A Recombination Hotspot in a Schizophrenia-Associated Region of GABRB2

Background: Schizophrenia is a major disorder with complex genetic mechanisms. Earlier, population genetic studies revealed the occurrence of strong positive selection in the GABRB2 gene encoding the β2 subunit of GABAA receptors, within a segment of 3,551 bp harboring twenty-nine single nucleotide polymorphisms (SNPs) and containing schizophrenia-associated SNPs and haplotypes. Methodology/Principal Findings:In the present study, the possible occurrence of recombination in this 'S1-S29' segment was assessed. The occurrence of hotspot recombination was indicated by high resolution recombination rate estimation, haplotype diversity, abundance of rare haplotypes, recurrent mutations and torsos in haplotype networks, and experimental haplotyping of somatic and sperm DNA. The sub-segment distribution of relative recombination strength, measured by the ratio of haplotype diversity (Hd) over mutation rate (θ), was indicative of a human specific Alu-Yi6 insertion serving as a central recombining sequence facilitating homologous recombination. Local anomalous DNA conformation attributable to the Alu-Yi6 element, as suggested by enhanced DNase I sensitivity and obstruction to DNA sequencing, could be a contributing factor of the increased sequence diversity. Linkage disequilibrium (LD) analysis yielded prominent low LD points that supported ongoing recombination. LD contrast revealed significant dissimilarity between control and schizophrenic cohorts. Among the large array of inferred haplotypes, H26 and H73 were identified to be protective, and H19 and H81 risk-conferring, toward the development of schizophrenia. Conclusions/Significance: The co-occurrence of hotspot recombination and positive selection in the S1-S29 segment of GABRB2 has provided a plausible contribution to the molecular genetics mechanisms for schizophrenia. The present findings therefore suggest that genome regions characterized by the co-occurrence of positive selection and hotspot recombination, two interacting factors both affecting genetic diversity, merit close scrutiny with respect to the etiology of common complex disorders. © 2010 Ng et al

AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome

<p>Abstract</p> <p>Background</p> <p>To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance.</p> <p>Results</p> <p>Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA.</p> <p>Conclusions</p> <p>AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.</p

Alternative-Splicing in the Exon-10 Region of GABAA Receptor β2 Subunit Gene: Relationships between Novel Isoforms and Psychotic Disorders

BACKGROUND: Non-coding single nucleotide polymorphisms (SNPs) in GABRB2, the gene for beta(2)-subunit of gamma-aminobutyric acid type A (GABA(A)) receptor, have been associated with schizophrenia (SCZ) and quantitatively correlated to mRNA expression and alternative splicing. METHODS AND FINDINGS: Expression of the Exon 10 region of GABRB2 from minigene constructs revealed this region to be an "alternative splicing hotspot" that readily gave rise to differently spliced isoforms depending on intron sequences. This led to a search in human brain cDNA libraries, and the discovery of two novel isoforms, beta(2S1) and beta(2S2), bearing variations in the neighborhood of Exon-10. Quantitative real-time PCR analysis of postmortem brain samples showed increased beta(2S1) expression and decreased beta(2S2) expression in both SCZ and bipolar disorder (BPD) compared to controls. Disease-control differences were significantly correlated with SNP rs187269 in BPD males for both beta(2S1) and beta(2S2) expressions, and significantly correlated with SNPs rs2546620 and rs187269 in SCZ males for beta(2S2) expression. Moreover, site-directed mutagenesis indicated that Thr(365), a potential phosphorylation site in Exon-10, played a key role in determining the time profile of the ATP-dependent electrophysiological current run-down. CONCLUSION: This study therefore provided experimental evidence for the importance of non-coding sequences in the Exon-10 region in GABRB2 with respect to beta(2)-subunit splicing diversity and the etiologies of SCZ and BPD

Social Cognitive Role of Schizophrenia Candidate Gene GABRB2

10.1371/journal.pone.0062322PLoS ONE84

Positive Selection within the Schizophrenia-Associated GABA(A) Receptor β(2) Gene

The gamma-aminobutyric acid type-A (GABA(A)) receptor plays a major role in inhibitory neurotransmissions. Intronic SNPs and haplotypes in GABRB2, the gene for GABA(A) receptor β(2) subunit, are associated with schizophrenia and correlated with the expression of two alternatively spliced β(2) isoforms. In the present study, using chimpanzee as an ancestral reference, high frequencies were observed for the derived (D) alleles of the four SNPs rs6556547, rs187269, rs1816071 and rs1816072 in GABRB2, suggesting the occurrence of positive selection for these derived alleles. Coalescence-based simulation showed that the population frequency spectra and the frequencies of H56, the haplotype having all four D alleles, significantly deviated from neutral-evolution expectation in various demographic models. Haplotypes containing the derived allele of rs1816072 displayed significantly less diversity compared to haplotypes containing its ancestral allele, further supporting positive selection. The variations in DD-genotype frequencies in five human populations provided a snapshot of the evolutionary history, which suggested that the positive selections of the D alleles are recent and likely ongoing. The divergence between the DD-genotype profiles of schizophrenic and control samples pointed to the schizophrenia-relevance of positive selections, with the schizophrenic samples showing weakened selections compared to the controls. These DD-genotypes were previously found to increase the expression of β(2), especially its long isoform. Electrophysiological analysis showed that this long β(2) isoform favored by the positive selections is more sensitive than the short isoform to the inhibition of GABA(A) receptor function by energy depletion. These findings represent the first demonstration of positive selection in a schizophrenia-associated gene

