Transcription profiling of human testicular tissue histologically scored as containing carcinoma in situ (CIS) in 50%, 75%, and 100% of the seminiferous tubules vs total RNA from testicular tissue with preserved normal and complete spermatogenesis and no CIS present
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Christian Schwager
PROVIDER: E-EMBL-2 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Testicular germ cell tumours (TGCTs) of young adult men, seminoma (SEM) and nonseminoma (NSEM), develop from a precursor cell, carcinoma in situ (CIS), which resembles foetal gonocytes and retains embryonic pluripotency. We used microarrays to analyse microRNA (miRNA) expression in 12 human testis samples with CIS cells and compared it to the miRNA expression profiles of normal adult testis, testis with Sertoli-cell-only (SCO) that lack germ cells, testis tumours (SEM and embryonal carcinoma, EC; an undifferentiated component of NSEM) and foetal male and female gonads. Principal component analysis revealed distinct miRNA expression profiles characteristic for each of the different tissue types. We identified several miRNAs that were unique to testis with CIS cells, foetal gonads, and testis tumours. These included miRNAs from the hsa-miR-371~373 and -302~367 clusters that have previously been reported in germ cell tumours and three miRNAs (hsa-miR-96, -141 and -200c) that were also expressed in human epididymis. We found several miRNAs that were upregulated in testis tumours: hsa-miR-9, -105 and the hsa-miR-182~183~96 cluster were highly expressed in SEM, while the hsa-miR-515~526 cluster was high in EC. We conclude that miRNA expression profile changes during testis development and that the miRNA profile of adult testis with CIS cells shares characteristic similarities with the expression in foetal gonocytes. We used Agilent microarrays to determine the expression of microRNAs in samples from testis. We first used Agilent-016436 Human miRNA Microarray 1.0 G4472A (GPL9081; miRNA ID version) on 4 samples: normal testis, testis with 30% carcinoma in situ (CIS) tubules, testis with 50% CIS tubules and testis with 99-100% CIS tubules. This allowed us to determine the correlation between miRNA expressiona and the content of CIS cells in the samples. This is the file with data from those four arrays. Next, we used Agilent-019118 Human miRNA Microarray 2.0 G4470B (GPL8936; Probe Name version) on 24 samples that included normal testis, testis with the precursor for testis cancer carcinoma in situ (CIS), Sertoli-cell-only testis (contains the somatic testis cells but no germ cells), seminom and non-seminom tumours, and foetal gonads. This constitute the main part of the experiment and the publication, but the data was submitted to GEO in an independent file.
2011-11-01 | E-GEOD-31824 | biostudies-arrayexpress
Project description:We employed Solexa sequencing technology to profile miRNAs and piRNA in normal human testis, three cases, pulled together
2014-01-21 | E-MTAB-1629 | biostudies-arrayexpress
Project description:The epididymis can be subdivided into three regions, the caput, corpus and cauda epididymidis, that have different characteristics and functions. Goal was to determine the differential pattern of gene expression along the regions of the human epididymis. Two-condition experiment, region 1 vs region 2. Replicates: 4 biological replicates from each epididymal region.
2010-08-25 | E-GEOD-23812 | biostudies-arrayexpress
Project description:We investigated the influence of extension of autosomal asynapsis on expression profiles during spermatogenesis. We used the mouse autosomal translocation T(16;17)43H (abbreviated T43H) and t12 haplotype, a natural variant of Chr 17 encompassing four adjacent non-overlapping inversions proximal to the T43H translocation breakpoint, as a model. The presence of t12 haplotype in trans to the T43H translocation resulted in stringent spermatogenic block and in more complete silencing of genes surrounding the T43H translocation break. Strikingly, silencing of the unsynapsed autosomal chromatin preceded the inactivation of the sex chromosomes (MSCI) and was apparent already in the population of pre-mid pachytene spermatocytes and testes of 15 days old males. Populations of pre-mid-pachytene spermatocytes were isolated from Ttf+/+T43H and t12+/+T43 males in three biological replicates. Their expression was compared to two biological replicates of the populations of pre-mid pachytene spermatocytes and mid-late pachytene spermatocytes obtained from C57BL/10J fertile males. Independently, testicular RNA was isolated from 15 days old Ttf+/+T43H and t12+/+T43 males in three biological replicates and the expression was compared to the testicular expression of two 15 days old C57BL/6J males.
2014-05-09 | E-GEOD-29177 | biostudies-arrayexpress
Project description:Autosomal trisomies and monosomies bring serious threats to embryonic development through transcriptional disarray primarily caused by the dosage effect of the aneuploid part of the genome. The present study compared the effect of a mouse viable 30 Mb segmental trisomy on the genome-wide transcriptional profile of somatic (liver) cells and male germ cells. While the 1.6-fold change in expression of triplicated genes reflected the gene dosage in liver cells, the extra copy was almost fully compensated in early pachytene spermatocytes, showing 1.18-fold increase. Allele-specific semi-quantitative evaluation of steady-state mRNA levels of the triplicated Amdhd2 gene revealed silencing evenly distributed among all three copies in these meiotic cells. Although more pronounced, the dosage compensation of trisomic genes was concordant with the incidence of HORMAD2 and γH2AX markers of unsynapsed chromatin. The possible explanations include insufficient sensitivity to detect both MSUC markers in the 30 Mb region of the chromosome, or an early silencing effect of another epigenetic factor. Taken together, our results indicate that the meiotic silencing of unsynapsed chromatin is the major but not the only factor driving the dosage compensation of triplicated genes in primary spermatocytes. We compared the global expression profiles in isolated popoulations of meiotic cells and liver cells of Ts43H trisomic males and their t121/D17 euploid siblings.
2016-03-30 | E-GEOD-54683 | biostudies-arrayexpress
Project description:The distal convoluted tubule (DCT) plays a key role in the fine-tuning of renal Mg2+ reabsorption. In recent years, hereditary magnesium (Mg2+) transport disorders have helped to identify important players in DCT Mg2+ homeostasis. Here, we report the Mg2+-sensitive transcriptional expression of the DCT transcriptome using gene expression microarray analysis. Mice expressing eGFP under a DCT-specific promoter were subjected to Mg2+-deficient or Mg2+-enriched diets. Subsequently, the Complex Object Parametric Analyzer and Sorter (COPAS) allowed isolation of eGFP-positive DCT cells. RNA extracts were subjected to pair-wise microarray analysis, high vs. low Mg2+. Of all genes in the genome, 46 were shown to be differentially expressed with a minimal fold-change of 2. Several known magnesiotropic genes, such as Trpm6 and Parvalbumin, were upregulated in the low Mg2+ fraction. Moreover, new genes were identified that are potentially involved in renal Mg2+ homeostasis. To confirm that the selected candidate genes are regulated by dietary Mg2+ availability, the expression levels of Slc41a3, Pcbd1, Tbc1d4 and Umod were determined by RT-PCR analysis. Indeed, all four genes were shown to be significantly upregulated in mice fed the Mg2+-deficient diet. In conclusion, by elucidating the Mg2+-sensitive DCT transcriptome, new candidate players in renal Mg2+ homeostasis were identified. RNA samples were isolated from PV-eGFP-positive tubules from mice fed on a low (L-samples) or high (H-samples) magnesium diet. Littermate H and L samples were labeled and put on mouse microarrays together. Two of the four sample sets were analyzed in dye-swap to compensate for dye-biases.
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