Clin Genet 2015: 88: 74–79 © 2014 John Wiley & Sons A/S. Printed in Singapore. All rights reserved Published by John Wiley & Sons Ltd CLINICAL doi: 10.1111/cge.12448 Short Report A founder in the TCIRG1 causes in the Ashkenazi Jewish population

,† ,† Anderson SL, Jalas C, Fedick A, Reid KF, Carpenter TO, Chirnomas D, S.L. Andersona , C. Jalasb , Treff NR, Ekstein J, Rubin BY. A founder mutation in the TCIRG1 gene A. Fedickc, K.F. Reida, causes osteopetrosis in the Ashkenazi Jewish population. T.O. Carpenterd,D. Clin Genet 2015: 88: 74–79. © John Wiley & Sons A/S. Published by John Chirnomasd, N.R. Treffc,e, Wiley & Sons Ltd, 2014 J. Eksteinf and B.Y. Rubina Osteopetrosis is a rare and heterogeneous characterized by aDepartment of Biological Sciences, dense mass that is a consequence of defective function and/or Fordham University, Bronx, NY 10458, development. Autosomal recessive osteopetrosis (ARO) is the most severe USA, bBonei Olam, Center for Rare form and is often fatal within the first years of life; early hematopoietic stem Jewish Genetic Disorders, Brooklyn, NY c transplant (HSCT) remains the only curative treatment for ARO. The 11204, USA, Department of majority of the ARO-causing are located in the TCIRG1 gene. We Microbiology and Molecular Genetics, Rutgers-Robert Wood Johnson Medical report here the identification and characterization of an A to T transversion in → School, Piscataway, NJ 08854, USA, the fourth base of the 2 donor splice site (c.117+4A T) in TCIRG1,a dYale University School of , mutation not previously seen in the Ashkenazi Jewish (AJ) population. Departments of Pediatrics Analysis of a random sample of individuals of AJ descent revealed a carrier (Endocrinology) and Orthopedics and frequency of approximately 1 in 350. Genotyping of five loci adjacent to the Rehabilitation, New Haven, CT 06520, c.117+4A→T-containing TCIRG1 revealed that the presence of this USA, eReproductive Medicine Associates mutation in the AJ population is due to a single founder. The identification of of New Jersey, Department of Research, this mutation will enable population and will facilitate the Morristown, NJ 07960, USA, and fDor identification and treatment of individuals homozygous for this mutation. Yeshorim, The Committee for Prevention of Jewish , Brooklyn, NY 11211, Conflict of interest USA The authors have declared no conflicting interests. †These authors contributed equally to the work.

Key words: Ashkenazi Jewish – founder mutation – osteopetrosis – TCIRG1 Corresponding author: B.Y. Rubin, Department of Biological Sciences, Fordham University, 441 E. Fordham Road, Bronx, NY 10458, USA. Tel.: +1 718 817 3637; fax: +1 718 817 2792; e-mail: [email protected]

Received 8 May 2014, revised and accepted for publication 19 June 2014

Osteopetrosis is a genetic disorder characterized by or even elevated levels of and are said to dense bone mass that is a consequence of defec- have an ‘osteoclast-rich’ form of osteopetrosis; in the tive osteoclast function and/or development (1). remaining 30%, there is a clear defect in the production Approximately 70% of patients present with normal and differentiation of these cells and these individuals

