Journal of Genetics (2019) 98:10 © Indian Academy of Sciences https://doi.org/10.1007/s12041-019-1055-8

RESEARCH NOTE

Spectrum of X-linked intellectual disabilities and psychiatric symptoms in a family harbouring a Xp22.12 microduplication encompassing the RPS6KA3

VERA ULIANA1, FRANCESCO BONATTI1, VALENTINA ZANATTA2, PAOLA MOZZONI1, DAVIDE MARTORANA3 and ANTONIO PERCESEPE1∗

1Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy 2TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, 21052 Busto Arsizio, Varese, Italy 3Medical Genetics, University Hospital of Parma, 43126 Parma, Italy *For correspondence. E-mail: [email protected].

Received 3 July 2018; revised 13 September 2018; accepted 10 January 2019; published online 21 February 2019

Abstract. Microduplications of the X are a rare cause of X-linked intellectual disability (XLID), a clinically and genetically heterogeneous spectrum of disorders. In the present study, a 950-kb Xp22.12 microduplication including the RPS6KA3 gene was detected in affected members of a family, including the proband (male), his mother and one maternal uncle. Four female carriers had major depression and one of them also had mild intellectual disability. The present and previous cases with overlapping microduplications suggest that Xp22.12 microduplications can be included in the neuropsychiatric copy number variations.

Keywords. Xp22.12 microduplication; RPS6KA3 gene; X-linked intellectual disabilities.

Introduction (Manouvrier-Hanu et al. 1999; Merienne et al. 1999; Jacquot et al. 2002; Field et al. 2006), which we report X-linked intellectual disability (XLID) is a common and in a family presenting with psychiatric signs and peculiar genetically heterogeneous disease arising from several dif- phenotypes of major depression in carrier females. ferent mutations along the (Gécz et al. 2009), including microduplications, which have been dis- covered in the latest years through the systematic employ- Clinical report ment of the array-CGH technology in the diagnostic work up of syndromic and nonsyndromic ID patients (Gécz The pedigree is shown in figure 1. The proband (III-1) et al. 2009). Among the X chromosome duplicated regions, is a 34-year-old male, with a mild/moderate intellectual few reports have described patients with the involve- disability, who was diagnosed at 25 years of age with ment of Xp22.12 region, encompassing the RPS6KA3 paranoid schizophrenia. Fragile X syndrome analysis was gene (Madrigal et al. 2007; Tejada et al. 2011; Mat- normal. The physical examination showed height 187 cm sumoto et al. 2013; Bertini et al. 2015). Loss-of-function (97◦ centile), weight 100 kg (body mass index 28.6) and mutations of RPS6KA3 cause instead the Coffin–Lowry head circumference 56.5 cm (75−90◦ centile); no facial dys- syndrome (MIM: 303600), an X-linked semidominant dis- morphisms, skeletal or other systemic abnormalities were order characterized by severe intellectual disability (ID), noted. growth retardation, facial dysmorphisms, digital abnor- The mother (II-2) is a 59-year-old female with a diag- malities and skeletal deformities with a wide spectrum nosis of major depression at about 30 years of age. She of expressivity (Pereira et al. 2010). The RPS6KA3 gene did not undergo a functional evaluation of her cognitive duplications are a much rarer condition and result in a mild skills, but her schooling and other activities were normal. or borderline ID phenotype with few associated features Two maternal uncles (II-3 and II-4), 52 and 60 years of

