Comparative Transcriptome Analyses Highlight Distinct Pathogenetic Mechanisms for Pleuropulmonary Blastoma and Congenital Pulmonary Airway Malformations

Abstract

Pleuropulmonary blastoma (PPB) and congenital pulmonary airway malformations (CPAM) are two rare cystic lung diseases occurring in childhood. PPB can evolve from a low-grade epithelial cyst lesion to a high-grade sarcoma with a poor prognosis, whereas CPAM usually has a favorable non-tumorous outcome. Clinical similarities complicate diagnosis and may delay appropriate care. PPB is associated with DICER1 mutations that disturb miRNA biogenesis, altering the miRNA repertoire. Conversely, KRAS mutations are detected in CPAM, but their implication remains unclear. To decipher the mechanisms underlying these diseases, we undertook a comprehensive analysis of molecular variations in CPAM and PPB lung lesions using genome-wide RNA-seq and miRNA-seq assays. Each pathology displayed a distinct expression profile revealing a unique etiology. CPAM presented misexpression of bronchial epithelial markers correlating with KRAS mutation, while changes in expression of distal lung epithelial and mesenchymal markers were PPB-specific. PPB also exhibited abnormal gain of expression of developmental transcription factors, likely due to perturbed Polycomb Repressive Complex 2 (PRC2) activity. Overexpression of miR-323a-3p, which targets the PRC2 subunit EED, correlated with decreased EED expression. Together, these observations propose a PPB pathogenetic mechanism connecting DICER1 mutations and altered miRNA profile to defective PRC2 activity, misexpression of developmental transcription factors, and cancer.

Keywords

Pleuropulmonary blastoma / Congenital pulmonary airway malformations / DICER syndrome / Lung development / microRNA

Acknowledgments

We thank Olivier Boucherat, Jean Charron and Tom Moss for comments on the manuscript and sharing reagents. We also thank Venkata Manem for guidance in bioinformatic analyses, Stéphane Dubois from the Next-Generation Sequencing Platform, Genomics Center, CRCHUQ-ULaval for help in RNA-seq assays, and Carl St-Pierre from the Cellular Imaging Unit CRCHUQ-ULaval for advice.

Author Contributions

Conceptualization: J.G., N.H., K.L.-T. and L.J.; Methodology: J.G., N.H., K.L.-T. and B.F.; Validation: J.G., N.H. and L.J.; Formal analysis: J.G., N.H. and L.J.; Resources: C.D., W.D.F. and L.J.; Data curation: J.G., N.H. and L.J.; Writing—original draft preparation: J.G. and L.J.; Writing—review and editing: J.G., N.H., K.L.-T., B.F., C.D., W.D.F. and L.J.; Supervision: L.J.; Project administration: L.J.; Funding acquisition: L.J. All the authors read and approved the manuscript before submission.

Ethics Statement

The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the respective institutional ethics committees and by the CHU de Québec-Université Laval research ethics committee (project MP-20-2020-4809, approved: 5 August 2019).

Informed Consent Statement

Informed consent was obtained from all subjects involved in the study.

Data Availability Statement

RNA-seq and miRNA-seq data are available through NCBI GEO (accession numbers GSE311205 and GSE311209) and exome data are available through SRA (accession number PRJNA1356925).

Funding

This work was supported by the Canadian Institutes of Health Research (FRN169158 to L.J.) and the Cancer Research Society (24217 to L.J.). B.F. holds studentships from NSERC (BESC M) and Fonds de Recherche du Québec en Santé (BF1-325367).

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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