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Series GSE12280 Query DataSets for GSE12280
Status Public on Oct 01, 2008
Title Specific genomic aberrations in squamous cell lung carcinoma with lymph node or distant metastasis
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary The majority of patients with squamous cell lung cancer (SCC) die because of metastatic disease. The genomic mechanisms underlying this metastatic behaviour are underexposed. We analyzed a cohort of patients with primary squamous cell carcinoma (SCC) using array-based comparative genomic hybridization (aCGH) to identify which genomic aberrations were related metastatic behaviour. The cohort consisted of 34 patients with a follow-up of at least 5 years, including 15 without any metastases, 8 with metastases in regional lymph nodes only, and 11 with metastases exclusively in distant organs within two years after surgery. Common alterations observed in at least 40% of all SCC were gains at 3q13-q29, 5p11-p15, 8q24, 19q13, 20p12-p13, 22q11-q13, and losses at 3p12-p14, 3p24, 4p15, 4q33-q35, 5q14-q23, 5q31-q35, 8p21-p22, 9p21-p24. Amplifications were observed at 2p15-p16, 3q24-q29, 8p11-p12, 8q23-q24, and 12p12, containing candidate oncogenes such as BCL11A, REL, ECT2, PIK3CA, ADAM9, MYC, and KRAS. Gains at 7q36, 8p12, 10q22, 12p12, loss at 4p14 and homozygous deletions at 4q33-q34.1 occurred significantly more frequent in SCC from patients with lymph node metastases. SCC from patients with distant metastases showed a significantly higher frequency of gain at 8q22-q24 and loss of 8p23 and 13q21, and a significantly lower frequency of gain at 2p12 and 2p16 and loss at 11q25 as compared to SCC from patients without metastases. In conclusion, we identified specific genomic aberrations in primary SCC that are related to lymph node or distant metastases. These loci can be further explored for their potential use as predictive or prognostic markers.
 
Overall design PATIENTS AND TISSUE SPECIMENS
We selected a total of 34 patients who presented with centrally located primary squamous cell lung carcinoma (SCC), including 15 patients without lymph node or distant organ metastases within 5 years after surgery; 8 patients with lymph node metastases at the time of surgery, but no distant metastases within 5 years after surgery; 11 patients presenting with distant metastases within 2 years after surgery (median 10 months, range 2-19) but without lymph node metastases. One patient of the ‘no metastases’ group died 3 years after surgery, not of disease. In one patient of the distant metastases group, metastasis presented at 28 months. Patients with both lymph node and distant metastases, and patients who were treated with chemotherapy before or directly after surgery were excluded.

LASER DISSECTION MICROSCOPY
For two SCC samples containing >90% tumour cells in the tissue section (samples T02 and T28), genomic DNA was isolated from the total tissue, in all other cases laser microdissection microscopy (LDM) was performed to obtain pure cell populations. Only vital tumour cells without apparent admixture of inflammatory cells through the tumour fields were selected for LDM. An area of approximately 25x106 μm2 was microdissected from 8μm sections by P.A.L.M. Microlaser Technology system (P.A.L.M., Bernried, Germany). Microdissected cells were immediately collected in SE buffer (75mM NaCl, 0.1mM EDTA) for DNA isolation.

DNA ISOLATION
Genomic DNA was isolated and purified using a standard salt-chloroform extraction protocol. The DNA concentration was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). For each sample, 100 ng genomic DNA was amplified using the BioScore kit (Enzo Life Sciences, Farmingdale, NY). Only SCC cases for which a high yield of amplified DNA was obtained in the amplification reaction were used for aCGH experiments.

ARRAY-BASED CGH (ACGH)
We started with a number of test hybridizations to determine if aCGH profiles of amplified DNA were comparable to those of non-amplified total DNA. We observed consistent profiles for amplified and non-amplified DNA indicating that amplification does not affect the aCGH results (data not shown).
An amount of 600 ng of (amplified) genomic DNA was labeled with Cy3-dUTP (Perkin Elmer, Langen, Germany) using the BioPrima DNA labeling System (Invitrogen Inc., Carlsbad, CA)11. Samples were inversely sex-matched with a normal reference DNA (labeled with Cy5-dUTP) as an internal control for gain or loss at the X chromosome. Hybridizations were included for further analysis only if the calculated ratio for the X-chromosomal BACs were as expected. The design and construction of the BAC-microarray, containing 6465 BACs, has been previously described. The array slides were processed according to the manufacturer’s instructions and as described previously. Arrays were scanned using an Agilent scanner (Agilent, Santa Clara, CA).
 
Contributor(s) Boelens MC, Kok K, van der Vlies P, van der Vries G, Sietsma H, Timens W, Postma DS, Groen HJ, van den Berg A
Citation(s) 19324446, 20832896
Submission date Jul 29, 2008
Last update date Mar 20, 2012
Contact name Mirjam Boelens
Organization name UMCG
Street address Hanzeplein 1
City Groningen
ZIP/Postal code 9713 GZ
Country Netherlands
 
Platforms (1)
GPL7096 UMCG_6.5KBAC_ARRAY
Samples (34)
GSM307984 T01(aCGH)
GSM307995 T02(aCGH)
GSM308016 T03(aCGH)
Relations
BioProject PRJNA113669

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12280_RAW.tar 31.5 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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