74 A founder mutation in the TCIRG1 gene causes osteopetrosis are classified as having an ‘osteoclast-poor’ form of was performed with the approval of the Fordham Univer- osteopetrosis. sity institutional review board (IRB). Autosomal recessive (‘malignant’) osteopetrosis (ARO) is the most severe form of the and is often fatal within the first years of life (1, 2). Infants Reverse transcriptase-polymerase chain reaction (RT-PCR) with ARO exhibit abnormal and dense bone structure, analysis of fetal cell RNA susceptibility to fractures, the absence of a bone mar- RNA was isolated from fetal cells obtained by chorionic row cavity, and thrombocytopenia. Excessive villus sampling (CVS) using RNeasy Plus Mini Kits bone development can cause cranial nerve entrapment. (Qiagen, Germantown, MD) and RT-PCR analysis was Untreated, ARO patients have a life expectancy of performed with OneStep RT-PCR Kits (Qiagen) using 3–4 years (3). TCIRG1-2F and -3R primers (located in 2 and 3, The majority of the ARO-causing mutations are respectively) (see Table S1, Supporting Information for located in the T-cell, immune regulator 1, ATPase, primer sequences). The RT-PCR products were analyzed H+transporting, lysosomal V0 subunit a3 (TCIRG1) on 2% agarose gels and purified for sequence analysis. gene (4, 5). Mammalian V- consist of at least 13 different subunits, organized into a cytoplasmic V1 domain and a membrane embedded V0 domain. The DNA sequencing V1 domain is responsible for the hydrolysis of ATPase DNA sequencing was performed by fluorescent dye and the V0 domain functions as a proton translocator terminator detection on an ABI 3730xl Analyzer (6). The a subunit, which is a component of the V0 (GENEWIZ, South Plainfield, NJ). domain, exists as four isoforms. The a3 isoform exists primarily in osteoclasts (7). The V-ATPase complex located in the membrane of the ruffled border of the analysis for population screening bone-bound osteoclasts releases protons and generates an acidic environment, required for the solubilization Genotyping was accomplished via an allelic discrim- of hydroxyapatite, in the resorption area beneath the ination assay. Sequence-specific forward and reverse osteoclast. The osteopetrosis-causing mutations in the primers were used to amplify a region around the poly- TCIRG1 gene generate a non-functional V-ATPase morphic sequence, then allelic discrimination was per- unable to generate an acidic environment. formed utilizing VIC- and FAM-labeled probes to detect As a result of historical founder effects, individ- the normal and mutant , respectively (see Table S1 uals of Ashkenazi Jewish (AJ) descent are subject for primer and probe sequences). to a variety of genetic disorders (8). The success of All from the individuals identified as being carriers were confirmed to be heterozygous for the genetic screening programs for this population has been → facilitated by the limited number of disease-causing c.117+4A T mutation by PCR amplification and mutations (9). A recent comprehensive carrier frequency sequencing of a 309 bp fragment surrounding the study on individuals of AJ descent has suggested an mutation, using primers located in 1 and expansion of the number of disorders that should be 2. The sequence of the primers, TCIRG1-int-1 and routinely tested for and has provided valuable carrier TCIRG1–int-2, are presented in Table S1. frequency information on 16 diseases prevalent in this population (10). Haplotype analysis We show the presence of a founder mutation in the TCIRG1 gene that is the genetic cause of ARO in Microsatellite marker analysis of the region adjacent to three families in which both parents are of AJ descent. the TCIRG1 gene was performed on the DNA of five Screening of a random population of individuals of AJ affected children and 12 carriers (the three sets of par- descent reveals the carrier frequency of this mutation ents of the affected children and the six unrelated indi- to be 1 in approximately 350. The identification of this viduals identified in the population frequency study). mutation in the AJ population supports its inclusion Amplification of the D11S4155, D11S987, D11S1917, in carrier screening programs and should facilitate D11S1337 and D11S4178 polymorphic microsatellite the diagnosis and treatment of ARO in individuals of markers, which are all within 0.4 MB of TCIRG1,was AJ descent. performed using the respective primers listed in Table S1. The forward ‘F’ primer of each pair was labeled on the 5′ end with 6-FAM™ (Fluorescein) dye (IDT, Coralville, Subjects and methods IA). The amplified products were run on an ABI 3730xl Analyzer at GENEWIZ (South Plainfield, NJ) and the subjects results analyzed using Peak Scanner v1.0 software (Life or cheek swab samples were obtained from Technologies, Grand Island, NY). For each marker ana- the affected children and their parents. Anonymous lyzed, the smallest PCR product obtained was interpreted blood samples from individuals of AJ descent were as having the least number of repeats; that size PCR obtained from the screening program (11). product was assigned an arbitrary allele number of ‘1,’ Genomic DNA was purified from blood using QIAamp not meant to imply the actual number of repeats, but DNA Blood Kits (Qiagen, Germantown, MD). This work the smallest relative number for a given marker within

