Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA254834 | ENA |
REPOSITORIES: ENA
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Project description:Several observations have pointed a link between small RNA pathway and testicular germ cell tumorigenesis. Yet, the role of small RNAs in testicular germ cell tumors (TGCTs) is still not completely understood. In this study, we characterized the expression profiles of sRNAs in 9 primary sporadic TGCTs and 2 normal testes (NTs) using a sequencing approach. Our data show comprehensive coverage of microRNAs (miRNAs) expressed in human TGCT tissues and NTs, including the identification of 29 candidate novel miRNAs. We identified the differentially expression of miR-506~514 cluster and miR-21, miR-223 in the TGCTs compared to NTs. Functionally, we showed that miR-514a-3p positively regulates apoptosis through directly regulating PEG3. We further demonstrate that PEG3 activates NF-kappa B pathway in human testicular germ cell tumors.
2015-01-16 | GSE59267 | GEO
Project description:We investigated how MEIOC affects testicular germ cells at the transition from mitosis to meiosis. We performed gene expression profiling analysis using data obtained from RNA-seq of preleptotene-enriched testes from wild-type and Meioc KO pups.
2024-04-16 | GSE230743 | GEO
Project description:Despite timely and successful surgery, 32% of patients with bilateral and 10% with unilateral cryptorchidism will develop azoospermia. Cryptorchid boys at risk of azoospermia display a typical testicular histology of impaired mini-puberty at the time of the orchidopexy. During mini-puberty increased gonadotropin and testosterone secretion stimulate transformation of gonocytes into Ad spermatogonia. In azoospermia risk group this transformation is to a great extent impaired. This study aimed to analyze data on whole genome expression signatures of undescended testes at risk of developing azoospermia. Twenty-three testicular biopsies from 22 boys were analyzed (19 testes from 18 boys with cryptorchidism) and 4 contralateral descended testes from patients with testicular agenesis. Expression profiling identified 483 genes not or under-expressed in the azoospermia risk group compared with the control and LAZR groups. Annotated loci were associated with spermatogenesis. Other significant genes were cellular defense response genes and hormone controlled loci involved in spermatogenesis. Some genes transcribed in normal adult meiotic and post-meiotic germ cells are activated in healthy juvenile Ad spermatogonia. Thus, molecular events initiating the testicular expression program at the onset of puberty and maintaining it during adulthood occur very early in prepubertal testes. This molecular event is to a great extent impaired in HAZR group lacking Ad spermatogonia (stem cells for spermatozoa) indicating impaired mini puberty.
2010-11-23 | E-GEOD-25518 | biostudies-arrayexpress
Project description:In addition to germ cell population, testes contain several types of somatic cells, including Sertoli cells, Leydig cells, and peritubular myoid (PTM) cells. PTM cells are a type of smooth muscle-like cells and have contraction ability. To identify a marker of PTM cells, we isolated primary cells and subsequently performed RNA-Seq of testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3), testicular Sertoli cells (Sertoli_1, Sertoli_2, Sertoli_3), testicular Leydig cells (Leydig_1, Leydig_2, Leydig_3), testicular germ cells (Germ_1, Germ_2, Germ_3), vascular smooth muscle cells (VSMC_1, VSMC_2, VSMC_3), intestinal smooth muscle cells (ISMC_1, ISMC_2, ISMC_3), and tracheal smooth muscle cells (TSMC_1, TSMC_2, TSMC_3) using BGISEQ-500 platform (BGI, China).
2019-01-19 | GSE125303 | GEO
Project description:In addition to germ cell population, testes contain several types of somatic cells, including Sertoli cells, Leydig cells, and peritubular myoid (PTM) cells. PTM cells are a type of smooth muscle-like cells and have contraction ability. To identify a marker of PTM cells, we isolated primary cells and subsequently performed miRNA-Seq of testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3), testicular Sertoli cells (Sertoli_1, Sertoli_2, Sertoli_3), testicular Leydig cells (Leydig_1, Leydig_2, Leydig_3), testicular germ cells (Germ_1, Germ_2, Germ_3), vascular smooth muscle cells (VSMC_1, VSMC_2, VSMC_3), intestinal smooth muscle cells (ISMC_1, ISMC_2, ISMC_3), and tracheal smooth muscle cells (TSMC_1, TSMC_2, TSMC_3) using BGISEQ-500 platform (BGI, China).
