTN, COMP and multiple collagens. IPF myofibroblasts had upregulated expression of several ribosomal protein L (RPL) genes, including RPL15 (adj pval 8.17 E-34), RPL10A (adj pval 7.07E-14), RPL27 (adj pval 1.80 E-20), RPL13 (adj pval 1.28E-22), and RPLP2 (adj pval 2.32 E-17), amongst others, when compared to IPF alveolar and adventitial fibroblasts. RPL10A was upregulated in total IPF versus control fibroblasts (adj pval 0.00348) as well. Amongst 51 RPL genes, 35 were upregulated in IPF myofibroblasts versus IPF alveolar and adventitial fibroblasts. In analogous comparison, 24 of 46 ribosomal protein S (RPS) genes were upregulated, with RPS2 the most upregulated (adj pval 3.86E-34). Conclusions Ribosomal protein genes are upregulated in IPF myofibroblasts, compared to both donor myofibroblasts and IPF alveolar and adventitial fibroblasts. These data support the hypothesis that ribosomal protein genes are differentially expressed across fibroblast populations in the fibrotic lung and in the transition between the normal and diseased states. These findings also provide a framework for investigating the relationship between specific ribosomal proteins, such as RPL10A, and post-transcriptional changes in sets of mRNAs that are translated by RPL10A-rich ribosomes. This abstract is funded by: NIH: 1R01HL173817-01A1 (DJK), 1K08HL16258 (EV)
Vakhshoorzadeh et al. (Fri,) studied this question.