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Figure 1. Pedigree of the family. Family members with intellectual disability are indicated with black shaded figures, whereas family members with mood disorders are shaded with grey. III-1, II-3 and II-4 also represent psychiatric disorders. The proband is indicated by an arrow. The results of the array-CGH are indicated in the box below the symbols of the family members: −/−, females without Xp22.12 microduplication; +/−, females heterozygous for the Xp22.12 microduplication; +, males hemizygous for Xp22.12 microduplication. age, respectively, are affected by mild/moderate intellectual 2(MAP7D2) and chromosome X open-reading frame 23 disability and psychosis. II-3 presented also one episode (BCLAF3). The proximal breakpoint is located between of seizures at about 25 years of age, treated thereafter. X:19624255 and X:19624315 (last normal and first dupli- A 50-year-old maternal aunt (II-7) was diagnosed with cated probes, respectively), the distal between X:20597582 depression in her third decade of life, whereas one of her and X:20622288 (last duplicated and first normal probes, daughters (III-9) presented a mild intellectual disability. respectively), according to the UCSC Genome Browser After informed consent, array-CGH analysis was per- (UCSC hg19, http://genome.ucsc.edu, on Human Febru- formed using commercially available oligonucleotide ary 2009 Assembly). microarrays containing about 180000 probes (PerkinElmer The duplication was identified in the proband (III-1), in oligo genome-wide CGX-HD Array 180K) with an aver- his mother (II-2) and in a maternal uncle (II-3) but was age resolution of about 60 kb in the critical regions not identified in the proband’s sister, a 37-year-old woman and 120 kb in the backbone. Array-CGH analysis iden- in good health status. The biological samples of the other tified a chromosome X interstitial duplication of about family members were not available. 950 kb [arr[GRCh37] Xp22.12(19651494_20597642)x2], To determine the presence of a dosage effect for the with minimal/maximal size between 946.15 and 997.91 RPS6KA3 gene, its transcript levels were analysed in kb, which includes eight : SH3KBP1, BCLAF3, peripheral blood mononuclear cells in the proband, his LOC729609, MIR23C, MAPD7D2, EIF1AX, mother and a normal male control by real-time quanti- SCARNA9L and RPSKA3. Of those, only RPS6KA3 tative PCR on an iCycler iQ Multicolor RealTime PCR (MIM: *300075) is a known disease gene, being associ- Detection (Syscules, USA). Each plate included a neg- ated to Coffin–Lowry syndrome and nonsyndromic ID ative control and a duplicate assay for each sample. (Field et al. 2006), whereas for the other seven genes Specific primers and locked nucleic acid probes were no evidence of a pathogenetic role exists: LOC729609, designed by the ProbeFinder software (Roche Diagnostics, microRNA 23c (MIR23c) and small Cajal body-specific Mannheim, Germany). The relative transcript quantifi- RNA 9-like (SCARNA9L) are miscellaneous small RNA cation of the RPS6KA3 gene was calculated using the genes; EIF1AX encodes a small eukaryotic initiation fac- 2−Ct normalization for a X-linked control gene, the tor (eIF4C) implied in the translation initiation pathway, guanine-phosphoribosyl-transferase (HPRT), located on SH3KBP1 is an 85-kD CBL-interacting protein which chromosome X. enhances tumour necrosis factor-mediated apoptotic cell The male affected proband presented mRNA levels death; very little is known for MAP7 domain containing more than double compared with normal male control Intellectual disabilities and psychiatric symptoms in Xp22.12 microduplication Page 3 of 7 10

(a)

(b)

Figure 2. (a) Map of the chromosome X genomic region involved in the rearrangement (from 19.5 to 21 Mb) and view of the genes within the duplicated region, downloaded from the Database of Genomic Variants (http://projects.tcag.ca/variation/). The duplication reported in the present study is compared with previously described patients carrying an overlapping rearrangement. (b) qPCR analysis for RPS6KA3 mRNA expression in peripheral blood lymphocytes of the male control, the carrier mother and the affected proband.

