A de novo splice site mutation in CASK causes FG syndrome-4 and congenital nystagmus.

Mutations in CASK cause X-linked intellectual disability, microcephaly with pontine and cerebellar hypoplasia, optic atrophy, nystagmus, feeding difficulties, GI hypomotility, and seizures. Here we present a patient with a de novo carboxyl-terminus splice site mutation in CASK (c.2521-2A>G) and clinical features of the rare FG syndrome-4 (FGS4). We provide further characterization of genotype-phenotype correlations in CASK mutations and the presentation of nystagmus and the FGS4 phenotype. There is considerable variability in clinical phenotype among patients with a CASK mutation, even among variants predicted to have similar functionality. Our patient presented with developmental delay, nystagmus, and severe gastrointestinal and gastroesophageal complications. From a cognitive and neuropsychological perspective, language skills and IQ are within normal range, although visual-motor, motor development, behavior, and working memory were impaired. The c.2521-2A>G splice mutation leads to skipping of exon 26 and a 9 base-pair deletion associated with a cryptic splice site, leading to a 28-AA and a 3-AA in-frame deletion, respectively (p.Ala841_Lys843del and p.Ala841_Glu868del). The predominant mutant transcripts contain an aberrant guanylate kinase domain and thus are predicted to degrade CASK's ability to interact with important neuronal and ocular development proteins, including FRMD7. Upregulation of CASK as well as dysregulation among a number of interactors is also evident by RNA-seq. This is the second CASK mutation known to us as cause of FGS4. © 2017 Wiley Periodicals, Inc.

Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants.

We conducted a systematic study of top susceptibility variants from a genome-wide association (GWA) study of bipolar disorder to gain insight into the functional consequences of genetic variation influencing disease risk. We report here the results of experiments to explore the effects of these susceptibility variants on DNA methylation and mRNA expression in human cerebellum samples. Among the top susceptibility variants, we identified an enrichment of cis regulatory loci on mRNA expression (eQTLs), and a significant excess of quantitative trait loci for DNA CpG methylation, hereafter referred to as methylation quantitative trait loci (mQTLs). Bipolar disorder susceptibility variants that cis regulate both cerebellar expression and methylation of the same gene are a very small proportion of bipolar disorder susceptibility variants. This finding suggests that mQTLs and eQTLs provide orthogonal ways of functionally annotating genetic variation within the context of studies of pathophysiology in brain. No lymphocyte mQTL enrichment was found, suggesting that mQTL enrichment was specific to the cerebellum, in contrast to eQTLs. Separately, we found that using mQTL information to restrict the number of single-nucleotide polymorphisms studied enhances our ability to detect a significant association. With this restriction a priori informed by the observed functional enrichment, we identified a significant association (rs12618769, P(bonferroni)<0.05) from two other GWA studies (TGen+GAIN; 2191 cases and 1434 controls) of bipolar disorder, which we replicated in an independent GWA study (WTCCC). Collectively, our findings highlight the importance of integrating functional annotation of genetic variants for gene expression and DNA methylation to advance the biological understanding of bipolar disorder.

Genome-wide SNP genotyping study using pooled DNA to identify candidate markers mediating susceptibility to end-stage renal disease attributed to Type 1 diabetes.

AIMS: Genetic factors play a major role in the progression of kidney disease in diabetes. To identify candidate single nucleotide polymorphisms (SNPs) with potential effects on susceptibility to end-stage renal disease (ESRD), we performed a whole genome association scan using pooled DNA from Caucasian individuals with Type 1 diabetes. METHODS: We utilized the Illumina Infinium II HumanHap 550 beadchip platform to genotype 555 352 SNPs in DNA pools comprised of 547 cases with ESRD and 549 control subjects with Type 1 diabetes duration > 20 years and no ESRD. Pooled probe intensity was used to predict mean allele frequency (MAF) for each locus. Individual genotyping was performed using the iPLEX assay in conjunction with the MassARRAY platform (Sequenom). RESULTS: We identified 2870 markers showing substantial differences in MAF (5.0-10.7%) between pools. To initiate validation of these findings, we genotyped 22 high-ranking markers in 462 individuals with ESRD and 470 unaffected control subjects selected from the genome-wide SNP genotyping study sample. We observed the strongest evidence for association between ESRD and rs1749824, located in the ZMIZ1 gene [OR = 1.47 (1.21-1.78) per copy of T allele; P = 8.1 x 10(-5)] and rs9298190, located in the musculin gene [OR = 1.56 (1.28-1.91) per copy of C allele; P = 1.6 x 10(-5)]. Evidence for nominal association with markers in or near the IRS2, TMPO, BID, KLRA1, ELMO1 and CNDP1 genes was also observed (P < or = 0.0006). CONCLUSIONS: These findings identify several novel loci which may contribute to ESRD susceptibility in individuals with Type 1 diabetes.

