Identification of TGCT genes involved in initiation and maintenance of transformed germ cells.
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE14481 | GEO | 2009/12/31
SECONDARY ACCESSION(S): PRJNA111493
REPOSITORIES: GEO
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Project description:Initially, we had compared gene expression differences in the embryonic gonads (E13.5) of the 129 and M19 strains by performing microarray analysis. These studies allowed us to identify downregulation of expression of the D19Bwg1357e, Zfp162 and Cox15 genes in the M19 strain. We next decided to examine gene expression profile changes in the embryonic gonads of 129 and M19 at additional stages so as to identify other TGCT genes from M19 that are also involved in initiation and maintenance of transformed germ cells. For this we isolated E13.5, E15.5 and E17.5 genital ridges from male embryos. Microarray analysis of E13.5, E15.5 and E17.5 genital ridges from male embryos of M19 and 129. Total RNA prepared from the embryonic gonads were analyzed on 12 Affymetrix mouse 430_2 arrays. The objective of the analysis is to determine the differentially expressed genes for the following comparisons: 1. Comparisons of the two strains at each stage, specifically: 1a. 129-E13-GR vs. M19-E13-GR 1b. 129-E15-GR vs. M19-E15-GR 1c. 129-E17-GR vs. M19-E17-GR 2. Comparisons of the different stage in strain 129, specifically: 2a. 129-E13-GR vs. 129-E15-GR 2b. 129-E15-GR vs. 129-E17-GR 3. Comparisons of the different stage in strain CSS, specifically: 3a. M19-E13-GR vs. M19-E15-GR 3b. M19-E15-GR vs. M19-E17-GR After data process and quality assessment, 38069 out of 45101 probe sets proceeded for further analysis to identify differentially expressed genes. Hierarchical cluster analysis shows that samples of two strains from the same stage were grouped together and separated from the other stages (Fig.8). The initial analysis indicates a number of trends in gene expression patterns. Moreover, downregulation of expression of D19Bwg1357e, Zfp162 and Cox15 genes in M19 was also verified in this analysis. These data are currently being analyzed with the help of Dr. Y. Ji and L. Xiao from the Department of Bioinformatics and Computational Biology and Department of Biostatistics at M.D. Anderson Cancer Center. The results are unpublished.
2009-12-30 | E-GEOD-14481 | biostudies-arrayexpress
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.
2009-01-13 | E-GEOD-14354 | biostudies-arrayexpress
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2016-06-15 | E-GEOD-63860 | biostudies-arrayexpress
Project description:Small RNA cloning from embryonic genital ridges.
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Project description:We used microarrays to profile global gene expression changes of Pou5f1-GFP-positive germ cells between E11.5 to E15.5. Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. Three timepoints were included in this study: E11.5 (male/female), E13.5 (male) and E15.5 (male). For each timepoint, three biological replicates were analyzed. The Pou5f1-GFP-negative (non-germ cell) fraction of E13.5 (male) gonads was also included as a control.
2013-01-25 | E-GEOD-38126 | biostudies-arrayexpress
Project description:Here, we present the fetal mouse intestine data from the project \\"Comparison of human and mouse mesenchyme identifies common and unique aspects of intestinal patterning\\". Whole intestines were harvested from fetuses from timed pregnant matings for wildtype C57BL/6 mice (Jax strain #000664). Fetal stages were confirmed according to the Theiler staging chart (https://www.emouseatlas.org/emap/ema/staging_criteria/staging_criteria.html). Whole intestines (from the common bile duct through the cecum) were collected at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5). Male and female intestines from each stage were pooled and dissociated to single cells for single cell RNA sequencing as previously described (Miller et al. 2020 Dev Cell). Specifically, E13.5 was 6 intestines, E14.5 was 5 intestines, E15.5 was 4 intestines, E16 was 3 intestines and E17.5 was 3 intestines.
2024-04-01 | E-MTAB-13201 | biostudies-arrayexpress
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2013-02-06 | GSE37716 | GEO