GluK2 Research Articles

Cryptic breakpoint identified by whole-genome mate-pair sequencing in a rare paternally inherited complex chromosomal rearrangement

BackgroundPrecise characterization of apparently balanced complex chromosomal rearrangements in non-affected individuals is crucial as they may result in reproductive failure, recurrent miscarriages or affected offspring.Case presentationWe present a family, where the non-affected father and daughter were found, using FISH and karyotyping, to be carriers of a three-way complex chromosomal rearrangement [t(6;7;10)(q16.2;q34;q26.1), de novo in the father]. The family suffered from two stillbirths, one miscarriage, and has a son with severe intellectual disability. In the present study, the family was revisited using whole-genome mate-pair sequencing. Interestingly, whole-genome mate-pair sequencing revealed a cryptic breakpoint on derivative (der) chromosome 6 rendering the rearrangement even more complex. FISH using a chromosome (chr) 6 custom-designed probe and a chr10 control probe confirmed that the interstitial chr6 segment, created by the two chr6 breakpoints, was translocated onto der(10). Breakpoints were successfully validated with Sanger sequencing, and small imbalances as well as microhomology were identified. Finally, the complex chromosomal rearrangement breakpoints disrupted the SIM1, GRIK2, CNTNAP2, and PTPRE genes without causing any phenotype development.ConclusionsIn contrast to the majority of maternally transmitted complex chromosomal rearrangement cases, our study investigated a rare case where a complex chromosomal rearrangement, which most probably resulted from a Type IV hexavalent during the pachytene stage of meiosis I, was stably transmitted from a fertile father to his non-affected daughter. Whole-genome mate-pair sequencing proved highly successful in identifying cryptic complexity, which consequently provided further insight into the meiotic segregation of chromosomes and the increased reproductive risk in individuals carrying the specific complex chromosomal rearrangement. We propose that such complex rearrangements should be characterized in detail using a combination of conventional cytogenetic and NGS-based approaches to aid in better prenatal preimplantation genetic diagnosis and counseling in couples with reproductive problems.

Increased Grik4 Gene Dosage Causes Imbalanced Circuit Output and Human Disease-Related Behaviors

Altered glutamatergic neurotransmission is thought to contribute to mental disorders and neurodegenerative diseases. Copy-number variation in genes associated with glutamatergic synapses represents a source of genetic variability, possibly underlying neurological and mental disease susceptibility. The GRIK4 gene encodes a high-affinity kainate receptor subunit of essentially unknown function, although de novo duplication of the 11q23.3-q24.1 locus to which it maps has been detected in autism and other disorders. To determine how changes in the dose of Grik4 affect synaptic activity, we studied mice overexpressing this gene in the forebrain. A mild gain in Grik4 enhances synaptic transmission, causing a persistent imbalance in inhibitory and excitatory activity and disturbing the circuits responsible for the main amygdala outputs. These changes in glutamatergic activity reverse when Grik4 levels are normalized; thus, they may account for the behavioral abnormalities in disorders like autism or schizophrenia.

Kainate Receptors Inhibit Glutamate Release Via Mobilization of Endocannabinoids in Striatal Direct Pathway Spiny Projection Neurons.

Kainate receptors are members of the glutamate receptor family that function by both generating ionotropic currents through an integral ion channel pore and coupling to downstream metabotropic signaling pathways. They are highly expressed in the striatum, yet their roles in regulating striatal synapses are not known. Using mice of both sexes, we demonstrate that GluK2-containing kainate receptors expressed in direct pathway spiny projection neurons (dSPNs) inhibit glutamate release at corticostriatal synapses in the dorsolateral striatum. This inhibition requires postsynaptic kainate-receptor-mediated mobilization of a retrograde endocannabinoid (eCB) signal and activation of presynaptic CB1 receptors. This pathway can be activated during repetitive 25 Hz trains of synaptic stimulation, causing short-term depression of corticostriatal synapses. This is the first study to demonstrate a role for kainate receptors in regulating eCB-mediated plasticity at the corticostriatal synapse and demonstrates an important role for these receptors in regulating basal ganglia circuits.SIGNIFICANCE STATEMENT The GRIK2 gene, encoding the GluK2 subunit of the kainate receptor, has been linked to several neuropsychiatric and neurodevelopmental disorders including obsessive compulsive disorder (OCD). Perseverative behaviors associated with OCD are known to result from pathophysiological changes in the striatum and kainate receptor knock-out mice have striatal-dependent phenotypes. However, the role of kainate receptors in striatal synapses is not known. We demonstrate that GluK2-containing kainate receptors regulate corticostriatal synapses by mobilizing endocannabinoids from direct pathway spiny projection neurons. Synaptic activation of GluK2 receptors during trains of synaptic input causes short-term synaptic depression, demonstrating a novel role for these receptors in regulating striatal circuits.

Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection

The genotyping of a single-nucleotide polymorphism (SNP) is addressed through methods based on loop-mediated isothermal amplification (LAMP) combined with user-friendly optical read-outs to cover the current demand for point-of-care DNA biomarker detection. The modification of primer design and reaction composition improved the assay selectivity yielding allele-specific results and reducing false-positive frequency. Furthermore, the reduced cost, ease of use and effectiveness of colorimetric detection (solution and hybridisation chip formats) were availed for the image capture by a smartphone, reching high sensitivity. In order to evaluate their discriminating capacities, LAMP-based methods were applied to human samples to genotype a SNP biomarker (rs1954787) located in the GRIK4 gene and related to the treatment response to anti-depressants drugs. Sensitive (limit of detection: 100 genomic DNA copies), reproducible (< 15% error), fast (around 70 min) and low-cost assays were accomplished. Patient subgroups were correctly discriminated, agreeing with reference sequencing techniques. The achieved analytical performances using the developed amplification-detection principles confirmed the approach potential for point-of-care optical DNA testing.

Abstract B39: Investigation of the effects of alterations in the glutamate receptor, GRIK2, on osteosarcoma tumorigenesis

Abstract Osteosarcoma is a primary, malignant bone tumor that mainly occurs in young adults and survival rates (60-70% over five years) have remained steady and novel treatment targets are needed. Osteosarcoma tumors exhibit chromosomal instability and are heterogeneous. In this study we identified recurrent copy number alterations in 44 flash-frozen osteosarcoma tumors obtained at biopsy with 25 blood-matched samples. Copy number losses were observed in 14% of tumors in the 6q16.3 region, specifically in the 5 intergenic space and first intron of the GRIK2 gene. GRIK2 encodes an ionotropic glutamate receptor that has been identified as a tumor-suppressor gene in gastric cancer, but the relationship between alterations in this region and osteosarcoma are still to be determined. We found that the focal deletions do not overlap with any coding sequence of GRIK2; however, there is a region of interest that contains a SETDB1 histone methyltransferase binding site that is shared by several deletions. The 5 intergenic space is enriched with H3K9Me3 histone marks which is indicative of transcriptional repression. SETDB1 is responsible for adding H3K9Me3 histone marks and deletion of this site may alter the expression of GRIK2. The goal of this study is to determine the relationship between noncoding deletions in 6q16.3 and GRIK2 by examining the effects of the deletions on the expression, function, and regulation on osteosarcoma cells in vitro. Gene expression levels of GRIK2 were quantified with RT-qPCR in both osteosarcoma tumors and cell lines. The functional role of GRIK2 was characterized in both U2-OS and SaOS-2 osteosarcoma cells through gain-of-function experiments. Cell viability was measured by the XTT assay and cell migration was quantified with a wound-healing assay. Apoptosis levels were assessed with an annexin V experiment. The effect of noncoding deletions of the SETDB1 binding site was examined using CRISPR/cas9 gene editing. Following transfection of a CRISPR/cas9 vector, U2-OS cells were sorted by fluorescence-activated cell sorting, grown for 7-10 days, and GRIK2 gene expression levels were measured. The expression levels of GRIK2 varied in tumors and were low in cell lines. Several tumors with focal deletions were among a subset of tumors with increased transcript levels relative to cell lines. Due to this observation, GRIK2 was overexpressed in U2-OS and SaOS-2 cells and found to result in decreased cell proliferation, migration, and increased apoptosis levels. Gene editing of the SETDB1 binding site was confirmed following DNA extraction and PCR of the deleted region. Following cell sorting and growth, GRIK2 transcript levels were increased in edited cells relative to untreated cells. Noncoding deletions in the 6q16.3 region were associated with increased expression levels of GRIK2 and overexpression of GRIK2 in vitro may result in a less aggressive phenotype. Gene editing of the SETDB1 binding site with CRISPR/cas9 demonstrated that focal deletions of the region may be involved in epigenetic regulation of GRIK2. Noncoding deletions of GRIK2 are linked to expression and functional changes in GRIK2 and further studies will examine GRIK2 as a potential target for therapeutic intervention. Citation Format: Justin G. Mayers, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis. Investigation of the effects of alterations in the glutamate receptor, GRIK2, on osteosarcoma tumorigenesis [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B39.