75 Anderson et al. the samples. A PCR product that was, for example, one Definitive demonstration of the disease-causing effect repeat larger was given an allele number of ‘2’ and so on. of base changes in the variant positions of donor splice sites is dependent on the ability to detect a patholog- ical effect of these changes. As the surviving individ- Results uals homozygous for the c.117+4A→T mutation all Clinical report received HSCT and therefore no longer had periph- eral blood cells bearing this mutation, the impact of Five patients of AJ descent exhibiting typical signs of the c.117+4A→T mutation was examined in fetal cells ARO were all born to nonconsanguineous AJ parents. homozygous for the mutation (derived from a fetus con- Patient 1 presented at 3 months of age with leuko- ceived by the parents of patient 1). DNA sequence anal- cytosis without fever, , bulging ysis of RT-PCR products generated from these cells and fontanelle and dysmorphic facial features typical of from two fetal cell samples not bearing this mutation osteopetrosis. On the basis of phenotypic presenta- (derived from unrelated pregnancies), using a primer tion of osteopetrosis, this child received an unrelated located at the 5′ end of 2 and a primer in exon 3 of hematopoietic stem cell transplant (HSCT) at 7 months the TCIRG1 gene, revealed that the cells containing the but died from infectious complications. c.117+4A→T mutation generated a smaller transcript Patient 2 was noted at 2 months of age to have an (Fig. 1b); sequencing analysis of the RT-PCR products increased head circumference as well as a bulging ante- revealed that the smaller transcript was missing the last rior fontanel. No diagnosis was made at the time. At part of exon 2 (Fig. 1b). This event 5 months, the child’s head circumference was greater involved the use of a cryptic splice donor site within exon than the upper limit of normal, the bulging anterior 2, resulting in a transcript that encoded 14 fewer amino fontanel had become more prominent and there was a acids in the TCIRG1-encoded , due to the splicing significant impairment of vision. X rays revealed the out of the last 42 nt of the exon (Fig. 1c). It is interesting presence of dense and the child was diagnosed to note that the homozygous presence of a c.117+4A→T as having osteopetrosis. At 9 months, the child received mutation in the TCIRG1 gene has also been noted in a HSCT from a fraternal twin brother. The transplan- a child with osteopetrosis born to consanguineous par- tation was successful and the child has continued to ents of Turkish descent. Characterization of the transcript develop well. generated from this allele in fibroblast cells also revealed Patients 3, 4 and 5 were born to a single couple. the use of the cryptic splice site in exon 2 (12). At 2 months, the parents noted the inability of patient 3 to see. Ocular examination revealed little pupillary response, atrophy of the optic nerve and a flat elec- Carrier frequency and haplotype analysis troretinogram (ERG). Compression of the optic nerve The identification of six unrelated individuals of AJ was noted on a computed tomography (CT) scan. A descent (the parents of the affected children), who are skeletal survey performed at 5 months revealed dense carriers of the c.117+4A→T mutation, prompted a study bones and the child was diagnosed as having osteopetro- of the frequency of this mutation in this population. sis. At 16 months, HSCT was performed with a matched Genotype analysis was performed using TaqMan tech- unrelated donor. The child died shortly thereafter from nology on 2092 DNA samples collected from a random complications associated with anesthesia. Skeletal sur- population of individuals of AJ descent. Two thousand veys were performed on patients 4 and 5 shortly after and eighty-eight samples were successfully amplified birth and both were determined to have osteopetrosis. and six individuals were determined to be heterozygous Both children received HSCT from unrelated matched for the c.117+4A→T bearing allele (Fig. 2). PCR ampli- donors and both continue to do well. fication and DNA sequence analysis of a 309 bp fragment encompassing the c.117+4A→T mutation performed on Identification and characterization of an ARO-causing the DNA of the six individuals found to be heterozygous homozygous mutation in TCIRG1 for the mutant allele and on the four samples that failed to amplify in the TaqMan assay confirmed the six indi- The suspected diagnosis of osteopetrosis in patient #1 viduals to be heterozygous for the c.117+4A→T allele prompted an analysis of the DNA sequence of the and the four samples that failed to amplify were homozy- patient’s TCIRG1, CLCN7 and OSTM1 . For this gous for the wildtype allele. The carrier frequency for analysis, the protein-encoding exonic regions with flank- this mutation was thus determined to be approximately 1 ing intronic sequences were amplified and sequenced. in 350. The homozygous presence of an A to T transversion was To examine whether the presence of this mutation detected in the fourth base of the intron 2 donor splice site in this population is due to a founder effect, haplo- (c.117+4A→T; NG_007878.1, nt 7377) in the child’s type analysis was performed using five microsatellite TCIRG1 gene and the parents were determined to be het- markers, D11S4155, D11S987, D11S1917, D11S1337 erozygous for this mutation (Fig. 1a). DNA amplification and D11S4178, located within 0.4 MB of the TCIRG1 and sequence analysis revealed that all of the remaining gene. The affected children were observed to be homozy- ARO patients were homozygous for the c.117 + 4A → T gous for the number of repeats at each of the five loci. mutation and all of their parents were heterozygous for Microsatellite markers that are ‘linked’ to a mutation this mutation (data not shown). would be expected to bear the same number of repeats

