Exome sequencing and pathway analysis for identification of genetic variability relevant for bronchopulmonary dysplasia (BPD) in preterm newborns: A pilot study.

BACKGROUND: Bronchopulmonary dysplasia (BPD) is the most common chronic lung disease in infancy, affecting preterm children with low birth weight. The disease has a multifactorial aetiology with a significant genetic component; until now published association studies have identified several candidate genes but only few of these data has been replicated. In this pilot study, we approached exome sequencing aimed at identifying non-common variants, which are expected to have a stronger phenotypic effect. MATERIALS AND METHODS: We performed this study on 26 Italian severely affected BPD preterm unrelated newborns, homogeneously selected from a large prospective cohort. We used an Illumina HiSeq 2000 for sequencing. Data analysis was focussed on genes previously associated to BPD susceptibility and to new candidates in related pathways, highlighted by a prioritization analysis performed using ToppGene Suite. RESULTS: By exome sequencing, we identified 3369 novel variants, with a median of 400 variations per sample. The top candidate genes highlighted were NOS2, MMP1, CRP, LBP and the toll-like receptor (TLR) family. All of them have been confirmed with Sanger sequencing. CONCLUSIONS: Potential candidate genes have been discovered in this preliminary study; the pathogenic role of identified variants will need to be confirmed with functional and segregation studies and possibly with further methods, able to evaluate the collective influence of rare variants. Moreover, additional candidates will be tested and genetic analysis will be extended to all affected children.

Genetic susceptibility to neonatal lung diseases.

Advances in molecular genetics have enabled improvement of knowledge in pathogenesis and diagnosis of either monogenic or multifactorial neonatal lung diseases. Variants in genes regulating surfactant function and metabolism are implicated in some rare and common respiratory diseases. Congenital surfactant deficiencies are rare diseases due to mutations in genes encoding surfactant proteins and cause significant and often lethal respiratory failure in newborns and interstitial lung disease in older children. Diagnosis is made by molecular analysis and eventually confirmed by histological analysis of lung tissue. A multifactorial contribution, resulting from interaction between multiple genes and environmental factors, has been supposed for respiratory distress syndrome (RDS) and bronchopulmonary dysplasia (BPD). Several potential candidate genes, especially regarding surfactant proteins and cytokines, have been shown in association with these diseases. Genetic variants predisposing to RDS or BPD are usually polymorphisms which are not causative, but can increase susceptibility to the disease. Identification of infants at risk of disease can be useful to provide them individualized therapies. (www.actabiomedica.it).

Genetic predisposing factors to bronchopulmonary dysplasia: preliminary data from a multicentre study.

Bronchopulmonary dysplasia (BPD) is the most frequent chronic lung disease in preterm newborn infants. It is a multifactorial disease caused by the interaction between environmental and genetic factors. The aim of this study is to identify genetic variants contributing to BPD development using next-generation sequencing (NGS) technology. We prospectively evaluated 378 premature newborn infants with a gestational age <32 weeks in a multicentre study from 12 Italian neonatal intensive care unit from 2009 to 2012. Infants were divided into two groups: normal controls (225) and BPD-affected infants (141) with mild (65, 46.1%), moderate (40, 28.4%) and severe (36, 25.5%) BPD. BPD was more frequent in infants with lower weight and gestational age. Antenatal steroid administration was more frequent in the control group. Postnatal infection, respiratory distress syndrome, patent ductus arterious, cerebral haemorrhage, surfactant administration, ventilatory support, diuretics and postnatal steroid administration correlated with severity of BPD. Among BPD, moderate and severe cases will be selected as BPD "extreme phenotypes", and in fact variations in 28-day oxygen need-based BPD were previously shown to be fully attributable to environmental effects whereas dependence on supplemental oxygen at 36 weeks seems to better reflect underlying genetic susceptibility. Exome analysis by NGS is in progress. Identifications of genetic markers predisposing to BPD may allow development of personalized and preventive treatments.

Analysis of nucleotide variations in genes of iron management in patients of Parkinson's disease and other movement disorders.

