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Papers in Press. First published October 27, 2005 as doi:10.1373/clinchem.2005.056192 Clinical Chemistry 52:1 000 – 000 (2006) Molecular Diagnostics and Genetics Population Differences in the Polyalanine Domain and 6 New Mutations in HLXB9 in Patients with Currarino Syndrome Mercè Garcia-Barceló,1,2 Man-ting So,1,2 Danny Ko-chun Lau,1 Thomas Yuk-yu Leon,1 Zheng-wei Yuan,1,3 Wei-song Cai,1,3 Vincent Chi-hang Lui,1 Ming Fu,1,4 Jo-Anne Herbrick,5 Emily Gutter,6 Virginia Proud,6 Long Li,4 Jacqueline Pierre-Louis,7 Kirk Aleck,8 Ernest van Heurn,9 Elena Belloni,10 Stephen W. Scherer,5 and Paul Kwong-hang Tam1,2* Background: The combination of partial absence of the sacrum, anorectal anomalies, and presacral mass constitutes Currarino syndrome (CS), which is associated with mutations in HLXB9. Methods: We analyzed HLXB9 mutations by direct sequencing in 5 CS families, 6 sporadic cases, and 97 healthy Chinese individuals and potentially pathologic expansion of HLXB9 GCC repeats in patients, 4 general populations [Chinese, Japanese, Yoruba, and the Utah subset of the Centre du Etude Polymorphisme Humain (CEPH)] from the HapMap project, and 45 Chinese individuals. Results: We identified 6 novel mutations, including 2 missense mutations affecting highly conserved residues (Ser185X, Trp215X, Ala26fs, Ala75fs, Met1Ile, and Arg273Cys). Allele and genotype distributions showed marked statistically significant differences. (GCC)11 was the most common allele overall; its frequency ranged from 90% in CEPH to 68% in Yoruba and 50% in Chinese and Japanese populations. (GCC)9 was almost as common as (GCC)11 in Chinese and Japanese populations, whereas its frequency was <10% in Yoruba and CEPH populations. The Yoruba population had the highest frequency of the largest alleles [(GCC)12 and (GCC)13], which were almost absent in the other groups. Conclusions: Lack of HLXB9 mutations in some patients and the presence of variable phenotypes suggest DNA alterations in HLXB9 noncoding regions and/or in other genes encoding HLXB9 regulatory molecules or protein partners. If HLXB9, like other homeobox genes, has a threshold beyond which triplet expansions are pathologic, those populations enriched with larger alleles would be at a higher risk. The data illustrate the importance of ethnicity adjustment if these polymorphic markers are to be used in association studies. 1 Department of Surgery, 2 Genome Research Center, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China. 3 Department of Pediatric Surgery, China Medical University, Shenyang, China. 4 Department of Surgery, Beijing Children’s Hospital, Beijing, China. 5 Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada. 6 Department of Pediatrics, Children’s Hospital of the King’s Daughters, Norfolk, VA. 7 Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada. 8 St. Joseph’s Hospital, CHC Phoenix Genetics Program, Phoenix, AZ. 9 Surgical Unit, University Hospital, Maastricht, The Netherlands. 10 IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, and IEO, Istituto Europero di Oncologia, Milan, Italy. * Address correspondence to this author at: Division of Paediatric Surgery, Department of Surgery, University of Hong Kong Medical Centre, Queen Mary Hospital, Hong Kong SAR, China. Fax 852-2817-3155; e-mail [email protected]. Received June 16, 2005; accepted October 10, 2005. Previously published online at DOI: 10.1373/clinchem.2005.056192 © 2006 American Association for Clinical Chemistry The Currarino syndrome (CS; OMIM 176450) has been described as a triad of partial sacral agenesis with intact first sacral vertebra (sickle-shaped sacrum), presacral mass, and anorectal malformations (1–3 ). The spectrum of anorectal malformations ranges from anal stenosis to imperforate anus with/without anal fistula to the spinal cord or to the urogenital system. Females are more frequently affected than males (2, 3 ). Isolated anorectal malformations have an estimated incidence of 1 in 5000 live