Abstract 5507: Investigation of the effects of alterations in the glutamate receptor, GRIK2 on osteosarcoma tumorigenesis

Abstract Osteosarcoma is a primary, malignant bone tumour mainly affecting young adults with a five-year survival rate of 60-70% depending on presentation of metastasis at diagnosis. Tumours are marked by genetic instability and heterogeneity and for this reason, molecular subtypes have yet to be characterized. Survival rates have remained consistent over the past few decades and novel molecular targets for treatment are needed. Current genomic strategies have identified recurrent copy number alterations. In a study of 44 flash frozen osteosarcoma tumours which were obtained at the time of biopsy and 25 blood-matched samples we identified recurrent copy number losses including a region at 6q16.3 in 14% of tumours. Focal deletions were observed in the 5’ intergenic space and first intron of the GRIK2 gene and do not overlap with any coding sequence. The relationship between alterations in this region and osteosarcoma tumourigenesis has yet to be explored in depth. GRIK2 encodes an ionotropic glutamate receptor that has been implicated as a tumour suppressor in gastric cancer. An interesting feature of the tumours was the overlap of focal deletions with a SETDB1 histone methyltransferase binding site indicating a potential connection with epigenetic regulation of GRIK2. The goal of this study is to examine the effects of non-coding, focal deletions on GRIK2 gene expression, function and regulation in osteosarcoma cells. GRIK2 transcript levels were measured in osteosarcoma tumours and cell lines using qRT-PCR. Functional assays were performed to characterize the role of GRIK2 in osteosarcoma cell proliferation, migration and apoptosis in vitro. Gene editing with CRISPR/cas9 was performed to examine the link between non-coding deletions and GRIK2 expression. GRIK2 transcript levels varied in tumours; several tumours with focal deletions had increased transcript levels relative to cell lines which demonstrated low expression levels. Due to the observation of low transcript levels, a gain of function approach was employed to examine GRIK2 function in vitro. Overexpression of GRIK2 decreased proliferation, migration and increased apoptosis in osteosarcoma cells. Gene editing of the SETDB1 binding site resulted in increased GRIK2 transcript levels relative to untreated cells. This study suggests that non-coding focal deletions are linked to high expression levels of GRIK2 which may confer a less aggressive phenotype and are involved in epigenetic regulation of the gene. Citation Format: Justin G. Mayers, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis. Investigation of the effects of alterations in the glutamate receptor, GRIK2 on osteosarcoma tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5507. doi:10.1158/1538-7445.AM2017-5507

Common variants in GRIK4 and major depressive disorder: An association study in the Chinese Han population.

