Article

Targeted Next-Generation Sequencing Appoints C16orf57 as Clericuzio-Type Poikiloderma with Neutropenia Gene

Università degli Studi di Milano, Dipartimento di Biologia e Genetica per le Scienze Mediche, Milan, Italy.
The American Journal of Human Genetics (Impact Factor: 10.99). 12/2009; 86(1):72-6. DOI: 10.1016/j.ajhg.2009.11.014
Source: PubMed

ABSTRACT Next-generation sequencing is a straightforward tool for the identification of disease genes in extended genomic regions. Autozygosity mapping was performed on a five-generation inbred Italian family with three siblings affected with Clericuzio-type poikiloderma with neutropenia (PN [MIM %604173]), a rare autosomal-recessive genodermatosis characterised by poikiloderma, pachyonychia, and chronic neutropenia. The siblings were initially diagnosed as affected with Rothmund-Thomson syndrome (RTS [MIM #268400]), with which PN shows phenotypic overlap. Linkage analysis on all living subjects of the family identified a large 16q region inherited identically by descent (IBD) in all affected family members. Deep sequencing of this 3.4 Mb region previously enriched with array capture revealed a homozygous c.504-2 A>C mismatch in all affected siblings. The mutation destroys the invariant AG acceptor site of intron 4 of the evolutionarily conserved C16orf57 gene. Two distinct deleterious mutations (c.502A>G and c.666_676+1del12) identified in an unrelated PN patient confirmed that the C16orf57 gene is responsible for PN. The function of the predicted C16orf57 gene is unknown, but its product has been shown to be interconnected to RECQL4 protein via SMAD4 proteins. The unravelled clinical and genetic identity of PN allows patients to undergo genetic testing and follow-up.

Download full-text

Full-text

Available from: Ludovica Volpi, Aug 31, 2015
0 Followers
 · 
257 Views
  • Source
    • "The diagnosis of our PN patients were made clinically and confirmed by molecular analysis for deleterious mutations in the causative gene, USB1, identified recently in 2010 [Volpi et al., 2010]. c.531delA homozygous deleterious mutation was detected in both patient's genomic DNA (Fig. 2C,D). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Poikiloderma with neutropenia (PN), is a rare genodermatosis associated with patognomic features of poikiloderma and permanent neutropenia. Three common recurrent mutations of related gene, USB1, were considered to be associated with three different ethnic origins. The most common recurrent mutation, c.531delA, has been detected in seven Caucasian patients in the literature. In this paper, we present review of all patients from the literature and report two additional patients of Turkish ancestry with the diagnosis of PN. The diagnosis of these two PN patients were made clinically and confirmed by molecular analysis which detected the most common recurrent mutation, c.531delA. Genotype-ethnic origin correlation hypothesis, therefore, has been strengthened with this result. Short stature in PN, is a common finding, which until now has never been treated with growth hormone (GH). One of our patients is the first patient with attempted treatment of short stature via GH administration. Finally, both of our patients had high-pitched voice and vocal cord nodules which might be considered as additional clinical findings not associated with PN before. © 2014 Wiley Periodicals, Inc.
    American Journal of Medical Genetics Part A 10/2014; 164(10). DOI:10.1002/ajmg.a.36683 · 2.05 Impact Factor
  • Source
    • "sequencing (NGS), either in combination with whole-exome capture or targeted capture of specific genomic regions, or used to directly sequence the entire genome (WGS) (Lupski et al., 2010; Ng et al., 2009; Volpi et al., 2010). Whole-exome sequencing was also successfully employed to identify a human CLCN7 mutation in osteopetrosis patients (Sui et al., 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Chloride/proton exchange by the lysosomal anion transporter ClC-7/Ostm1 is of pivotal importance for the physiology of lysosomes and bone resorption. Mice lacking either ClC-7 or Ostm1 develop a lysosomal storage disease and mutations in either protein have been found to underlie osteopetrosis in mice and humans. Some human disease-causing CLCN7 mutations accelerate the usually slow voltage-dependent gating of ClC-7/Ostm1. However, it has remained unclear whether the fastened kinetics is indeed causative for the disease. Here we identified and characterized a new deleterious ClC-7 mutation in Belgian Blue Cattle with a severe symptomatology including peri-natal lethality and in most cases gingival hamartomas. By autozygosity mapping and genome-wide sequencing we found a handful of candidate variants, including a cluster of three private SNPs causing the substitution of a conserved tyrosine in the CBS2 domain of ClC-7 by glutamine. The case for ClC-7 was strengthened by subsequent examination of affected calves that revealed severe osteopetrosis. The Y750Q mutation largely preserved the lysosomal localization and assembly of ClC-7/Ostm1, but drastically accelerated its activation by membrane depolarization. These data provide first evidence that accelerated ClC-7/Ostm1 gating per se is deleterious, highlighting a physiological importance of the slow voltage-activation of ClC-7/Ostm1 in lysosomal function and bone resorption.
    Disease Models and Mechanisms 10/2013; 7(1). DOI:10.1242/dmm.012500 · 5.54 Impact Factor
  • Source
    • "C16orf57 encodes a protein of unknown molecular function . To date, 19 distinct C16orf57 mutations have been identified in 31 patients with PN (for details, see Supplemental Table S1; Arnold et al. 2010; Tanaka et al. 2010; Volpi et al. 2010; Clericuzio et al. 2011; Colombo et al. 2012), all of which lead to the generation of truncated, and most likely nonfunctional, proteins. C16orf57 is also mutated in a subset of patients diagnosed with dyskeratosis congenita (DC) and Rothmund-Thomson syndrome (RTS) (Walne et al. 2010; Piard et al. 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: C16orf57 encodes a human protein of unknown function, and mutations in the gene occur in poikiloderma with neutropenia (PN), which is a rare, autosomal recessive disease. Interestingly, mutations in C16orf57 were also observed among patients diagnosed with Rothmund-Thomson syndrome (RTS) and dyskeratosis congenita (DC), which are caused by mutations in genes involved in DNA repair and telomere maintenance. A genetic screen in Saccharomyces cerevisiae revealed that the yeast ortholog of C16orf57, USB1 (YLR132C), is essential for U6 small nuclear RNA (snRNA) biogenesis and cell viability. Usb1 depletion destabilized U6 snRNA, leading to splicing defects and cell growth defects, which was suppressed by the presence of multiple copies of the U6 snRNA gene SNR6. Moreover, Usb1 is essential for the generation of a unique feature of U6 snRNA; namely, the 3'-terminal phosphate. RNAi experiments in human cells followed by biochemical and functional analyses confirmed that, similar to yeast, C16orf57 encodes a protein involved in the 2',3'-cyclic phosphate formation at the 3' end of U6 snRNA. Advanced bioinformatics predicted that C16orf57 encodes a phosphodiesterase whose putative catalytic activity is essential for its function in vivo. Our results predict an unexpected molecular basis for PN, DC, and RTS and provide insight into U6 snRNA 3' end formation.
    Genes & development 08/2012; 26(17):1911-25. DOI:10.1101/gad.193169.112 · 12.64 Impact Factor
Show more