The integrated single cell RNAseq analysis of lung cells in Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV) mouse model
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ABSTRACT:
PROVIDER: PRJNA737573 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14812326.fastq.gz | Fastqsanger.gz | |||
| SRR14812327.fastq.gz | Fastqsanger.gz | |||
| SRR14812328.fastq.gz | Fastqsanger.gz | |||
| SRR14812329.fastq.gz | Fastqsanger.gz |
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Project description:Non-coding copy number changes in 16q24.1 upstream of FOXF1 were identified in two patients with ACD. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.
2012-07-11 | GSE39257 | GEO
Project description:Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in the etiology of ACDMPV.
| S-EPMC5518754 | biostudies-literature
Project description:Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare, lethal cause of neonatal respiratory failure and persistent pulmonary hypertension. We present a presumptive prenatal diagnosis of ACDMPV based on chorionic villus sampling of a FOXF1 mutation in a fetus with extra-pulmonary anomalies often associated with ACDMPV.
| S-EPMC5476418 | biostudies-literature
Project description:Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a lethal neonatal lung disease characterised by severe pulmonary hypertension, abnormal vasculature and intractable hypoxaemia. Mechanisms linking abnormal lung vasculature with severe hypoxaemia in ACD/MPV are unknown. We investigated whether bronchopulmonary anastomoses form right-to-left shunt pathways in ACD/MVP. We studied 2 infants who died of ACD/MPV postmortem with direct injections of coloured ink into the pulmonary artery, bronchial artery and pulmonary veins. Extensive histological evaluations included serial sectioning, immunostaining and 3-dimensional reconstruction demonstrated striking intrapulmonary vascular pathways linking the systemic and pulmonary circulations that bypass the alveolar capillary bed. These data support the role of prominent right-to-left intrapulmonary vascular shunt pathways in the pathophysiology of ACD/MPV.
| S-EPMC4405163 | biostudies-literature
Project description:Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, fatal, developmental lung disorder, which usually presents as persistent pulmonary hypertension of the newborn (PPHN) unresponsive to treatment. The authors present their own experience with three cases admitted during the last 15 years.
| S-EPMC4009999 | biostudies-literature
Project description:Analysis of genes dysregulated in the lungs of neonates with ACDMPV neonate lungs compared to control lungs Total RNA extracted by eight ACDMPV lungs compared to total RNA extracted from five control lungs
2014-03-01 | E-GEOD-54780 | biostudies-arrayexpress
Project description:BackgroundAlveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a fatal congenital lung disorder strongly associated with genomic alterations in the Forkhead box F1 (FOXF1) gene and its regulatory region. However, little is known about how FOXF1 genomic alterations cause ACD/MPV and what molecular mechanisms are affected by these mutations. Therefore, the effect of ACD/MPV patient-specific mutations in the FOXF1 gene on the molecular function of FOXF1 was studied.MethodsEpitope-tagged FOXF1 constructs containing one of the ACD/MPV-associated mutations were expressed in mammalian cell lines to study the effect of FOXF1 mutations on protein function. EMSA binding assays and luciferase assays were performed to study the effect on target gene binding and activation. Immunoprecipitation followed by SDS‒PAGE and western blotting were used to study protein‒protein interactions. Protein phosphorylation was studied using phos-tag western blotting.ResultsAn overview of the localization of ACD/MPV-associated FOXF1 mutations revealed that the G91-S101 region was frequently mutated. A three-dimensional model of the forkhead DNA-binding domain of FOXF1 showed that the G91-S101 region consists of an α-helix and is predicted to be important for DNA binding. We showed that FOXF1 missense mutations in this region differentially affect the DNA binding of the FOXF1 protein and influence the transcriptional regulation of target genes depending on the location of the mutation. Furthermore, we showed that some of these mutations can affect the FOXF1 protein at the posttranscriptional level, as shown by altered phosphorylation by MST1 and MST2 kinases.ConclusionMissense mutations in the coding region of the FOXF1 gene alter the molecular function of the FOXF1 protein at multiple levels, such as phosphorylation, DNA binding and target gene activation. These results indicate that FOXF1 molecular pathways may be differentially affected in ACD/MPV patients carrying missense mutations in the DNA-binding domain and may explain the phenotypic heterogeneity of ACD/MPV.
| S-EPMC11536904 | biostudies-literature
Project description:BackgroundAlveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a lethal neonatal lung disorder characterized by the decrease of the alveolar units, abnormalities in the air-blood barrier of the lung, and impaired gas exchange. Typically, it affects a full-term newborn; the symptoms usually start within a few hours after birth, resulting in severe respiratory distress and pulmonary hypertension. In most of the cases, this disorder is refractory to conventional pulmonary support.Case presentationWe report a case of a newborn male of 29 weeks gestational age, with birth weight of 850 g and intrauterine growth restriction. Severe respiratory distress appeared a few minutes after birth; non-invasive ventilatory support was provided in the delivery room and, as a consequence of persistent respiratory failure, he was admitted to the neonatal intensive care unit (NICU) where mechanical ventilation was required. Due to the symptoms and pulmonary ultrasound pattern suggestive of respiratory distress syndrome, surfactant treatment was administered. Lung ultrasound (LU) was used for monitoring the responsiveness to surfactant; severe pulmonary hypertension ensued, followed by respiratory failure, refractory shock, and death within 48 h. Owing to the poor response to the established therapy, ACD/MPV was suspected. The diagnosis was confirmed through autopsy. The main goal of this case report is to show the role of LU for monitoring the evolution of this disorder.ConclusionLU could provide essential information to help diagnose and follow-up the underlying cause of persistent pulmonary hypertension of the newborn in an earlier and more effective way than chest X-ray. LU is suitable for routine monitoring of lung disease in the NICU.
| S-EPMC9922097 | biostudies-literature
Project description:Analysis of genes dysregulated in the lungs of neonates with ACDMPV neonate lungs compared to control lungs
2014-03-01 | GSE54780 | GEO
Project description:Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV) is a rare congenital pulmonary disease that affects newborns. Most patients with ACDMPV are born at full term and are healthy. The main clinical manifestations are refractory pulmonary hypertension and pulmonary failure with gastrointestinal, urinary, or cardiac malformations. ACDMPV often progresses rapidly, but no conventional biological or imaging tests other than genetic testing are available for its diagnosis. Lung biopsy is currently the gold standard for diagnosis. We herein report two cases of ACDMPV confirmed by pathological examination and discuss their ultrasonographic findings.
| S-EPMC9528008 | biostudies-literature