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| Status |
Public on Dec 10, 2014 |
| Title |
Affymetrix SNP array data for lung cancer samples |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
Lung cancer is the leading cause of death from malignant diseases worldwide, with the non-small cell (NSCLC) subtype accounting for the majority of cases. NSCLC is characterized by frequent genomic imbalances and copy number variations (CNVs), but the epigenetic aberrations that are associated with clinical prognosis and therapeutic failure remain not completely identify. In the present study, a total of 55 lung cancer patients were included and we conducted genomic and genetic expression analyses, immunohistochemical protein detection, DNA methylation and chromatin immunoprecipitation assays to obtain genetic and epigenetic profiles associated to prognosis and chemoresponse of NSCLC patients. Finally, siRNA transfection-mediated genetic silencing and cisplatinum cellular cytotoxicity assays in NSCLC cell lines A-427 and INER-37 were assesed to described chemoresistance mechanisms involved. Our results identified high frequencies of CNVs (60% of cases) in the 7p22.3-p21.1 and 7p15.3-p15.2 cytogenetic regions. However, overexpression of genes, such as MEOX2, HDAC9, TWIST1 and AhR, at 7p21.2-p21.1 locus occurred despite the absence of CNVs and little changes in DNA methylation. In contrast, the promoter sequences of MEOX2 and TWIST1 displayed significantly lower/decrease in the repressive histone mark H3K27me3 and increased in the active histone mark H3K4me3 levels. Finally these results correlate with poor survival in NSCLC patients and cellular chemoresistance to oncologic drugs in NSCLC cell lines in a MEOX2 and TWIST1 overexpression dependent-manner. In conclusion, we report for the first time that MEOX2 participates in chemoresistance irrespective of high CNV, but it is significantly dependent upon H3K27me3 enrichment probably associated with aggressiveness and chemotherapy failure in NSCLC patients, however additional clinical studies must be performed to confirm our findings as new probable clinical markers in NSCLC patients.
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| Overall design |
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen, and paraffin embedded lung tumor samples
Copy number analysis of Affymetrix 500K SNP arrays was performed for 33 lung tumor samples, including lung precursor metaplasia, lung tumors and cell lines. Six samples were also hybridized on the Affymetrix SNP 6.0 array
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| Contributor(s) |
Avila-Moreno F, Hidalgo-Miranda A, Zuniga-Ramos J |
| Citation(s) |
25460568 |
| Submission date |
Oct 16, 2014 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Alfredo Hidalgo-Miranda |
| E-mail(s) |
ahidalgo@inmegen.gob.mx
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| Phone |
+52-55-53501966
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| Organization name |
National Institute of Genomic Medicine
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| Street address |
Periferico Sur 4124, Torre Zafiro II, piso 6
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| City |
Mexico City |
| ZIP/Postal code |
01900 |
| Country |
Mexico |
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| Platforms (3) |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL3720 |
[Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (66)
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| GSM1526610 |
