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Genetics Roundup: Motley Crew of Variants Kicks Off 2013

12 March 2013. Genetic studies of schizophrenia in the past two months have served up more leads of both the rare and common variety. While some of the rare ones incriminate single genes already familiar to schizophrenia researchers, one implicates a whole new territory on chromosome 16. These findings are complemented by two studies pointing to contributions by common variants to mental illness. One study finds that common variants may have "hyperlocal" effects on risk for bipolar disorder in a single family, not just across a population; a second study fingers a common variant that combines with an environmental factor to increase risk for schizophrenia. These varied findings highlight the complexity of the genetic basis of schizophrenia.

Distal 16p11.2
The first study, published online January 16 in JAMA Psychiatry, reports a rare deletion on the far end of 16p11.2 that is associated with schizophrenia in large, and multiple, samples. If you’re thinking you’ve heard of 16p11.2 before, you have: it harbors a locus known for its "mirror phenotypes," with duplications associated with microcephaly, schizophrenia, and autism, and deletions with macrocephaly and autism (see SRF related news story), and recently a common variant there has been associated with psychosis (see SRF related news story). But the new study implicates a completely different, non-overlapping section 600 kilobases away. A transatlantic collaboration led by Todd Lencz of Zucker Hillside Hospital in Glen Oaks, New York, and George Kirov of Cardiff University in Cardiff, U.K., looked for copy number variations (CNVs) in two separate samples, one from Bulgaria, and one of Ashkenazi Jews.

First authors Saurav Guha and Elliott Rees and colleagues found a 220 kb deletion in the distal part of 16p11.2 in two cases from each sample. As ever, the challenge with rare variants is to convincingly link them to disease, so to gather supporting evidence, the researchers scoured eight independent samples for this deletion. This, combined with the events from the initial discovery samples, garnered a total of 13 deletions in 13,850 cases of schizophrenia (0.094 percent) and three among 19,954 controls (0.015 percent). The difference in frequency amounted to an odds ratio of 6.25 (p = 0.001), meaning that the deletion was associated with over a sixfold increase in risk for schizophrenia.

The exact size of the deletion varied among carriers, but all deletions were missing nine genes, some of which have been linked to neurological diseases, or insulin or leptin function. This jibes with previous work that has linked distal 16p11.2 deletions to developmental delay and obesity (e.g., Bachmann-Gagescu et al., 2010).

Do not pass up NPAS3
Taking a more focused approach, Frederick Nucifora of Johns Hopkins University in Baltimore, Maryland, and colleagues sequenced the neuronal PAS domain protein 3 (NPAS3) gene in 34 families affected by multiple cases of schizophrenia. NPAS3 encodes a transcription factor, and has been associated with schizophrenia before, via common variants (Pickard et al., 2009) and rare, gene-disrupting mutations (Kamnasaran et al., 2003). In a brief report published online January 22 in Molecular Psychiatry, first author Lan Yu and colleagues describe a point mutation found in one of these families that converts a valine to an isoleucine in the resulting protein. The mutation was found in a mother and two of her children, all three of whom had schizophrenia. It was also found in another child, who had major depression. Additional risk alleles could be at work in this family, however, because non-carriers in the family also had psychiatric disorders. Still, the mutation seemed potentially pathogenic, as mutant copies of NPAS3 in cultured mouse neurons limited the growth of neuronal processes—something consistent with a role in neuronal wiring, and in line with the idea that schizophrenia stems from disrupted neurodevelopment.

Studying families densely affected by mental illness can be a good way to find a variant with a strong effect, but this is not always the end result, according to another brief report published online December 18, 2012, in Molecular Psychiatry. A team led by Patrick Sullivan of the University of North Carolina in Chapel Hill, together with Markus Nöthen of the University of Bonn, Germany, and Marcella Rietschel of Heidelberg University in Mannheim, Germany, studied a Spanish family with 18 cases of bipolar disorder and seven cases of major depressive disorder. Sequencing the parts of the genome held in common among the family members did not turn up any strong leads, nor did looking for CNVs in the entire genome. But when the researchers added up the risk contributed by common variants linked to bipolar disorder (PGC Bipolar Disorder Working Group, 2011), the risk scores in affected family members were significantly greater than those from the unaffected. These risk scores were similar to those found in an affected sample of unrelated cases, and suggest that an enrichment for multiple, common variants may underlie mental illness in some families.

