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Radioproteomics stratifies molecular response to antifibrotic treatment in pulmonary fibrosis
David Lauer, Cheryl Y. Magnin, Luca R. Kolly, Huijuan Wang, Matthias Brunner, Mamta Chabria, Grazia M. Cereghetti, Hubert S. Gabryś, Stephanie Tanadini-Lang, Anne-Christine Uldry, Manfred Heller, Stijn E. Verleden, Kerstin Klein, Adela-Cristina Sarbu, Manuela Funke-Chambour, Lukas Ebner, Oliver Distler, Britta Maurer, Janine Gote-Schniering
David Lauer, Cheryl Y. Magnin, Luca R. Kolly, Huijuan Wang, Matthias Brunner, Mamta Chabria, Grazia M. Cereghetti, Hubert S. Gabryś, Stephanie Tanadini-Lang, Anne-Christine Uldry, Manfred Heller, Stijn E. Verleden, Kerstin Klein, Adela-Cristina Sarbu, Manuela Funke-Chambour, Lukas Ebner, Oliver Distler, Britta Maurer, Janine Gote-Schniering
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Research Article Pulmonology Therapeutics

Radioproteomics stratifies molecular response to antifibrotic treatment in pulmonary fibrosis

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Abstract

Antifibrotic therapy with nintedanib is the clinical mainstay in the treatment of progressive fibrosing interstitial lung disease (ILD). High-dimensional medical image analysis, known as radiomics, provides quantitative insights into organ-scale pathophysiology, generating digital disease fingerprints. Here, we performed an integrative analysis of radiomic and proteomic profiles (radioproteomics) to assess whether changes in radiomic signatures can stratify the degree of antifibrotic response to nintedanib in (experimental) fibrosing ILD. Unsupervised clustering of delta radiomic profiles revealed 2 distinct imaging phenotypes in mice treated with nintedanib, contrary to conventional densitometry readouts, which showed a more uniform response. Integrative analysis of delta radiomics and proteomics demonstrated that these phenotypes reflected different treatment response states, as further evidenced on transcriptional and cellular levels. Importantly, radioproteomics signatures paralleled disease- and drug-related biological pathway activity with high specificity, including extracellular matrix (ECM) remodeling, cell cycle activity, wound healing, and metabolic activity. Evaluation of the preclinical molecular response–defining features, particularly those linked to ECM remodeling, in a cohort of nintedanib-treated fibrosing patients with ILD, accurately stratified patients based on their extent of lung function decline. In conclusion, delta radiomics has great potential to serve as a noninvasive and readily accessible surrogate of molecular response phenotypes in fibrosing ILD. This could pave the way for personalized treatment strategies and improved patient outcomes.

Authors

David Lauer, Cheryl Y. Magnin, Luca R. Kolly, Huijuan Wang, Matthias Brunner, Mamta Chabria, Grazia M. Cereghetti, Hubert S. Gabryś, Stephanie Tanadini-Lang, Anne-Christine Uldry, Manfred Heller, Stijn E. Verleden, Kerstin Klein, Adela-Cristina Sarbu, Manuela Funke-Chambour, Lukas Ebner, Oliver Distler, Britta Maurer, Janine Gote-Schniering

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Figure 2

Delta radiomic phenotypes reflect molecular response to antifibrotic treatment.

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Delta radiomic phenotypes reflect molecular response to antifibrotic tre...
(A) Volcano plot of the DE proteins between clusters 1 and 2. Proteins with log2 fold change (log2FC) > 0.3 and P < 0.05 were considered significantly different. Down- and upregulated proteins are highlighted in blue and red, respectively. (B) GO pathway analysis of the down- and upregulated DE proteins. Terms marked with an asterisks are of cellular compartment (CC) ontology; all others are of biological process (BP) ontology. (C) Heatmap of DE proteins included in Reactome pathways “extracellular matrix organization,” “receptor tyrosine kinase signaling,” and “cytokine signaling” and their expression in clusters 1 and 2 compared with vehicle-treated mice. (D) Analysis workflow and bar chart depicting the results from cell type deconvolution analysis. The change of the indicated cell type signature between clusters 1 and 2 is expressed as signed log10 enrichment P value. (E) Representative immunofluorescence stainings of fibrotic regions in clusters 1 and 2. Images show nuclei (DAPI), AT2 cells (proSP-C), myofibroblasts (α-SMA), and AT1 cells (PDPN). Regions are 500 × 500 μm in size. Scale bar: 100 μm. (F) Percentage of α-SMA+ cells in fibrotic regions of cluster 1 and cluster 2 samples. Mann-Whitney U test was used to compare the groups.

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