Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis
Abstract Background Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-11-01
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| Series: | Respiratory Research |
| Online Access: | https://doi.org/10.1186/s12931-023-02572-6 |
| _version_ | 1797556969130688512 |
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| author | Rachel Z. Blumhagen Jonathan S. Kurche Carlyne D. Cool Avram D. Walts David Heinz Tasha E. Fingerlin Ivana V. Yang David A. Schwartz |
| author_facet | Rachel Z. Blumhagen Jonathan S. Kurche Carlyne D. Cool Avram D. Walts David Heinz Tasha E. Fingerlin Ivana V. Yang David A. Schwartz |
| author_sort | Rachel Z. Blumhagen |
| collection | DOAJ |
| description | Abstract Background Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these pathologically heterogeneous regions of the IPF lung is critical to understanding the distribution and extent of fibrotic lung disease and identifying potential therapeutic targets. Application of a spatial transcriptomics platform would provide more detailed spatial resolution of transcriptional signals compared to previous single cell or bulk RNA-Seq studies. Methods We performed spatial transcriptomics using GeoMx Nanostring Digital Spatial Profiling on formalin-fixed paraffin-embedded (FFPE) tissue from 32 IPF and 12 control subjects and identified 231 regions of interest (ROIs). We compared normal-appearing lung parenchyma and airways between IPF and controls with histologically normal lung tissue, as well as histologically distinct regions within IPF (normal-appearing lung parenchyma, transition zones containing fibroblastic foci, areas of dense fibrosis, and honeycomb epithelium metaplasia). Results We identified 254 differentially expressed genes (DEGs) between IPF and controls in histologically normal-appearing regions of lung parenchyma; pathway analysis identified disease processes such as EIF2 signaling (important for cap-dependent mRNA translation), epithelial adherens junction signaling, HIF1α signaling, and integrin signaling. Within IPF, we identified 173 DEGs between transition and normal-appearing lung parenchyma and 198 DEGs between dense fibrosis and normal lung parenchyma; pathways dysregulated in both transition and dense fibrotic areas include EIF2 signaling pathway activation (upstream of endoplasmic reticulum (ER) stress proteins ATF4 and CHOP) and wound healing signaling pathway deactivation. Through cell deconvolution of transcriptome data and immunofluorescence staining, we confirmed loss of alveolar parenchymal signals (AGER, SFTPB, SFTPC), gain of secretory cell markers (SCGB3A2, MUC5B) as well as dysregulation of the upstream regulator ATF4, in histologically normal-appearing tissue in IPF. Conclusions Our findings demonstrate that histologically normal-appearing regions from the IPF lung are transcriptionally distinct when compared to similar lung tissue from controls with histologically normal lung tissue, and that transition zones and areas of dense fibrosis within the IPF lung demonstrate activation of ER stress and deactivation of wound healing pathways. |
| first_indexed | 2024-03-10T17:10:42Z |
| format | Article |
| id | doaj.art-01706a12d28340c886415da719d291ac |
| institution | Directory Open Access Journal |
| issn | 1465-993X |
| language | English |
| last_indexed | 2024-03-10T17:10:42Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Respiratory Research |
| spelling | doaj.art-01706a12d28340c886415da719d291ac2023-11-20T10:40:31ZengBMCRespiratory Research1465-993X2023-11-0124111210.1186/s12931-023-02572-6Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosisRachel Z. Blumhagen0Jonathan S. Kurche1Carlyne D. Cool2Avram D. Walts3David Heinz4Tasha E. Fingerlin5Ivana V. Yang6David A. Schwartz7Center for Genes, Environment and Health, National Jewish HealthDepartment of Medicine, University of Colorado Anschutz Medical CampusDepartment of Medicine, University of Colorado Anschutz Medical CampusDepartment of Medicine, University of Colorado Anschutz Medical CampusPathology Laboratory, National Jewish HealthCenter for Genes, Environment and Health, National Jewish HealthDepartment of Medicine, University of Colorado Anschutz Medical CampusDepartment of Medicine, University of Colorado Anschutz Medical CampusAbstract Background Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these pathologically heterogeneous regions of the IPF lung is critical to understanding the distribution and extent of fibrotic lung disease and identifying potential therapeutic targets. Application of a spatial transcriptomics platform would provide more detailed spatial resolution of transcriptional signals compared to previous single cell or bulk RNA-Seq studies. Methods We performed spatial transcriptomics using GeoMx Nanostring Digital Spatial Profiling on formalin-fixed paraffin-embedded (FFPE) tissue from 32 IPF and 12 control subjects and identified 231 regions of interest (ROIs). We compared normal-appearing lung parenchyma and airways between IPF and controls with histologically normal lung tissue, as well as histologically distinct regions within IPF (normal-appearing lung parenchyma, transition zones containing fibroblastic foci, areas of dense fibrosis, and honeycomb epithelium metaplasia). Results We identified 254 differentially expressed genes (DEGs) between IPF and controls in histologically normal-appearing regions of lung parenchyma; pathway analysis identified disease processes such as EIF2 signaling (important for cap-dependent mRNA translation), epithelial adherens junction signaling, HIF1α signaling, and integrin signaling. Within IPF, we identified 173 DEGs between transition and normal-appearing lung parenchyma and 198 DEGs between dense fibrosis and normal lung parenchyma; pathways dysregulated in both transition and dense fibrotic areas include EIF2 signaling pathway activation (upstream of endoplasmic reticulum (ER) stress proteins ATF4 and CHOP) and wound healing signaling pathway deactivation. Through cell deconvolution of transcriptome data and immunofluorescence staining, we confirmed loss of alveolar parenchymal signals (AGER, SFTPB, SFTPC), gain of secretory cell markers (SCGB3A2, MUC5B) as well as dysregulation of the upstream regulator ATF4, in histologically normal-appearing tissue in IPF. Conclusions Our findings demonstrate that histologically normal-appearing regions from the IPF lung are transcriptionally distinct when compared to similar lung tissue from controls with histologically normal lung tissue, and that transition zones and areas of dense fibrosis within the IPF lung demonstrate activation of ER stress and deactivation of wound healing pathways.https://doi.org/10.1186/s12931-023-02572-6 |
| spellingShingle | Rachel Z. Blumhagen Jonathan S. Kurche Carlyne D. Cool Avram D. Walts David Heinz Tasha E. Fingerlin Ivana V. Yang David A. Schwartz Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis Respiratory Research |
| title | Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis |
| title_full | Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis |
| title_fullStr | Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis |
| title_full_unstemmed | Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis |
| title_short | Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis |
| title_sort | spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis |
| url | https://doi.org/10.1186/s12931-023-02572-6 |
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