Niitsu Takayuki, Kataoka Toshiaki, Fukushima Kiyoharu, Motooka Daisuke, Shichino Shigeyuki, Natsume-Kitatani Yayoi, Kitamura Hideya, Niwa Takashi, Baba Tomohisa, Okuzaki Daisuke, Kumanogoh Atsushi, Akira Shizuo, Okudela Koji, Ogura Takashi
Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.
Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan.
J Pathol. 2025 Sep;267(1):79-91. doi: 10.1002/path.6451. Epub 2025 Jul 28.
Interstitial lung diseases (ILDs) encompass a diverse group of pulmonary disorders, with progressive fibrosis leading to poor prognosis. Here we aimed to identify key molecules involved in progressive fibrosis across various ILDs, using spatial transcriptomics (ST). ST analysis (Visium) was performed on lung cryobiopsy specimens from five patients with various ILDs. Two cases, rich in young fibrotic lesions, as defined by fibroblastic foci and destructive alveolar organization, were selected for spatial high-dimensional weighted gene coexpression network analysis (hdWGCNA) to identify key gene networks with biological significance in active fibrosis. We utilized public single-cell RNA sequencing datasets of various ILDs, performed enrichment analysis and trajectory-based differential expression analysis, and quantified cell-cell communication to evaluate the involvement of the spatially extracted module in fibrosis. Immunohistochemical staining of the extracted molecules was performed. Using hdWGCNA, we identified a distinct gene module (the SM2 module) enriched in young fibrotic lesions. The SM2 module was characterized by distinct features of fibroblast activation that were represented across various lesions. Key hub genes within this module, including COL1A2, COL3A1, COL1A1, and SPARC, formed a robust coexpression network. Immunohistochemical staining showed that SPARC, a component of the SM2 module, was highly expressed in young fibrotic lesions, but not in old scarring lesions, across various ILDs. To assess the prognostic significance of SPARC immunohistochemical expression, we extended our analysis to a cohort of 71 patients with unclassifiable ILDs (uILDs), a particularly heterogeneous subtype with unclear pathogenesis and limited treatment options. Higher SPARC levels in the upper, lower, or both lung lobes in uILD were significantly associated with poor overall survival. In summary, an integrated cross-disease approach using ST revealed key gene expression patterns central to active fibrosis and successfully identified SPARC as a potentially beneficial prognostic marker. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
间质性肺疾病（ILDs）包括多种肺部疾病，进行性纤维化会导致预后不良。在此，我们旨在利用空间转录组学（ST）确定各种ILDs中参与进行性纤维化的关键分子。对5例患有各种ILDs的患者的肺冷冻活检标本进行了ST分析（Visium）。选择了2例富含年轻纤维化病变的病例（根据成纤维细胞灶和破坏性肺泡结构定义）进行空间高维加权基因共表达网络分析（hdWGCNA），以识别在活动性纤维化中具有生物学意义的关键基因网络。我们利用各种ILDs的公开单细胞RNA测序数据集，进行富集分析和基于轨迹的差异表达分析，并量化细胞间通讯，以评估空间提取模块在纤维化中的参与情况。对提取的分子进行免疫组织化学染色。使用hdWGCNA，我们确定了一个在年轻纤维化病变中富集的独特基因模块（SM2模块）。SM2模块具有成纤维细胞活化的独特特征，在各种病变中均有体现。该模块内的关键枢纽基因，包括COL1A2、COL3A1、COL1A1和SPARC，形成了一个强大的共表达网络。免疫组织化学染色显示，SM2模块的组成部分SPARC在各种ILDs的年轻纤维化病变中高表达，但在陈旧性瘢痕病变中不表达。为了评估SPARC免疫组织化学表达的预后意义，我们将分析扩展至71例无法分类的ILDs（uILDs）患者队列，这是一种特别异质性的亚型，发病机制不明且治疗选择有限。uILD患者上叶、下叶或双肺叶中较高的SPARC水平与较差的总生存期显著相关。总之，使用ST的综合跨疾病方法揭示了活动性纤维化核心的关键基因表达模式，并成功将SPARC鉴定为一种潜在有益的预后标志物。© 2025作者。《病理学杂志》由John Wiley & Sons Ltd代表大不列颠及爱尔兰病理学会出版。