births, but the incidence of the complete triad is unknown. CS is associated with mutations in the homeobox gene HLXB9 and may segregate in families as an autosomal dominant trait, mainly as a result of haploinsufficiency 1 Copyright © 2005 by The American Association for Clinical Chemistry 2 Garcia-Barceló et al.: HLXB9 in Currarino Patients and the General Population (4, 5 ). The phenotype of the disease is variable (39% of patients present with a severe phenotype, 29% are clinically apparent, 28% have changes apparent only on x-ray, and 4% are asymptomatic), indicating that the manifestation and severity of the disease might depend not only on HLXB9 mutations, but also on the effect of other, as yet unknown, genes that could act as modifiers. Primarily because of its great phenotypic variability, CS is frequently misdiagnosed. A combined diagnostic protocol (6 ) includes a plain anteroposterior radiograph of the sacrum as the first step. If hemisacrum is present, molecular analysis of the HLXB9 gene and radiologic study of parents and relatives are indicated to distinguish between sporadic and familial cases of CS. HLXB9 has 3 exons encoding a 403-amino acid protein. The HLXB9 protein functions as a transcription factor regulating gene expression in both developing and adult tissues, although little is known about target genes or protein partners. Structurally, HLXB9 contains a homeodomain, a highly conserved region of 82 amino acids, and a polyalanine region consisting of 16 alanines (Fig. 1). Polyalanine tracts, coded by imperfect trinucleotide repeats (GCN) (7, 8 ), contain ⬃20 alanines. Polyalanine expansions have been described in 9 genes (HOXD13, RUNX2, ZIC2, HOXA13, FOXL2, SOX3, ARX, PHOX2B, and PABPN1) as the cause of congenital defects (8, 9 ). Except for PABPN1, all of these genes code for transcription factors with important roles during development and differentiation, as is the case for HLXB9 (10 ). To date, 25 CS-causing HLXB9 heterozygous mutations have been identified. All missense mutations are clustered in the homeodomain, whereas nonsense and frameshift mutations are mostly on the NH2 terminus of the protein (2, 11 ). We report HLXB9 mutations found in 5 CS families and 6 sporadic cases. In addition, we present an analysis of the distribution of the polyalanine tract polymorphisms in 4 different populations [Chinese, Japanese, Yoruba, and Centre du Etude Polymorphisme Humain (CEPH)] from the haplotype mapping (HapMap) project. Participants and Methods patients and controls After obtaining informed consent, we studied 31 individuals (18 patients and their relatives). All patients presented with the complete Currarino triad. Six of the affected individuals had no family history of CS and were classified as sporadic cases (S1 through S6 in Table 1). Patient S4 was also affected with Poland syndrome [congenital underdevelopment or absence of the chest muscle and bone (pectoralis and sternal) on one side of the body and cutaneous syndactyly of the hand on the same side], and patient S6 with club foot. Parents of these sporadic CS patients were also included in the study when available. In the remaining affected individuals, CS was classified as familial because characteristics of the CS phenotype had been observed in some family members. These familial cases were distributed in 5 families (F1 through F5), all of Caucasian origin, whose phenotypes and family structures are depicted in Fig. 2. We studied 97 healthy Chinese individuals from Hong Kong as controls. We also analyzed the polyalanine region of HLXB9 in 270 samples representing individuals from 4 different populations. These samples included a panel of 30 trios from the Yoruba in Ibadan, Nigeria; a panel of 30 trios from the CEPH collection (US Utah residents with ancestry from northern and western Europe); and a panel of 45 unrelated Japanese individuals in Tokyo and 45 unrelated Han Chinese individuals in Beijing, all represented in the HapMap project. We measured GCC repeats [(GCC)n] in 48 