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Impaired AMPK control of alveolar epithelial cell metabolism promotes pulmonary fibrosis
Luis R. Rodríguez, Konstantinos-Dionysios Alysandratos, Jeremy Katzen, Aditi Murthy, Willy Roque Barboza, Yaniv Tomer, Sarah Bui, Rebeca Acín-Pérez, Anton Petcherski, Kasey Minakin, Paige Carson, Swati Iyer, Katrina Chavez, Charlotte H. Cooper, Apoorva Babu, Aaron I. Weiner, Andrew E. Vaughan, Zoltan Arany, Orian S. Shirihai, Darrell N. Kotton, Michael F. Beers
Luis R. Rodríguez, Konstantinos-Dionysios Alysandratos, Jeremy Katzen, Aditi Murthy, Willy Roque Barboza, Yaniv Tomer, Sarah Bui, Rebeca Acín-Pérez, Anton Petcherski, Kasey Minakin, Paige Carson, Swati Iyer, Katrina Chavez, Charlotte H. Cooper, Apoorva Babu, Aaron I. Weiner, Andrew E. Vaughan, Zoltan Arany, Orian S. Shirihai, Darrell N. Kotton, Michael F. Beers
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Research Article Metabolism Pulmonology

Impaired AMPK control of alveolar epithelial cell metabolism promotes pulmonary fibrosis

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Abstract

Alveolar epithelial type II (AT2) cell dysfunction is implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). We previously demonstrated that expression of an AT2 cell–exclusive disease-associated protein isoform (SP-CI73T) in murine and patient-specific induced pluripotent stem cell–derived (iPSC-derived) AT2 cells leads to a block in late macroautophagy and promotes time-dependent mitochondrial impairments; however, how a metabolically dysfunctional AT2 cell results in fibrosis remains elusive. Here, using murine and human iPSC-derived AT2 cell models expressing SP-CI73T, we characterize the molecular mechanisms governing alterations in AT2 cell metabolism that lead to increased glycolysis, decreased mitochondrial biogenesis, disrupted fatty acid oxidation, accumulation of impaired mitochondria, and diminished AT2 cell progenitor capacity manifesting as reduced AT2 cell self-renewal and accumulation of transitional epithelial cells. We identify deficient AMPK signaling as a critical component of AT2 cell dysfunction and demonstrate that targeting this druggable signaling hub can rescue the aberrant AT2 cell metabolic phenotype and mitigate lung fibrosis in vivo.

Authors

Luis R. Rodríguez, Konstantinos-Dionysios Alysandratos, Jeremy Katzen, Aditi Murthy, Willy Roque Barboza, Yaniv Tomer, Sarah Bui, Rebeca Acín-Pérez, Anton Petcherski, Kasey Minakin, Paige Carson, Swati Iyer, Katrina Chavez, Charlotte H. Cooper, Apoorva Babu, Aaron I. Weiner, Andrew E. Vaughan, Zoltan Arany, Orian S. Shirihai, Darrell N. Kotton, Michael F. Beers

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Figure 4

Metabolic alterations and emergence of an epithelial transitional state in response to in vivo SftpcI73T expression.

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Metabolic alterations and emergence of an epithelial transitional state ...
(A) Uniform manifold approximation and projection (UMAP) visualization of 35,002 lung cells profiled by scRNA-Seq in GSE234604 (56) color-coded by cell lineage with subset analysis of 2,500 distal epithelial cells. (B) Gradient dot plot of key distal epithelial genes used to annotate AT1 (cluster 1), AT2 (clusters 2, 4), and transitional subclusters (clusters 3, 5). (C) Dendrogram of top 20 DEGs and their associated log2FC for each cluster as determined by FDR. A subset of cluster-defining genes is highlighted. (D) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs (FDR < 0.05, log2FC > 1 & <–1) in cluster 2 compared with other clusters. (E) Gradient dot plot of KEGG pathway enrichment analysis of upregulated DEGs (FDR < 0.05, log2FC > 1) across clusters. (F) Color-coded UMAPs by genotype and time point and frequency table denoting cluster distributions within biological samples. (G) Volcano plot of differential expression analysis (FDR < 0.05, log2FC > 1 or <–1) comparing the early (cluster 3) and late (cluster 5) transitional clusters highlighting decreased expression of AT1 cell marker genes (Hopx, Ager, Cav1, Pdpn, Aqp5) and increased expression of transitional cell marker genes (Cldn4, Krt8, Krt18, Gdf15, Sppr1a) in the early transitional cell cluster. (H) Pseudotime trajectory analysis with starting node set in the AT2 cell cluster. (I) Gradient dot plot of indicated transitional state gene modules (Supplemental Table 1) (58, 60, 62–69) across distal epithelial clusters. (J) KEGG pathway module scores for AMPK and PPAR signaling demonstrate progressive downregulation from the AT2 cell cluster to transitional cell clusters.

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