A genome-wide association study identifies a new variant associated with word reading fluency in Chinese children

Reading disability exhibited defects in different cognitive domains, including word reading fluency, word reading accuracy, phonological awareness, rapid automatized naming and morphological awareness. To identify the genetic basis of Chinese reading disability, we conducted a genome-wide association study (GWAS) of the cognitive traits related to Chinese reading disability in 2284 unrelated Chinese children. Among the traits analyzed in the present GWAS, we detected one genome-wide significant association (p < 5 × 10⁻⁸) on word reading fluency for one SNP on 4p16.2, within EVC genes (rs6446395, p = 7.33 × 10⁻¹⁰). Rs6446395 also showed significant association with Chinese character reading accuracy (p = 2.95 × 10⁻⁴), phonological awareness (p = 7.11 × 10⁻³) and rapid automatized naming (p = 4.71 × 10⁻³), implying multiple effects of this variant. The eQTL data showed that rs6446395 affected EVC expression in the cerebellum. Gene-based analyses identified a gene (PRDM10) to be associated with word reading fluency at the genome-wide level. Our study discovered a new candidate susceptibility variant for reading ability and provided new insights into the genetics of developmental dyslexia in Chinese children.     

Genomewide association study for susceptibility genes contributing to familial Parkinson disease

Five genes have been identified that contribute to Mendelian forms of Parkinson disease (PD); however, mutations have been found in fewer than 5% of patients, suggesting that additional genes contribute to disease risk. Unlike previous studies that focused primarily on sporadic PD, we have performed the first genomewide association study (GWAS) in familial PD. Genotyping was performed with the Illumina HumanCNV370Duo array in 857 familial PD cases and 867 controls. A logistic model was employed to test for association under additive and recessive modes of inheritance after adjusting for gender and age. No result met genomewide significance based on a conservative Bonferroni correction. The strongest association result was with SNPs in the GAK/DGKQ region on chromosome 4 (additive model: p = 3.4 × 10⁻⁶; OR = 1.69). Consistent evidence of association was also observed to the chromosomal regions containing SNCA (additive model: p = 5.5 × 10⁻⁵; OR = 1.35) and MAPT (recessive model: p = 2.0 × 10⁻⁵; OR = 0.56). Both of these genes have been implicated previously in PD susceptibility; however, neither was identified in previous GWAS studies of PD. Meta-analysis was performed using data from a previous case–control GWAS, and yielded improved p values for several regions, including GAK/DGKQ (additive model: p = 2.5 × 10⁻⁷) and the MAPT region (recessive model: p = 9.8 × 10⁻⁶; additive model: p = 4.8 × 10⁻⁵). These data suggest the identification of new susceptibility alleles for PD in the GAK/DGKQ region, and also provide further support for the role of SNCA and MAPT in PD susceptibility. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. N. Pankratz and J. B. Wilk are joint first authors.     

Candidate Agtr2 influenced genes and pathways identified by expression profiling in the developing brain of Agtr2 mice

Intellectual disability (ID) is a common developmental disability observed in 1 to 3% of the human population. A possible role for the Angiotensin II type 2 receptor (AGTR2) in brain function, affecting learning, memory, and behavior, has been suggested in humans and rodents. Mice lacking the Agtr2 gene (Agtr2^−/y) showed significant impairment in their spatial memory and exhibited abnormal dendritic spine morphology. To identify Agtr2 influenced genes and pathways, we performed whole genome microarray analysis on RNA isolated from brains of Agtr2^−/y and control male mice at embryonic day 15 (E15) and postnatal day one (P1). The gene expression profiles of the Agtr2^−/y brain samples were significantly different when compared to profiles of the age-matched control brains. We identified 62 differently expressed genes (p ≤ 0.005) at E15 and in P1 brains of the Agtr2^−/y mice. We verified the differential expression of several of these genes in brain samples using quantitative RT-PCR. Differentially expressed genes encode molecules involved in multiple cellular processes including microtubule functions associated with dendritic spine morphology. This study provides insight into Agtr2 influenced candidate genes and suggests that expression dysregulation of these genes may modulate Agtr2 actions in the brain that influences learning and memory.     