76 A founder mutation in the TCIRG1 gene causes osteopetrosis

Table 1. The c.117+4A>T allele and its associated haplotype

Individuala c.117 + 4 D11S4155b D11S987b D11S1917b D11S1337b D11S4178b

A1 TT 2, 2 7, 7 3, 3 1, 1 1, 1 A2 TT 2, 2 7, 7 3, 3 1, 1 1, 1 A3 TT 2, 2 7, 7 3, 3 1, 1 1, 1 A4 TT 2, 2 7, 7 3, 3 1, 1 1, 1 A5 TT 2, 2 7, 7 3, 3 1, 1 1, 1 C1 TA 2,4 5,7 1, 31,11,1 C2 TA 2,4 4,73,31,6 1, 1 C3 TA 2,4 5,73,31,5 1,3 C4 TA 2,3 2,7 1, 31,11,1 C5 TA 2,3 2,7 3,3 1,1 1,1 C6 TA 2,4 5,7 1, 31,5 1,3 C7 TA 2,4 5,7 1, 31,11,1 C8 TA1,2 5, 73,31,4 1, 1 C9 TA 2,4 4,7 1, 31,4 1,4 C10 TA 2,4 4,73,5 1, 1 1, 1 C11 TA 2,4 1,7 1, 31,11,1 C12 TA 2, 52,7 3,3 1,7 1, 1 aA = affected, C = carrier. bA designation of "1" for the dinucleotide repeat markers is a relative number and represents the least number of repeats seen for a given marker in this cohort of 17 individuals. Bolded letters/numbers represent variants present on the mutant allele. for each of the markers if the affected child inherited the Discussion same allele from each parent. The parents and all other carriers were found to be at least heterozygous for the We present the first demonstration of the existence number of repeats for each of the markers that all of the of ARO in the AJ population and demonstrate the affected children were homozygous for (Table 1). This disease-causing mutation to be an A to T transversion finding strongly supports the notion that this mutation is in the fourth base of the intron 2 donor splice site → the result of a founder effect. (c.117+4A T) of the TCIRG1 gene. This mutation

