Evaluation of an algorithm of tagging SNPs selection by linkage disequilibrium

Genetic Overlap Between Attention Deficit/Hyperactivity Disorder and Autism Spectrum Disorder in SHANK2 Gene

Background: Recent findings indicated a high comorbidity between attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD), as well as shared genetic influences on them. The latter might contribute at least partly to the former clinical scenario. This study aimed at investigating whether SHANK genes were potential pleiotropic genes to the two said disorders, underlying their genetic overlap.

Methods: This study recruited 298 boys with ADHD (including 256 family trios of 1 ADHD boy and his 2 biological parents), 134 boys with ASD, 109 boys with both ADHD and ASD, and 232 typically developing boys as community controls. They were aged between 6 and 11 years old.

Results: There was no significant difference in allele frequency of a number of single nucleotide polymorphisms (SNPs) in SHANK2/SHANK3 between the three clinical groups (ADHD, ASD, and ADHD + ASD) and between the two control groups (community controls and pseudo-controls), respectively. The three clinical groups and the two control groups were thus, respectively, combined. A comparison between the two aggregated samples identified significant evidence of disease association for three SHANK2 SNPs with both ADHD and ASD, even after multiple testing correction: rs11236616 (OR = 0.762, permuted p = 0.0376), rs7106631 (OR = 0.720, permuted p = 0.0034), and rs9888288 (OR = 0.770, permuted p = 0.0407). Comparisons among individual groups pointed to a similar trend of findings.

Conclusion:SHANK2 could be considered a potential pleiotropic gene underlying the genetic overlap between ADHD and ASD. This might contribute partly to their high comorbidity in the afflicted children.

Anxiety and depression with neurogenesis defects in exchange protein directly activated by cAMP 2-deficient mice are ameliorated by a selective serotonin reuptake inhibitor, Prozac

Intracellular cAMP and serotonin are important modulators of anxiety and depression. Fluoxetine, a selective serotonin reuptake inhibitor (SSRI) also known as Prozac, is widely used against depression, potentially by activating cAMP response element-binding protein (CREB) and increasing brain-derived neurotrophic factor (BDNF) through protein kinase A (PKA). However, the role of Epac1 and Epac2 (Rap guanine nucleotide exchange factors, RAPGEF3 and RAPGEF4, respectively) as potential downstream targets of SSRI/cAMP in mood regulations is not yet clear. Here, we investigated the phenotypes of Epac1 (Epac1(-/-)) or Epac2 (Epac2(-/-)) knockout mice by comparing them with their wild-type counterparts. Surprisingly, Epac2(-/-) mice exhibited a wide range of mood disorders, including anxiety and depression with learning and memory deficits in contextual and cued fear-conditioning tests without affecting Epac1 expression or PKA activity. Interestingly, rs17746510, one of the three single-nucleotide polymorphisms (SNPs) in RAPGEF4 associated with cognitive decline in Chinese Alzheimer's disease (AD) patients, was significantly correlated with apathy and mood disturbance, whereas no significant association was observed between RAPGEF3 SNPs and the risk of AD or neuropsychiatric inventory scores. To further determine the detailed role of Epac2 in SSRI/serotonin/cAMP-involved mood disorders, we treated Epac2(-/-) mice with a SSRI, Prozac. The alteration in open field behavior and impaired hippocampal cell proliferation in Epac2(-/-) mice were alleviated by Prozac. Taken together, Epac2 gene polymorphism is a putative risk factor for mood disorders in AD patients in part by affecting the hippocampal neurogenesis.

