functionality and bioactivity of food compounds: topic
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expression profiling
Poltronieri Palmiro
Monday, 07 July 2008 08:47 UTC
GenXpro is a German company based in the Frankfurt Innovation Zentrum. It is leaded by Peter Winter and Prof. Gunter Kahl, two scientists that developed SuperSAGE. On friday 4th of july, Dr. Winter held a seminar in Lecce on SuperSAGE and SuperTAG arrays, two methods the company applies for whole expression profiling, combined to 454 sequencing. The advantage of this method is that it does not require experimental replicates to be performed, no dye swaps and other DNA arrays constrains as no signals from low abundant transcripts.
Although at the moment it can look as an expensive method, considering that 7-8 replicates in DNA arrays technology cost up to 4000 euro, and provide information on 20% of the transcriptome, superSAGE is a convenient technology. Most importantly, GenXpro in two years will bring on the market new diagnostic kits, not only for profiling of polyA- mRNAs, but also for riboregulators, and for epigenetic profiling.
This is good news for the whole scientific community, and a revolution in the genomic studies field.
This SuperTAG will be applied by GenXpro in the screening of the effects of compounds on chicken embryos, an important tool in toxicology studies.
Are you using expression profiling for testing the effects of bioactives on cell cultures or in animal models?
Share with this newsgroup your experiments, your opinion on the efficience of current methods, and your comments on the technologies available today.
Recently GSK and NCI have posted the results of expression profiling of 200 cancer cell lines on caArray, an open-source, web and programmatically accessible array data management system.
This system was based on Affy chips, so that is is mainly based on protein coding genes, and does not contain antisense transcripts.
Other type of experiments with bioactives are designed using primary cell cultures (also not tumoral), keratinocytes, stem cells, since cancer cell lines often contain amplifications and chromosome rearrangements.
In addition, Laser Capture Microdissection
can help in isolating specific types of cells, tissues and concentrate the study on a homogenous group of cells.
Post your contribution to this topic, and we will be happy to discuss it!
Updated 07 July 2008 09:14 UTC
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Replies
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Recentyl two new papers offer a methodology that can be considered competing with the GenXpro SuperSAGE-DNA microarray expression profiling.
In the first paper, Piero Carninci- based method of Cap analysis of gene expression is improved. It costitutes a pooled CAP tag system, which enables to measure the dynamic changes in gene expression (Maeda N et al, Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra-highthroughput sequencer, Biotechniques 2008, 45, july 95-97.
In the second paper, Nature Biotechnol 26, march 2008, GK Geiss at el. at Nanostring Technologies Inc., show how direct multiplexed measurements of gene expression can be achieved with color coded probe pairs. This last method is simple, does not rely on DNA sequencing, but has constrains since it cannot find any new transcript (transfrag or splice variant). It needs preliminary knowledge on a series of mRNAs, on which they design two sets of probes. The GenXpro and the Riken systems instead can discover new transcripts and slice variants, by deepening the analysis of the cDNA pool, however they rely on various enzymatic steps and correct addition of tags.
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