Genome-wide linkage analysis of ADHD using high-density SNP arrays: novel loci at 5q13.1 and 14q12.

Previous genome-wide linkage studies applied the affected sib-pair design; one investigated extended pedigrees of a genetic isolate. Here, results of a genome-wide high-density linkage scan of attention-deficit/hyperactivity disorder (ADHD) using an array-based genotyping of approximately 50 K single nucleotide polymorphism (SNPs) markers are presented. We investigated eight extended pedigrees of German origin that were non-related, not part of a genetic isolate and ascertained on the basis of clinical referral. Two parametric analyses maximizing LOD scores (MOD) and a non-parametric analysis for both a broad and a narrow phenotype approach were conducted. Novel linkage loci across all families were detected at 2q35, 5q13.1, 6q22-23 and 14q12, within individual families at 18q11.2-12.3. Further linkage regions at 7q21.11, 9q22 and 16q24.1 in all families, and at 1q25.1, 1q25.3, 9q31.1-33.1, 9q33, 12p13.33, 15q11.2-13.3 and 16p12.3-12.2 in individual families replicate previous findings. High-resolution linkage mapping points to several novel candidate genes characterized by dense expression in the brain and potential impact on disorder-relevant synaptic transmission. Our study provides further evidence for common gene effects throughout different populations despite the complex multifactorial etiology of ADHD.

Structural insights into the mechanical regulation of molecular recognition sites.

Intriguing experimental and computational data are emerging to suggest that mechanical forces regulate the functional states of some proteins by stretching them into nonequilibrium states. Using the extracellular matrix protein fibronectin as an example, we discuss molecular design principles that might control the exposure of a protein's recognition sites, and/or their relative distances, in a force-dependent manner. Fibronectin regulates many cellular functions by binding directly to integrins. Although integrins have a key role in the transduction of force across the cell membrane by coupling the extracellular matrix to the cytoskeleton, the studies reviewed here suggest that fibronectin might be one of the molecules responsible for the initial transformation of mechanical force into a biochemical signal.

Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort.

OBJECTIVES: CSF levels of Aß1-42, t-tau, and p-tau181p are potential early diagnostic markers for probable Alzheimer disease (AD). The influence of genetic variation on these markers has been investigated for candidate genes but not on a genome-wide basis. We report a genome-wide association study (GWAS) of CSF biomarkers (Aß1-42, t-tau, p-tau181p, p-tau181p/Aß1-42, and t-tau/Aß1-42). METHODS: A total of 374 non-Hispanic Caucasian participants in the Alzheimer's Disease Neuroimaging Initiative cohort with quality-controlled CSF and genotype data were included in this analysis. The main effect of single nucleotide polymorphisms (SNPs) under an additive genetic model was assessed on each of 5 CSF biomarkers. The p values of all SNPs for each CSF biomarker were adjusted for multiple comparisons by the Bonferroni method. We focused on SNPs with corrected p<0.01 (uncorrected p<3.10×10(-8)) and secondarily examined SNPs with uncorrected p values less than 10(-5) to identify potential candidates. RESULTS: Four SNPs in the regions of the APOE, LOC100129500, TOMM40, and EPC2 genes reached genome-wide significance for associations with one or more CSF biomarkers. SNPs in CCDC134, ABCG2, SREBF2, and NFATC4, although not reaching genome-wide significance, were identified as potential candidates. CONCLUSIONS: In addition to known candidate genes, APOE, TOMM40, and one hypothetical gene LOC100129500 partially overlapping APOE; one novel gene, EPC2, and several other interesting genes were associated with CSF biomarkers that are related to AD. These findings, especially the new EPC2 results, require replication in independent cohorts.

Peer weight norm misperception as a risk factor for being over and underweight among UK secondary school students.

