Multiple correlations of mRNA expression and protein abundance in human cytokine profile

Abstract

With the development of genomic study, researchers found that it is insufficient to predict protein expression from quantitative mRNA data in large scale, which is contrary to the traditional opinion that mRNA expression correlates with protein abundance at the single gene level. To try to solve the apparent conflicting views, here we set up a series of research models and chose soluble cytokines as targets. First, human peripheral blood mononuclear cell (PBMC) from one health donor was treated with 16 continuously changing conditions, the protein and mRNA profile were analyzed by multiplex Luminex and genomic microarray, respectively. Among the tested genes, around half mRNA correlated well with their corresponding proteins (ρ > 0.8), however if we put all the genes together, the correlation coefficient for the 16 conditions varied from 0.29 to 0.71. Second, PBMC from 14 healthy donors were stimulated with the same condition and it was found that the correlation coefficient went down (ρ < 0.6). Third, 28 rheumatoid arthritis (RA) patients were tested for their response to the same external stimuli and it turned out different individual displayed different protein expression pattern as expect. Lastly, autoimmune disease cohorts (8 diseases including RA, 103 patients in total) were assayed on the whole view. It was observed that there was still some similarity in the protein profile among patients from the single disease type although completely different patterns were displayed across different disease categories. This study built a good bridge between single gene analysis and the whole genome study and may give a reasonable explanation for the two conflicting views in current biological science.

Cytokine mRNA and protein expression by cell cultures of epithelial ovarian cancer—Methodological considerations on the choice of analytical method for cytokine analyses

“…We obtained a negative correlation coefficient suggesting that the translation of mRNA to protein was not dependent on mRNA abundancy but probably on other mechanisms. In contrast to the findings in our kinetic experiments, a much variable but positive correlation coefficient of 0.29 to 0.71 was found in a study of cytokine mRNA and protein expression by human PBMCs, where similarly to our protein analyses, a multiplex Luminex ® methodology was used 24 . The reason is not known, and several biological and technical factors could have contributed to this discrepancy.…”

“…Samples taken from patients show a “snap‐shot” of cytokine levels at an unknown time point in the process from transcription of the gene to degradation of the protein. Several studies have been performed to seek for correlation between protein abundance and mRNA expression in human material, with varying results and opposing views 13,18,21‐26 . Diverging results are to be expected considering methods used for each analysis, what material is analyzed and the handling of this material, making obtained results specific for a given system.…”

“…For example, different cellular sources were used—PBMCs, a natural cellular source for induction and production of cytokines vs our study where ovarian cancer cells were used, as well as different methods for mRNA detection—we used RT‐qPCR and they used microarrays. The overall conclusion of the authors 24 was that it is insufficient to predict protein abundance from quantitative mRNA data. Results consistent with our findings, that is negative correlation coefficient, were found in a study of mRNA and protein expression for a subgroup of proteins including several HSP types, haptoglobin, various cytokeratins, Rab proteins, and others in 76 cases of lung adenocarcinomas 25 .…”

“…In other subgroups of proteins in this investigation, 25 no correlation between mRNA and protein expression was found. There are several more studies confirming that the abundancy of protein expression and mRNA levels is poorly correlated 13,22‐26 …”

Evaluation by hierarchical clustering of multiple cytokine expression after phytohemagglutinin stimulation

“…Cytokine expression data were obtained from a previously published study in which the experimental materials and methods are described in detail [18]. Briefly, human peripheral blood mononuclear cells (PBMCs) from one healthy donor were isolated from whole blood by density gradient centrifugation and cultured in four different stimulation media, designated as A: IL-4+IL-6; B: IL-4+IL-6+H 2 O 2 ; C: IL-4+IL-6+PHA; and D: IL-4+IL-6+PHA+H 2 O 2 .…”