Project description:Chromosome substitution strains (CSS or consomic strains) are useful for mapping phenotypes to chromosomes. However, huge efforts are needed to identify the gene(s) responsible for the phenotype in the complex context of the chromosome. Here, we report the identification of candidate disease genes from a CSS using a combination of genetic and genomic approaches as well as by using knowledge about the germ cell tumor disease etiology. We utilized the CSS, 129.MOLF-Chr 19 chromosome substitution strain (or M19), in which males develop germ cell tumors of the testes at an extremely high rate. We are able to identify 3 protein-coding genes and 1 microRNA on chromosome 19 that have previously not been implicated to be testicular tumor susceptibility genes. Our findings suggest that changes in gene expression levels in the gonadal tissues of multiple genes from Chr 19 likely contribute to the high TGCT incidence of the M19 strain. Our data advances the use of CSS to identify disease susceptibility genes and demonstrates that the 129.MOLF-Chr 19 strain serves as a useful model to elucidate the genetics and biology of germ cell transformation and tumor development. For gene expression profiling, we used male gonads from different developmental stages, E13.5 and PN1, from the M19 and 129 strains. The idea was to detect the common gene expression changes in the gonads at stages when germ cells are known to transform to embryonal carcinoma (EC) cells. E13.5 stage was chosen because tumor development is reported to start around E13.5 in 129 strains (Stevens 1973b; Stevens and Hummel 1957). PN1 stage gonads were chosen because our studies with M19;Oct4-GFP mice, as described above, showed that both germ cells and EC cells are present at this stage suggesting that germ cell transformation may also be ongoing at this stage in the testes of M19 strain. We also compared gene expression differences in gonads to that of embryos to determine whether gene expression differences are specific to the gonads. Our goal was to identify gene(s) whose expression is consistently changed in the gonads at E13.5 and PN1 in the M19 as these would likely be candidate TGCT susceptibility gene(s). Fig. 3A indicates the 3 different tissue samples collected from the M19 and 129 strains: gonads (genital ridges) dissected from male E13.5 embryos and from PN1 mice and male embryos at E13. Because tumor incidence in M19 is approximately 80% we anticipated that gene expression changes could be masked because ~20% of cells/tissues within a sample may have normal levels of gene expression or 20% of the testes may have normal gene expression. Moreover, the amount of RNA extracted from a single genital ridge or PN1 testis is insufficient for a microarray experiment. To minimize the effect of individual samples and to isolate sufficient RNA for microarray analysis from these small sized gonads, we pooled RNA from multiple samples (Table 1). Six RNA pooled samples were prepared (Fig.3A and Supplementary Table 2): E13.5 gonad RNA from males of 129 (129-GR) and M19 (M1-GR); PN1 testes RNA from 129 (129-NBT) and M19 (M1-NBT); E13.5 embryo RNA from males of 129 (129-E) and M19 (M1-E). The six RNA samples were hybridized to six Affymetrix mouse genome genechips individually. Hierarchical clustering analysis revealed a dendrogram in which gene expression profiles of the same tissue type clustered together (Fig. 3B). Profiles of the gonads, E13.5 and PN1, were related more closely than to those of embryos. Comparison of the expression profiles of E13.5 gonads from M19 and 129 revealed 10 genes with more than a 2-fold difference in expression levels (Fig. 3A and Supplementary Table 3A). Six of the 10 genes mapped to Chr 19. For the PN1 testes, 266 genes showed significant fold changes between the two strains and of these 13 genes mapped to Chr 19 (Fig. 3A and Supplementary Table 3C). For the E13.5 embryos, 35 genes showed greater than a 2-fold change in expression between the M19 and 129 and 5 out of 35 genes mapped to Chr 19 (Fig. 3A and Supplementary Table 3B). By analyzing the data of differentially expressed genes present in the 3 samples, as well as selecting those that map to Chr 19, we were able to exclude a majority of the genes but found 3 genes in common. The 3 genes map to Chr 19 and were found to be downregulated in the M19 strain E13.5 and PN1 gonads as well as E13.5 embryos. These are Zfp162, D19Bwg1357e and Cox15. These 3 genes have not been previously implicated in testicular tumorigenesis and are novel TGCT candidate susceptibility genes.

Project description:Methoxyacetic acid (MAA) is the active metabolite of the widely used industrial chemical ethylene glycol monomethyl ether, an established testicular toxicant. MAA induces the degradation of testicular germ cells in association with changes in gene expression in both germ cells and Sertoli cells of the testis. This study investigates the impact of MAA on gene expression in testicular Leydig cells, which play a critical role in germ cell survival and male reproductive function. Cultured mouse TM3 Leydig cells were treated with MAA for 3, 8, and 24 h and global gene expression was monitored by microarray analysis. A total of 3,912 MAA-responsive genes were identified. Ingenuity Pathway analysis identified reproductive system disease, inflammatory disease and connective tissue disorder as the top biological functions affected by MAA. The MAA-responsive genes were classified into 1,366 early responders, 1,387 mid-responders, and 1,138 late responders, based on the time required for MAA to elicit a response. Analysis of enriched functional clusters for each subgroup identified 106 MAA early response genes involved in transcription regulation, including 32 genes associated with developmental processes and 60 DNA-binding proteins that responded to MAA rapidly but transiently, and which may contribute to the downstream effects of MAA seen for large numbers of mid and late response genes. Genes within the phosphatidylinositol/phospholipase C/calcium signaling pathway, whose activity is required for potentiation of nuclear receptor signaling by MAA, were also enriched in the set of early MAA response genes. These findings on the progressive changes in gene expression induced by MAA in Leydig cells may help elucidate the signaling pathways perturbed by this testicular toxicant and explain its mechanism of toxicity at the gene level. Mouse TM3 Leydig cells (American Type Culture Collection, Manassas, VA) were grown in DMEM-F12 medium containing 5% horse serum and 2.5% FBS. Cells were grown to ~60% confluence and treated with culture medium alone, or with culture medium containing 1 mM or 5 mM MAA for either 3, 8 or 24 h. Total RNA was then isolated using TRIzol reagent, followed by incubation with RQ1 RNAse-free DNAse for 1 h at 37Â°C and then heating at 75Â°C for 5 min using the manufacturerâs protocol. A total of 6 cultures of TM3 cells were independently treated with MAA under each of the 6 treatment conditions specified above (i.e., 1 mM or 5 mM MAA for either 3, 8 or 24 h), and the corresponding 6 sets of RNA samples were validated by RNA integrity analysis (Agilent Bioanalyzer). Each RNA sample was also validated by qPCR analysis using SYBR Green I-based chemistry and primers specific for 3 genes known to respond to MAA (Cyp17a1, Shbg, and Igfbp3) to verify consistency of the MAA responses. The 6 RNA samples were then used to prepare two independent pools (n=3 RNA samples each) for microarray analysis with dye swaps. Sample labeling, hybridization to microarrays, scanning and calculation of normalized expression ratios were carried out at the Wayne State University Institute of Environmental Health Sciences microarray facility using Alexa 555 and Alexa 647 aminoallyl-aRNA samples

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