Myoid differentiation in dermatofibrosarcoma protuberans and its fibrosarcomatous variant: 10 years’ experience in a tertiary hospital

Dermatofibrosarcoma protuberans (DFSP) is a relatively rare, locally aggressive, and dermal-based fibroblastic tumor. There are several histological variants, in which the usual emphasis is on fibrosarcomatous DFSP, as it acquires metastatic potential. Myoid differentiation in DFSP is rare, and more often found in fibrosarcomatous DFSP. Myoid differentiation is defined as tumor cells with brightly eosinophilic cytoplasm, well-defined cytoplasmic margins, and vesicular nuclei. In this study, we aim at characterizing the immunostaining pattern regarding myoid differentiation in DFSP, and discuss the potential pitfall in making the diagnosis. A total of ten cases of DFSP were found in the past ten years in our hospital. Two of them show focal myoid differentiation, including the only case of fibrosarcomatous DFSP. Around 5% of the tumor area in the traditional DFSP case shows myoid differentiation, while around 10% of the tumor area in fibrosarcomatous DFSP shows myoid differentiation. The myoid areas show positive staining, albeit patchy to focal, for smooth muscle markers, including smooth muscle actin, muscle-specific actin, caldesmon, and calponin. Staining for CD34, in those areas, is weak or negative. This may create diagnostic difficulty with smooth muscle tumors or myofibroblastic lesions, especially in a small biopsy sample. In difficult cases, the detection of COL1A1-PDGFB fusion by fluorescence in situ hybridization is helpful, as this is a characteristic chromosomal translocation found in the large majority of DFSP

Compositions and methods for the targeted delivery of agents to treat liver cancer

Most of the cytotoxic drugs used in cancer chemotherapy have narrow chemotherapeutic utility and effectiveness and serious side effects at high dosages. As a result, drug delivery systems have been developed to modify the biodistribution of cytotoxic drugs, improving their selectivity for tumors or reducing the damage to normal tissues. This invention can further improve the performance of drug delivery systems. Liposomes have been used extensively in delivery system for cytotoxic drugs used in cancer chemotherapy. Such use of liposomes as a drug delivery system has provided a means to improve the therapeutic utility of some conventional drugs. Since many liposomes are rapidly taken up by the cells of the mononuclear phagocyte system or reticuloendothelial system, they have been effective in delivering drugs to organs. However, their rapid clearance from the bloodstream has also limited their utility for transporting drugs to disease sites. Introduction of this new method overcomes this problem. The novel invention provides compositions containing an effective amount of specific therapeutic agent encapsulated in a liposome coupled to a desialyated glycoprotein, e.g., desialyated glycoprotein-1. The new compositions can prolong the circulation of liposomes successfully

Epidermoid cyst in an intrapancreatic accessory spleen with abnormally high CEA level in cyst fluid: a case report

Epidermoid cyst in an intrapancreatic accessory spleen is a rare benign lesion that is difficult to diagnose preoperatively. Cyst fluid analysis for biochemistry markers has been widely used to aid the diagnosis of pancreatic cysts. A high cyst fluid carcinoembryonic antigen (CEA) level (&gt;800 ng/mL) is said to be useful in distinguishing intraductal papillary mucinous neoplasm (IPMN) and mucinous cystic neoplasm (MCN) from other non-mucinous cysts. We herein report a case of epidermoid cyst in an intrapancreatic accessory spleen with abnormally high CEA level (3582 ng/mL) in the cyst fluid, suggesting a potential pitfall in using cyst fluid CEA level as an indicator of mucinous neoplasms

Application of machine learning to development of copy number variation-based prediction of cancer risk

In the present study, recurrent copy number variations (CNVs) from non-tumor blood cell DNAs of Caucasian non-cancer subjects and glioma, myeloma, and colorectal cancer-patients, and Korean non-cancer subjects and hepatocellular carcinoma, gastric cancer, and colorectal cancer patients, were found to reveal for each of the two ethnic cohorts highly significant differences between cancer patients and controls with respect to the number of CN-losses and size-distribution of CN-gains, suggesting the existence of recurrent constitutional CNV-features useful for prediction of predisposition to cancer. Upon identification by machine learning, such CNV-features could extensively discriminate between cancer-patient and control DNAs. When the CNV-features selected from a learning-group of Caucasian or Korean mixed DNAs consisting of both cancer-patient and control DNAs were employed to make predictions on the cancer predisposition of an unseen test group of mixed DNAs, the average prediction accuracy was 93.6% for the Caucasian cohort and 86.5% for the Korean cohort. © the authors