Lung precursor metaplasia, nsp [1032-05-1-3] |
| GSM1526611 |
Lung precursor metaplasia, sty [1032-05-1-4] |
| GSM1526612 |
Lung Epithelium without cellular atypias, and metaplasia, nsp [1278-05-23] |
| GSM1526613 |
Lung Epithelium without cellular atypias, and metaplasia, sty [1278-05-24] |
| GSM1526614 |
NSCLC SCC-MD, tumor nsp [1352-06-13] |
| GSM1526615 |
NSCLC SCC-MD, tumor sty [1352-06-14] |
| GSM1526616 |
NSCLC SCC-PD, tumor nsp [1479-06-13] |
| GSM1526617 |
NSCLC SCC-PD, tumor sty [1479-06-14] |
| GSM1526618 |
NSCLC SCC-MD (IV), tumor nsp [1551-063] |
| GSM1526619 |
NSCLC SCC-MD (IV), tumor sty [1551-064] |
| GSM1526620 |
Lung precursor Metaplasia, nsp [293-06-3] |
| GSM1526621 |
Lung precursor Metaplasia, sty [293-06-4] |
| GSM1526622 |
NSCLC SCC-PD, nsp [708-06-103] |
| GSM1526623 |
NSCLC SCC-PD, sty [708-06-104] |
| GSM1526624 |
Lung precursor metaplasia-displasia, nsp [834-06-2-3] |
| GSM1526625 |
Lung precursor metaplasia-displasia, sty [834-06-2-4] |
| GSM1526626 |
NSCLC SCC-BD, nsp [897-06-23] |
| GSM1526627 |
NSCLC SCC-BD, sty [897-06-24] |
| GSM1526628 |
A427 lung adenocarcinoma cell line, nsp [A427_3] |
| GSM1526629 |
A427 lung adenocarcinoma cell line, sty [A427_4] |
| GSM1526630 |
SCLC, nsp [GOA290508_N_3] |
| GSM1526631 |
SCLC, sty [GOA290508_N_4] |
| GSM1526632 |
SCLC, nsp [GOA290508_T_3] |
| GSM1526633 |
SCLC, sty [GOA290508_T_4] |
| GSM1526634 |
NSCLC, nsp [INER_13] |
| GSM1526635 |
NSCLC, sty [INER_14] |
| GSM1526636 |
AD, nsp [INER_223] |
| GSM1526637 |
AD, sty [INER_224] |
| GSM1526638 |
AD-PD, nsp [INER_253] |
| GSM1526639 |
AD-PD, sty [INER_254] |
| GSM1526640 |
NSCLC, nsp [INER_33] |
| GSM1526641 |
NSCLC, sty [INER_34] |
| GSM1526642 |
SCLC, nsp [INER_53] |
| GSM1526643 |
SCLC, sty [INER_54] |
| GSM1526644 |
AD-MD, nsp [INER_73] |
| GSM1526645 |
AD-MD, sty [INER_74] |
| GSM1526646 |
SCLC, nsp [INER_83] |
| GSM1526647 |
SCLC, sty [INER_84] |
| GSM1526648 |
NSCLC AD (Mexican Mestizo) cell line, nsp [INER-37_3] |
| GSM1526649 |
NSCLC AD (Mexican Mestizo) cell line, sty [INER-37_4] |
| GSM1526650 |
NSCLC, nsp [NRJ270508_N1_3] |
| GSM1526651 |
NSCLC, sty [NRJ270508_N1_4] |
| GSM1526652 |
NSCLC, nsp [NRJ270508_T1_3] |
| GSM1526653 |
NSCLC, sty [NRJ270508_T1_4] |
| GSM1526654 |
SCLC, nsp [OTB0702083] |
| GSM1526655 |
SCLC, sty [OTB0702084] |
| GSM1526656 |
SCLC, nsp [OTB070208N_3] |
| GSM1526657 |
SCLC, sty [OTB070208N_4] |
| GSM1526658 |
SCLC nsp [Q045-07-A3] |
| GSM1526659 |
SCLC, sty [Q045-07-A4] |
| GSM1526660 |
SCC, sty [Q1235-06-23] |
| GSM1526661 |
SCC, nsp [Q1235-06-A4] |
| GSM1526662 |
AD-PD, nsp [Q1488-06-23_2] |
| GSM1526663 |
AD-PD, sty [Q1488-06-24] |
| GSM1526664 |
SCLC, nsp [Q177-083] |
| GSM1526665 |
SCLC, sty [Q177-084] |
| GSM1526666 |
NSCLC, nsp [Q4-07-13] |
| GSM1526667 |
NSCLC, sty [Q4-07-14] |
| GSM1526668 |
NSCLC cell line SK-1 nsp [SK-13] |
| GSM1526669 |
NSCLC cell line SK-1 sty [SK-14] |
| GSM1526670 |
SKMES-1 [SK-1-6] |
| GSM1526671 |
NSCLC [1479-06-6] |
| GSM1526672 |
NSCLC [897-06-6] |
| GSM1526673 |
NSCLC [1551-06-6] |
| GSM1526674 |
Lung Precursor Metaplasia [834-06-6] |
| GSM1526675 |
Lung Epithelium without Cellular Atypias, and metaplasia [1278-05-6] |
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| Relations |
| BioProject |
PRJNA266490 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62407_CN_matrix_FFPE.txt.gz |
14.3 Mb |
(ftp)(http) |
TXT |
| GSE62407_CN_matrix_Fresh_Frozen.txt.gz |
26.3 Mb |
(ftp)(http) |
TXT |
| GSE62407_RAW.tar |
2.0 Gb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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