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.

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Available from: Ludovica Volpi, Aug 31, 2015
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    • "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). "
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    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
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    • "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). "
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    • "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). "
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    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.
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