Psychiatry Research 215 (2014) 255–257

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Letter to the Editor

Absence of low frequency variants associated with schizophrenia at the ultraconserved non-coding region of TCF4 To the Editor: TCF4 is a transcription factor involved in the development of central nervous system strongly associated with schizophrenia, as revealed by genome-wide association studies (GWAS) (Steinberg et al., 2011). Haploinsufficiency of TCF4 causes the Pitt–Hopkins syndrome, a syndrome characterized by intellectual disability, wide mouth, and hyperventilation. The haploinsufficiency is due to mutations causing premature stop codons, missense mutations, translocations or deletions (Whalen et al., 2012). Bejerano et al. (2004) have described the existence of ultraconserved elements (UCEs) within the human genome, defined as sequences of at least 200 bp with 100% homology between human, mouse and rat genomes. Experimental validation of many of these UCEs in transgenic mouse embryos revealed that most non-coding UCEs are regulatory elements involved in gene expression during development. One of the tested elements with enhancer activity was UC435, an ultraconserved non-coding sequence 227 bp long located within TCF4. UC435 drives expression in hindbrain, midbrain and neural tube (VISTA enhancer browser, dataset ID: hs376). Visual inspection of the ENCODE Project's results at the UCSC genome browser revealed that UC435 is a target of the p300 protein in a neuroblastoma cell line (ENCODE Project Consortium, 2012). This protein is a histone acetyltransferase linked to enhancer activity, which provides further evidence for the role of UC435 as an enhancer. This gene presents another UCE described by Bejerano et al. (2004), UC436. Nevertheless, unlike UC435, almost half of UC436 involves a coding exon of TCF4. Furthermore, there is no experimental evidence showing the role of UC436 as an enhancer. Because of that, here we focused on UC435, testing for the existence of highly penetrant alleles associated with schizophrenia at this UCE. Sample consists of 528 schizophrenic cases and 270 controls from Galicia (NW Spain). Cases are subjects attending public hospitals at the Galician health service meeting the DSMIV criteria for schizophrenia. Controls are blood donors from the same geographical origin, and represent an unbiased subset of the full collection described in Carrera et al. (2012). Further description of the subjects is presented in Carrera et al. (2012). The study was approved by the appropriate ethical committee (Comité Ético de Investigación Clínica de Galicia). Identification of UC435 homologous sequences at other mammalian genomes was done by BLAST searches using as query the sequence of UC435 (chr18:53089931-53090157 at human genome build 37) against the refseq_genomic database from the NCBI server. Detection of variants at the 1000 Genome Project Phase I, based on the sequencing of 1092 individuals sampled from 14 populations drawn from Europe, East Asia, sub-Saharan Africa and 0165-1781/$ - see front matter & 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.psychres.2013.10.008