A diagnostic spectrum
The inhibitory synapse takes center stage in a study published online February 7 in Human Molecular Genetics. Led by Steven Scherer of The Hospital for Sick Children in Toronto, Canada, the study reports deletions and point mutations in gephryin (GPHN), a molecular organizer of inhibitory synapses, in schizophrenia, autism, and seizures. GPHN encodes a protein that forms a bridge between glycine or γ-aminobutyric acid (GABA) receptors and the interior cytoskeleton, and promotes their clustering at the postsynaptic side of an inhibitory synapse. Previous research has implicated GPHN in schizophrenia (Lencz et al., 2007), and the molecule has fallen under further suspicion because of its interactions with other schizophrenia- and autism-associated molecules, including neurexins and neuroligins.

First author Anath Lionel and colleagues combed GPHN for CNVs or point mutations in people with schizophrenia, autism, or seizure disorders. This search turned up small deletions within the protein-coding part of the gene in six cases of either schizophrenia, autism, or seizure disorder (out of 8,775 surveyed) and in three controls (out of 27,019), and protein-changing "missense" mutations in six cases of autism. The results implicate GPHN in autism for the first time, and add GPHN to the list of genetic risk factors shared between autism and schizophrenia. The findings also fit with ideas of impaired inhibitory transmission in schizophrenia (see SRF Hypothesis; see also SRF related news story), and highlight the machinery of inhibitory synapses alongside that of its excitatory counterparts (see SRF related news story).

The precise type of mutation may determine the resulting disorder, according to another paper published online February 5 in Human Molecular Genetics. Liesbeth Rooms of University of Antwerp, Belgium, and colleagues set their sights on the ANK3 gene, a well-established risk factor for bipolar disorder and schizophrenia (see SRF related news story). Like GPHN, ANK3 also bridges membrane-bound receptors to the cytoskeleton, though ANK3 connects with voltage-gated sodium channels that cluster at action potential-propagating zones along the axon. First authors Zafar Iqbal, Geert Vandeweyer, and Monique van der Voet report inactivating disruptions to ANK3 in people with intellectual disability. The researchers suggest that a drastic loss of ANK3 function leads to intellectual disability, whereas subtler changes like those introduced by common variants would promote less severe psychiatric conditions. If true, then genes with an established link to intellectual disability may warrant special attention in the hunt for risk alleles contributing to complex psychiatric disorders.

Consider cytomegalovirus
While it is clear that the effects of genetic risk alleles may be modulated by environment, it is harder to know which of the seemingly infinite environmental factors to study. As previously reported in a dispatch from WCPG 2012 (see SRF related conference story), a team has been exploring whether cytomegalovirus infection of mothers during pregnancy might interact with genetic risk factors carried by their fetuses. Cytomegalovirus targets the nervous system, and maternal infection with it has been connected to schizophrenia risk (see SRF related news story). Led by Anders Børglum of Aarhus University in Denmark, and published online January 29 in Molecular Psychiatry, the study plumbs Danish population databases that contain mental health information on all people born in Denmark since 1981, as well as stored blood spots collected upon their birth. DNA extracted from the babies’ blood can give clues about their genetic risk for the disorder, and antibodies detected in the blood can give a readout as to whether the mother was infected with cytomegalovirus at the time of birth because newborns do not yet make their own antibodies.

