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Series GSE6567 Query DataSets for GSE6567
Status Public on May 07, 2007
Title Chromosome 8 BAC Array CGH and Expression Studies Identify Amplification and Overexpression of TRMT12 in Breast Cancer
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by genome tiling array
Summary Genomic changes in chromosome 8 are commonly observed in breast cancer cell lines and tumors. Fine mapping of such genomic changes, and evaluation of associated expression changes, are expected to provide reagents for diagnosis, insights into understanding the disease, and open up avenues for novel therapeutic intervention. We made an effort to search for genes on chromosome 8 with altered copy number and expression. A high resolution (0.1Mb) bacterial artificial chromosome (BAC) array of chromosome 8 that can detect single copy changes was developed using Phi29 DNA polymerase amplified BAC DNA. Hybridization of DNA from a breast cancer cell line (SKBR3) with two known amplified regions (8q21 and 8q24) resulted in resolving this region into 6 distinct amplicons, in addition identified 3 deleted regions. The boundaries and the peak of each region were verified by FISH, and the extent of amplification/deletion for each region was validated by qPCR. Using these BAC arrays, CGH was performed with a total of eight breast cancer cell lines, and common regions of genomic amplification/deletion were identified by segmentation analysis. Two consensus regions in 8q24 included a 1.2 Mb region (125.3-126.5 Mb) and a 1.0 Mb region (128.1-129.1 Mb) that were amplified in 7/8 cell lines, and in the 8q21 region there was a smaller 0.88 Mb region (86.62-87.50 Mb) amplified in 4/8 cell lines. A global expression analysis was performed for all these cell lines using a high-density oligonucleotide array to identify the genes whose expression correlated with amplification/deletion. Representative genes from 5 commonly amplified regions (REXO1L1, TMEM55A, TRMT12, MTSS1, EIF2C2, MYC) and 2 deleted regions (DPYSL2, NRG1 and NDRG1) were verified by qPCR and RT-qPCR for genomic and expression changes. Validation by RT-qPCR using RNA from 30 breast tumors showed that the TRMT12 (125.5 Mb) gene were overexpressed in many of the tumors. TRMT12 is homolog of a yeast gene encoding tRNA methyltransferase involved in biosythesis of a modified base in a tRNA. It would be interesting to explore the role of TRMT12 and the RNA processing pathway in tumorigenesis.
Keywords: Comparative Genomic Hybridization (CGH), Breast cancer cell lines, Expression, BAC array, Oligo expression array
Overall design A high-density BAC arrays for chromosome 8 was generated by printing on glass slides BAC DNAs amplified using Phi29 DNA polymerases. These arrays were used to evaluate copy number changes in chromosome 8 for 8 breast cancer cell lines. Segmentation analysis identified common regions of copy number gain/loss. RNA from these 8 cell lines was analyzed for global expression changes using an oligonucleotide (HEEBO) expression array. The consistent expression changes in genes for chromosome were identified, and a fraction of these genes validated by RT-qPCR. Overexpression in tumor RNA was validated for two genes that showed genomic amplification.
Contributor(s) Rodriguez VW, Chen Y, Elkahloun AG, Chandrasekharappa SC
Citation(s) 17440925
Submission date Dec 19, 2006
Last update date Jan 18, 2013
Contact name Christopher Pan
Organization name NIH
Department NHGRI
Street address Rm 5228, Bldg 50, South Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL4611 Illumina Human 49K Oligo array (HEEBO-7 set)
GPL4615 Chr8 BACs 5.7K DNA array
Samples (42)
GSM149960 NHGRI_T47D_HB7-16
GSM149961 NHGRI_BT474_HB7-17
GSM149962 NHGRI_MDA435_HB7-18
BioProject PRJNA98741

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
GSE6567_RAW.tar 77.3 Mb (http)(custom) TAR (of TXT)

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