Michael P. Moreau

Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism

We have undertaken a genome-wide analysis of rare copy-number variation (CNV) in 1124 autism spectrum disorder (ASD) families, each comprised of a single proband, unaffected parents, and, in most kindreds, an unaffected sibling. We find significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome, characterized by a highly social personality. We identify rare recurrent de novo CNVs at five additional regions, including 16p13.2 (encompassing genes USP7 and C16orf72) and Cadherin 13, and implement a rigorous approach to evaluating the statistical significance of these observations. Overall, large de novo CNVs, particularly those encompassing multiple genes, confer substantial risks (OR = 5.6; CI = 2.6-12.0, p = 2.4 × 10(-7)). We estimate there are 130-234 ASD-related CNV regions in the human genome and present compelling evidence, based on cumulative data, for association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin 1.

Altered microRNA expression profiles in postmortem brain samples from individuals with schizophrenia and bipolar disorder.

BACKGROUND MicroRNAs (miRNAs) are potent regulators of gene expression with proposed roles in brain development and function. We hypothesized that miRNA expression profiles are altered in individuals with severe psychiatric disorders. METHODS With real-time quantitative polymerase chain reaction, we compared the expression of 435 miRNAs and 18 small nucleolar RNAs in postmortem brain tissue samples from individuals with schizophrenia, individuals with bipolar disorder, and psychiatrically healthy control subjects (n = 35 each group). Detailed demographic data, sample selection and storage conditions, and drug and substance exposure histories were available for all subjects. Bayesian model averaging was used to simultaneously assess the impact of these covariates as well as the psychiatric phenotype on miRNA expression profiles. RESULTS Of the variables considered, sample storage time, brain pH, alcohol at time of death, and postmortem interval were found to affect the greatest proportion of miRNAs. Of miRNAs analyzed, 19% exhibited positive evidence of altered expression due to a diagnosis of schizophrenia or bipolar disorder. Both conditions were associated with reduced miRNA expression levels, with a much more pronounced effect observed for bipolar disorder. CONCLUSIONS This study suggests that modest underexpression of several miRNAs might be involved in the complex pathogenesis of major psychosis.

Association of synapsin 2 with schizophrenia in families of Northern European ancestry

The synapsin 2 (Syn2) gene (3p25) is implicated in synaptogenesis, neurotransmitter release, and the localization of nitric oxide synthase to the proximity of its targets. In this study we investigated linkage and association between the Syn2 locus and schizophrenia. 37 pedigrees of Northern European ancestry from the NIMH Human Genetics Initiative collection were used. Four microsatellites and twenty SNPs were genotyped. Linkage (FASTLINK) and association (TRANSMIT, PDTPHASE) between markers and schizophrenia were evaluated. A maximum heterogeneity LOD of 1.93 was observed at marker D3S3434 with a recessive mode of inheritance. Significant results were obtained for association with schizophrenia using TRANSMIT (minimum nominal p=0.0000005) and PDTPHASE (minimum nominal p=0.014) using single marker analyses. Haplotype analysis using markers in introns 5 and 6 of Syn2 provided a single haplotype that is significantly associated with schizophrenia using TRANSMIT (nominal p<0.00000001) and PDTPHASE (nominal p=0.02). Simulation studies confirm the global significance of these results, but demonstrate that the small p-values generated by the bootstrap routine of TRANSMIT can be consistently anticonservative. Review of the literature suggests that Syn2 is likely to be involved in the etiology or pathogenesis of schizophrenia.

Chronological Changes in MicroRNA Expression in the Developing Human Brain

Objective MicroRNAs (miRNAs) are endogenously expressed noncoding RNA molecules that are believed to regulate multiple neurobiological processes. Expression studies have revealed distinct temporal expression patterns in the developing rodent and porcine brain, but comprehensive profiling in the developing human brain has not been previously reported. Methods We performed microarray and TaqMan-based expression analysis of all annotated mature miRNAs (miRBase 10.0) as well as 373 novel, predicted miRNAs. Expression levels were measured in 48 post-mortem brain tissue samples, representing gestational ages 14–24 weeks, as well as early postnatal and adult time points. Results Expression levels of 312 miRNAs changed significantly between at least two of the broad age categories, defined as fetal, young, and adult. Conclusions We have constructed a miRNA expression atlas of the developing human brain, and we propose a classification scheme to guide future studies of neurobiological function.

