Microarray analysis of promoter methylation in lung cancers.

Aberrant DNA methylation is an important event in carcinogenesis. Of the various regions of a gene that can be methylated in cancers, the promoter is the most important for the regulation of gene expression. Here, we describe a microarray analysis of DNA methylation in the promoter regions of genes using a newly developed promoter-associated methylated DNA amplification DNA chip (PMAD). For each sample, methylated Hpa II-resistant DNA fragments and Msp I-cleaved (unmethylated+methylated) DNA fragments were amplified and labeled with Cy3 and Cy5 respectively, then hybridized to a microarray containing the promoters of 288 cancer-related genes. Signals from Hpa II-resistant (methylated) DNA (Cy3) were normalized to signals from Msp I-cleaved (unmethylated+methylated) DNA fragments (Cy5). Normalized signals from lung cancer cell lines were compared to signals from normal lung cells. About 10.9% of the cancer-related genes were hypermethylated in lung cancer cell lines. Notably, HIC1, IRF7, ASC, RIPK3, RASSF1A, FABP3, PRKCDBP, and PAX3 genes were hypermethylated in most lung cancer cell lines examined. The expression profiles of these genes correlated to the methylation profiles of the genes, indicating that the microarray analysis of DNA methylation in the promoter region of the genes is convenient for epigenetic study. Further analysis of primary tumors indicated that the frequency of hypermethylation was high for ASC (82%) and PAX3 (86%) in all tumor types, and high for RIPK3 in small cell carcinoma (57%). This demonstrates that our PMAD method is effective at finding epigenetic changes during cancer.

Human netrin-G1 isoforms show evidence of differential expression.

The recently identified netrins-G1 and -G2 form a distinct subgroup within the UNC-6/netrin gene family of axon guidance molecules. In this study, we determined the size and structure of the exon/intron layout of the human netrin-G1 (NTNG1) and -G2 (NTNG2) genes. Northern analysis of both genes showed limited nonneuronal but wide brain expression, particularly for NTNG2. Reverse transcriptase PCR detected nine alternatively spliced isoforms including four novel variants of NTNG1 from adult brain. A semiquantitative assay established that major expression was restricted to isoforms G1c, G1d, G1a, and G1e in the brain and to G1c in the kidney. There is also evidence of developmental regulation of these isoforms between fetal and adult brain. In conclusion, NTNG1 may use alternative splicing to diversify its function in a developmentally and tissue-specific manner.

Case-control association study of human netrin G1 gene in Japanese schizophrenia.

The exact etiology of schizophrenia remains undetermined but accumulating evidence suggests that disturbances in neurodevelopment may represent one contributory factor. Netrin G1, a recently cloned gene from the mouse, has been shown to play a potential role in the formation of neural circuitry. To determine whether this gene is involved in the development of psychosis, we performed a genetic association study of human netrin G1 gene in schizophrenia. First, we determined the human genomic structure of netrin G1 by direct comparisons between cDNA and genome sequences, and by database searches. For the subsequent examination of heterozygosity, we selected 10 single nucleotide polymorphisms (SNPs) for an association test in case (n = 180) and control (n = 180) samples. Among these SNPs, IVS8-1467C>T showed significant allelic association (nominal P = 0.020) with disease. This SNP is located in a haplotype block of approximately 40 kb and haplotypes in this block also displayed significant association (most significant P = 0.017). These findings suggest that netrin G1 or a nearby gene may contribute to the overall genetic risk for schizophrenia.

Association between schizophrenia with ocular misalignment and polyalanine length variation in PMX2B.

The increased incidence of minor physical anomalies (MPAs) in schizophrenia is the fundamental basis for the neurodevelopmental hypothesis of schizophrenia etiology. Ocular misalignment, or strabismus, falls into the category of MPAs, but this phenotype has not been assessed in schizophrenia. This study reveals that a subtype of strabismus, constant exotropia, displays marked association with schizophrenia (P=0.00000000906). To assess the genetic mechanisms, we examined the transcription factor genes ARIX (recently identified as a causative gene for syndromic strabismus) and its paralogue, PMX2B. We identified frequent deletion/insertion polymorphisms in the 20-alanine homopolymer stretch of PMX2B, with a modest association between these functional polymorphisms and constant exotropia in schizophrenia (P=0.029). The polymorphisms were also associated with overall schizophrenia (P=0.012) and more specifically with schizophrenia manifesting strabismus (P=0.004). These results suggest a possible interaction between PMX2B and other schizophrenia-precipitating factors, increasing the risk of the combined phenotypes. This study also highlights the unique nature of the polyalanine length variations found in PMX2B. In contrast with other transcription factor genes, the variations in PMX2B show a high prevalence, with deletions being more common than insertions. Additionally, the polymorphisms are of ancient origin and stably transmitted, with mild phenotypic effects. In summary, our study lends further support to the disruption of neurodevelopment in the etiology of schizophrenia, by demonstrating the association of a specific MPA, in this case, constant exotropia with schizophrenia, along with molecular variations in a possible causative gene.