Homozygosity Mapping and Whole-Exome Sequencing to Detect SLC45A2 and G6PC3 Mutations in a Single Patient with Oculocutaneous Albinism and Neutropenia Andrew R
Total Page：16
File Type：pdf, Size：1020Kb
See related commentary on pg 1971 ORIGINAL ARTICLE Homozygosity Mapping and Whole-Exome Sequencing to Detect SLC45A2 and G6PC3 Mutations in a Single Patient with Oculocutaneous Albinism and Neutropenia Andrew R. Cullinane1, Thierry Vilboux1, Kevin O’Brien2, James A. Curry1, Dawn M. Maynard1, Hannah Carlson-Donohoe1, Carla Ciccone1, NISC Comparative Sequencing Program3, Thomas C. Markello1, Meral Gunay-Aygun2, Marjan Huizing1 and William A. Gahl1,2 We evaluated a 32-year-old woman whose oculocutaneous albinism (OCA), bleeding diathesis, neutropenia, and history of recurrent infections prompted consideration of the diagnosis of Hermansky–Pudlak syndrome type 2. This was ruled out because of the presence of platelet d-granules and absence of AP3B1 mutations. As parental consanguinity suggested an autosomal recessive mode of inheritance, we employed homozygosity mapping, followed by whole-exome sequencing, to identify two candidate disease-causing genes, SLC45A2 and G6PC3. Conventional dideoxy sequencing confirmed pathogenic mutations in SLC45A2, associated with OCA type 4 (OCA-4), and G6PC3, associated with neutropenia. The substantial reduction of SLC45A2 protein in the patient’s melanocytes caused the mislocalization of tyrosinase from melanosomes to the plasma membrane and also led to the incorporation of tyrosinase into exosomes and secretion into the culture medium, explaining the hypopigmentation in OCA-4. Our patient’s G6PC3 mRNA expression level was also reduced, leading to increased apoptosis of her fibroblasts under endoplasmic reticulum stress. To our knowledge, this report describes the first North American patient with OCA-4, the first culture of human OCA-4 melanocytes, and the use of homozygosity mapping, followed by whole-exome sequencing, to identify disease-causing mutations in multiple genes in a single affected individual. Journal of Investigative Dermatology (2011) 131, 2017–2025; doi:10.1038/jid.2011.157; published online 16 June 2011 INTRODUCTION polymorphism (SNP) arrays, followed by the next-generation Until recently, molecular diagnostics for patients with rare sequencing technique of whole-exome sequencing (Ng et al., disorders relied upon sequencing of genes identified as 2009, 2010; Otto et al., 2010). This reduces the amount of candidates by virtue of the clinical phenotypes. Now, data generated and is more cost effective than whole-genome massively parallel (‘‘next generation’’) sequencing allows sequencing (Teer and Mullikin, 2010). for unfocused detection of disease-causing mutations, with- We illustrate the benefit of next-generation sequencing in out the bias introduced by phenotype. This critical advantage a patient with oculocutaneous albinism (OCA) and con- can be particularly important for patients with clinical genital neutropenia. OCA is a group of autosomal recessively manifestations that point to complex diseases. The process inherited hypopigmentary disorders that affect melanin that is generally employed involves single-nucleotide pigment synthesis or trafficking of pigmentary enzymes or organelles (King et al., 2002) in the skin, hair, and eyes 1Medical Genetics Branch, National Human Genome Research Institute (Gronskov et al., 2007). Four genes are associated with OCA: (NHGRI), National Institutes of Health, Bethesda, Maryland, USA; 2Intramural TYR (OCA-1; Tomita et al., 1989), OCA2 (OCA-2; Rinchik Office of Rare Diseases Research, Office of the Director, National Institutes of et al., 1993), TYRP1 (OCA-3; Boissy et al., 1996), and Health, Bethesda, Maryland, USA and 3National Institutes of Health Intramural Sequencing Center (NISC), National Human Genome Research SLC45A2 (OCA-4; Newton et al., 2001). Mutations in these Institute, National Institutes of Health, Bethesda, Maryland, USA genes rarely cause phenotypic features other than albinism, Correspondence: Andrew R. Cullinane, Medical Genetics Branch, National but certain syndromes have OCA as an obligate component. Human Genome Research Institute (NHGRI), National Institutes of Health, Hermansky–Pudlak syndrome (HPS), e.g., is characterized by Bethesda, Maryland 20892, USA. E-mail: [email protected] OCA and a bleeding diathesis. There are 8 known human Abbreviations: ER, endoplasmic reticulum; HPS, Hermansky–Pudlak HPS genes (HPS1–8) (Oh et al., 1996; Dell’Angelica et al., syndrome; OCA, oculocutaneous albinism; SNP, single-nucleotide polymorphism 1999; Anikster et al., 2001; Suzuki et al., 2002; Li et al., Received 12 January 2011; revised 31 March 2011; accepted 5 April 2011; 2003; Zhang et al., 2003; Morgan et al., 2006), whose protein published online 16 June 2011 products are involved in the biogenesis of