A PIN1 polymorphism that prevents its suppression by AP4 associates with delayed onset of Alzheimer's disease

Alzheimer's disease (AD), the most common form of dementia, is characterized by the presence of neurofibrillary tangles composed of tau and senile plaques of amyloid-beta peptides (Aβ) derived from amyloid precursor protein (APP). Pin1 is a unique prolyl isomerase that has been shown to protect against age-dependent neurodegeneration by acting on phosphorylated tau and APP to suppress tangle formation and amyloidogenic APP processing. Here we report a functional polymorphism, rs2287839, in the Pin1 promoter that is significantly associated with a 3-year delay in the average age at onset (AAO) of late-onset AD in a Chinese population. More significantly, the Pin1 polymorphism rs2287839 is located within the consensus binding motif for the brain-selective transcription factor, AP4 (CAGCTG) and almost completely abolishes the ability of AP4 to bind and suppress the Pin1 promoter, as shown by chromatin immunoprecipitation, electrophoretic mobility shift assay, and promoter luciferase assay. Moreover, overexpression or knockdown of AP4 resulted in an 80% reduction or 2-fold increase in endogenous Pin1 levels, respectively. Thus, AP4 is a novel transcriptional repressor of Pin1 expression and the Pin1 promoter single nucleotide polymorphism (SNP) identified in this study that prevents such suppression is associated with delayed onset of AD. These results indicate that regulation of Pin1 by AP4 plays a critical role in determining age at onset of AD and might be a novel therapeutic target to delay the onset of AD.

Molecular cloning, expression and polymorphism of the porcine apolipoprotein A5 gene in a Jinhua × Pietrain F2 reference population

As a newly described member of the apolipoprotein gene family, apolipoprotein A5 (APOA5) has been suggested to play a key role in the triglyceride metabolism in both human and mice. The aim of this study was to identify the porcine (Sus scrofa) APOA5 gene, determine its mRNA and its mutations that are associated with lipid accumulation. The porcine APOA5 cDNA was amplified by reverse transcriptase polymerase chain reaction using the information of the mouse or other mammals. It had been determined that the open reading frame of the porcine APOA5 gene consists of 1092 bp, which encodes a predicted protein composed of 363 amino acids with a similarity to bovine (80.43%) and to human (78.47%). The expression analysis indicated that the porcine APOA5 gene was expressed in hypophysis, fat and liver. Twelve single nucleotide polymorphisms (SNPs), including 4 SNPs in the 5' end, 1 SNP in second intron, 1 SNP in third exon and 6 SNPs in the 3' end, were identified in the porcine APOA5 gene and genotyped on the Jinhua × Pietrain F2 reference population, it had revealed that the SNP of C1834T was significantly associated with average backfat thickness and leaf fat weight (P < 0.01 and P < 0.05, respectively). In conclusion, this study has got basic information of the porcine APOA5 gene and provides evidence that the APOA5 gene could be a potential candidate gene for fat deposition.

Polymorphisms of the estrogen receptor alpha (ESR1) gene and the risk of Alzheimer's disease in a southern Chinese community

BACKGROUND

Alzheimer's disease (AD) is a neurodegenerative disease with a higher prevalence in women. Expression of estrogen receptor 1 (ESR1) gene has been identified throughout the brain. Owing to the putative neuroprotective effects of estrogen, estrogen receptor gene is a potential candidate modulating the development of AD. Preliminary associations between two polymorphisms of ESR1 (PvuII and XbaI) gene and AD have been reported.

METHODS

In this study, 16 single nucleotide polymorphisms (SNPs) of the ESR1 gene (including four commonly studied ESR1 SNPs and 12 other tagging SNPs selected from the HapMap database) were investigated to further evaluate the association between ESR1 polymorphisms and the risk of AD in the Chinese population.

RESULTS

A total of 233 Chinese AD patients and 245 age-matched elderly control subjects were recruited. Genetic associations were analyzed by chi-square test and interaction effect was analysed by logistic regression analysis. Five SNPs (clustered between intron 3 and intron 7) were associated with the risk of AD (p-value ranges from 0.001 to 0.035); another two SNPs (located on exon 2 and intron 2) were shown to modulate the age-at-onset (AAO) in AD (p-value = 0.036 and 0.011).

CONCLUSIONS

ESR1 gene polymorphisms may be associated with the AAO in AD. The present results provided information for possible associations between certain polymorphisms of ESR1 gene and the risk of AD.