2019-01-19 | GSE125302 | GEO
Project description:Comparison of miRNA expression profiles in malignant germ cell tumors compared to non-malignant control group. Use of bioinformatic algorithm Sylamer to interrogate mRNA expression profiles from malignant germ cell tumors for enrichment or depletion of binding sites for differentially expressed miRNAs. Use of Gene Ontology (GO) analysis to demonstrate functional significance of differentially expressed miRNAs in malignant germ cell tumors. mRNA profiling: Analyzed global mRNA expresion profiles from 21 pediatric samples (17 malignant germ cell tumors, 1 benign germ cell tumor and 3 gonadal controls) using Sylamer (van Dongen et al, Nature Methods 2008, PMID 18978784) to study functional significance of differentially expressed miRNAs in malignant germ cell tumors. 16 of these files previously published - Palmer et al, Cancer Research 2008, PMID 18519683; GEO Accession Number GSE10615. Similarly, re-analyzed published global mRNA expresion profiles from 25 adult samples (20 malignant germ cell tumors and 5 testis controls) using Sylamer (van Dongen et al, Nature Methods 2008, PMID 18978784) to study functional significance of differentially expressed miRNAs in malignant germ cell tumors. These files previously published - Korkola at al, Cancer Research 2006, PMID 16424014; GEO Accession Number GSE3218. miRNA profiling: Analyzed global miRNA expression files from 48 samples including 32 pediatric gonadal and extragonadal germ cell tumors, 2 adult testicular seminomas, 8 gonadal and developmental control samples and 6 germ cell tumor cell lines. Re-analyzed published data (TaqMan MicroRNA Assays) from study of miRNA expression in adult gonadal germ cell tumors (Gillis et al, J Pathol 2007, PMID 17893849) and compared with pediatric findings. Re-analyzed data linked below as supplementary file.
2010-03-14 | E-GEOD-18155 | biostudies-arrayexpress
Project description:Very recently, a number of independent studies showed that serum levels of embryonic micro-RNA (miR) clusters 371-3 and 302abc/367 are predictive for the presence of testicular type II germ cell tumors. These miRs could be used to sensitively detect SE and EC components which are indeed known to express these miRs [1-7]. This study investigates ca 750 miRs in a high throughput approach to validate these previously identified markers and identify novel potential miR markers for testicular type II germ cell tumors. 1. Belge, G., et al., Serum levels of microRNAs miR-371-3: a novel class of serum biomarkers for testicular germ cell tumors? Eur Urol, 2012. 61(5): p. 1068-9. 2. Dieckmann, K.P., et al., MicroRNAs miR-371-3 in serum as diagnostic tools in the management of testicular germ cell tumours. Br J Cancer, 2012. 107(10): p. 1754-60. 3. Gillis, A.J., et al., Targeted serum miRNA (TSmiR) test for diagnosis and follow-up of (testicular) germ cell cancer patients: a proof of principle. Mol Oncol, 2013. 7(6): p. 1083-92. 4. Gillis, A.J., et al., High-throughput microRNAome analysis in human germ cell tumours. J Pathol, 2007. 213(3): p. 319-28. 5. Murray, M.J. and N. Coleman, Testicular cancer: a new generation of biomarkers for malignant germ cell tumours. Nat Rev Urol, 2012. 9(6): p. 298-300. 6. Murray, M.J., et al., Identification of microRNAs From the miR-371~373 and miR-302 clusters as potential serum biomarkers of malignant germ cell tumors. Am J Clin Pathol, 2011. 135(1): p. 119-25. 7. Voorhoeve, P.M., et al., A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell, 2006. 124(6): p. 1169-81.
2014-10-02 | GSE59520 | GEO
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.
2009-01-13 | GSE14354 | GEO
Project description:Genomic DNA from 6 pure EC and 2 normal testis was fragmented and immunoprecipitated with anti-5mC monoclonal antibodies by MeDIP. After IP, DNA was purified and amplified using Whole Genome Amplification. Subsequently, DNA was biotin-labeled and hybridized to Human Tiling Array 2.0R Chips (Affymetrix) according to the manufacturer’s instruction. Raw data (CEL files) were normalized and analyzed by TAS (Affymetrix). Technical replicate of MeDIP-chip procedure was performed. Testicular embryonic carcinoma (EC) is a major subtype of non-seminomatous germ cell tumors (NSGCTs) in males. To identify epigenetic changes during testicular tumorigenesis, we profiled the DNA methylation of 6 ECs. These samples represent different stages (stage I and stage III) and different extent of invasiveness. Non-cancerous testicular tissues were included. A total of 1167 tumor-hypermethylated differential methylated regions (DMRs) were identified across the genome. Among them, 40 genes/ncRNA were found to have hypermethylated promoters. Interestingly, we found several hypermethylated sex-linked genes, including X-linked genes STAG2, SPANXD/E, MIR1184, Y-linked genes RBMY1A1/1B/1D and FAM197Y2P. Expression of RBMY1A was confirmed by immunohistochemistry in normal germ cells, but lost in EC and seminoma. Our genome-wide analysis identified methylation changes in several previously unknown genes for testicular ECs, which might provide insight into the crosstalk between normal germ cell development and carcinogenesis. A total of 8 DNA samples, including 6 EC and 2 normal testicular tissues
2015-03-12 | E-GEOD-66784 | biostudies-arrayexpress
Project description:Sheep testes undergo a dramatic rate of development with structural changes during sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three sexual maturity (3 month-old) rams were sequenced using 10x Genomic platform single-cell sequencing (scRNA-seq).Nine testicular somatic cell types and five male germ cell types were observed.The study revealed significant changes in germline stem cells during sexual maturation. Candidate factors and pathways for the regulation of germ and somatic cell development were identified that represent the scientific basis for the development of a livestock stem cell breeding program.
2021-12-30 | GSE184343 | GEO