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12 Smith-Magenis Syndrome Deletion, Reciprocal Duplication Dup(17)(P11.2P11.2), and Other Proximal 17P Rearrangements

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12 Smith-Magenis Syndrome Deletion, Reciprocal Duplication Dup(17)(P11.2P11.2), and Other Proximal 17P Rearrangements Chapter 12 / SMS Deletion 179 12 Smith-Magenis Syndrome Deletion, Reciprocal Duplication dup(17)(p11.2p11.2), and Other Proximal 17p Rearrangements Pawel Stankiewicz, MD, PhD, Weimin Bi, PhD, and James R. Lupski, MD, PhD CONTENTS INTRODUCTION CONSTITUTIONAL RECURRENT GENOMIC DISORDERS IN PROXIMAL 17P SMS-REPS, LCR LOCATED AT THE BREAKPOINTS OF THE COMMON DELETION SUMMARY REFERENCES INTRODUCTION An approx 4-Mb genomic segment on chromosome 17p11.2 commonly deleted in 70–80% of patients with the Smith-Magenis syndrome (SMS) is flanked by large, complex, highly identical (approx 98.7%), and directly oriented, proximal (approx 256 kb) and distal (approx 176 kb) low-copy repeats (LCRs), termed SMS-REPs. These LCR copies mediate nonallelic homologous recombination (NAHR), resulting in both SMS deletion and the reciprocal dupli- cation dup(17)(p11.2p11.2). A third copy, the middle SMS-REP (approx 241 kb) is inverted and located between them. Several additional large LCR17ps have been identified fomented by breakpoint mapping in patients with deletions ascertained because of an SMS phenotype. LCRs in proximal 17p constitute more than 23% of the analyzed genome sequence, approx fourfold higher than predictions based on virtual analysis of the entire human genome. LCRs appear to play a significant role not only in common recurrent deletions and duplications, but also in other rearrangements including unusual sized (i.e., uncommon, recurrent and nonrecur- rent) chromosomal deletions, reciprocal translocations, and marker chromosomes. DNA sequence analysis from both common and unusual sized recurrent SMS deletions and common dup(17)(p11.2p11.2) reveals “recombination hotspots” or a remarkable positional preference for strand exchange in NAHR events. Large palindromic LCRs, mapping between proximal and middle SMS-REPs, are responsible for the origin of a recurrent somatic isochromosome From: Genomic Disorders: The Genomic Basis of Disease Edited by: J. R. Lupski and P. Stankiewicz © Humana Press, Totowa, NJ 179 180 Part IV / Genomic Rearrangements and Disease Traits i(17q), one of the most common recurrent structural abnormalities observed in human neo- plasms, suggesting genome architecture may play a role in mitotic as well as meiotic rearrange- ments. LCRs in proximal 17p are also prominent features in the genome evolution of this region whereby several serial segmental duplications have played an important role in chromosome evolution accompanying primate speciation. The gene- and LCR-rich, human genomic region 17p11.2-p12 is rearranged in a variety of different constitutional, evolutionary, and cancer-associated structural chromosome aberra- tions, and thus is an excellent model to investigate the role of genome architecture in DNA rearrangements (1–9). CONSTITUTIONAL RECURRENT GENOMIC DISORDERS IN PROXIMAL 17p Similar to Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuronopathy with pressure palsies (HNPP), the LCR-mediated NAHR mechanism is responsible for two other constitutional genomic disorders in proximal chromosome 17p: SMS and the dup(17)(p11.2p11.2) syndrome. Smith-Magenis Syndrome SMS (MIM 182290) is a multiple congenital anomalies and mental retardation disorder associated with an interstitial deletion within chromosome 17p11.2 (10–13). Clinical charac- teristics include minor craniofacial and skeletal anomalies such as brachycephaly, frontal bossing, synophrys, midfacial hypoplasia, short stature, and brachydactyly, neurobehavioral abnormalities such as aggressive and self-injurious behavior and sleep disturbances, oph- thalmic, otolaryngological, cardiac, and renal anomalies (13,14). As defined by fluorescence in situ hybridization (FISH) and by a unique de novo junction fragment identified in pulsed-field gel electrophoresis, 70–80% of SMS patients harbor a common approx 4-Mb deletion within 17p11.2 (3,12,15,16). Approximately 20–25% SMS patients have either smaller or larger sized deletions (16–19). Recently, premature termination codon mutations in the retinoic acid inducible-1 gene, RAI1, which maps within the SMS critical region, have been found in five SMS-like patients without deletion (20–21), suggesting RAI1 haploinsufficiency causes SMS. Bioinformatics analyses of the dosage sensitive RAI1 gene, and comparative genomics between human and mouse orthologs, revealed a zinc finger like-PHD domain at the carboxyl terminus that is conserved in the trithorax group of chroma- tin-based transcriptional regulators, suggesting that RAI1 might be involved in chromatin remodeling (21). These findings suggest RAI1 is involved in transcriptional control through a