Association of rare non-coding SNVs in the lung-specific FOXF1 enhancer with a mitigation of the lethal ACDMPV phenotype

Authors	SZAFRANSKI Przemyslaw LIU Qian KAROLAK Justyna A. SONG Xiaofei DE LEEUW Nicole FAAS Brigitte GERYCHOVÁ Romana JANKŮ Petr JEŽOVÁ Marta VALÁŠKOVÁ Iveta GIBBS Kathleen A. SURREY Lea F. POISSON Virginie BERUBE Denis OLIGNY Luc L. MICHAUD Jacques L. POPEK Edwina STANKIEWICZ Pawel
Year of publication	2019
Type	Article in Periodical
Magazine / Source	Human Genetics
MU Faculty or unit	Faculty of Medicine
Citation
Web	http://dx.doi.org/10.1007/s00439-019-02073-x
Doi	http://dx.doi.org/10.1007/s00439-019-02073-x
Keywords	ALVEOLAR-CAPILLARY DYSPLASIA; MICE HETEROZYGOUS NULL; PULMONARY VEINS; GENE FOXF1; MISALIGNMENT; TRANSCRIPTION; VARIANTS; VESSELS; HAPLOINSUFFICIENCY; EXPRESSION
Description	Haploinsufficiency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. In one case, the deletion of the maternal allele of the FOXF1 enhancer caused pulmonary hypertension and histopathologically diagnosed MPV without the typical ACD features. In the second case, the deletion of the paternal enhancer resulted in ACDMPV rather than the expected neonatal lethality. In both cases, FOXF1 expression in lung tissue was higher than usually seen or expected in patients with similar deletions, suggesting an increased activity of the remaining allele of the enhancer. Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Moreover, in a family with three histopathologically-diagnosed ACDMPV siblings whose missense FOXF1 mutation was inherited from the healthy non-mosaic carrier mother, we have identified a rare SNV rs28571077-A within 2-kb of the above-mentioned non-coding SNVs in the FOXF1 enhancer in the mother, that was absent in the affected newborns and 13 unrelated ACDMPV patients with CNV deletions of this genomic region. Based on the low population frequencies of these three variants, their absence in ACDMPV patients, the results of reporter assay, RNAi and EMSA experiments, and in silico predictions, we propose that the described SNVs might have acted on FOXF1 enhancer as hypermorphs.