Genetic association of complex traits: using idiopathic scoliosis as an example

Although the exact etiology of adolescent idiopathic scoliosis is still undefined, genetic factors play an important role. Some patients have familial genetic disease that appears to have an autosomal dominant pattern. Linkage studies of these families revealed multiple potential genetic loci that may predispose individuals to the condition. Additional genetic analysis is required to identify the disease-predisposition genes of the loci found in the linkage studies. The initial localization of potential critical loci through large family-based population studies now needs fine mapping by association studies using high-density polymorphic markers (single nucleotide polymorphisms or SNPs). These markers are now available as a result of the Human Genome Project, International HapMap Project, and other genetic diversity projects. The application of this emerging data in a large association study of affected individuals and controls is integral for the identification of putative genes. With these complementary approaches, we will be able to progress with mutational analysis of hopefully a small set of candidate genes in the near future. In this commentary, we illustrate what is possible in the genomic era, and indicate what we should expect from genetic studies in adolescent idiopathic scoliosis, a complex trait disease.

The alpha(1S) subunit of the L-type calcium channel is not a predisposition gene for thyrotoxic periodic paralysis

OBJECTIVE

Thyrotoxic periodic paralysis (TTP) has been associated with genetic variations in the gene encoding the alpha 1 subunit of the L-type calcium channel (CACNA1S). Mutations in CACNA1S are known to account for the majority of cases of familial hypokalaemic periodic paralysis (HOKPP). In this study we have examined 48 genetic polymorphisms in the CACNA1S gene and genotyped a tagging set of representative polymorphisms to determine the role of this gene in TPP.

DESIGN AND PATIENTS

A genetic association study was carried out with 98 TPP patients and 162 male thyrotoxic controls. Among 47 polymorphisms evaluated for linkage disequilibrium (LD) and the spectrum of haplotypes in the Chinese population, 31 were selected as tagging single-nucleotide polymorphisms (SNPs) for genotyping the whole sample. A new genotyping protocol was used to analyse an insertion/deletion (I/D) polymorphism.

RESULTS

We studied the LD among 47 polymorphisms in the CACNA1S gene, which comprised a set of high-density markers with an average of one SNP every 2 kb. Subsequently, 31 tagSNPs were genotyped for all the samples. The gene is composed of three LD blocks. With this block structure, we were confident that variations of the gene were comprehensively covered by the tagSNPs. No significant association was found between the polymorphisms and TPP.

CONCLUSION

We established the LD structure of this calcium channel subunit gene (CACNA1S) for the first time. However, its genetic variations are not associated with TPP in Chinese patients.

Association of prostaglandin-endoperoxide synthase 2 (PTGS2) polymorphisms and Alzheimer's disease in Chinese

Cyclooxygenase-2 (COX-2, encoded by the gene prostaglandin-endoperoxide synthase 2, PTGS2) is a key enzyme in the conversion of arachidonic acid to prostaglandins. The prostaglandins produced by COX-2 are involved in inflammation and pain response in different tissues in the body. Enhanced COX-2 expression had been found in regions of brains from patients with Alzheimer's disease (AD). Here, we proceeded to test the hypothesis that polymorphisms of the PTGS2 gene predispose to AD. IVS5-275 T>G and Ex10+837 T>C in addition to three tagging SNPs from HapMap database, which provided a comprehensive coverage of genetic variations in the PTGS2 gene in Chinese were genotyped among 257 AD patients and 244 age-matched healthy Chinese subjects. Genetic associations were analyzed by chi(2)-test and haplotypes analysis. Although the previously reported protective polymorphism (rs20417, -765 G/C) for AD in PTGS2 gene was not polymorphic in the Chinese population, SNPs in both the promoter (-2319 G>T) and 3' region (Ex10+837 T>C) of PTGS2 were associated with the risk of AD (p=0.01 and 0.03, respectively). Carriers of Ex10+837 T allele had a 1.5-fold increase in the risk of AD. This study suggested that PTGS2 gene was a predisposition gene and arachidonic acid metabolism might be involved in the pathogenesis of AD. It provided further evidence to support a role of inflammation in the development and progression of AD.