BACKGROUND: Erroneous perceptions of peer weight norms may be important risk factors for being underweight and overweight. This study assessed misperceptions of peer weight norms and their association with being overweight or underweight among UK youth. METHODS: Anonymous surveys were conducted among students (n=2104) attending schools in a Greater London borough in Fall 2007. Students' perceptions of the weight norm for same sex peers in their year in their school (years 5 through 11) are compared with the aggregate self-reports of weight for these same sex and year cohorts in each school. Variation in perceptions is compared with personal body mass index (BMI) on the basis of self-reported height and weight. RESULTS: A total of 34% of males and 32% of females overestimated peer weight norms by more than 5% (10 kg on average). Similarly, 37% of males and 43% of females underestimated peer weight norms by more than 5% (7 kg on average). For both males and females, overestimating peer weight norms was associated with a greater risk for being overweight and underestimating peer weight norms was associated with a greater risk for being underweight. Perceived peer weight norm was the strongest predictor of BMI among females compared with estimated actual weight norms of peers (based on the mean of self-reported weight) and demographic factors, and one of the two strongest predictors among males in linear regression analyses, including schools as fixed effects. CONCLUSIONS: Pervasive misperceptions of peer weight norms may contribute to unhealthy weight-related behaviors and help perpetuate students' overweight or underweight status. Future research should examine perceptions of other weight-related peer norms and explore what may create misperceptions. Addressing pervasive misperceptions of weight could perhaps be included as a part of interventions aimed at reducing unhealthy weight and related behaviors.

Regulation of the 2-oxoglutarate dehydrogenase lipoate succinyltransferase complex from cauliflower by nucleotide. Pre-steady state kinetics and physical studies.

Analysis of the binding of thiamin pyrophosphate to the 2-oxoglutarate dehydrogenaselipoate succinyltransferase multienzyme complex using pre-steady state kinetic methods revealed that the presence of 2-oxoglutarate is not necessary for binding, although it does stabilize the complex by slowing the rate of dissociation of the holoenzyme. The rate of binding of thiamin-PPi to the enzyme and the subsequent enzyme activation are not limited by a reaction at C-2 of the thiazolium ring of thiamin-PPi since no kinetic isotope effect is observed when 2-D-thiamin-PPi is substituted for the protonated cofactor. The presence of 5'-AMP, which activates the reaction producing both a V and a Km response, causes a significant increase in kon for thiamin-PPi. The AMP analog 1,N6-ethenoadenosine-5'-monophosphate (epsilon-AMP) also activates the reaction, but shows only a K effect, with no influence on V. This effector reduces Kd for the thiamin-PPi2-oxoglutarate dehydrogenase complex by increasing kon. The change in kon for thiamin-PPi in response to changes in hydrogen ion concentration shows pK values which are unaffected by the addition of AMP, in this respect resembling the steady state kinetic response of V/Km and differing from the pH profile of V. The dissociation constant of holoenzyme is relatively insensitive to pH over the range pH 6 to 9, but in the presence of AMP the Kd, which is decreased in the range from pH 7 to 8, increases sharply at higher or lower pH values.

Structural mapping of rabbit muscle phosphofructokinase. Distance between the adenosine cyclic 3',5'-phosphate binding site and a reactive sulfhydryl group.

The cAMP binding site of rabbit muscle phosphofructokinase has been labeled with the fluorescent molecule 5'-(p-fluorosulfonylbenzoyl)-2-aza-1,N6-ethenoadenosine. The most reactive sulfhydry- group of this modified enzyme, which is catalytically active, has been labeled with 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole and with N-]4-(dimethylamino)-3,5-dinitrophenyl]maleimide. The calculated distances between the cAMP binding site and the most reactive sulfhydryl group, as determined by resonance energy transfer measurements, are 31 and 26 A, respectively, for the two sulfhydryl group labels. Both steady-state and fluorescent -ifetime techniques were used to measure the energy transfer efficiencies in 50 mM potassium phosphate (pH 8.0) and 1 mM ethylenediaminetetraacetic acid, and a value of 2/3 was assumed for the donor-acceptor orientation factor. If the difference in calculated distances is attributed to a difference in the orientation factor for the two donor-acceptor ,airs, the actual distance between the cAMP ligand binding site and the most reactive sulfhydryl group on phosphofructokinase is shown to be 28 +/- 6 A.