SNPs in SNCA,MCCC1, DLG2, GBF1 and MBNL2 are associated with Parkinson's disease in southern Chinese population

Numerous single nucleotide polymorphisms (SNPs), which have been identified as susceptibility factors for Parkinson's disease (PD) as per genome‐wide association studies, have not been fully characterized for PD patients in China. This study aimed to replicate the relationship between 12 novel SNPs of 12 genes and PD risk in southern Chinese population. Twelve SNPs of 12 genes were detected in 231 PD patients and 249 controls, using the SNaPshot technique. Meta‐analysis was used to assess heterogeneity of effect sizes between this study and published data. The impact of SNPs on gene expression was investigated by analysing the SNP‐gene association in the expression quantitative trait loci (eQTL) data sets. rs8180209 of SNCA (allele model: P = .047, OR = 0.77; additive model: P = .047, OR = 0.77), rs2270968 of MCCC1 (dominant model: P = .024, OR = 1.52), rs7479949 of DLG2 (recessive model; P = .019, OR = 1.52), rs10748818 of GBF1 (additive model: P < .001, OR = 0.37), and rs4771268 of MBNL2 (recessive model: P = .003, OR = 0.48) were replicated to be significantly associated with the increased risk of PD. Noteworthy, a meta‐analysis of previous studies suggested rs8180209, rs2270968, rs7479949 and rs4771268 were in line with those of our cohort. Our study replicated five novel functional SNPs in SNCA, MCCC1, DLG2, GBF1 and MBNL2 could be associated with increased risk of PD in southern Chinese population.     

Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.     

Atypical Genetic Locus Associated with the zwf Gene Encoding the Glucose 6-Phosphate Dehydrogenase from Enterococcus mundtii CRL35

The zwf gene encoding glucose 6-phosphate dehydrogenase (G6PD, EC.1.1.1.49) from Enterococcus mundtii CRL35 was cloned as a 4921 bp EcoRI fragment and analyzed. The predicted zwf gene product consists of 506 residues with a molecular mass of 58.4 kDa, and is fully active in Escherichia coli as demonstrated by its heterologous expression in the zwf-negative mutant E. coli Su294. It shows a high degree of sequence identity (40–60%) to G6PDs described in other bacteria. Upstream of the zwf gene, a homolog of the DtxR family was identified (ORF D). Analysis of the 5′ sequence of ORF D revealed a potential promoter sequence, which would suggest the presence of an operon-like structure between ORF D and the zwf gene. Finally, it was found that Fe²⁺ levels have an important role as a modulator of G6PD activity. This is the first report of this type of regulation of G6PD activity. A possible involvement in oxidative stress is discussed.     

Gene expression differences in mice divergently selected for methamphetamine sensitivity

In an effort to identify genes that may be important for drug-abuse liability, we mapped behavioral quantitative trait loci (bQTL) for sensitivity to the locomotor stimulant effect of methamphetamine (MA) using two mouse lines that were selectively bred for high MA-induced activity (HMACT) or low MA-induced activity (LMACT). We then examined gene expression differences between these lines in the nucleus accumbens, using 20 U74Av2 Affymetrix microarrays and quantitative polymerase chain reaction (qPCR). Expression differences were detected for several genes, including Casein Kinase 1 Epsilon (Csnkle), glutamate receptor, ionotropic, AMPA1 (GluR1), GABA B1 receptor (Gabbr1), and dopamine- and cAMP-regulated phosphoprotein of 32 kDa (Darpp-32). We used the database to identify QTL that regulate the expression of the genes identified by the microarrays (expression QTL; eQTL). This approach identified an eQTL for Csnkle on Chromosome 15 (LOD=3.8) that comapped with a bQTL for the MA stimulation phenotype (LOD=4.5), suggesting that a single allele may cause both traits. The chromosomal region containing this QTL has previously been associated with sensitivity to the stimulant effects of cocaine. These results suggest that selection was associated with (and likely caused) altered gene expression that is partially attributable to different frequencies of gene expression polymorphisms. Combining classical genetics with analysis of whole-genome gene expression and bioinformatic resources provides a powerful method for provisionally identifying genes that influence complex traits. The identified genes provide excellent candidates for future hypothesis-driven studies, translational genetic studies, and pharmacological interventions.     

Expression and activity of V‐H+‐ATPase in gill and kidney of marbled eel Anguilla marmorata in response to salinity challenge

The full‐length complementary (c)DNA of vacuolar‐type‐H⁺‐ATPase B1 gene (vhab1) in marbled eel Anguilla marmorata with 1741 base pairs (bp) was identified. It contained a 1512 bp open reading frame encoding a polypeptide with 503 amino acids (55·9 kDa), an 83 bp 5′‐untranslated region (UTR) and a 146 bp 3′‐UTR. The expression levels of A. marmorata vhab1 in gill and kidney of A. marmorata were evaluated at different intervals during the exposure to various salinities (0, 10 and 25). The results indicated that the expression levels of A. marmorata vhab1 messenger (m)RNA in gill and kidney had a significant increase and reached the highest level at 1 h in brackish water (BW, salinity 10) group and 6 h in seawater (SW, salinity 25) group. Therefore, salinity did affect the relative expression level of A. marmorata vhab1 mRNA in gills, which exhibited the enhancement by c. 44 times in SW group when compared with that in fresh water. No remarkable difference in the expression of A. marmorata vhab1 mRNA was observed after 15 days of SW exposure (P > 0·05). V‐H⁺‐ATPase activity exhibited an increase by two‐ to three‐fold when compared with that in gill and kidney from the control group. The consequence primarily suggested that A. marmorata vhab1 gene product in elvers from A. marmorata plays an important role in adaptation response to SW.     