The researchers first did a straightforward genomewide association study (GWAS) by surveying single nucleotide polymorphisms (SNPs) in 888 people with schizophrenia and 882 controls. Not surprisingly for the smallish sample size, no one SNP reached genomewide significance (i.e., p <5 x 10-8). Follow-up analyses in a separate Danish sample and a German-Dutch sample also did not produce any genomewide significant signals, nor did combining the samples. When looking for SNPs that boosted risk for schizophrenia in the presence of maternal cytomegalovirus infection, the researchers found one flagging CTNNA3, a gene encoding a cell adhesion protein. On its own, cytomegalovirus infection did not increase risk for schizophrenia, nor did the SNP marking CTNNA3, but when combined they produced a fivefold increase in risk (p = 7.3 x 10-7). Though other confounding factors, such as socioeconomic status, may explain this result (i.e., socioeconomic status correlates with cytomegalovirus infection, and with schizophrenia risk), it suggests that considering environmental factors in concert with GWAS may reveal entirely new leads.—Michele Solis.

References:
Børglum AD, Demontis D, Grove J, Pallesen J, Hollegaard MV, Pedersen CB, Hedemand A, Mattheisen M; GROUP investigators, Uitterlinden A, Nyegaard M, Orntoft T, Wiuf C, Didriksen M, Nordentoft M, Nöthen MM, Rietschel M, Ophoff RA, Cichon S, Yolken RH, Hougaard DM, Mortensen PB, Mors O. Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci. Mol Psychiatry. 2013 Jan 29. Abstract

Collins AL, Kim Y, Szatkiewicz JP, Bloom RJ, Hilliard CE, Quackenbush CR, Meier S, Rivas F, Mayoral F, Cichon S, Nöthen MM, Rietschel M, Sullivan PF. Identifying bipolar disorder susceptibility loci in a densely affected pedigree. Mol Psychiatry. 2012 Dec 18. Abstract

Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, Malhotra AK, Rietschel M, Nöthen MM, Degenhardt F, Priebe L, Breuer R, Strohmaier J, Ruderfer DM, Moran JL, Chambert KD, Sanders AR, Shi J, Kendler K, Riley B, O'Neill T, Walsh D, Malhotra D, Corvin A, Purcell S, Sklar P, Iwata N, Hultman CM, Sullivan PF, Sebat J, McCarthy S, Gejman PV, Levinson DF, Owen MJ, O'Donovan MC, Lencz T, Kirov G, . Implication of a rare deletion at distal 16p11.2 in schizophrenia. JAMA Psychiatry. 2013 Mar 1; 70(3):253-60. Abstract

Iqbal Z, Vandeweyer G, van der Voet M, Waryah AM, Zahoor MY, Besseling JA, Roca LT, Vulto-van Silfhout AT, Nijhof B, Kramer JM, Van der Aa N, Ansar M, Peeters H, Helsmoortel C, Gilissen C, E L M Vissers L, Veltman JA, de Brouwer AP, Frank Kooy R, Riazuddin S, Schenck A, van Bokhoven H, Rooms L. Homozygous and heterozygous disruptions of ANK3: at the crossroads of neurodevelopmental and psychiatric disorders. Hum Mol Genet. 2013 Feb 18. Abstract

Lionel AC, Vaags AK, Sato D, Gazzellone MJ, Mitchell EB, Chen HY, Costain G, Walker S, Egger G, Thiruvahindrapuram B, Merico D, Prasad A, Anagnostou E, Fombonne E, Zwaigenbaum L, Roberts W, Szatmari P, Fernandez BA, Georgieva L, Brzustowicz LM, Roetzer K, Kaschnitz W, Vincent JB, Windpassinger C, Marshall CR, Trifiletti RR, Kirmani S, Kirov G, Petek E, Hodge JC, Bassett AS, Scherer SW. Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures. Hum Mol Genet. 2013 Feb 20. Abstract

Yu L, Arbez N, Nucifora LG, Sell GL, Delisi LE, Ross CA, Margolis RL, Nucifora FC Jr. A mutation in NPAS3 segregates with mental illness in a small family. Mol Psychiatry. 2013 Jan 22. Abstract

 
Comments on News and Primary Papers
Primary Papers: A mutation in NPAS3 segregates with mental illness in a small family.

Comment by:  Ben Pickard
Submitted 5 February 2013 Posted 5 February 2013

The paper by Yu et al. places another tick next to the...  Read more


View all comments by Ben Pickard
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