Gene expression analysis comparing between pure- and mixed type testicular seminoma
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PROVIDER: PRJNA704085 | ENA |
REPOSITORIES: ENA
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Project description:We hypothesized that the comparison between pure type seminoma and seminoma components in mixed tumor (mixed type seminoma) could reveal early changes of the reprogramming process; however, only a little data is available. We performed gene expression microarray analysis of 6 pure type and 6 mixed type seminomas, and the hierarchical clustering analysis properly grouped each type of seminomas into a separated cluster. Supervised analysis between these groups identified 154 significantly dysregulated genes (Storey-adjusted q < 0.05). The genes with the highest overexpression in mixed type seminomas compared with the pure type seminomas included MT1 isoforms, PRSS8, TSC22D1, and SLC39A4; down-regulated genes included DEFB123, LMTK2, and MTRF. Functional annotation analysis of the differently expressed genes revealed the top-ranking categories related to cellular zinc metabolism, consisting of MT-1 isoforms and SLC39A4.
2021-02-23 | GSE167294 | GEO
Project description:Gene expression patterns of testicular seminoma were analysed applying oligonucleotide microarrays in 40 specimens of different tumour stages (pT1, pT2, pT3) and in 3 normal testes. Experiment Overall Design: A total of 40 pure seminoma including 22 samples of tumour stage 1 (pT1), 14 samples of tumour stage 2 (pT2) and 4 of tumour stage 3 (pT3) as well as three normal testicular samples of high-quality mRNA were used for microarray analyses.
2008-11-06 | E-GEOD-8607 | biostudies-arrayexpress
Project description:Gene expression patterns of testicular seminoma were analysed applying oligonucleotide microarrays in 40 specimens of different tumour stages (pT1, pT2, pT3) and in 3 normal testes. Keywords: ordered
2007-07-31 | GSE8607 | GEO
Project description:Testicular cancer is the most common solid malignancy in young men. Given the many histological classifications of testicular tumours, seminoma is one of the most treatable cancers. The survival rate in early-stage disease was more than 90%. Thus, seminoma at the cellular and molecular levels, especially at the single-cell level, is worth studying. We performed a single-cell RNA sequencing (scRNA-seq) study on a patient who was diagnosed with testicular seminoma with lymph node metastasis. This study presented tumour tissue, PBMC, pelvic and renal hilus lymph node in a total of 18,206 high-quality single-cell transcriptome information. The characteristics of metastatic cell lineage were revealed by the comparison between different tumour cell subtypes at the scRNA level. A single-cell map of testicular seminoma with lymph node metastasis was constructed by scRNA-seq. We discovered the gene expression characteristics of the tumour cells in testicular seminoma, especially metastatic tumour cells. KRT8 and KRT18 were commonly expressed in the three tumour cell subtypes. However, TCF7L1, SCG3 and SV2C were the specifically expressed genes of tumour cell subtypes in primary tumour sites. Some molecular markers specifically expressed by the metastatic cell lineage, such as POU5F1, were identified. We revealed the molecular characteristics of testicular seminoma at the single-cell level, especially the metastatic tumour cells. This study could provide new insights into the diagnosis and treatment of testicular seminoma.
2022-03-25 | GSE197778 | GEO
Project description:Purpose: The aim of the present study was to examine the biological differences between seminomas with occult and clinically apparent metastases at the time of diagnosis of the primary tumor to gain insight into the biology of these tumors and facilitate the identification of novel predictors of seminoma metastasis. Materials and Methods: Total RNA including small RNAs was isolated from testicular tumors of patients with pure seminoma presenting with lymphogenic metastasis (n=5, clinical stage IIb/c) and occult metastasis (n=5, clinical stage I). The regulation of biological processes was examined (1) throughout the mRNA transcriptome (whole genome microarrays, 8x60K Array, Agilent and 4 samples per group) and (2) the miRNA transcriptome employing small RNA next generation sequencing (SOLID, Life Technologies). Protein coding genes (mRNAs) and small RNAs showing a significant (> 2-fold) difference between the groups were identified. Finally (3), we examined 95 candidate miRNAs in 36 apparent metastasized and another 5 occult metastasized seminoma using logistic regression analysis. Results: Among 19,596 genes, on average 12,894 mRNAs appeared expressed (65.8%, SD +/- 2.4; range, 62.0–69.3%) and 16.99×106/13.94×106 small RNA reads were identified for apparent/occult metastasized seminoma. These reads on average convert into 9,901/9,675 small RNAs including 422/404 mature microRNAs. None of these mRNAs/small RNAs met our selection criteria for candidate genes. From 95 candidate miRNAs 44 appeared expressed, with 3 of them showing weak but significant (p=0.047-0.049) differences among both groups. Conclusions: Occult and apparent metastasized seminomas are biologically almost indistinguishable and probably represent no separate tumor entities. These findings may simplify future research on seminoma metastasis.
