Identification of unique and common low abundance tumour-specific transcripts by suppression subtractive hybridization and oligonucleotide probe array analysis

Most human cancers are characterized by genetic aberrations accompanied by altered expression and function of numerous genes. Applying genome-wide, microarray gene expression analysis to identify deregulated genes in different tumour types can provide potential gene candidates as diagnostic and prog...

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Vydané v:	Oncogene Ročník 27; číslo 29; s. 4128 - 4136
Hlavní autori:	Liu, B H, Goh, C H K, Ooi, L L P J, Hui, K M
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London Nature Publishing Group UK 03.07.2008 Nature Publishing Nature Publishing Group
Predmet:	Abundance Antisense RNA Antisense therapy Apoptosis Biological and medical sciences Biopsy Breast cancer Breast carcinoma Cancer Care and treatment Cell Biology Cell physiology Cell transformation and carcinogenesis. Action of oncogenes and antioncogenes Deoxyribonucleic acid DNA DNA microarrays DNA Probes - genetics DNA, Complementary DNA, Neoplasm - genetics DNA, Neoplasm - metabolism Drug development Fundamental and applied biological sciences. Psychology Gastroenterology. Liver. Pancreas. Abdomen Gene expression Gene Expression Profiling - methods Genes, Neoplasm Genetic aspects Genomics Genomics - methods Gynecology. Andrology. Obstetrics Hepatocellular carcinoma Human Genetics Humans Hybridization Internal Medicine Liver cancer Liver. Biliary tract. Portal circulation. Exocrine pancreas Mammary gland diseases Medical diagnosis Medical sciences Medicine Medicine & Public Health Methods Molecular and cellular biology Nasopharyngeal carcinoma Neoplasms - genetics Neoplasms - metabolism Neoplasms - pathology Nucleic acid hybridization Oligonucleotide Array Sequence Analysis - methods Oligonucleotides oncogenomics Oncology Research methodology Ribonucleic acid Risk factors RNA RNA, Neoplasm - biosynthesis RNA, Neoplasm - genetics Throat cancer Transcription, Genetic Tumors Singapore breast cancer affymetrix GeneChip arrays nasopharyngeal carcinoma suppression subtractive hybridization hepatocellular carcinoma low abundance transcripts Breast disease Suppression Hepatic disease Hepatocellular carcinoma Breast cancer Identification Malignant tumor Nasopharynx carcinoma Gene expression Carcinogenesis Mammary gland diseases ENT disease Digestive diseases Pharynx disease Oligonucleotide Cancer
ISSN:	0950-9232, 1476-5594, 1476-5594
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Popis
Shrnutí:	Most human cancers are characterized by genetic aberrations accompanied by altered expression and function of numerous genes. Applying genome-wide, microarray gene expression analysis to identify deregulated genes in different tumour types can provide potential gene candidates as diagnostic and prognostic tools and promising targets for drug development. However, the detection of deregulated genes with low levels of expression remains a major challenge. In this study, we have designed a strategy, termed modified suppression subtractive hybridization (mSSH), to identify genes encoding rare transcripts. The strategy entails incorporating the T 7 -promoter sequence at the 5′ end of the noncoding cDNA strand during first strand cDNA synthesis to generate unidirectional antisense RNA from the resultant cDNA following conventional SSH. These transcripts are subsequently analysed by Affymetrix oligonucleotide gene arrays. Here, we have used five hepatocellular carcinoma (HCC), five breast carcinoma and four nasopharyngeal carcinoma (NPC) biopsies separately as testers and their corresponding normal biopsies as drivers to enrich for low abundance tumour type-specific transcripts. The total detectable number of probe sets following mSSH was reduced almost 10-fold in comparison to those detected for the same resected tumour tissues without undergoing subtraction, thus yielding a subtraction efficacy of over 90%. Using this experimental approach, we have identified 48 HCC-specific, 45 breast carcinoma-specific, and 83 NPC-specific genes. In addition, 115 genes were upregulated in all the three cancer types. When compared to gene-profiling data obtained without mSSH, the majority of these identified transcripts were of low abundance in the original cancer tissues. mSSH can therefore serve as a comprehensive molecular strategy for pursuing functional genomic studies of human cancers.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	0950-9232 1476-5594 1476-5594
DOI:	10.1038/onc.2008.50