(2.33 versus 0.88-fold change), supporting the hypothesis brought about the knowledge of several new syndromes, of a gene dosage effect for the RPS6KA3 gene, whereas which have been recognized through the reverse pheno- no differences were found for the carrier mother (0.62 fold typing of patients sharing the same mutation or genomic change) (figure 2b). rearrangement (Potocki et al. 2007; Koolen et al. 2012). With time, a pathogenetic role for specific CNVs has Discussion been identified also in patients with subtler phenotypes, such as mild nonsyndromic ID, psychiatric and, as in the The widespread use of the array-based technology for present report, mood disorders (Gécz et al. 2009; Ste- the diagnosis of syndromic and nonsyndromic ID has fansson et al. 2014; Uliana and Percesepe 2016). Here 10 Page 4 of 7 Vera Uliana et al. Maternal About 1 Mb (hg19) Inheritance Size Position 20498961 20597642 20890343 20700691 X:19915395- X:20060343- X:19651494- X:19651193- Other keratosis features features Dysmorphic disorders No No NR Maternal No No NR Maternal No No No Maternal Neuropsychiatric disability Intellectual difficulties delayed language difficulties delayed language difficulties Sex Age (years) ) ) 2013 ) ( 2007 ( 2011 ( et al. et al. Phenotypic features of subjects with Xp22.12 duplication reported in present case, literature and DECIPHER database. et al. MotherMaternal grandmotherMatsumoto F NR F No NR No No No No No No No NR Maternal Maternal uncle M 22 Learning Table 1. Present case ProbandMaternal uncleMotherMadrigal M M 63 F 34 Yes 59 Mild/moderate Schizophrenia No Psychosis No Depression No No No Epilepsy No Maternal About 950 kb NR NR ProbandMaternal uncleMaternal uncleMotherTejada M M M NR NR NR F Yes Yes Mild NR No NR Dyslexia NR NR Mild NR NR NR NR NR NR NR Maternal NR About 850 kb NR NR Maternal uncle M 36 Learning Brother M 5 Learning Proband M 8 Mild No No Follicular Intellectual disabilities and psychiatric symptoms in Xp22.12 microduplication Page 5 of 7 10 Maternal About 650 kb Maternal About 1 Mb Maternal About 700 kb Maternal About 500 kb (hg19) Inheritance Size Position 20833589 20597641 20553271 20355406 X:20208171- X:19874277- Other features anomalies, hearing loss hypospadia features Dysmorphic disorders ADHD No No Maternal NR NR Strabismus, NR NR NR X:19842599- Neuropsychiatric disability Intellectual developmental level developmental delay impairment Sex Age (years) ) ) 2015 ( contd ( et al. Table 1 ProbandBrotherSisterMaternal brother M M M F 15 4 13 Mild Borderline 11 Mild/moderate No No ADHD No NoNR, not No reported; ADHD, attention deficit and hyperactivity disorders. No Epilepsy Epilepsy No Maternal Maternal About 600 kb Maternal Proband M 12 Mild No Mild EEG MotherMaternal uncleDECIPHER 283026 M M F NR NR Language disorders 38 Mild NR No NR No No NR Similar to proband No NR X:19563240- No NR NR Maternal sisterMotherBertini F F 11 No NR No No Depression No No No No Maternal Likely paternal DECIPHER 276374 M 5 Global DECIPHER 269161 F NR Cognitive 10 Page 6 of 7 Vera Uliana et al. we describe a family in which mild ID segregates with a References Xp22.12 microduplication and all the affected males also present psychiatric disorders, whereas the carrier females Bertini V., Cambi F., Bruno R., Toschi B., Forli F., Berrettini have mood disorders and in one case ID. The rearrange- S. et al. 2015 625 kb microduplication at Xp22.12 including ment involves one gene, RPS6KA3, related to syndromic RPS6KA3 in a child with mild intellectual disability. J. Hum. Genet. 60, 777–780. ID (Coffin–Lowry syndrome), whose duplication can be Field M., Tarpey P., Boyle J., Edkins S., Goodship J., Luo Y. considered causative of the XLID in the family, in agree- et al. 2006 Mutations in the RSK2(RPS6KA3) gene cause ment with few other previously reported cases (figure 2a), Coffin-Lowry syndrome and nonsyndromic X-linked mental which have established the duplications of the Xp22.12 retardation. Clin. Genet. 70, 509–515. region encompassing the RPS6KA3 as a cause of mild ID Gécz J., Shoubridge C. and Corbett M. 2009 The genetic land- scape of intellectual disability arising from chromosome X. or borderline intellectual quotient (Madrigal et al. 2007; Trends Genet. 25, 308–316. Tejada et al. 2011; Matsumoto et al. 2013). Two of those Hauge C. and Frödin M. 2006 RSK and MSK in MAP kinase studies have found two times higher RPS6KA3 expres- signalling. J. Cell Sci. 119, 3021–3023. sion levels in affected males with Xp22.12 duplications Jacquot S., Zeniou M., Touraine R. and Hanauer A. 2002 than in normal males (Tejada et al. 2011; Matsumoto X-linked Coffin-Lowry syndrome (CLS, MIM 303600, RPS6KA3 gene, protein product known under various et al. 2013): these results were also confirmed in our names: pp90(rsk2), RSK2, ISPK, MAPKAP1). Eur. J. Hum. study (figure 2b). One study reported two males who also Genet. 