Major depressive disorder (MDD) is a common and complex mental disorder. Recent studies found that genetic variants located in GRIK4, which encoded glutamate ionotropic receptor kainate type subunit 4, was associated with the MDD. In this study, we intended to investigate whether GRIK4 gene was associated with MDD. So five single nucleotide polymorphisms (SNPs) were selected and genotyped (rs79526501, rs11218016, rs4582985, rs6589847, rs56275759) in 568 MDD patients and 846 healthy controls from Chinese Han population. The results showed that rs56275759 demonstrated statistically significant differences between MDD patients and control subjects both in allelic frequencies (p value=0.011) and genotypic frequencies (p value=0.029). Rs4582985 was excluded from the further analysis for its deviation from the Hardy-Weinberg equilibrium. Strong linkage disequilibrium (LD) was found among rs11218016, rs6589847 and rs56275759, and this block was significantly associated with MDD. In summary, our results firstly indicated that rs56275759 of GRIK4 gene might be associated with MDD in Chinese Han population.

A gain-of-function mutation in the GRIK2 gene causes neurodevelopmental deficits.

Objective:To identify inherited or de novo mutations associated with a suite of neurodevelopmental abnormalities in a 10-year-old patient displaying ataxia, motor and speech delay, and intellectual disability.Methods:We performed whole-exome sequencing of the proband and her parents. A pathogenic gene variant was identified as damaging based on sequence conservation, gene function, and association with disorders having similar phenotypic profiles. Functional characterization of the mutated protein was performed in vitro using a heterologous expression system.Results:A single de novo point mutation in the GRIK2 gene was identified as causative for the neurologic symptoms of the proband. The mutation is predicted to change a codon for alanine to that of a threonine at position 657 (A657T) in the GluK2 kainate receptor (KAR) subunit, a member of the ionotropic glutamate receptor gene family. Whole-cell voltage-clamp recordings revealed that KARs incorporating the GluK2(A657T) subunits show profoundly altered channel gating and are constitutively active in nominally glutamate-free extracellular media.Conclusions:In this study, we associate a de novo gain-of-function mutation in the GRIK2 gene with deficits in motor and higher order cognitive function. These results suggest that disruption of physiologic KAR function precludes appropriate development of the nervous system.

Identifying and retargeting transcriptional hot spots in the human genome.

Mammalian cell line development requires streamlined methodologies that will reduce both the cost and time to identify candidate cell lines. Improvements in site-specific genomic editing techniques can result in flexible, predictable, and robust cell line engineering. However, an outstanding question in the field is the specific site of integration. Here, we seek to identify productive loci within the human genome that will result in stable, high expression of heterologous DNA. Using an unbiased, random integration approach and a green fluorescent reporter construct, we identify ten single-integrant, recombinant human cell lines that exhibit stable, high-level expression. From these cell lines, eight unique corresponding integration loci were identified. These loci are concentrated in non-protein coding regions or intronic regions of protein coding genes. Expression mapping of the surrounding genes reveals minimal disruption of endogenous gene expression. Finally, we demonstrate that targeted de novo integration at one of the identified loci, the 12(th) exon-intron region of the GRIK1 gene on chromosome 21, results in superior expression and stability compared to the standard, illegitimate integration approach at levels approaching 4-fold. The information identified here along with recent advances in site-specific genomic editing techniques can lead to expedited cell line development.

Association between polymorphism of GIuR6 gene and domestic violence in Uygur population on alcoholics in Xinjiang

Objective To investigate the association between glutamate receptor-6 (GIuR6/GRIK2) gene polymorphism and domestic violence in Xinjiang Uygur population on alcoholics. Methods The methods of polymerase chain reaction (PCR) and DNA sequencing technique were conducted to detect rs6922753 and rs2227283 single nucleotide polymorphism of GLUR6 gene in a 104 domestic violence perpetrators on alcoholics and 80 non-domestic violence perpetrators on alcoholics. The association between the polymorphisms and violent behavior was analyzed with SPSS 17.0. Results The frequency of allele (χ2=4.935) and genotype (χ2=7.622) of rs6922753 polymorphisms in the domestic violence group were statistically different from those in the non-domestic violence group (P 0.05). Conclusions GIuR6 gene polymorphism may be associated with domestic violence in Xinjiang Uygur population on alcoholics. Key words: UYGUR NATIONALITY; Alcohol-related disorders/CO/GE; Domestic violence; Receptors, glutamate/GE

Multiplex PCR Analysis of 17 (11 Novels) STR Markers Linked to Six Autosomal Recessive Intellectual Disability Genes in Iranian Population.

