Integrated spatial and single-cell transcriptomics reveal PAK kinase as a therapeutic target in fibroblastic foci and dense fibrosis of idiopathic pulmonary fibrosis
Naoaki Watanabe, Masahiro Yoshida, Yuta Hirano, Shota Fujimoto, Sachi Matsubayashi, Takashi Ishiguro, Nobumasa Takahashi, Yoshihiko Shimizu, Noboru Takayanagi, Yoshinori Kawabata, Yutaro Mori, Koji Okamoto, Shunsuke Minagawa, Kazuyoshi Kuwano, Jun Araya, Yusuke Yamamoto, Yu Fujita
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterised by progressive fibrosis of lung parenchyma. The histopathology of IPF exhibits temporal and spatial heterogeneity, including immature fibroblastic foci (FF) and densely collagenised fibrosis. FF serve as dynamic niches of pro-fibrotic fibroblasts and play a pivotal role in fibrosis progression and transition into dense fibrosis (DF). Here, we integrated single-cell RNA sequencing (scRNA-seq) with spatial transcriptomics to elucidate cellular heterogeneity and the novel cell type involved not only in FF formation, but also in DF development. We identified a novel myofibroblast population, WNT5A + CTHRC1 + myofibroblasts, enriched in both FF and DF regions, underscoring their pivotal role in fibrosis progression. Differential gene expression analysis revealed the activation of p21-activated kinase (PAK)2 in these fibrotic areas, including WNT5A + CTHRC1 + myofibroblasts. PAK inhibition significantly suppressed transforming growth factor-β-induced myofibroblast differentiation and collagen production in IPF-derived fibroblasts. Furthermore, in a bleomycin-induced lung fibrosis mouse model, intraperitoneal administration of the PAK inhibitor significantly attenuated fibrotic progression. This study highlights the therapeutic potential of PAK inhibition for IPF, particularly targeting pathogenic fibroblasts within both FF and DF regions. By leveraging spatial transcriptomics and scRNA-seq, we provide a comprehensive molecular and cellular atlas of FF and DF in IPF lung tissue, offering new insights into fibrosis progression and therapeutic intervention.