Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues

Schmitt, Armin O.; Specht, Thomas; Beckmann, Georg; Dahl, Edgar; Pilarsky, Christian; Hinzmann, Bernd; Rosenthal, André

doi:10.1093/nar/27.21.4251

Cited by 120 publications

(82 citation statements)

References 32 publications

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“…By statistical evaluation of the frequency of the sequences for specific genes it is possible to develop an expression profile at different environmental conditions for genes of different cDNA libraries. Thereby it is possible to investigate the up-and down regulation of genes (Schmitt et al, 1999) or to compare the gene expression under different conditions (Rafalski et al, 1998). The establishment of ESTs from E. huxleyi at different stages of viral infection could thus be an effective means for expression analysis of virus infected cultures for which the viral genome is known.…”

Section: Introductionmentioning

confidence: 99%

Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection

Kegel

Allen

Metfies

et al. 2007

Gene

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Blooms of the coccolithophorid Emiliania huxleyi can be infected by viruses, which can lead to bloom-termination. This pilot study used an expressed sequence tag (EST) approach to get a first view of gene-expression changes that occur during viral infection of E. huxleyi. cDNA libraries were constructed from uninfected cultures and 6, 12, and 24 h after infection with E. huxleyi-specific virus 86 (EhV-86). From each library 60-90 ESTs were randomly selected and annotated manually with PhyloGena. Viral genes were identified using BLAST-Search of the known viral genome. The data of this study show, that 6 h after viral infection the algal transcriptome changed significantly although few viral transcripts were present. At this point, changes mainly concerned transcripts related to photosynthesis and protein metabolism. However, after 24 h viral transcripts were most abundant. Viral transcripts found at this stage of viral infection encode proteins involved in protein degradation, nucleic acid degradation, transcription and replication.

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Section: Introductionmentioning

confidence: 99%

Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection

Kegel

Allen

Metfies

et al. 2007

Gene

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“…In all, 40% of primary breast tumors exhibited aberrant methylation of TMS1 (Conway et al, 2000). TMS1 was also identified in an 'in silico' screen for mRNAs that were under-represented in breast cancer cDNA libraries (Schmitt et al, 1999). In a recent large-scale gene expression profiling study, TMS1 was found to be downregulated by at least twofold in 27 of 117 primary breast tumors (van 't Veer et al, 2002).…”

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confidence: 99%

Effects of methylation on expression of TMS1/ASC in human breast cancer cells

2003

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Gene silencing associated with aberrant methylation of promoter region CpG islands is one mechanism in which tumor suppressor genes are inactivated in human cancers. Recently, we identified a novel gene, Target of Methylation-associated Silencing-1 (TMS1) (also called ASC), which is aberrantly methylated and silenced in human breast cancers. To further investigate the mechanism of TMS1 silencing, we defined the transcription initiation site and detailed the DNA methylation pattern of the TMS1 CpG island in normal breast epithelial cells, breast cancer cell lines, and primary tumors. We find that in normal cells, the TMS1 CpG island lies within a 1.2 kb unmethylated domain, the 5 0 boundary of which is in close proximity to the transcription initiation site. In breast cancer cell lines, this boundary appeared to be unstable in that methylation tended to accumulate in the 5 0 end of the CpG island relative to normal epithelial cells. In contrast, the 3 0 methylation boundary remained intact. Gene silencing was not correlated with the methylation of specific CpG sites nor the inability to transactivate the TMS1 promoter, but was correlated with the percentage of alleles in the population exhibiting dense methylation across the entire CpG island. Using 5-aza-deoxycytidine to reactivate TMS1 in methylated and silent cell lines, and a cassette methylation strategy to determine the impact of methylation on different parts of the promoter, we find that demethylation of a small region immediately surrounding the transcription start site is critical to TMS1 expression. Our data support the idea that gene silencing and dense methylation are tightly coupled events that affect individual chromosomal copies of TMS1 in an all-or-none manner. The transition to this stably repressed state may be facilitated by spreading of methylation into the proximal promoter and direct effects of methylation on TMS1 transcription.

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“…With respect to the identification of cancer-associated gene products with potential relevance to cancer vaccine targets, EST database mining has resulted in the discovery of a prostate cancer-related gene, PAGE-1/GAGE-B, 16 a Ewing's sarcoma-associated gene, XAGE-1, 17 and a number of differentially expressed transcripts in breast cancer 18 and glioblastoma multiforme. 19 In order to identify new CT gene products, the current study mined the Unignene database, a compilation of both EST and Genbank databases, for transcripts expressed exclusively in cancer and normal testis.…”

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confidence: 99%

Identification of cancer/testis genes by database mining and mRNA expression analysis

Scanlan

Gordon

Williamson

et al. 2002

Intl Journal of Cancer

120

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Cancer/testis (CT) antigens are immunogenic proteins expressed predominantly in gametogenic tissue and cancer; they are considered promising target molecules for cancer vaccines. The identification of new CT genes is essential to the development of polyvalent cancer vaccines designed to overcome tumor heterogeneity and antigen loss. In the current study, a search for new CT genes was conducted by mining the Unigene database for gene clusters that contain expressed sequence tags derived solely from both normal testis and tumor-derived cDNA libraries. This search identified 1,325 different cancer/testis-associated Unigene clusters. The mRNA expression pattern of 73 cancer/testis-associated Unigene clusters was assessed by reverse transcriptase polymerase chain reaction. Three gene products, CT15/ Hs.177959, CT16/Hs.245431 and CT17/Hs.178062, were detected only in testis and in tumor tissue. CT15 is equivalent to ADAM2/fertilin-␤. CT16, an uncharacterized gene product, has homology (30 -50%) to members of the GAGE gene family and is 89% identical to CT16.2/Hs.293317, indicating that CT16 and CT16.2 are members of a new GAGE gene family. The uncharacterized gene product, CT17, has homology (30%) to phospholipase A1. RT-PCR analysis showed that CT15 is expressed exclusively in renal cancer, whereas CT16 and CT17 are expressed in a range of human cancers. Realtime RT-PCR analysis of newly defined CT genes and the prototype CT antigens, MAGE-3 and NY-ESO-1, revealed low levels (less than 3% of the level detected in testis) of CT15, CT16 and NY-ESO-1 in a limited range of normal, non-gametogenic tissues. This study demonstrates the merits of database mining with respect to the identification of tissue-restricted gene products expressed in cancer.

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Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues

Cited by 120 publications

References 32 publications

Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection

Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection

Effects of methylation on expression of TMS1/ASC in human breast cancer cells

Identification of cancer/testis genes by database mining and mRNA expression analysis

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