the Americas (1000 Genomes Project Consortium, 2012) was done by searching the UCSC genome browser using UC435 coordinates. Variation at UC435 in our sample was examined by high resolution melting analysis (HRMA) using Idaho Technology (Salt Lake City, Utah, USA). Changes in melting curves were measured using the Lightscanner instrument (Idaho Technology). PCR primers were 5′-AAGCATTTGGGAATTGTGAG-3′ and 5′-AGAGTGGAAGTGAAATTTGTTTTT-3′, leading to an amplicon of 254 bp. PCR conditions were: 94 1C, 2 min; 35 cycles of 94 1C, 30 s, 59 1C, 30 s, and 72 1C, 1 min; and a final extension of 72 1C, 10 min. Amplifications were performed in the presence of LCGreen plus dye following manufacturer's instructions (Idaho Technology). Sequencing of selected samples was performed using Big-Dye terminator chemistry and an ABI3710 sequencer (Applied Biosystems Foster City, CA). There is just one change in 22 placental mammal reference sequences from different orders, corresponding to position 1 of UC435 in the Chinese hamster, suggesting that the edges of the element are approximate. Extending the comparison to three marsupial genomes, two of them are identical and one, corresponding to the Tasmanian devil, presents a single change (Fig. 1). Searching for the presence of any variant at the 1000 Genomes Project identified 3 rare variants within UC435, two detected once, rs186334179 (present in a Japanese subject from Tokyo) and rs181478739 (also in a Japanese from Tokyo), and the other (rs190709022) present in two Luhya subjects from Webuye, Kenya (Fig. 1). HMRA of our samples did not detect any variant. A few samples presenting anomalous curves were processed again, leading to normal curves. Sequencing of the nine samples with more different melting curves confirmed the absence of nucleotide differences. An analysis of the common polygenic component in schizophrenia strongly suggests that a substantial fraction of genetic susceptibility to schizophrenia may affect gene expression (Richards et al., 2012). De novo mutational events in sporadic schizophrenia cases suggest that those genes with a biased expression in early development, like TCF4, represent a substantial contribution to the disease (Xu et al., 2012). Taking into account that haploinsufficiency of TCF4 leads to Pitt–Hopkins syndrome, the level of expression of TCF4 must be tightly regulated. In agreement with this, Williams et al. (2011) suggest that there are no common alleles with moderately large effects on expression of this gene (>20% in difference) as measured in adult brains. Here, we confirmed that UC435 is an ultraconserved element, with no change in the reference sequence of 22 placental mammals. Surprisingly, low frequency variants at UC435 are present in samples from the 1000 Genome Project. The existence of low frequency variants at this UCE in humans and the absence of any change in the 22 reference sequences for placental mammals strongly suggest that variations are slightly deleterious and,

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Letter to the Editor / Psychiatry Research 215 (2014) 255–257

UC435

chr18:53089931

chr18:53090157

Fig. 1. Location and sequence of UC435. Variations detected by the 1000 Genome Project are shown as lowercase letters. Changes among mammalian reference genomes are shown as underlined letters.

because of that, they do not reach fixation (i.e., replacement of the old variant by the new one). The HRMA technique is highly effective in the detection of rare variants present in heterozygosity (Vossen et al., 2009). Assuming that there were not false negatives in our results, we have a probability higher than 80% to detect a variant at population frequency higher than 0.15% in a sample of 528 cases. Therefore, we can discard allelic variants at UC435 with a combination of frequencies and effects similar to many recurrent copy number variants (CNVs) that confer moderate risk to schizophrenia. For instance, duplication at 16p11.2, and deletions at 1q21.1, 15q13.3, or 22q11.2, present a frequency in schizophrenic patients higher than 0.15% but clearly lower than 0.1% in controls (Malhotra and Sebat, 2012). Further analyses with larger sample sizes will be necessary to test for variants causing a weaker effect on schizophrenia risk or variants at lower frequency causing stronger effect.

Acknowledgment This work was supported by Grant FIS/FEDER PI11/00770 to JC.

