Article Review on "Genome-Wide Gene Expression Analysis"

Article Review 5 pages (1396 words) Sources: 3

[EXCERPT] . . . .

Both the Z-score and the number of genes affected by culture conditions per gene class are presented. There are shortcomings as well. Figure 5c is missing error bars and is therefore unconvincing in terms of significance and Figure 3 seems redundant when compared to the information provided by Table 2.

Results

The results section contains three subsections that are clearly identified with headings. The first section outlines the experiments that were used to validate the model system before conducting subsequent experiments. The next section presents the micro-array experiments and the statistical calculations performed. The relative numbers of upregulated and downregulated genes are given for each condition and each tumor line. The last section describes the array data validation experiments using semi-quantitative RT-PCR and Western blotting.

The organization of the results section is also intuitive, moving from experiments that characterize the model, to a comprehensive genome-wide approach to finding genes that may mediate radio- and chemo-resistance, to validation of a select few gene candidates using semi-quantitative RT-PCR and Western blotting.

While the use of Western blotting here is appropriate, the use of semiquantitative RT-PCR seems antiquated. Many laboratories today are using real-time RT-PCR, which avoids the possibility of signal quenching caused by analyzing ethidium-stained bands in an agarose gel (Choquer, Boccara, and Vidal-Cros, 2003). The other disadvantage of the RT-PCR approach used by these authors is that the PCR reactions may have progressed beyond the exponential amplification phase and plateaued, thereby reducing the validity of between sample comparisons. There was no mention of terminating the PCR reactions within the exponential phase of amplification in the methods section, therefore the RT-PCR data may not be reliable.

Discussion

The discussion section is well-written and takes pains to reference the relevant work of others. The authors also discussed how their findings aligned with the work of others, and in what way they did not. For example, gene expression patterns have been shown in the past to vary significantly between cells grown in 2D and 3D cultures. In addition, researchers had noted previously that tumor cells are more resistant to cancer treatment modalities when grown in 3d, compared to cells grown in a monolayer. The findings presented in the current article confirm these findings. What is novel about the findings in the current article is that the gene classes found to be differentially regulated in 3D cultures differ substantially those found to be relevant to cells grown in monolayer. In the current study, cells grown in 3D differentially regulate genes involved in extracellular matrix interactions and biological processes, while genes involved in DNA repair were more active in cells grown in 2D. Proposed future experiments will attempt to determine how the different gene classes may be involved in radio- and chemo-resistance, and whether the transcriptome or proteome is differentially responsible for tumorigenesis.

References

All in-text citations match the reference list and vice versa. There were 44 references cited. Of these, 10 were review papers and one was an edited book. All articles, except the book, were published in peer-reviewed journals. Close to 57% of the references were published in 2007 or more recently. The older publications were clustered into three groups, with the first cluster appearing at the beginning of the introduction and the next two clusters providing supporting information in the methods section. The clustering of older published works would be expected at these points in the manuscript. This analysis also suggests the current research findings are contemporary and at the cutting-edge of research efforts in this field.

The acknowledgements are consistent with the norm. Researchers often acknowledge the gift of reagents, cell lines, and animal models that are difficult, time-consuming, and/or too expensive to reproduce. While some principal investigators will include technical personnel in the authors section, this is not always the case and may depend on the magnitude of the contribution.

References

Choquer, M., Boccara, M., and Vidal-Cros, A. (2003). A semi-quantitative RT-PCR method to readily compare expression levels within Botrytis cinerea multigenic families in vitro and in planta. Curr Genet 43: 303-309.

Zschenker, O., Streichert, T., Hehlgans, S., and Cordes, N. (2012). Genome-wide gene expression analysis in cancer cells reveals 3D growth to affect ECM and processes associated… READ MORE

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