additional healthy Chinese from Hong Kong. sequence and data analysis We used PCR amplification and direct sequencing to screen for DNA variants in the coding regions and basic promoter of the HLXB9 gene. Sequencing was performed with the Big DyeTM Terminator (Ver. 3.0) Cycle Kit (Applied Biosystems) and an ABI 3100 sequencer (Applied Biosystems). Primers (designed from GenBank sequence NT_007741.12), PCR, and sequencing conditions are available in the Data Supplement that accompanies the online version of this article at http://www.clinchem. Table 1. Phenotype, HLXB9 mutation, and GCC-repeat analyses of the sporadic CS patients. Mutation/(GCC)n genotype Patient S1a S2a S3d S4d S5a S6a a (M)b (M) (F) (M) (F) (M) Phenotype Proband Father Mother CS CS CS CS ⫹ Poland syndrome CS CS ⫹ club foot Arg273Cys; (GCC)11/(GCC)11 ⫺; (GCC)11/(GCC)11 ⫺; (GCC)11/(GCC)11 ⫺; (GCC)11/(GCC)11 ⫺; (GCC)9/(GCC)11 Ser185X; (GCC)9/(GCC)11 NA ⫺; (GCC)11/(GCC)12 NA ⫺; (GCC)11/(GCC)11 ⫺; (GCC)9/(GCC)11 Ser185X; (GCC)9/(GCC)11 ⫺;c (GCC)11/(GCC)11 ⫺; (GCC)9/(GCC)11 NA ⫺; (GCC)11/(GCC)11 ⫺; (GCC)11/(GCC)11 ⫺; (GCC)11/(GCC)12 Chinese origin. M, male; F, female; NA, not available. c ⫺, no mutation detected. d Caucasian origin. b 3 Clinical Chemistry 52, No. 1, 2006 org/content/vol52/issue1/. Hardy–Weinberg equilibrium was tested according to the procedure described by Guo and Thompson (12 ). Results mutation analysis We identified 6 novel heterozygous mutations (Fig. 1), including 2 nonsense (Ser185X and Trp215X), 2 frameshifts (Ala26fs and Ala75fs), and 2 missense mutations affecting highly conserved amino acids such as the initiating methionine (Met1Ile) and Arg 31 (Arg273Cys) of the homeodomain region. Met1Ile is the first HLXB9 missense mutation localized outside the homeodomain. All frameshift and nonsense mutations described predict truncated proteins that, if stably translated, would lack the homeodomain region, possibly affecting its DNA-binding and transcription-regulation activities. The mutations described below were detected in 2 of 6 sporadic cases (Table 1) and in 4 of the 5 CS families (Fig. 2 and Table 2). These mutations were not observed in 97 Hong Kong Chinese (this study) or in 87 Caucasian controls (5 ). sporadic cases Among the sporadic cases (Table 1), only 2 male patients (S1 and S6) harbored HLXB9 mutations. S1 had a c815C⬎T transition leading to a substitution of residue 273 of the protein (arginine) with a cysteine (Arg273Cys). This missense mutation affects a highly conserved amino acid (amino acid 31 of the homeodomain R31 within helix 2) involved in the binding of the HLXB9 protein to the target DNA (13–15 ). R31 also contributes to the correct packaging of helices II and III by forming a salt bridge with a conserved glutamate residue at position 42 in helix III (14, 16 –18 ). Missense mutations in R31 have been found in the human homeobox genes PITX2, MSXI, MSX2, LMX1B, and HOXD13 and are associated with 5 different developmental diseases: iridogoniodysgenesis syndrome, tooth agenesis, enlarged parietal foramina, nail-patella syndrome, and several digital anomalies, respectively (18, 19 ). Studies of these homeobox genes have demonstrated the in vivo relevance of this mutation, which has even been defined as a “hot spot” for disease (18, 20 ). Functional analyses revealed that substitution of the R31 residue by a histidine reduces the capability of the protein to bind DNA and also the ability to activate transcription (21, 22 ). Patient S6 harbored a c554C⬎A transversion originating the nonsense mutation Ser185X (TGC changes to stop codon TGA), which predicts a truncated protein consisting of only 185 amino acids. Interestingly, Ser185X was also found in the apparently healthy father of S6. familial cases Family 2. Three affected members (II2, II3, and III1) harbored a c3G⬎A transition predicting a methionine (ATG) to isoleucine (ATA) change at the initiating codon. Interestingly, Met1Ile is the first HXLB9 missense mutation found that is not clustered in the homeodomain