scholarly journals Frequent copy number gains of SLC2A3 and ETV1 in testicular embryonal carcinomas

2020 ◽  
Vol 27 (9) ◽  
pp. 457-468
Author(s):  
Andreas M Hoff ◽  
Sigrid M Kraggerud ◽  
Sharmini Alagaratnam ◽  
Kaja C G Berg ◽  
Bjarne Johannessen ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Target Genes ◽  
Copy Number Gain ◽  
The Cancer Genome Atlas ◽  
Dna Copy Number ◽  
Testicular Germ Cell ◽  
Testicular Germ Cell Tumours ◽  
Candidate Target ◽  
Copy Number Changes

Testicular germ cell tumours (TGCTs) appear as different histological subtypes or mixtures of these. They show similar, multiple DNA copy number changes, where gain of 12p is pathognomonic. However, few high-resolution analyses have been performed and focal DNA copy number changes with corresponding candidate target genes remain poorly described for individual subtypes. We present the first high-resolution DNA copy number aberration (CNA) analysis on the subtype embryonal carcinomas (ECs), including 13 primary ECs and 5 EC cell lines. We identified recurrent gains and losses and allele-specific CNAs. Within these regions, we nominate 30 genes that may be of interest to the EC subtype. By in silico analysis of data from 150 TGCTs from The Cancer Genome Atlas (TCGA), we further investigated CNAs, RNA expression, somatic mutations and fusion transcripts of these genes. Among primary ECs, ploidy ranged between 2.3 and 5.0, and the most common aberrations were DNA copy number gains at chromosome (arm) 7, 8, 12p, and 17, losses at 4, 10, 11, and 18, replicating known TGCT genome characteristics. Gain of whole or parts of 12p was found in all samples, including a highly amplified 100 kbp segment at 12p13.31, containing SLC2A3. Gain at 7p21, encompassing ETV1, was the second most frequent aberration. In conclusion, we present novel CNAs and the genes located within these regions, where the copy number gain of SLC2A3 and ETV1 are of interest, and which copy number levels also correlate with expression in TGCTs.

High-resolution array CGH of metanephric adenomas: lack of DNA copy number changes

2010 ◽  
Vol 56 (2) ◽  
pp. 212-216 ◽  
Author(s):  
Adrianna Szponar ◽  
Maria V Yusenko ◽  
Gyula Kovacs
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Array Cgh ◽  
Dna Copy Number ◽  
Copy Number Changes

P34: Analysing DNA copy number changes in lung carcinomas and adjacent bronchial epithelium by means of high-resolution array CGH

2005 ◽  
Vol 48 (4) ◽  
pp. 500-501
Author(s):  
Artur Muradyan ◽  
Helmut Popper ◽  
Iris Halbwedl ◽  
Wei Chen ◽  
Claus Hultschig ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Array Cgh ◽  
Bronchial Epithelium ◽  
Dna Copy Number ◽  
Lung Carcinomas ◽  
Copy Number Changes

scholarly journals LINC00467 Is Upregulated by DNA Copy Number Amplification and Hypomethylation and Shows ceRNA Potential in Lung Adenocarcinoma

2022 ◽  
Vol 12 ◽  
Author(s):  
Wen Wang ◽  
Hao Bo ◽  
Yumei Liang ◽  
Guoli Li
Keyword(s):  
Lung Adenocarcinoma ◽  
Copy Number ◽  
Target Genes ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Dna Copy Number ◽  
Cerna Network ◽  
Cancer Genome Atlas ◽  
Copy Number Amplification ◽  
Genome Atlas