Non-syndromic autosomal recessive intellectual disability (NS-ARID) is a heterogeneous neurodevelopmental disease. More research is needed to study the NS-ARID genes. Using STR markers linked to a specific gene, we can perform homozygosity mapping and prenatal diagnosis. One approach to investigate the NS-ARID genes in large families is homozygosity mapping. In this study, we surveyed allele frequency and allele heterozygosity of 17 NS-ARID STR markers linked to the six NS-ARID genes in Iranian population. The test group consisted of 120 unrelated healthy individuals. STR markers were designed using SERV software. Also, genotyping was done using multiplex PCR. Data was analyzed by Gene Mapper software. Allele frequency and observed heterozygosity rates were estimated using PowerStatV12. Deviation from the Hardy-Weinberg equilibrium (HWE) was performed based on the Exact test. Out of 17 STR loci, 11 were novel. In total, 166 alleles were detected for the 17 markers. According to our study, the D9MAN1B1SD7.4, D19S872, D6GRIK2SI1.7, D19TECRSDI.8, D1ST3GAL3SIO.5, and D14ZC3H14SD5.3 STR loci were found to be the most informative and polymorphic STR markers for MAN1B1, ZNF526, GRIK2, TECR, ST3GAL3, and ZC3H14 genes, respectively. We also performed other statistical analyses on these STR markers and found that all of the 17 STRs were polymorphic and met the Hardy-Weinberg equilibrium. Finding novel STRs, with high allele heterozygosity, is one of the most significant outcomes of the present study. These findings can be useful for homozygosity mapping, PGD, and PND practices for the NS-ARID.

Exploring Genetic Factors Involved in Huntington Disease Age of Onset: E2F2 as a New Potential Modifier Gene.

Age of onset (AO) of Huntington disease (HD) is mainly determined by the length of the CAG repeat expansion (CAGexp) in exon 1 of the HTT gene. Additional genetic variation has been suggested to contribute to AO, although the mechanism by which it could affect AO is presently unknown. The aim of this study is to explore the contribution of candidate genetic factors to HD AO in order to gain insight into the pathogenic mechanisms underlying this disorder. For that purpose, two AO definitions were used: the earliest age with unequivocal signs of HD (earliest AO or eAO), and the first motor symptoms age (motor AO or mAO). Multiple linear regression analyses were performed between genetic variation within 20 candidate genes and eAO or mAO, using DNA and clinical information of 253 HD patients from REGISTRY project. Gene expression analyses were carried out by RT-qPCR with an independent sample of 35 HD patients from Basque Country Hospitals. We found suggestive association signals between HD eAO and/or mAO and genetic variation within the E2F2, ATF7IP, GRIN2A, GRIN2B, LINC01559, HIP1 and GRIK2 genes. Among them, the most significant was the association between eAO and rs2742976, mapping to the promoter region of E2F2 transcription factor. Furthermore, rs2742976 T allele patient carriers exhibited significantly lower lymphocyte E2F2 gene expression, suggesting a possible implication of E2F2-dependent transcriptional activity in HD pathogenesis. Thus, E2F2 emerges as a new potential HD AO modifier factor.

Gene-gene interaction of μ-opioid receptor and GluR5 kainate receptor subunit is associated with smoking behavior in a Greek population: presence of a dose allele effect.