region (2, 11 ). The c3G nucleotide is conserved 100% in the initiation codons of all eukaryotes and in most prokaryotes (23 ). A mutation in the initiating codon would likely lead to loss of the signal for initiation of translation, suggesting either that no protein is produced or the translation initiation site moves up- or downstream. In HLXB9, the next in-frame ATG codon would correspond to methionine 223. Translation initiation from this internal ATG site would yield a 180-amino acid protein lacking the N-terminal domain (which is supposed to be involved in Fig. 1. Schematic drawing showing the HLXB9 gene and the HLXB9 protein with the mutations identified in this study. Correspondence between HLXB9 coding regions and HLXB9 protein is also represented. Nucleotide positions are defined in relation to the first nucleotide of the start codon, which is designated position ⫹1, and according to RefSeq NM_005515.2, which comprises 11 GCC repeats. The amino acid residues are numbered according to RefSeq NP_005506, starting at the initiator methionine residue. 4 Garcia-Barceló et al.: HLXB9 in Currarino Patients and the General Population Table 2. HLXB9 mutation and GCC-repeat analyses of the familial CS patients.a Family Family member(s) analyzed Mutation/(GCC)n genotype F1 II2 III7;III8 II2; II3;III1 I1 I2 II1 I1; II3 I2 II3 II4; III1 III2 ⫺;b (GCC)9/(GCC)11 ⫺; (GCC)11/(GCC)11 Met1Ile; (GCC)11/(GCC)11 ⫺; (GCC)9/(GCC)12 Ala26fs; (GCC)11/(GCC)11 Ala26fs; (GCC)11/(GCC)12 Ala75fs; (GCC)11/(GCC)12 (GCC)11/(GCC)11 Trp213X; (GCC)11/(GCC)11 ⫺; (GCC)9/(GCC)11 Trp213X; (GCC)9/(GCC)11 F2 F3 F4 F5 a b For kinship and phenotypes, see Fig. 2. ⫺, no mutation detected. stop codon 153 codons away from Ala-75 (Ala75fs). The predicted truncated protein would be 175 amino acids shorter than the wild-type HLXB9. Fig. 2. Pedigrees of the 5 families included in this study. A, ventricular septal defect; B, neurogenic bladder, azoospermia, and left unilateral renal hypoplasia with chronic interstitial nephritis; C, neurogenic bladder and mitral valve prolapse; D, urinary reflux; E, sacral dimple with bony outgrowth. ⴱ, individual screened for HLBX9 mutations. protein–protein interactions), whereas translation initiation from ATA would yield smaller amounts of wild-type HLXB9 protein (24 ). Either scenario could account for the affected individuals of family 2, who harbored the same mutation but showed different phenotypes. Remarkably, the mother (I2) of the affected sisters (II2 and II3) and her asymptomatic daughter (II1) had no abnormal x-ray findings and no complaints. Unfortunately, DNA of those asymptomatic family members who seemed to have transmitted this mutation was not available for analysis. Family 3. A 77delC was observed in the mother (I2) and daughter (II1) but was absent in the father (I1). DNA samples from the rest of the family were not available. This deletion replaces the alanine of codon 26 with a glycine and introduces a frameshift that originates a stop codon 196 codons away from Ala-26 (Ala26fs), predicting a truncated protein with 222 amino acids instead of 403. Family 4. Both I1 and II3 harbored a duplication of 17 bp (c196_212dup) in exon 1 that originates the replacement of Ala-75 by proline, creating a frameshift that generates a Family 5. A c638G⬎A transition was detected in 2 family members (II3 and III2). This transition originates the nonsense mutation Trp213X (TGG changes to stop codon TGA), which predicts a truncated protein consisting of only 213 amino acids. The severity of the phenotype differed considerably between the mother (II3) and son (III2). Interestingly, family member III1, who did not carry Trp213X, presented with a phenotype (sacral dimple with no abnormal magnetic resonance imaging findings) almost identical to that of her brother (sacral dimple with a bony outgrowth and no abnormal magnetic resonance imaging findings). Chromosomal microdeletions affecting the HLXB9 gene, which have been described in some Currarino patients (4 ), can be detected