Narrowing the FOXF1 distant enhancer region on 16q24.1 critical for ACDMPV

Abstract

BackgroundAlveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal lung developmental disorder caused by heterozygous point mutations or genomic deletions involving FOXF1 or its 60-kb tissue-specific enhancer region mapping 270 kb upstream of FOXF1 and involving fetal lung-expressed long non-coding RNA genes and CpG-enriched sites. Recently, we have proposed that the FOXF1 locus at 16q24.1 may be a subject of genomic imprinting.FindingsUsing custom-designed aCGH and Sanger sequencing, we have identified a novel de novo 104 kb genomic deletion upstream of FOXF1 in a patient with histopathologically verified full phenotype of ACDMPV. This deletion allowed us to further narrow the FOXF1 enhancer region and identify its critical 15-kb core interval, essential for lung development. This interval harbors binding sites for lung-expressed transcription factors, including GATA3, ESR1, and YY1, and is flanked by the lncRNA genes and CpG islands. Bisulfite sequencing of one of these CpG islands on the non-deleted allele showed that it is predominantly methylated on the maternal chromosome 16.ConclusionsSubstantial narrowing and bisulfite sequencing of the FOXF1 enhancer region on 16q24.1 provided new insights into its regulatory function and genomic imprinting.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0278-2) contains supplementary material, which is available to authorized users.

Genotype–phenotype correlation in two Polish neonates with alveolar capillary dysplasia

“…Whereas the CNV deletion in Patient 1 involved FOXF1, the CNV deletion observed in Patient 2 removed the upstream FOXF1 enhancer, leaving the FOXF1 gene intact. These findings further confirm that the non-coding genomic interval mapping upstream to FOXF1 is essential for human lung development [14].…”

Maternal mutations ofFOXF1cause alveolar capillary dysplasia despite not being imprinted

“…Allele‐specific expression analysis for FOXF1 failed to identify the evidence of maternal expression, and detailed methylation screening did not find any evidence for allelic methylation, a key epigenetic feature associated with imprinted loci. This is despite previous reports of modest maternal methylation within the newly defined critical region defined by minimal deletion overlap (Szafranski et al., ). However, it must be noted that the methylation experiments performed by Szafranski et al 2016. were not performed using SNPs, and the methylation profile was inferred from patient samples carrying deletions.…”

“…This includes six of the 10 CpGs within the proposed DMRs (region 1 in Fig. C) mapping within the critical region (Szafranski et al., ; Szafranski et al., ).…”

Alveolar capillary dysplasia with misalignment of the pulmonary veins: clinical, histological, and genetic aspects

“… 49 This regulatory region was identified by defining the shortest region of overlapping genomic deletions in ACD/MPV patients. 50 , 51 The remaining 55 cases were not genetically tested due to insufficient DNA quality. 49 Additionally, a variety of heterozygous genomic variants in the FOXF1 locus of ACD/MPV patients have been reported by other research groups.…”