Dioscin and methylprotodioscin isolated from the root of Asparagus cochinchinensis suppressed the gene expression and production of airway MUC5AC mucin induced by phorbol ester and growth factor

BackgroundThe root of Asparagus cochinchinensis (Lour.) Merr. has been utilized as mucoregulators and expectorants for controlling the airway inflammatory diseases in folk medicine.Hypothesis/purposeWe investigated whether dioscin and methylprotodioscin isolated from the root of Asparagus cochinchinensis (Lour.) Merr. suppress the gene expression and production of airway MUC5AC mucin induced by phorbol ester and growth factor.Study designConfluent NCI-H292 cells were pretreated with dioscin or methylprotodioscin for 30 min and then stimulated with EGF or PMA for 24 h. The MUC5AC mucin gene expression was measured by RT-PCR. Production of MUC5AC mucin protein was measured by ELISA.Results(1) Dioscin and methylprotodioscin suppressed the expression of MUC5AC mucin gene induced by EGF or PMA; (2) dioscin suppressed the production of MUC5AC mucin induced by either EGF at 10⁻⁵ M (p < 0.05) and 10⁻⁶ M (p < 0.05) or PMA at 10⁻⁴ M (p < 0.05), 10⁻⁵ M (p < 0.05) and 10⁻⁶ M (p < 0.05); (3) methylprotodioscin also suppressed the production of MUC5AC mucin induced by either EGF at 10⁻⁴ M (p < 0.05) or PMA at 10⁻⁴ M (p < 0.05).ConclusionThese results suggest that dioscin and methylprotodioscin isolated from the root of Asparagus cochinchinensis suppress the gene expression and production of MUC5AC mucin, by directly acting on airway epithelial cells, and the results are consistent with the traditional use of Asparagus cochinchinensis as remedy for diverse inflammatory pulmonary diseases.     

NSAIDs protect dopaminergic neurons against 6‐OHDA and MPP+ toxicity

Endogenous and environmental neurotoxins are among the suspected causes of the loss of dopaminergic (DA) neurons in Parkinson's disease (PD). Non‐steroidal anti‐inflammatory drugs (NSAIDs) reduce inflammation by inhibiting cyclooxygenase (COX)‐dependent synthesis of prostaglandins (PG) from arachidonic acid. NSAIDs decrease the incidence of Alzheimer's disease, but little is known about their potential benefit for PD. Therefore, we examined whether NSAIDs could protect DA neurons from neurotoxic insults. NSAIDs can protect DA neurons against excitotoxicity (Casper et al. 2000), and against 6‐hydroxydopamine (6‐OHDA) toxicity (Carrasco et al. 2001). Here, we compared in primary mesencephalic/DA neuron cultures the effect of NSAIDs on the toxicity of 1‐methyl‐phenylpyridinium (MPP⁺) or 6‐OHDA. 6‐OHDA significantly (*p < 0.0001) increased PG production, whereas MPP⁺ did not (p < 0.05). We then compared the competitive/unspecific COX inhibitors ibuprofen and naproxen and the noncompetitive/unspecific inhibitor acetylsalicylic acid (ASA, aspirin) for their ability to protect DA neurons against either 6‐OHDA or MPP⁺ toxicity. Interestingly, all three nonselective COX inhibitors protected DA neurons in cultures against both 6‐OHDA and MPP⁺ (p < 0.05), despite the difference in PG induction by 6‐OHDA vs. MPP⁺. The selective COX‐2 inhibitor NS398 did protect DA neurons against 5 μm MPP⁺ (*p < 0.05), but failed to protect DA neurons against 5 μm 6‐OHDA (p < 0.05). Our results suggest that COX‐inhibitors may have neuroprotective benefits unrelated to inhibition of PG synthesis, and that 6‐OHDA and MPP⁺ have partially overlapping mechanisms of neurodegeneration possibly involving COX activity. Acknowledgement: Supported, in part, by the International Federation for Parkinson's disease, NY, NY.