Fig. 1.(a) Electropherograms showing sequence of the first six nt of TCIRG1 intron 2. Polymerase chain reaction (PCR) product from wildtype DNA contains an ‘A’ (green) in the fourth base in both alleles; from DNA of the autosomal recessive osteopetrosis (ARO)-affected individual (a homozygote), a ‘T’ (red) in both alleles; from parental (heterozygote) DNA, an ‘A’ (green) on one allele overlapped with a ‘T’ (red) from the other allele. (b)RNA was subjected to RT-PCR with primers located in exons 2 and 3 with an expected product size of 167 bp. TCIRG1 transcripts from cells homozygous for the mutation (ARO) generated a smaller product, which sequencing revealed to be 125 bp in size, representing a loss of 42 nucleotides at the end of exon 2, while the products from the unrelated fetal cells (WT) were of the expected size. Electropherograms show nt 74–79 of exon 2 (in red), followed either by the first 6 nt of exon 3 (also in red), due to the exclusion of the last 42 nt of exon 2 (ARO-affected), or nt 80–85 (in blue) of exon2(wildtype). (c) The c.117+4A→T mutation results in the splicing out of the last 42 nt (in blue) of exon 2, encoding 14 amino acids, in addition to the normally spliced out intron 2. The 42 nt are spliced out of the TCIRG1 transcript due to the use of a cryptic splice donor site (‘gt’ in blue, italicized text) when the c.117+4A→T mutation in intron 2 is present. The removal of the 42 nt results in the loss of 14 amino acids (bold, upper-case letters) from the cytoplasmic portion of the TCIRG1 protein.

77 Anderson et al.

Fig. 2. Carrier frequency determination by allelic discrimination assay. Two thousand and ninety-two DNA samples were assayed for the presence of the c.117+4A→T mutation. Six heterozygotes were discovered among the 2088 that were successfully amplified, demonstrating a carrier frequency of approximately 1 in 350. alters the splicing of the gene transcript and encodes The homozygous presence of this mutation in five a protein missing 14 amino acids from the hydrophilic affected children and its heterozygous presence in the N-terminal, cytoplasmically located portion of the a3 six parents of the children and six unrelated individuals, subunit of the V-ATPase. all of whom share the same haplotype as the affected The TCIRG1 gene encodes two isoforms of the a3 children on at least one allele in the region adjacent to the subunit of V-ATPase: (i) isoform a, which is 830 amino TCIRG1 gene, identify the c.117+4A→Tmutationasthe acids long, highly expressed in osteoclasts and essen- first founder mutation in TCIRG1 in the AJ population. tial for their function; and (ii) isoform b, which is In light of its frequency in this population and the transcribed from exon 5 of the TCIRG1 gene and is significant mortality and medical challenges associated missing the first 216 amino acids of isoform a.This with osteopetrosis, its inclusion in routine carrier testing latter form is expressed by and essential for activation should be considered. of T-cells. The fact that the longer isoform a is essential for V-ATPase function in osteoclasts, as evidenced Supporting Information by the ARO-causing mutations in the region of the Additional supporting information may be found in the online TCIRG1 gene that encodes amino acids 1–216 (e.g. version of this article at the publisher’s web-site. c.118–1G→A (13), c.197-1G→A (13), c.480_481insG (13), c.117+4A→T and others), suggests the presence of an essential element(s) within these amino acids, all Acknowledgements of which lie within the cytoplasmic domain of the a3 This work was funded by a grant from Bonei Olam, The Center for subunit. It is not known at this time what role amino Rare Jewish Genetic Disorders. acids 26–39, the portion of the first 216 amino acids of the a3 subunit lost as a consequence of the c.117+4A→T References mutation, play in the loss of function of V-ATPase, but 1. Tolar J, Teitelbaum SL, Orchard PJ. Osteopetrosis. N Engl J Med 2004: it is apparently sufficient to cause severe disease. 351: 2839–2849. The demonstrated presence of this disease-causing 2. Mazzolari E, Forino C, Razza A, Porta F, Villa A, Notarangelo LD. mutation in individuals of AJ descent will facilitate the A single-center experience in 20 patients with infantile malignant diagnosis of infants who present with osteopetrosis-like osteopetrosis. Am J Hematol 2009: 84: 473–479. 3. Balemans W, Van Wesenbeeck L, Van Hul W. A clinical and molecular symptoms and thereby accelerate the search for suitable overview of the human osteopetroses. Calcif Tissue Int 2005: 77: hematopoietic stem cell donors. 263–274.

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