multi-protein complex, and its function may be altered in individuals with SMS. Interestingly, despite a common deletion size, the only constant objectively defined features among patients with SMS are sleep disturbances, low adaptive functioning, and mental retar- dation. There is no pathognomonic clinical feature, no characteristic cardiovascular defect, renal anomaly, otolaryngological, nor ophthalmic abnormality in SMS (22). The Emerging Clinical Phenotype of the dup(17)(p11.2p11.2) Syndrome: The Homologous Recombination Reciprocal of the Common SMS Deletion The common SMS deletion region is duplicated in patients with a milder, predominantly neurobehavioral phenotype and the reciprocal chromosome duplication—dup(17)(p11.2p11.2) Chapter 12 / SMS Deletion 181 (5,23). Similar to SMS patients with common deletion, subjects with common duplication dup(17)(p11.2p11.2) also manifest marked variability in the physical features and behavioral profile. Clinical findings include dysmorphic craniofacial features, hypotonia and failure to thrive, oropharyngeal dysphasia, neurocognitive impairment, and behavioral problems includ- ing autistic, aggressive, and self-injurious behavior. Structural cardiac anomalies including aortic root enlargement, have been identified. However, the frequency of organ system devel- opmental abnormalities appears to be less than that observed for patients deleted for this genomic interval (i.e., SMS). Sleep disturbances are seen in all patients yet the findings are distinct from those of deletion 17p11.2. It is predicted that the incidence of dup(17)(p11.2p11.2) may be equal to that of SMS given the reciprocal nature of the common rearrangements responsible for the conditions. However, as this duplication is difficult to detect by routine cytogenetic analysis, many of these patients are currently probably not ascertained. Systematic clinical evaluation of a cohort of patients with dup(17)(p11.2p11.2) will be necessary to determine the features most characteristic of this microduplication syndrome. The relatively high frequency of constitutional genomic disorders in proximal chromosome 17p is further substantiated by the identification of an individual with two distinct megabase- sized DNA rearrangements of this genomic interval. These included both a de novo dup(17)(p11.2p11.2) and an inherited HNPP deletion on the other homolog. These rearrange- ments were associated with mild delay and a family history of autosomal dominant carpal tunnel syndrome (24). SMS-REPS, LCR LOCATED AT THE BREAKPOINTS OF THE COMMON DELETION Physical mapping studies have demonstrated that the SMS common deletion interval is flanked by large (approx 200 kb), highly identical (>98%), LCR gene clusters termed proximal and distal SMS-REPs (1,3,7) that during either maternal or paternal gametogenesis act as substrates for NAHR (8,25). To delineate the genomic structure (size, orientation, sequence identity, gene content) and evolution of the SMS-REPs, we constructed and sequenced a complete approx 5-Mb bacterial and P1-derived artificial chromosome (BAC/PAC) contig in 17p11.2-p12. Our analysis revealed that both the proximal SMS-REP (approx 256 kb) and the distal copy (approx 176 kb) are located in the same orientation and derived from a progenitor copy, whereas the middle SMS-REP (approx 241 kb) is inverted and appears to have been derived from the proximal copy. This architecture likely explains why the common SMS deletions occur between proximal and distal SMS-REPs. There are four regions of significant stretches of identity between the proximal and the distal SMS-REPs (A, B, C, and D regions in Fig. 1A). The sum of these high sequence similarity regions is approx 170 kb (169,905 bp), and the identity is greater than 98% with the exception of the D region (>95%) (Table 1). The largest conserved segment (region A in Fig. 1A) is 126 kb in size. Two large sequence blocks (between A and B, and between C and D) in the proximal SMS-REP are absent in the distal SMS-REP. Two smaller blocks, flanking areas of the B region in the distal SMS-REP are absent in the proximal SMS-REP (Fig. 1A). FISH analysis using SMS-REP-specific BAC clones as probes revealed strong hybridiza- tion signals on metaphase chromosomes 17p11.2 and three strong signals on the interphase chromosomes. However, SMS-REP-specific BACs also showed weaker hybridization signals in interphase analysis and metaphase spreads; these map to chromosome 17p13.1, 17p12, 182 Part IV / Genomic Rearrangements and Disease Traits Fig. 1. Sequence-based genomic structure of the Smith-Magenis syndrome (SMS)-REPs. (A) There are four regions of sequence identity more than 95% between the proximal and the distal SMS-REPs (A, B, C, and D). The A, B, and C sequence blocks have more than 98% identity between distal and proximal REPs, whereas the D regions (green) show more than 95% identity. The thick blue lines represent
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