The capacity to act as an electron donor and acceptor makes iron an essential cofactor of many vital processes. Its balance in the body has to be tightly regulated since its excess can be harmful by favouring oxidative damage, while its deficiency can impair fundamental activities like erythropoiesis. In the brain, an accumulation of iron or an increase in its availability has been associated with the development and/or progression of different degenerative processes, including Parkinson's disease, while iron paucity seems to be associated with cognitive deficits, motor dysfunction, and restless legs syndrome. In the search of DNA sequence variations affecting the individual predisposition to develop movement disorders, we scanned by DHPLC the exons and intronic boundary regions of ceruloplasmin, iron regulatory protein 2, hemopexin, hepcidin and hemojuvelin genes in cohorts of subjects affected by Parkinson's disease and idiopathic neurodegeneration with brain iron accumulation (NBIA). Both novel and known sequence variations were identified in most of the genes, but none of them seemed to be significantly associated to the movement diseases of interest.

Sequence variations in mitochondrial ferritin: distribution in healthy controls and different types of patients.

The storage of iron in the cells is mainly accomplished by cytosolic ferritins. The perturbation of ferritin function may result in accumulation of excess iron in cells and tissues and increased oxidative stress, common features of different genetic and acquired disorders. Mutations in L-ferritin have been associated with neuroferritinopathy, a rare and severe movement disorder with abnormal brain iron storage. Recently, a novel form of ferritin has been discovered, which localizes in the mitochondrial matrix and plays an important role in iron homeostasis in these organelles. The possible association of sequence variations in the mitochondrial ferritin (FtMt) gene with disorders with aberrant iron distribution has not been investigated yet. We set up a denaturing high-performance liquid chromatography (DHPLC)-based screening for FtMt and analyzed the genomic DNA of patients with myelodysplastic syndromes (# 63) or with Parkinson's disease (# 332) and other movement disorders such as pantothenate kinase-associated neurodegeneration (# 7), restless legs syndrome (# 23), and suspected neuroferritinopathy (# 7) and of control subjects (# 342). We detected eight different types of substitution, all at the heterozygous state. Six of them caused amino acid changes, but none of them was predicted to drastically perturb FtMt structure and/or function. The c + 134C > A (P45H) variation, which was the most common (# 28), was less represented in the Parkinson's population, although not significantly (p = 0.07). The analysis suggests that sequence variations in the coding region of FtMt are not involved in the development of myelodysplastic syndromes and Parkinson's disease.

High resolution melting for the identification of mutations in the iron responsive element of the ferritin light chain gene.

BACKGROUND: Among the causes of hyperferritinemia, hereditary hyperferritinemia cataract syndrome (HHCS) is an autosomal dominant disease characterized by distinctive cataracts and high serum ferritin. It is caused by mutations in the iron responsive element (IRE) of the ferritin light chain gene (FTL). METHODS: To speed up and simplify mutational scanning in this genomic region, we developed a protocol based on high-resolution melting (HRM) analysis. RESULTS: Validation was carried out using 18 wild-type and 14 DNA samples carrying different mutations, each analyzed in replicates of 20. The method allowed for correct identification and genotyping of all mutant samples, and each variant generated a specific profile distinguishable from the wild type. A 5.5% proportion of false positive results were obtained. In addition, in two patients with HHCS, two new mutations were identified by HRM based on an altered melting profile. These mutations were subsequently characterized by direct sequencing (7C>G+40A>G and 49A>C). CONCLUSIONS: The high reliability of HRM in detecting known and new DNA variations indicate that this could be an effective and sensitive method for molecular scanning of mutations in the IRE of the FTL gene in patients presenting with either HHCS or unexplained hyperferritinemia.

Analysis of ferritin genes in Parkinson disease.

BACKGROUND: Genes that regulate iron metabolism may be involved in increasing brain iron content in Parkinson disease (PD). The ferritin L-chain is one of these genes, but the rare insertional mutations that cause neuroferritinopathy with basal ganglia degeneration have not yet been identified in PD. METHODS: We used denaturing HPLC (DHPLC) to investigate 124 PD patients and 180 controls for variations in the coding and in the 5' untranslated regions of the H- and L-ferritin genes. RESULTS: In the H-ferritin gene, we found one new and rather common intronic polymorphism and the K54R substitution in two controls. The L-ferritin gene showed a very common L55L polymorphism and four other types of DNA variations, three of which were in the patient cohort. A mutation of the conserved His133 to Pro was found in a PD patient and in his daughter. The patient did not show signs of neuroferritinopathy, but the mutation was associated with low L-ferritin levels and with mild chronic anemia. CONCLUSIONS: The results support the hypothesis that DNA variations in the ferritin genes are not a common cause for PD.