10, 2–5. presented epilepsy, one carrier female with a pervasive Koolen D. A., Kramer J. M., Neveling K., Nillesen W. M., development disorder and another with depression (Mat- Moore-Barton H. L., Elmslie F. V. et al. 2012 Muta- sumoto et al. 2013), whereas one additional study reported tions in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome. Nat. Genet. 44, a duplication partially encompassing RPS6KA3 associ- 639–641. ated with XLID (Bertini et al. 2015); finally, a duplication Madrigal I., Rodríguez-Revenga L., Armengol L., González E., including RPS6KA3 was associated with a more severe Rodriguez B., Badenas C. et al. 2007 X-chromosome tiling phenotype in one family, likely because of the large size path array detection of copy number variants in patients with of the rearrangement, extending for 8.5 Mb and involv- chromosome X-linked mental retardation. BMC Genomics 8, 443. ing also other relevant genes for intellectual disability, like Manouvrier-Hanu S., Amiel J., Jacquot S., Merienne K., CDKL5 (Tzschach et al. 2008) (table 1). When analysing Moerman A., Coëslier A. et al. 1999 Unreported RSK2 the international copy number variation databases report- missense mutation in two male sibs with an unusually ing patients with ID and/or congenital malformations, mild form of Coffin-Lowry syndrome. J. Med. Genet. 36, in particular DECIPHER (https://decipher.sanger.ac.uk) 775–778. Matsumoto A., Kuwajima M., Miyake K., Kojima K., and ISCA (http://dbsearch.clinicalgenome.org), three phe- Nakashima N., Jimbo E. F. et al. 2013 An Xp22.12 microdu- notypically characterized DECIPHER cases had similar plication including RPS6KA3 identified in a family with duplications and no other rearrangements (table 1). The variably affected intellectual and behavioral disabilities. J. two ISCA cases with a pathogenic Xp22.12 duplica- Hum. Genet. 58, 755–757. tion include one with developmental delay (nssv579201) Merienne K., Jacquot S., Pannetier S., Zeniou M., Bankier A., Gecz J. et al. 1999 A missense mutation in RPS6KA3 (RSK2) and one with microcephaly (nssv579202). In the ISCA responsible for non-specific mental retardation. Nat. Genet. 22, database, no information about other rearrangements of 13–14. the patients or about their family were reported, and Pereira M. P., Heron D. and Hanauer A. 2007 The first large therefore they have not been included in figure 2aorin duplication of the RSK2 gene identified in a Coffin-Lowry table 1. syndrome patient. Hum. Genet. 122, 541–543. Pereira P.M., Schneider A., Pannetier S., Heron D. and Hanauer The present report indicates that the Xp22.12 microdu- A. 2010 Coffin-Lowry syndrome. Eur. J. Hum. Genet. 18, 627– plication including the RPS6KA3, a known cause of 633. nonsyndromic mild XLID, confers a high risk for depres- Potocki L., Bi W., Treadwell-Deering D., Carvalho C. M., Eifert sion in carrier females in the context of a wide spectrum A.,FriedmanE.M.et al. 2007 Characterization of Potocki- of expressivity, which in affected males is featured, among Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage- sensitive critical interval that can convey an autism the others, also by psychosis, suggesting that the Xp22.12 phenotype. Am. J. Hum. Genet. 80, 633–649. duplications can be finally considered in the number of the Stefansson H., Meyer-Lindenberg A., Steinberg S., Magnusdot- neuropsychiatric CNVs. tir B., Morgen K., Arnarsdottir S. et al. 2014 CNVs conferring risk of autism or schizophrenia affect cognition in controls. Nature 505, 361–366. Tejada M. I., Martínez-Bouzas C., García-Ribes A., Lar- Acknowledgements rucea S., Acquadro F., Cigudosa J. C. et al. 2011 A child with mild X-linked intellectual disability and a microdu- This work was supported by the ‘Fondazione Emma ed Ernesto plication at Xp22.12 including RPS6KA3. Pediatrics 128, Rulfo per la Genetica Medica’ (Italy). This study makes used of e1029–1033. data generated by the DECIPHER Consortium. We are indebted Tzschach A., Chen W., Erdogan F., Hoeller A., Ropers H. H., to the family members for their collaboration. Castellan C. et al. 2008 Characterization of interstitial Xp Intellectual disabilities and psychiatric symptoms in Xp22.12 microduplication Page 7 of 7 10

duplications in two families by tiling path array CGH. Am. Uliana V. and Percesepe A. 2016 Reverse phenotyping comes of J. Med. Genet. A 46, 197–203. age. Mol. Genet. Metab. 118, 230–231.

Corresponding editor: S. Ganesh