Improvements to bead-based oligonucleotide ligation SNP genotyping assays

We describe a bead-based, multiplexed, oligonucleotide ligation assay (OLA) performed on the Luminex flow cytometer. Differences between this method and those previously reported include the use of far fewer beads and the use of a universal oligonucleotide for signal detection. These innovations serve to significantly reduce the cost of the assay, while maintaining robustness and accuracy. Comparisons are made between the Luminex OLA and both pyrosequencing and direct sequencing. Experiments to assess conversion rates, call rates, and concordance across technical replicates are also presented.

NOS1AP protein levels are altered in BA46 and cerebellum of patients with schizophrenia.

Dear Editors, Brzustowicz and colleagues (2004) identified significant linkage disequilibrium between schizophrenia and markers within the gene encoding nitric oxide synthase 1 (neuronal; NOS1) adaptor protein (NOS1AP; also termed carboxyl-terminal PDZ ligand of nNOS or CAPON). Quantitative real-time PCR (qRT-PCR) analysis of mRNA from human postmortem dorsolateral prefrontal cortex further revealed that expression of the short isoform of the NOS1AP gene (NOS1AP-S) is significantly increased in patients with schizophrenia (Xu, et al., 2005). More recently, the group also identified a functional risk allele within NOS1AP and showed that this change increased NOS1AP mRNA expression in a cell culture system (Wratten, et al., 2009). Despite these recent reports establishing linkage between NOS1AP and schizophrenia, little is known about NOS1AP protein expression in the brains of affected patients. Previous reports described two distinct NOS1AP isoforms: full-length NOS1AP-L (10 exons, ~75kD) and NOS1AP-S, a C-terminal specific transcript that encodes only the PDZ domain (Jaffrey, et al., 1998; Xu, et al., 2005). We have now identified a novel isoform, NOS1AP-S’ (Figure 1A), in mouse and human tissue using qRT-PCR (data not shown). To evaluate the expression levels of these three NOS1AP isoforms in human brain tissue, postmortem samples from Brodmann’s Area (BA) 46, BA11, Medial Temporal Lobe (MTL), Occipital Lobe (OL), and cerebellum of unaffected patients and those with schizophrenia were obtained from the Human Brain and Spinal Fluid Resource Center (Los Angeles, CA) and subjected to Western blotting with normalization to GAPDH or actin, as previously described (Xu, et al., 2005). Investigators were blinded to all subject information until after statistical analysis. The logarithms of the normalized values for subjects with schizophrenia and unaffected control patients within the same brain region were compared using the standard t-test. Correction for testing of multiple expression levels was made using permutations of case/control labels. Secondary examination of linear models with other covariates was based on the AICc model selection criterion (Burnham, 2002). The L (p = 0.0067; reported p-values are nominal), S´ (p = 0.0082) and S (p = 0.0041) isoforms were increased in BA46 of patients with schizophrenia (Figure 1B) at a nominal significance level, although only the increase in the S isoform was significant (p<0.05) under permutation-based multiple testing adjustment. These data are consistent with previous reports strongly implicating this region in the etiology of schizophrenia (Barch, 2005; Bunney and Bunney, 2000; Xu, et al., 2005). The L (p = 0.0031), S (p = 0.0060), and S´ (p = 0.0156) isoforms were decreased in cerebellum of affected individuals (Figure 1B), although only the decrease of the L isoform was significant under adjustment. While some reports have indicated that schizophrenia may affect the cerebellum, the results are not as consistently observed as in other regions, namely the prefrontal cortex (Avila, et al., 2002; Kapoor, et al., 2006). There were no significant differences in NOS1AP expression between control and affected patients in BA11, the MTL, or the OL (Figure 1B). Additional analysis of NOS1AP expression reveals that no significant changes were evident in BA11, the MTL, or the OL of patients with schizophrenia versus those who are unaffected. While some studies have reported a role for BA11 in schizophrenia, others find no changes in expression of NMDA receptor pathway proteins (Toro and Deakin, 2005). Figure 1 (A) NOS1AP isoforms. The intron/exon boundaries and the predicted transcriptional (arrow) and translational (ATG) start sites for the different NOS1AP isoforms are illustrated. The new NOS1AP isoform is characterized by a unique 5’ exon and transcriptional ... Our data show an alteration of three NOS1AP isoforms in specific regions of the brain for patients diagnosed with schizophrenia. Initially identified in rat, NOS1AP plays a role in the inhibition of glutamate neurotransmission via disruption of NOS1 binding to Postsynaptic Density Protein-95 and -93. This results in uncoupling of NOS1 from the NMDA receptor, and ultimately, inhibition of receptor function (Brzustowicz, 2008; Jaffrey, et al., 1998; Xu, et al., 2005). These data suggest a role for NOS1AP in glutamate receptor hypofunction and manifestation of schizophrenia.

Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome- Wide Association Study

Fifty percent of variability in HIV-1 susceptibility is attributable to host genetics. Thus identifying genetic associations is essential to understanding pathogenesis of HIV-1 and important for targeting drug development. To date, however, CCR5 remains the only gene conclusively associated with HIV acquisition. To identify novel host genetic determinants of HIV-1 acquisition, we conducted a genome-wide association study among a high-risk sample of 3,136 injection drug users (IDUs) from the Urban Health Study (UHS). In addition to being IDUs, HIV- controls were frequency-matched to cases on environmental exposures to enhance detection of genetic effects. We tested independent replication in the Women’s Interagency HIV Study (N=2,533). We also examined publicly available gene expression data to link SNPs associated with HIV acquisition to known mechanisms affecting HIV replication/infectivity. Analysis of the UHS nominated eight genetic regions for replication testing. SNP rs4878712 in FRMPD1 met multiple testing correction for independent replication (P=1.38x10-4), although the UHS-WIHS meta-analysis p-value did not reach genome-wide significance (P=4.47x10-7 vs. P<5.0x10-8) Gene expression analyses provided promising biological support for the protective G allele at rs4878712 lowering risk of HIV: (1) the G allele was associated with reduced expression of FBXO10 (r=-0.49, P=6.9x10-5); (2) FBXO10 is a component of the Skp1-Cul1-F-box protein E3 ubiquitin ligase complex that targets Bcl-2 protein for degradation; (3) lower FBXO10 expression was associated with higher BCL2 expression (r=-0.49, P=8x10-5); (4) higher basal levels of Bcl-2 are known to reduce HIV replication and infectivity in human and animal in vitro studies. These results suggest new potential biological pathways by which host genetics affect susceptibility to HIV upon exposure for follow-up in subsequent studies.

Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

Bacterial communities in the mouse caecum and faeces are known to be altered by changes in dietary fat. The microbiota of the mouse small intestine, by contrast, has not been extensively profiled and it is unclear whether small intestinal bacterial communities shift with dietary fat levels. We compared the microbiota in the small intestine, caecum and colon in mice fed a low-fat (LF) or high-fat (HF) diet using 16S rRNA gene sequencing. The relative abundance of major phyla in the small intestine, Bacteriodetes, Firmicutes and Proteobacteria, was similar to that in the caecum and colon; the relative abundance of Verrucomicrobia was significantly reduced in the small intestine compared to the large intestine. Several genera were uniquely detected in the small intestine and included the aerotolerant anaerobe, Lactobacillus spp. The most abundant genera in the small intestine were accounted for by anaerobic bacteria and were identical to those identified in the large intestine. An HF diet was associated with significant weight gain and adiposity and with changes in the bacterial communities throughout the intestine, with changes in the small intestine differing from those in the caecum and colon. Prominent Gram-negative bacteria including genera of the phylum Bacteroidetes and a genus of Proteobacteria significantly changed in the large intestine. The mechanistic links between these changes and the development of obesity, perhaps involving metabolic endotoxemia, remain to be determined.