Components of nicotine reward system can potentially influence smoking behavior. The μ-opioid receptor (OPRM1) binds the endogenous opioid peptide β-endorphin and mediates the reinforcing effects of nicotine, while the GluR5 kainate receptor subunit (encoded by GRIK1 gene), a binding site for known mediators of glutamate neurotransmission, potentially affects the glutaminergic system that is also indirectly implicated in the reward system. In the present study, OPRM1 A118G and GRIK1 rs2832407C>A polymorphisms and their interactions were analyzed in 132 smoking initiators (SI) and 144 non-initiators (NI) of Greek origin, using the PCR-RFLP method. No differences were found in the genotype or allele distribution of OPRM1 A118G and GRIK1 rs2832407C>A between SI and NI. However, we found a significant interaction of OPRM1 A118G and GRIK1 rs2832407C>A genotypes associated with smoking initiation in a model adjusted for age, sex, BMI and type 2 diabetes mellitus (odds ratio=1.341, 95% CI 1.024-1.755, p=0.033). A dose effect of OPRM1 and GRIK1 variant alleles was present. Increased number of variant alleles (from 0 to 4) was associated with smoking initiation in the same adjusted model (odds ratio=1.537, 95% CI 1.030-2.293, p=0.036). Smoking phenotype is a complex interaction of genetic and environmental factors. In the present study, we have shown that gene-gene interaction of components of different systems associated with nicotine reinforcing effects, such as OPRM1 and GRIK1, rather than one gene polymorphism, is associated with smoking behavior.

GRIK4 polymorphism and its association with antidepressant response in depressed patients: a meta-analysis.

This study aimed to evaluate the relationship between a human GRIK4 gene polymorphism (rs1954787) and responsiveness to antidepressant treatment in depressed patients. A meta-analysis was carried out on five studies. Pooled odds ratios (ORs), 95% CIs and a χ(2) test measuring heterogeneity were calculated. A test of publication bias was also conducted. Alleles and genotypes from a total of 2169 depressed patients were analyzed. The results showed that the C allele appeared more frequently than the T allele in responders to treatment (OR: 1.22; 95% CI: 1.035-1.445; z = 2.36; p = 0.018). Similarly, CC homozygotes were more likely than TT homozygotes to respond to treatment (OR: 1.45; 95% CI: 1.107-1.913; z = 2.69; p = 0.007). No evidence of publication bias was detected. Subjects possessing the C allele or CC genotype of the GRIK4 polymorphism rs1954787 are more likely to respond to antidepressant treatment relative to subjects harboring the T allele and TT genotype. Additional replication of this result is required before this association can be considered definitive, after which it may become possible to employ this marker in conjunction with other known predictors in order to anticipate the outcomes of treatment with antidepressant medications.

Toward Personalized Medicine in the Pharmacotherapy of Alcohol Use Disorder: Targeting Patient Genes and Patient Goals

Toward Personalized Medicine in the Pharmacotherapy of Alcohol Use Disorder: Targeting Patient Genes and Patient Goals

TAA repeat variation in the GRIK2 gene does not influence age at onset in Huntington’s disease

Huntington’s disease is a neurodegenerative disorder caused by an expanded CAG trinucleotide repeat whose length is the major determinant of age at onset but remaining variation appears to be due in part to the effect of genetic modifiers. GRIK2, which encodes GluR6, a mediator of excitatory neurotransmission in the brain, has been suggested in several studies to be a modifier gene based upon a 3’ untranslated region TAA trinucleotide repeat polymorphism. Prior to investing in detailed studies of the functional impact of this polymorphism, we sought to confirm its effect on age at onset in a much larger dataset than in previous investigations. We genotyped the HD CAG repeat and the GRIK2 TAA repeat in DNA samples from 2,911 Huntington’s disease subjects with known age at onset, and tested for a potential modifier effect of GRIK2 using a variety of statistical approaches. Unlike previous reports, we detected no evidence of an influence of the GRIK2 TAA repeat polymorphism on age at motor onset. Similarly, the GRIK2 polymorphism did not show significant modifier effect on psychiatric and cognitive age at onset in HD. Comprehensive analytical methods applied to a much larger sample than in previous studies do not support a role for GRIK2 as a genetic modifier of age at onset of clinical symptoms in Huntington’s disease.

Pharmacogenetics of glutamate system genes and SSRI-associated sexual dysfunction

We examined whether polymorphisms in the GRIK2, GRIA3 and GRIA1 genes were associated with selective serotonin reuptake inhibitor (SSRI)-associated sexual dysfunction in 114 participants treated for depression. One polymorphism in GRIA1 (rs1994862) was associated with arousal dysfunction, providing further evidence for the role of GRIA1 in mechanisms underlying SSRI-associated sexual side effects.

