CRISPR interference interrogation of COPD GWAS genes reveals the functional significance of desmoplakin in iPSC-derived alveolar epithelial cells

Abstract

Genome-wide association studies (GWAS) have identified dozens of loci associated with chronic obstructive pulmonary disease (COPD) susceptibility; however, the function of associated genes in the cell type(s) affected in disease remains poorly understood, partly due to a lack of cell models that recapitulate human alveolar biology. Here, we apply CRISPR interference to interrogate the function of nine genes implicated in COPD by GWAS in induced pluripotent stem cell–derived type 2 alveolar epithelial cells (iAT2s). We find that multiple genes implicated by GWAS affect iAT2 function, including differentiation potential, maturation, and/or proliferation. Detailed characterization of the GWAS gene DSP demonstrates that it regulates iAT2 cell-cell junctions, proliferation, mitochondrial function, and response to cigarette smoke–induced injury. Our approach thus elucidates the biological function, as well as disease-relevant consequences of dysfunction, of genes implicated in COPD by GWAS in type 2 alveolar epithelial cells.

Breathing new life into the study of COPD with genes identified from genome-wide association studies

“…In addition, as mentioned above, the cellular distribution of HHIP differs between mice and humans; abundant expression of HHIP in human AT2 cells might dictate alternative outcomes in response to injury in humans. We recently applied induced pluripotent stem cell-derived AT2 (iAT2) cells to interrogate the function of COPD GWAS genes, and found that HHIP expression regulated SFTPC expression in iAT2 cells but did not alter other aspects of AT2 cells (such as proliferation or differentiation capacity) [ 83 ]. Future studies, potentially employing iAT2 cells or precision-cut lung slices, elucidating responses to injury ( e.g.…”

“…Mechanistically, the absence of Fam13a in mice is protective through increased β-catenin signalling and subsequent increased cellular proliferation [ 84 ] and decreased fatty acid oxidation and associated cellular stress [ 96 ], suggesting that elevated FAM13A expression in COPD patients might impede lung epithelial repair in response to injury. To explore the function of FAM13A in human AT2 cells, we recently applied CRISPR interference to knock down full-length FAM13A in iAT2 cells [ 83 ]. Surprisingly, in contrast to the in vivo mouse studies, loss of FAM13A slowed iAT2 proliferation [ 83 ], potentially on the basis of differences in FAM13A isoforms expressed in mice versus humans.…”

“…To explore the function of FAM13A in human AT2 cells, we recently applied CRISPR interference to knock down full-length FAM13A in iAT2 cells [ 83 ]. Surprisingly, in contrast to the in vivo mouse studies, loss of FAM13A slowed iAT2 proliferation [ 83 ], potentially on the basis of differences in FAM13A isoforms expressed in mice versus humans. Further work is thus needed to differentiate the function of differential isoforms of FAM13A in COPD pathogenesis in humans.…”

“…Owing to lethality among Dsp −/− mice, it has not been straightforward to investigate the effect of cigarette smoke or ageing in the global absence of DSP. To address this question, we recently characterised the functional role of DSP in the lung using a combination of human iAT2 cells and mice lacking Dsp in lung epithelium [ 83 ]. DSP expression modulates the formation of desmosomes, as well as tight junctions, adherens junctions and cytoskeletal organisation in AT2 cells [ 83 ].…”

“…To address this question, we recently characterised the functional role of DSP in the lung using a combination of human iAT2 cells and mice lacking Dsp in lung epithelium [ 83 ]. DSP expression modulates the formation of desmosomes, as well as tight junctions, adherens junctions and cytoskeletal organisation in AT2 cells [ 83 ]. Intriguingly, reduction or ablation of DSP expression increased AT2 proliferation through extracellular signal-regulated kinase (ERK) signalling, both in iAT2 cells and in vivo [ 83 ].…”