by fluorescence in situ hybridization or copy number analysis, which were not performed in this study. Thus, patients with no detected mutation may have had a deletion affecting either completely or partially one HLXB9 allele. analysis of the length of the polyalanine tracts (GCC)11 was the most common allele among all individuals analyzed, although the (GCC)8, (GCC)9, and (GCC)12 alleles were also observed (Tables 1 and 2). We could not establish any correlation between the number of GCC repeats in patients and the presence of disease or with the variable penetrance of the HLXB9 mutations. A larger number of patients is required, however, to draw any conclusion regarding association of any given GCC allele with the disease. All (GCC)n alleles present in patients were also present in the controls. Surprisingly, statistically significant differences in the global (GCC)n allele and genotype distributions were observed between the healthy Chinese analyzed in this study and the Caucasian controls described previously by Belloni et al. (5 ). Comparison Clinical Chemistry 52, No. 1, 2006 (Table 3) revealed highly statistically significant differences for alleles (GCC)9, (GCC)11, and (GCC)12 and most of the genotypes including them. Most strikingly, in the Caucasian population, the frequency of (GCC)11 was 90%, but the frequency of this allele in Chinese was considerably lower (50%). These differences in allele frequencies are reflected in the genotype composition of the populations. We then investigated the (GCC)n allele and genotype distributions in other populations. A summary of the population genetic characteristics of HLXB9 is presented in Fig. 3. No deviation from Hardy–Weinberg equilibrium was observed in any of the populations. The (GCC)n allele and genotype distributions of the Hong Kong Chinese population matched those of Japanese and Chinese populations, the population described by Belloni et al. (5 ), and the CEPH individuals. In the Chinese and Japanese individuals, (GCC)9 was almost as common as (GCC)11, whereas its frequency was ⬎10% in the Yoruba and CEPH populations. The Yoruba population had the highest frequencies of the largest alleles [(GCC)12, 26.6%; (GCC)13, 2.7%], which were almost absent elsewhere. Whereas 80% of the CEPH individuals were represented by 1 main genotype [(GCC)11/ (GCC)11], genotype diversity was increased in the Yoruba population, in which (GCC)11/(GCC)11 and (GCC)11/ (GCC)12 were equally represented, and was highest in the Chinese and Japanese populations. Discussion The CS phenotype related to HLXB9 mutations is attributed to haploinsufficiency, whereby the wild-type allele Table 3. Allele and genotype distributions of the GCC repeats at the HLXB9 locus in Chinese (this study) and Caucasian (5 ) populations. Frequency (%) Alleles (GCC)8 (GCC)9 (GCC)11 (GCC)12 (GCC)13 Genotypes (GCC)9/(GCC)9 (GCC)11/(GCC)11 (GCC)12/(GCC)12 (GCC)8/(GCC)11 (GCC)9/(GCC)11 (GCC)9/(GCC)12 (GCC)11/(GCC)12 (GCC)12/(GCC)13 a b Chinese populationa Caucasian populationb 2 (P) 0.4 33.0 50.0 16.2 0.4 0.6 7.5 90.2 1.7 0.0 0.13 (0.71) 39.75 (⬍0.000001) 77.45 (⬍0.000001) 23.72 (⬍0.000001) 0.60 (0.64) 12.4 26.2 2.8 0.7 31.0 10.3 15.9 0.7 1.2 81.6 0.0 1.2 12.6 0.0 3.4 0.0 9.17 (0.0024) 67.00 (⬍0.000001) 2.44 (0.20) 0.13 (0.72) 10.04 (0.0015) 9.62 (0.0019) 8.42 (0.0037) 0.60 (0.64) This study; n ⫽ 145 individuals. Belloni et al. (5 ); n ⫽ 87 individuals. 5 Fig. 3. Allele (top) and genotype (bottom) distributions of the GCC repeats at the HLXB9 locus in 4 human populations. cannot provide sufficient HLXB9 protein (4 ). Thus, a mutation in one allele that leads to a ⬎50% decrease in gene product may cause symptoms. The phenotypic variability observed among family members carrying the same mutation and the unpredictability of the phenotype, however, can best be explained by the effects of other genes (4, 5, 11 ). Sensitivity to modifier genes is inherent to gene products whose correct functioning depends on relative amounts of interacting products, a characteristic intrinsic