Lung adenocarcinoma (LUAD) is the most common histological lung cancer, and it is the leading cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis. LINC00467 is a novel lncRNA that is abnormally expressed in several cancer types including LUAD. However, its function and regulatory mechanism in LUAD progression remain unclear. In this study, based on The Cancer Genome Atlas data mining, we demonstrated that DNA copy number amplification and hypomethylation was positively correlated with LINC00467 expression in LUAD. In addition, DNA copy number amplification was significantly associated with distant metastasis, immune infiltration and poor survival. Microarray analysis demonstrated that LINC00467 knockdown in the LUAD A549 cell line led to a distinct microRNA expression profile that impacted various target genes involved in multiple biological processes. This finding suggests that LINC00467 may regulate LUAD progression by functioning as a competing endogenous RNA (ceRNA). Finally, we constructed a ceRNA network that included two microRNAs (hsa-miR-1225-5p, hsa-miR-575) and five mRNAs (BARX2, BCL9, KCNK1, KIAA1324, TMEM182) specific to LINC00467 in LUAD. Subsequent Kaplan-Meier survival analysis in both The Cancer Genome Atlas and Gene Expression Omnibus databases revealed that two genes, BARX2 and BCL9, were potential prognostic biomarkers for LUAD patients. In conclusion, our data provide possible mechanisms underlying the abnormal upregulation of LINC00467 as well as a comprehensive view of the LINC00467-mediated ceRNA network in LUAD, thereby highlighting its potential role in diagnosis and therapy.

scholarly journals Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation

2021 ◽  
Vol 22 (3) ◽  
pp. 1146
Author(s):  
Reinhard Ullmann ◽  
Benjamin Valentin Becker ◽  
Simone Rothmiller ◽  
Annette Schmidt ◽  
Horst Thiermann ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Cell Line ◽  
Copy Number ◽  
Resistant Cell ◽  
Resistant Cell Line ◽  
Chromosomal Translocations ◽  
Dna Copy Number ◽  
Mutational Signatures ◽  
Copy Number Changes ◽  
And Oxidative Stress

Sulfur mustard (SM) is a chemical warfare agent that can damage DNA via alkylation and oxidative stress. Because of its genotoxicity, SM is cancerogenic and the progenitor of many chemotherapeutics. Previously, we developed an SM-resistant cell line via chronic exposure of the popular keratinocyte cell line HaCaT to increasing doses of SM over a period of 40 months. In this study, we compared the genomic landscape of the SM-resistant cell line HaCaT/SM to its sensitive parental line HaCaT in order to gain insights into genetic changes associated with continuous alkylation and oxidative stress. We established chromosome numbers by cytogenetics, analyzed DNA copy number changes by means of array Comparative Genomic Hybridization (array CGH), employed the genome-wide chromosome conformation capture technique Hi-C to detect chromosomal translocations, and derived mutational signatures by whole-genome sequencing. We observed that chronic SM exposure eliminated the initially prevailing hypotetraploid cell population in favor of a hyperdiploid one, which contrasts with previous observations that link polyploidization to increased tolerance and adaptability toward genotoxic stress. Furthermore, we observed an accumulation of chromosomal translocations, frequently flanked by DNA copy number changes, which indicates a high rate of DNA double-strand breaks and their misrepair. HaCaT/SM-specific single-nucleotide variants showed enrichment of C > A and T > A transversions and a lower rate of deaminated cytosines in the CpG dinucleotide context. Given the frequent use of HaCaT in toxicology, this study provides a valuable data source with respect to the original genotype of HaCaT and the mutational signatures associated with chronic alkylation and oxidative stress.

scholarly journals Recurring DNA copy number gain at chromosome 9p13 plays a role in the activation of multiple candidate oncogenes in progressing oral premalignant lesions

2014 ◽  
Vol 3 (5) ◽  
pp. 1170-1184 ◽  
Author(s):  
Rebecca Towle ◽  
Ivy F. L. Tsui ◽  
Yuqi Zhu ◽  
Sara MacLellan ◽  
Catherine F. Poh ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Gain ◽  
Premalignant Lesions ◽  
Dna Copy Number

Genome-Wide High-Resolution Screening in Dupuytren's Disease Reveals Common Regions of DNA Copy Number Alterations

2010 ◽  
Vol 35 (7) ◽  
pp. 1172-1183.e7 ◽  
Author(s):  
Barbara B. Shih ◽  
May Tassabehji ◽  
James S. Watson ◽  
Angus D. McGrouther ◽  
Ardeshir Bayat
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Dupuytren’S Disease ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Dupuytren's Disease ◽  
Genome Wide ◽  
Dna Copy Number Alterations
Sign in / Sign up

Export Citation Format

Share Document