{"doi":"10.1183/13993003.00474-2022","title":"Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity","abstract":"Background In idiopathic pulmonary fibrosis (IPF), myofibroblasts are key effectors of fibrosis and architectural distortion by excessive deposition of extracellular matrix and their acquired contractile capacity. Single-cell RNA-sequencing (scRNA-seq) has precisely defined the IPF myofibroblast transcriptome, but identifying critical transcription factor activity by this approach is imprecise. Methods We performed single-nucleus assay for transposase-accessible chromatin sequencing on explanted lungs from patients with IPF (n=3) and donor controls (n=2) and integrated this with a larger scRNA-seq dataset (10 IPF, eight controls) to identify differentially accessible chromatin regions and enriched transcription factor motifs within lung cell populations. We performed RNA-sequencing on pulmonary fibroblasts of bleomycin-injured Twist1- overexpressing COL1A2 Cre-ER mice to examine alterations in fibrosis-relevant pathways following Twist1 overexpression in collagen-producing cells. Results TWIST1, and other E-box transcription factor motifs, were significantly enriched in open chromatin of IPF myofibroblasts compared to both IPF nonmyogenic (log 2 fold change (FC) 8.909, adjusted p-value 1.82×10 −35 ) and control fibroblasts (log 2 FC 8.975, adjusted p-value 3.72×10 −28 ). TWIST1 expression was selectively upregulated in IPF myofibroblasts (log 2 FC 3.136, adjusted p-value 1.41×10 − 24 ), with two regions of TWIST1 having significantly increased accessibility in IPF myofibroblasts. Overexpression of Twist1 in COL1A2-expressing fibroblasts of bleomycin-injured mice resulted in increased collagen synthesis and upregulation of genes with enriched chromatin accessibility in IPF myofibroblasts. Conclusions Our studies utilising human multiomic single-cell analyses combined with in vivo murine disease models confirm a critical regulatory function for TWIST1 in IPF myofibroblast activity in the fibrotic lung. Understanding the global process of opening TWIST1 and other E-box transcription factor motifs that govern myofibroblast differentiation may identify new therapeutic interventions for fibrotic pulmonary diseases.","journal":"European Respiratory Journal","year":2023,"id":331056,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9505,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":821146,"name":"Harinath Bahudhanapati","orcid":null,"position":1,"is_corresponding":false},{"id":474273,"name":"Jiangning Tan","orcid":null,"position":2,"is_corresponding":false},{"id":12145,"name":"Tracy Tabib","orcid":"0000-0003-4053-988X","position":3,"is_corresponding":false},{"id":820860,"name":"Daniel I. Sullivan","orcid":"0000-0001-5277-521X","position":4,"is_corresponding":false},{"id":270743,"name":"Mehdi Nouraie","orcid":"0000-0001-7465-0581","position":5,"is_corresponding":false},{"id":270566,"name":"John Sembrat","orcid":"0000-0003-4108-803X","position":6,"is_corresponding":false},{"id":191790,"name":"Li Fan","orcid":null,"position":7,"is_corresponding":false},{"id":279535,"name":"Kong Chen","orcid":"0000-0001-6980-5454","position":8,"is_corresponding":false},{"id":279404,"name":"Silvia Liu","orcid":"0000-0002-1840-9520","position":9,"is_corresponding":false},{"id":237173,"name":"Mauricio Rojas","orcid":"0000-0001-7340-4784","position":10,"is_corresponding":false},{"id":1055470,"name":"Audrey Lafargue","orcid":"0000-0001-9551-2815","position":11,"is_corresponding":false},{"id":232233,"name":"Dean W. Felsher","orcid":"0000-0003-2496-523X","position":12,"is_corresponding":false},{"id":262587,"name":"Phuoc T. Tran","orcid":"0000-0002-0147-0376","position":13,"is_corresponding":false},{"id":352759,"name":"Daniel J. Kass","orcid":"0000-0001-6597-7830","position":14,"is_corresponding":false},{"id":7274,"name":"Robert Lafyatis","orcid":"0000-0002-9398-5034","position":15,"is_corresponding":false},{"id":270565,"name":"Eleanor Valenzi","orcid":"0000-0003-0656-6542","position":0,"is_corresponding":true}],"reference_count":48,"raw_metadata":null,"created_at":"2026-07-19T01:09:14.691473Z","pmid":"37142338","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}