miRNA Expression in Fibroblastic Foci within Idiopathic Pulmonary Fibrosis Lungs Reveals Novel Disease-Relevant Pathways
Laura Sabater, J Gossart, Inmaculada Hernández, Daniel Rico, Andy Blanchard, Lee A. Borthwick, Andrew J. Fisher, Joaquim Majó Fernández, Kasim Jiwa, Amy Collins, Giuseppe Abbate, Fiona Oakley, Derek A. Mann, Jelena Mann
Abstract
miRNAs are 22 nucleotides long and belong to a class of noncoding RNAs that plays an important role in regulating gene expression at a post-transcriptional level. Studies show aberrant levels of miRNAs to be associated with profibrotic processes in idiopathic pulmonary fibrosis (IPF). However, most of these studies used whole IPF tissue or in vitro monocultures in which fibrosis was artificially induced. The current study used laser microdissection to collect fibroblastic foci (FF), the key pathologic lesion in IPF, isolated miRNAs, and compared their expression levels with those found in whole IPF lung tissue and/or in vitro cultured fibroblast from IPF or normal lungs. Sequencing libraries were generated, and data generated were bioinformatically analyzed. A total of 18 miRNAs were significantly overexpressed in FF tissue when compared with whole IPF tissue. Of those, 15 were unique to FF. Comparison of FF with cultured IPF fibroblasts also revealed differences in miRNA composition that impacted several signaling pathways. The miRNA composition of FF is both overlapping and distinct from that of whole IPF tissue or cultured IPF fibroblasts and highlights the importance of characterizing FF biology as a phenotypically and functionally discrete tissue microenvironment. miRNAs are 22 nucleotides long and belong to a class of noncoding RNAs that plays an important role in regulating gene expression at a post-transcriptional level. Studies show aberrant levels of miRNAs to be associated with profibrotic processes in idiopathic pulmonary fibrosis (IPF). However, most of these studies used whole IPF tissue or in vitro monocultures in which fibrosis was artificially induced. The current study used laser microdissection to collect fibroblastic foci (FF), the key pathologic lesion in IPF, isolated miRNAs, and compared their expression levels with those found in whole IPF lung tissue and/or in vitro cultured fibroblast from IPF or normal lungs. Sequencing libraries were generated, and data generated were bioinformatically analyzed. A total of 18 miRNAs were significantly overexpressed in FF tissue when compared with whole IPF tissue. Of those, 15 were unique to FF. Comparison of FF with cultured IPF fibroblasts also revealed differences in miRNA composition that impacted several signaling pathways. The miRNA composition of FF is both overlapping and distinct from that of whole IPF tissue or cultured IPF fibroblasts and highlights the importance of characterizing FF biology as a phenotypically and functionally discrete tissue microenvironment. Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic lung disease characterized by a restrictive ventilatory defect and impaired gas transfer due to deposition of fibrotic tissue in the lung interstitium. The incidence of IPF has been reported as ranging from 2.8 to 18 cases per 100,000.1Hutchinson J. Fogarty A. Hubbard R. McKeever T. Global incidence and mortality of idiopathic pulmonary fibrosis: a systematic review.Eur Respir J. 2015; 46: 795-806Crossref PubMed Scopus (543) Google Scholar With 6000 new patients/year presenting and a disease prevalence of approximately 32,000 in the United Kingdom (British Lung Foundation UK IPF Statistics, https://www.blf.org.uk/support-for-you/idiopathic-pulmonary-fibrosis-ipf/statistics, last accessed February 2, 2022), it appears to be increasing steadily. IPF has a poor prognosis, with a median survival of 2 to 4 years from diagnosis, making post-diagnosis survival worse than many cancers.2Ley B. Collard H.R. King T.E. Clinical course and prediction of survival in idiopathic pulmonary fibrosis.Am J Respir Crit Care Med. 2011; 183: 431-440Crossref PubMed Scopus (1170) Google Scholar The etiology of IPF remains unclear, but growing evidence points towards complex interactions between genetic risk factors and environmental insults on a background of age-associated predisposition as the key contributors.3Fingerlin T.E. Murphy E. Zhang W. Peljto A.L. Brown K.K. Steele M.P. et al.Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.Nat Genet. 2013; 45: 613-620Crossref PubMed Scopus (553) Google Scholar, 4Molyneaux P.L. Cox M.J. Willis-Owen S.A.G. Mallia P. Russell K.E. Russell A.M. Murphy E. Johnston S.L. Schwartz D.A. Wells A.U. Cookson W.O.C. Maher T.M. Moffatt M.F. The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis.Am J Respir Crit Care Med. 2014; 190: 906-913Crossref PubMed Scopus (377) Google Scholar, 5Alder J.K. 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A phase 3 trial of pirfenidone in patients with idiopathic pulmonary fibrosis.N Engl J Med. 2014; 370: 2083-2092Crossref PubMed Scopus (2597) Google Scholar,7Richeldi L. du Bois R.M. Raghu G. Azuma A. Brown K.K. Costabel U. Cottin V. Flaherty K.R. Hansell D.M. Inoue Y. Kim D.S. Kolb M. Nicholson A.G. Noble P.W. Selman M. Taniguchi H. Brun M. Le Maulf F. Girard M. Stowasser S. Schlenker-Herceg R. Disse B. Collard H.R. Efficacy and safety of nintedanib in idiopathic pulmonary fibrosis.N Engl J Med. 2014; 370: 2071-2082Crossref PubMed Scopus (2939) Google Scholar Lung transplantation is the only option that offers hope for long-term survival, but it is only available to highly selected individuals.8Kistler K.D. Nalysnyk L. Rotella P. Esser D. Lung transplantation in idiopathic pulmonary fibrosis: a systematic review of the literature.BMC Pulm Med. 2014; 14: 139Crossref PubMed Scopus (99) Google Scholar The pathology of IPF is characterized by disruption of normal lung architecture due to deposition of excessive collagen and extracellular matrix in the alveolar walls, and of of fibroblasts and which are as fibroblastic foci on of A. P. F. G. M. S. A. J.A. P.M. Hansell D.M. Nicholson A.G. I. Brown K.K. L. of fibroblast foci in idiopathic pulmonary PubMed Google interactions in pulmonary Respir Crit Care Med. PubMed Scopus Google Scholar The foci discrete of lung and and are of importance to the progression of of the that the the FF in the lung to and excessive extracellular matrix is to to new that halt or reverse the disease miRNAs are noncoding RNAs that gene expression in a post-transcriptional to the of their with by the and a miRNA expression levels several and T. 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