lysosome-related & 2011 The Society for Investigative Dermatology www.jidonline.org 2017 AR Cullinane et al. Homozygosity Mapping and Whole-Exome Sequencing organelles (Huizing et al., 2008). HPS commonly has other disease-associated genes, i.e., SLC45A2 causing OCA-4 and phenotypic features such as pulmonary fibrosis, which is G6PC3 causing neutropenia. Neither of these genes would associated with subtypes 1 and 4 (Oh et al., 1996; Suzuki have been pursued according to standard practice. We et al., 2002). conclude that SNP array analysis, along with whole-exome Congenital neutropenia is a heterogeneous group sequencing, can be useful in identifying disease-causing of hereditary disorders characterized by life-threatening mutations in a single affected individual, especially if the bacterial infections early in life due to a paucity of mature family is consanguineous and suitable for homozygosity neutrophils (Welte et al., 2006; Boztug et al., 2008). mapping. Mutations in several genes, including ELA2, HAX1, WAS, GFI1, and recently G6PC3 (Horwitz et al., 1999; Devriendt RESULTS et al., 2001; Person et al., 2003; Klein et al., 2007; Boztug Case report et al., 2009), cause such conditions. Neutropenia also occurs A 32-year-old Caucasian female presented to the National in patients with HPS-2 disease, due to mutations in AP3B1, Institutes of Health (NIH) Clinical Center with a history of which encodes the b-3A subunit of adaptor complex-3 inflammatory bowel disease, primary neutropenia and (Dell’Angelica et al., 1999). Most congenitally neutropenic thrombocytopenia, and a surgically repaired atrial septal patients, including those with HPS-2, respond to recombinant defect. Her medical history revealed that she was diagnosed human granulocyte colony-stimulating factor, which with OCA shortly after birth, and subsequent eye examina- increases neutrophil counts and decreases the number and tions confirmed the presence of ocular albinism (Figure 1a). severity of infections (Bonilla et al., 1989). The patient was hospitalized for E. coli sepsis in the neonatal In this article, we describe a patient of consanguineous period with a white cell count as high as 12 K mlÀ1; her parentage who presented with findings that suggested the platelet count was 130 K mlÀ1. In her first year of life, she possible diagnosis of HPS-2, i.e., OCA and neutropenia. suffered from recurrent ear and bladder infections. At 3 years When no mutations were found in AP3B1, we performed of age, she was hospitalized for pneumonia and was homozygosity mapping on a SNP array and whole-exome leukopenic, with a white blood cell count of 2,800 K mlÀ1. sequencing using the patient’s genomic DNA. This allowed Thereafter, she continued to have recurrent lower urinary us to identify disease-causing mutations in two different tract infections and was placed on prophylactic antibiotics. T GGA CC GG Control T G G A G G C C Patient G A CC A G C T 12345678910111213Control G C AAT G C T Patient 14 15 1716 18 19 20 21 22 x Figure 1. Clinical findings and DNA analysis. (a) Fair skin and classic red hair in our patient, typical for oculocutaneous albinism type 4 patients. (b) Prominent superficial venous pattern seen in all previously described G6PC3 mutation-positive neutropenia patients. (c) Pedigree showing affected and unaffected individuals; our patient is depicted by the red box. Note the consanguineous background of the family. (d) Regions of homozygosity in the genome of the patient (shown within red boxes). (e) Chromatogram of the mutation in SLC45A2 (c.986delC, p.T329RfsX68). (f) Chromatogram of the mutation in G6PC3 (c.829C4T, p.Q277X). Control sequences are shown for comparison. Photograph published with patient’s permission. 2018 Journal of Investigative Dermatology (2011), Volume 131 AR Cullinane et al. Homozygosity Mapping and Whole-Exome Sequencing Throughout childhood and adolescence, she had symptoms Other immunological, autoimmune, and infectious dis- of colitis, chronic abdominal pain, bloody diarrhea, recurrent ease studies were normal. She had a minimal decrease in her skin infections, easy bruising, and heavy menstrual periods. She total immunoglobulin A level, but other tests of immune was eventually diagnosed with Crohn’s disease at 16 years of competency were normal, and an assay for HIV was negative. age and failed medical therapy, resulting in a hemicolectomy at Her soluble IL-2R level was also normal. The antinuclear 17 years of age. Despite this surgery, she continued to have antigen level, extractable nuclear antigen panel, and assays symptoms of inflammatory bowel disease and has received for antibodies to platelets and neutrophils were all negative. antibiotics and immunosuppressive therapy intermittently. The patient’s parents were first cousins (Figure 1c). Because of her persistent cytopenias and history of Her brother had albinism,