to homeobox genes. The transcription factors encoded by homeobox genes are expressed in different cell types and regulate the expression of many target genes, controlling the formation of organs and body structures during development. The specificity of these processes is achieved only through their interaction with cell- or tissue-specific protein partners (25 ). HXLB9 mutations may hamper the interaction of the HXLB9 protein with its tissue-specific partners, and as a result, multiple body structures would be affected to a different degree and with different phenotypic consequences. In addition, mutations in genes encoding HLXB9 protein partners or transcriptional regulators may influence HLXB9 expression, increasing the chances of phenotypic variability and accounting for patients with no HLXB9 mutations. Conversely, the normal phenotype of healthy individuals harboring mutations may be related to variations in expression of the nonmutated HLXB9 allele in different tissues and at different developmental stages. The CS phenotype caused by mutations in HLXB9 may therefore be sensitive to modifications elsewhere in the genome affecting HLXB9 protein partners or transcriptional regulators. 6 Garcia-Barceló et al.: HLXB9 in Currarino Patients and the General Population The mutations described in this study are likely to lead to a 50% decrease in protein function, although because of the lack of direct functional evidence their pathogenicity can only be inferred. No correlation between type or location of the mutation in the protein and severity of the phenotype could be established. As in previous studies, HLXB9 mutations were found in nearly all patients with familial CS and in only 30% of the patients with sporadic CS (2–5, 11, 26 )). Those sporadic patients with HLXB9 mutations may be descendents of asymptomatic individuals in whom signs of the condition can be detected only by radiologic analysis. Anorectal, pelvic ultrasound, and pelvic x-ray examinations should be conducted on relatives of patients with the sporadic form of CS to distinguish between familial and sporadic CS. Such examinations may have been revelatory in the case of patient S6 and his asymptomatic father (both harboring Ser185X), on whom no radiologic examination was conducted. Although both pathologic and nonpathologic polyalanine polymorphisms for several genes have been found in the general population, there is little information regarding their distribution in different ethnic populations (8, 27–31 ). To our knowledge, ethnic differences in polyalanine polymorphism frequencies have been described only for the RPL14 and the MICA genes (27, 28 ). It is tempting to speculate that if there was a threshold beyond which expansions are pathologic, those populations enriched with alleles with higher number of repeats would be at higher risk. In the PABPN1 gene (encoding an mRNA polyadenylation factor), the wild-type allele consists of 6 triplets (GCG6), and expansions of 2–7 triplets are pathologic and associated with oculopharyngeal muscular dystrophy (10 ). One triplet expansion (GCG7) acts as a modifier of the dominant disease phenotype caused by expansion of more than 1 triplet (GCG7/ GCG⬎7) or, in homozygosis, (GCG7/GCG7) as a mutation. Most interestingly, and perhaps relevant to the ethnic variety in the distribution of polyalanine polymorphisms, is that in the PABPN1 gene GCG7 is also found in 2% of healthy Caucasians in combination with GCG6. In this instance, there is a clear cutoff between wild-type and mutant alleles that clearly shows how a different ethnic distribution of this allele could translate into an ethnicityspecific disease risk. Because rare polymorphisms exist in 4 of the 9 genes in which alanine expansions cause disease, it is most important to screen similar sequences in other pathologies (8 ). Our analysis of the HLXB9 triplets indicates that alleles (GCC)8, (GCC)12, and (GCC)13 are the rarest in the populations studied. 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