Comparative analysis of a 3' end tag PCR and a linear RNA amplification approach for microarray analysis

LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue

Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.

Amplification biases: possible differences among deviating gene expressions

Background

Gene expression profiling has become a tool of choice to study pathological or developmental questions but in most cases the material is scarce and requires sample amplification. Two main procedures have been used: in vitro transcription (IVT) and polymerase chain reaction (PCR), the former known as linear and the latter as exponential. Previous reports identified enzymatic pitfalls in PCR and IVT protocols; however the possible differences between the sequences affected by these amplification defaults were only rarely explored.

Results

Screening a bovine cDNA array dedicated to embryonic stages with embryonic (n = 3) and somatic tissues (n = 2), we proceeded to moderate amplifications starting from 1 μg of total RNA (global PCR or IVT one round). Whatever the tissue, 16% of the probes were involved in deviating gene expressions due to amplification defaults. These distortions were likely due to the molecular features of the affected sequences (position within a gene, GC content, hairpin number) but also to the relative abundance of these transcripts within the tissues. These deviating genes mainly encoded housekeeping genes from physiological or cellular processes (70%) and constituted 2 subsets which did not overlap (molecular features, signal intensities, gene ID). However, the differential expressions identified between embryonic stages were both reliable (minor intersect with biased expressions) and relevant (biologically validated). In addition, the relative expression levels of those genes were biologically similar between amplified and unamplified samples.

Conclusion

Conversely to the most recent reports which challenged the use of intense amplification procedures on minute amounts of RNA, we chose moderate PCR and IVT amplifications for our gene profiling study. Conclusively, it appeared that systematic biases arose even with moderate amplification procedures, independently of (i) the sample used: brain, ovary or embryos, (ii) the enzymatic properties initially inferred (exponential or linear) and (iii) the preliminary optimization of the protocols. Moreover the use of an in-house developed array, small-sized but well suited to the tissues we worked with, was of real interest for the search of differential expressions.

Protein abundance ratios for global studies of prokaryotes

The use of multidimensional capillary HPLC combined with MS/MS has allowed high qualitative and quantitative proteome coverage of prokaryotic organisms. The determination of protein abundance change between two or more conditions has matured to the point that false discovery rates can be very low and for smaller proteomes coverage is sufficiently high to explicitly consider false negative error. Selected aspects of using these methods for global protein abundance assessments are reviewed. These include instrumental issues that influence the reliability of abundance ratios; a comparison of sources of nonlinearity, errors, and data compression in proteomics and spotted cDNA arrays; strengths and weaknesses of spectral counting versus stable isotope metabolic labeling; and a survey of microbiological applications of global abundance analysis at the protein level. Proteomic results for two organisms that have been studied extensively using these methods are reviewed in greater detail. Spectral counting and metabolic labeling data are compared and the utility of proteomics for global gene regulation studies are discussed for the methanogenic Archaeon Methanococcus maripaludis. The oral pathogen Porphyromonas gingivalis is discussed as an example of an organism where a large percentage of the proteome differs in relative abundance between the intracellular and extracellular phenotype.

Comparison of target labeling methods for use with Affymetrix GeneChips

Background

Several different commercial one-cycle labeling kits are available for preparation of the target for use with the Affymetrix GeneChip platform. However, there have been no evaluations of these different kits to determine if comparable results were generated. We report on the cRNA target synthesis, labeling efficiency and hybridization results using the One-Cycle Target Labeling Assay™ (Affymetrix), the BioArray RNA Amplification and Labeling System™ (Enzo Life Sciences), and the Superscript RNA Amplification System (Invitrogen Life Technologies).

Results

The only notable difference between kits was in the yield of cRNA target synthesized during in vitro transcription, where the BioArray assay had to be repeated several times in order to have sufficient target. However, each kit resulted in comparable signal and detection calls when hybridized to the Affymetrix GeneChip.

Conclusion

These 3 one-cycle labeling kits produce comparable hybridization results. This provides users with several kit options and flexibility when using the Affymetrix system.