Buechler, M. B. et al. Cross-tissue organization of the fibroblast lineage. Nature 593, 575–579 (2021).
Tsukui, T. et al. Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis. Nat. Commun. 11, 1920 (2020).
Plikus, M. V. et al. Fibroblasts: origins, definitions, and functions in health and disease. Cell 184, 3852–3872 (2021).
Hinz, B. & Lagares, D. Evasion of apoptosis by myofibroblasts: a hallmark of fibrotic diseases. Nat. Rev. Rheumatol. 16, 11–31 (2020).
Henderson, N. C., Rieder, F. & Wynn, T. A. Fibrosis: from mechanisms to medicines. Nature 587, 555–566 (2020).
Ruiz-Villalba, A. et al. Single-cell RNA sequencing analysis reveals a crucial role for CTHRC1 (collagen triple helix repeat containing 1) cardiac fibroblasts after myocardial infarction. Circulation 142, 1831–1847 (2020).
Melms, J. C. et al. A molecular single-cell lung atlas of lethal COVID-19. Nature 595, 114–119 (2021).
Pakshir, P. et al. The myofibroblast at a glance. J. Cell Sci. 133, jcs227900 (2020).
Friedman, S. L., Sheppard, D., Duffield, J. S. & Violette, S. Therapy for fibrotic diseases: nearing the starting line. Sci. Transl. Med. 5, 167sr1 (2013).
Narvaez del Pilar, O., Gacha Garay, M. J. & Chen, J. Three-axis classification of mouse lung mesenchymal cells reveals two populations of myofibroblasts. Development 149, dev200081 (2022).
McGowan, S. E. & Torday, J. S. The pulmonary lipofibroblast (lipid interstitial cell) and its contributions to alveolar development. Annu. Rev. Physiol. 59, 43–62 (1997).
Barkauskas, C. E. et al. Type 2 alveolar cells are stem cells in adult lung. J. Clin. Invest. 123, 3025–3036 (2013).
Hasegawa, K. et al. Fraction of MHCII and EpCAM expression characterizes distal lung epithelial cells for alveolar type 2 cell isolation. Respir. Res. 18, 150 (2017).
Gurczynski, S. J. & Moore, B. B. IL-17 in the lung: the good, the bad, and the ugly. Am. J. Physiol. 314, L6–L16 (2018).
Croft, A. P. et al. Distinct fibroblast subsets drive inflammation and damage in arthritis. Nature 570, 246–251 (2019).
Öhlund, D. et al. Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer. J. Exp. Med. 214, 579–596 (2017).
Boyd, D. F. et al. Exuberant fibroblast activity compromises lung function via ADAMTS4. Nature 587, 466–471 (2020).
Korsunsky, I. et al. Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases. Med 3, 481–518.e14 (2022).
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
Liu, W. et al. Antiflammin-1 attenuates bleomycin-induced pulmonary fibrosis in mice. Respir. Res. 14, 101 (2013).
Strobel, B. et al. Time and phenotype-dependent transcriptome analysis in AAV-TGFβ1 and Bleomycin-induced lung fibrosis models. Sci. Rep. 12, 12190 (2022).
Elyada, E. et al. Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Cancer Discov. 9, 1102–1123 (2019).
Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci. Adv. 6, eaba1983 (2020).
Habermann, A. C. et al. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci. Adv. 6, eaba1972 (2020).
Katzenstein, A.-L. A. & Myers, J. L. Idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 157, 1301–1315 (1998).
Barratt, S. L., Creamer, A., Hayton, C. & Chaudhuri, N. Idiopathic pulmonary fibrosis (IPF): an overview. J. Clin. Med. 7, 201 (2018).
Kuhn, C. et al. An immunohistochemical study of architectural remodeling and connective tissue synthesis in pulmonary fibrosis. Am. Rev. Respir. Dis. 140, 1693–1703 (1989).
Massagué, J. & Sheppard, D. TGF-β signaling in health and disease. Cell 186, 4007–4037 (2023).
Valenzi, E. et al. Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease. Ann. Rheum. Dis. 78, 1379–1387 (2019).
Dominguez, C. X. et al. Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy. Cancer Discov. 10, 232–253 (2020).
Binks, A. P., Beyer, M., Miller, R. & LeClair, R. J. Cthrc1 lowers pulmonary collagen associated with bleomycin‐induced fibrosis and protects lung function. Physiol. Rep. 5, e13115 (2017).
Li, J. et al. Autocrine CTHRC1 activates hepatic stellate cells and promotes liver fibrosis by activating TGF-β signaling. EBioMedicine 40, 43–55 (2019).
Voehringer, D., Liang, H.-E. & Locksley, R. M. Homeostasis and effector function of lymphopenia-induced ‘memory-like’ T cells in constitutively T cell-depleted mice. J. Immunol. 180, 4742–4753 (2008).
Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).
Yata, Y. et al. DNase I-hypersensitive sites enhance alpha1(I) collagen gene expression in hepatic stellate cells. Hepatology 37, 267–276 (2003).
Redente, E. F. et al. Age and sex dimorphisms contribute to the severity of bleomycin-induced lung injury and fibrosis. Am. J. Physiol. 301, L510–L518 (2011).
Henderson, N. C. et al. Targeting of αv integrin identifies a core molecular pathway that regulates fibrosis in several organs. Nat. Med. 19, 1617–1624 (2013).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337.e4 (2019).
Haghverdi, L., Lun, A. T. L., Morgan, M. D. & Marioni, J. C. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat. Biotechnol. 36, 421–427 (2018).
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
Marsh, S., Salmon, M. & Hoffman, P. samuel-marsh/scCustomize: version 1.1.1. Zenodo https://doi.org/10.5281/zenodo.7534950 (2023).
Susaki, E. A. et al. Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat. Commun. 11, 1982 (2020).
Meeker, A. K., Heaphy, C. M., Davis, C. M., Roy, S. & Platz, E. A. Photochemical pre-bleaching of formalin-fixed archival prostate tissues significantly reduces autofluorescence to facilitate multiplex immunofluorescence staining. Preprint at bioRxiv https://doi.org/10.1101/2021.11.09.467916 (2021).
Crowley, G. et al. Quantitative lung morphology: semi-automated measurement of mean linear intercept. BMC Pulm. Med. 19, 206 (2019).