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Malhotra, D., Sebat, J., 2012. CNVs: harbingers of a rare variant revolution in psychiatric genetics. Cell 148, 1223–1241. Richards, A.L., Jones, L., Moskvina, V., Kirov, G., Gejman, P.V., Levinson, D.F., Sanders, A.R., Molecular Genetics of Schizophrenia Collaboration (MGS), International Schizophrenia Consortium (ISC), Purcell, S., Visscher, P.M., Craddock, N., Owen, M.J., Holmans, P., O’Donovan, M.C., 2012. Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain. Molecular Psychiatry 17, 193–201. Steinberg, S., de Jong, S., Irish Schizophrenia Genomics Consortium, Andreassen, O. A., Werge, T., Børglum, A.D., Mors, O., Mortensen, P.B., Gustafsson, O., Costas, J., Pietiläinen, O.P., Demontis, D., Papiol, S., Huttenlocher, J., Mattheisen, M., Breuer, R., Vassos, E., Giegling, I., Fraser, G., Walker, N., Tuulio-Henriksson, A., Suvisaari, J., Lönnqvist, J., Paunio, T., Agartz, I., Melle, I., Djurovic, S., Strengman, E., Genetic Risk and Outcome in Psychosis (GROUP), Jürgens, G., Glenthøj, B., Terenius, L., Hougaard, D.M., Ørntoft, T., Wiuf, C., Didriksen, M., Hollegaard, M. V., Nordentoft, M., van Winkel, R., Kenis, G., Abramova, L., Kaleda, V., Arrojo, M., Sanjuán, J., Arango, C., Sperling, S., Rossner, M., Ribolsi, M., Magni, V., Siracusano, A., Christiansen, C., Kiemeney, L.A., Veldink, J., van den Berg, L., Ingason, A., Muglia, P., Murray, R., Nöthen, M.M., Sigurdsson, E., Petursson, H., Thorsteinsdottir, U., Kong, A., Rubino, I.A., De Hert, M., Réthelyi, J.M., Bitter, I., Jönsson, E.G., Golimbet, V., Carracedo, A., Ehrenreich, H., Craddock, N, Owen, M. J., O’Donovan, M.C., Wellcome Trust Case Control Consortium 2, Ruggeri, M., Tosato, S., Peltonen, L., Ophoff, R.A., Collier, D.A., St Clair, D., Rietschel, M., Cichon, S., Stefansson, H., Rujescu, D., Stefansson, K., 2011. Common variants at VRK2 and TCF4 conferring risk of schizophrenia. Human Molecular Genetics 20, 4076–4081. Vossen, R.H., Aten, E., Roos, A., den Dunnen, J.T., 2009. High-resolution melting analysis (HRMA): more than just sequence variant screening. Human Mutation 30, 860–866. Whalen, S., Héron, D., Gaillon, T., Moldovan, O., Rossi, M., Devillard, F., Giuliano, F., Soares, G., Mathieu-Dramard, M., Afenjar, A., Charles, P., Mignot, C., Burglen, L., Van Maldergem, L., Piard, J., Aftimos, S., Mancini, G., Dias, P., Philip, N., Goldenberg, A., Le Merrer, M., Rio, M., Josifova, D., Van Hagen, J.M., Lacombe, D., Edery, P., Dupuis-Girod, S., Putoux, A., Sanlaville, D., Fischer, R., Drévillon, L., Briand-Suleau, A., Metay, C., Goossens, M., Amiel, J., Jacquette, A., Giurgea, I., 2012. Novel comprehensive diagnostic strategy in Pitt–Hopkins syndrome: clinical score and further delineation of the TCF4 mutational spectrum. Human Mutation 33, 64–72. Williams, H.J., Moskvina, V., Smith, R.L., Dwyer, S., Russo, G., Owen, M.J., O’Donovan, M.C., 2011. Association between TCF4 and schizophrenia does not exert its effect by common nonsynonymous variation or by influencing cis-acting regulation of mRNA expression in adult human brain. American Journal of Medical Genetics. Part B. Neuropsychiatric Genetics 156B, 781–784. Xu, B., Ionita-Laza, I., Roos, J.L., Boone, B., Woodrick, S., Sun, Y., Levy, S., Gogos, J.A., Karayiorgou, M., 2012. De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nature Genetics 44, 1365–1369.

Letter to the Editor / Psychiatry Research 215 (2014) 255–257

Javier González-Penas Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain

Manuel Arrojo, Mario Páramo, Eduardo Paz, Santiago Agra, Ramón Ramos-Ríos, Julio Brenlla Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain

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Javier Costas n Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain E-mail address: [email protected] Received 8 May 2013 Available online 22 October 2013

n Corresponding autor at: Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Hospital Clínico Universitario, edificio Consultas, andar-2, Grupo de xenética de enfermidades psiquiátricas, despacho 15, E-15706 Santiago de Compostela, Spain. Tel.: þ 34 981955452; fax: þ 34 981951473.

Absence of low frequency variants associated with schizophrenia at the ultraconserved non-coding region of TCF4.

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