2014-02-21 | GSE55198 | GEO
Project description:Testicular germ cells tumors (TGCTs) have a high sensitivity to cisplatin-based chemotherapy and a high cure rate, although with possible serious adverse effects. In the search for tumor suppressive drugs, the RANKL inhibitor Denosumab, used to treat osteoporosis came up as a candidate since RANKL signaling was recently identified in the testis. RANKL signals through the receptor RANK and this signaling is antagonized by the decoy receptor OPG. Here, we demonstrate expression of RANKL, RANK, and OPG in germ cell neoplasia in situ (GCNIS), TGCTs, and TGCT-derived cell lines. RANKL inhibition reduced proliferation of seminoma-derived TCam-2 cells but had no effect on embryonal carcinoma-derived NTera2 cells in vitro. Denosumab did not potentiate the effect of cisplatin treatment in vitro but inhibition of RANKL in vivo resulted in reduced tumor growth in a TCam-2 but not a NTera2 xenograft model. Moreover, Denosumab treatment decreased proliferation in human testicular GCNIS tissue culture in vitro. In TGCT patients, serum RANKL was not linked with tumor burden, relapse, or other prognostic markers. In conclusion, this study shows that the RANKL signaling system is expressed in GCNIS and seminoma where RANKL inhibition suppress tumor growth in vitro and in vivo. Future studies are needed to determine whether RANKL is important for the malignant transformation and the transition from GCNIS to invasive tumors.
2022-04-19 | GSE197389 | 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:Purpose: The aim of the present study was to examine the biological differences between seminomas with occult and clinically apparent metastases at the time of diagnosis of the primary tumor to gain insight into the biology of these tumors and facilitate the identification of novel predictors of seminoma metastasis. Materials and Methods: Total RNA including small RNAs was isolated from testicular tumors of patients with pure seminoma presenting with lymphogenic metastasis (n=5, clinical stage IIb/c) and occult metastasis (n=5, clinical stage I). The regulation of biological processes was examined (1) throughout the mRNA transcriptome (whole genome microarrays, 8x60K Array, Agilent and 4 samples per group) and (2) the miRNA transcriptome employing small RNA next generation sequencing (SOLID, Life Technologies). Protein coding genes (mRNAs) and small RNAs showing a significant (> 2-fold) difference between the groups were identified. Finally (3), we examined 95 candidate miRNAs in 36 apparent metastasized and another 5 occult metastasized seminoma using logistic regression analysis. Results: Among 19,596 genes, on average 12,894 mRNAs appeared expressed (65.8%, SD +/- 2.4; range, 62.0M-bM-^@M-^S69.3%) and 16.99M-CM-^W106/13.94M-CM-^W106 small RNA reads were identified for apparent/occult metastasized seminoma. These reads on average convert into 9,901/9,675 small RNAs including 422/404 mature microRNAs. None of these mRNAs/small RNAs met our selection criteria for candidate genes. From 95 candidate miRNAs 44 appeared expressed, with 3 of them showing weak but significant (p=0.047-0.049) differences among both groups. Conclusions: Occult and apparent metastasized seminomas are biologically almost indistinguishable and probably represent no separate tumor entities. These findings may simplify future research on seminoma metastasis. Regarding the genome-wide expression profiling we analyzed gene expression changes in human seminoma samples with occult or lymphatic metastasis using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays in 8x60K format in combination with a one-color based hybridization protocol. Microarray signals were detected using the Agilent DNA Microarray Scanner. Differential RNA expression was assessed by applying appropriate biostatistics to the data set. GeneSpring GX12.6 analysis software was used to normalize and analyze the raw data. Different filtering approaches were applied to identify up- and downregulated transcripts in the comparisons of interest. Identified differentially expressed genes were further characterized for their involvement in biological pathways and processes based on the Panther database. For mRNA transcriptome analysis we used 4 samples per group. Only significant and > 2-fold differences in gene expression between the two groups were considered for comparisons, and unadjusted p-values and those adjusted for multiple comparisons (false discovery rate) were calculated. All gene candidates underwent gene set enrichment analyses using PANTHER pathway software (http://www.pantherdb.org/), which groups genes with similar biological functions based on their annotation.
2014-02-21 | E-GEOD-55198 | biostudies-arrayexpress
Project description:We have isolated highly pure testicular extracellular vesicles using a newly established testis dissociation method. We then used shotgun proteomic approach to examine the proteins carried by and expressed on the testicular extracellular vesicles.
2022-02-17 | PXD021766 | Pride
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.
2015-03-12 | GSE66784 | GEO