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| Status |
Public on Aug 29, 2019 |
| Title |
Molecular basis of cisplatin resistance in testicular germ cell tumors |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
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| Summary |
The emergence of cisplatin (CDDP) resistance is the main cause of treatment failure and death in patients with testicular germ cell tumors (TGCT), but its biologic background is poorly understood. To study the molecular basis of CDDP resistance in TGCT we prepared and sequenced CDDP-exposed TGCT cell lines as well as 31 primary patients’ samples. Long-term exposure to CDDP increased the CDDP resistance 10 times in the NCCIT cell line, while no major resistance was achieved in Tera-2. Development of CDDP resistance was accompanied by changes in the cell cycle (increase in G1 and decrease in S-fraction), increased number of acquired mutations, of which 3 were present within ATRX gene, as well as changes in gene expression pattern. Copy number variation analysis showed, apart from obligatory gain of 12p, several other large-scale gains (chr 1, 17, 20, 21) and losses (chr X), with additional more CNVs found in CDDP-resistant cells (e.g., further losses on chr 1, 4, 18, and gain on chr 8). In the patients’ samples, those who developed CDDP resistance and died of TGCT (2/31) showed high numbers of acquired aberrations, both SNPs and CNVs, and harbored mutations in genes potentially relevant to TGCT development (e.g., TRERF1, TFAP2C in one patient, MAP2K1 and NSD1 in another one). Among all primary tumor samples, the most commonly mutated gene was NSD1, affected in 9/31 patients. This gene encoding histone methyl transferase was also downregulated and identified among the 50 most differentially expressed genes in CDDP-resistant NCCIT cell line. Interestingly, 2/31 TGCT patients harbored mutations in the ATRX gene encoding a chromatin modifier that has been shown to have a critical function in sexual differentiation. Our research newly highlights its probable involvement also in testicular tumors. Both findings support the emerging role of altered epigenetic gene regulation in TGCT and CDDP resistance development. This submission includes complete cell lines sequencing data and processed files. The patients data are available from the authors on request.
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| Overall design |
sensitive and resistant TGCT cell lines
Long-term cultured cell lines are long-term cultured cells that have never been exposed to cisplatin and are cisplatin sensitive, they were used as a control to distinguish between changes occuring during long term cultures without any relation to cisplatin exposure and those related to cisplatin exposition and resistance.
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| Contributor(s) |
Boublikova L, Bakardjieva-Mihaylova V, Stuchly J, Svaton M |
| Citation(s) |
31500094 |
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| Submission date |
Aug 28, 2019 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Jan Stuchly |
| Organization name |
Charles University in Prague, 2nd Faculty of Medicne
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| Department |
Department of Paediatric Hematology/Oncology
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| Street address |
V Uvalu 84
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| City |
Prague |
| ZIP/Postal code |
15006 |
| Country |
Czech Republic |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA562689 |
| SRA |
SRP219813 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE136560_NCCIT.call.cns.txt.gz |
96.9 Kb |
(ftp)(http) |
TXT |
| GSE136560_NCCIT_CDDP.call.cns.txt.gz |
96.1 Kb |
(ftp)(http) |
TXT |
| GSE136560_NCCIT_output_report__coding.csv.gz |
6.0 Mb |
(ftp)(http) |
CSV |
| GSE136560_Tera-2.call.cns.txt.gz |
107.6 Kb |
(ftp)(http) |
TXT |
| GSE136560_Tera-2_CDDP.call.cns.txt.gz |
104.6 Kb |
(ftp)(http) |
TXT |
| GSE136560_Tera2_output_report_coding.csv.gz |
6.2 Mb |
(ftp)(http) |
CSV |
| GSE136560_deseq_counts_gene_annot.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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