Genetic association study of individual symptoms in depression

The heritability of some individual depressive symptoms has been well established. However, the causal genes related to individual depressive symptoms and genetic effects on the courses of individual depressive symptoms are still unclear. We examined these issues in 241 Korean patients who met the DSM-IV-TR criteria for major depression. Patients entered a 12-week clinical trial with antidepressants. A total of 1399 single-nucleotide polymorphisms (SNPs) of 79 candidate genes were assessed. The rs557762 and the TT haplotype in the 11th haplotype block of the GRIA3 gene were associated with feelings of guilt in females. The GGCCGGGC haplotype in the first haplotype block of TPH1 was significantly associated with middle insomnia. The ACAG haplotype in the 13th haplotype block of the GRIK2 gene was associated with somatic anxiety. Moreover, the effect of the rs557762 on guilt significantly varied across times. Our results indicate that there are associations between particular gene polymorphisms and some individual depressive symptoms. These results could contribute to understanding the biological mechanisms of depression.

DNA methylation biomarkers for lung cancer

Changes in DNA methylation patterns are an important characteristic of human cancer including lung cancer. In particular, hypermethylation of CpG islands is a signature of malignant progression. Methylated CpG islands are promising diagnostic markers for the early detection of cancer. However, the full extent and sequence context of DNA hypermethylation in lung cancer has remained unknown. We have used the methylated CpG island recovery assay and high-resolution microarray analysis to find hypermethylated CpG islands in squamous cell carcinomas (SCC) and adenocarcinomas of the lung. Each tumor contained several hundred hypermethylated CpG islands. In an initial microarray screen, 36 CpG islands were methylated in five of five (=100%) of the SCC tumors tested and 52 CpG islands were methylated in at least 75% of the adenocarcinomas tested (n=8). Using sodium-bisulfite-based approaches, 12 CpG islands (associated with the BARHL2, EVX2, IRX2, MEIS1, MSX1, NR2E1, OC2, OSR1, OTX1, PAX6, TFAP2A, and ZNF577 genes) were confirmed to be methylated in 85% to 100% of the squamous cell carcinomas and 11 CpG islands (associated with the CHAD, DLX4, GRIK2, KCNG3, NR2E1, OSR1, OTX1, OTX2, PROX1, RUNX1, and VAX1 genes) were methylated in >80% of the adenocarcinomas. From the list of genes that were methylated in lung adenocarcinomas, we identified the gene FAT4 and found that this gene was methylated in 39% of the tumors. FAT4 is the closest mammalian homologue of the Drosophila tumor suppressor Fat which is an important component of the Hippo growth control pathway. Many of these newly discovered methylated CpG islands hold promise for becoming biomarkers for the early detection of lung cancer.

Two-stage genome-wide association study identifies variants in CAMSAP1L1 as susceptibility loci for epilepsy in Chinese

In the majority of patients, epilepsy is a complex disorder with multiple susceptibility genes interacting with environmental factors. However, we understand little about its genetic risks. Here, we report the first genome-wide association study (GWAS) to identify common susceptibility variants of epilepsy in Chinese. This two-stage GWAS included a total of 1087 patients and 3444 matched controls. In the combined analysis of the two stages, the strongest signals were observed with two highly correlated variants, rs2292096 [G] [P= 1.0 × 10(-8), odds ratio (OR) = 0.63] and rs6660197 [T] (P= 9.9 × 10(-7), OR = 0.69), with the former reaching genome-wide significance, on 1q32.1 in the CAMSAP1L1 gene, which encodes a cytoskeletal protein. We also refined a previously reported association with rs9390754 (P= 1.7 × 10(-5)) on 6q21 in the GRIK2 gene, which encodes a glutamate receptor, and identified several other loci in genes involved in neurotransmission or neuronal networking that warrant further investigation. Our results suggest that common genetic variants may increase the susceptibility to epilepsy in Chinese.