Selbach et al. and Baek et al. present two nice papers that make an important methodological step forward, as both look directly to protein expression as it is modulated by miRNA. They both confirm that miRNA regulates large amounts of proteins, likely directly by binding to seeds in the 3’ ends of their target mRNA, but apparently also in a more indirect way by the regulation of the expression of some master regulators (e.g., Dicer in the Selbach paper). The big challenge is now to dissect the functional significance of this type of regulation and how the hundreds of microRNAs act together to regulate the overall expression pattern of proteins in cells and tissues in real life. There were already some hints in the past showing that specific microRNAs can reprogram cells in, for instance, a neuronal phenotype.

In vivo studies in the intact animals are now needed to correlate loss or gain of specific microRNAs to specific phenotypes, and those studies should be combined with a systematic analysis to see how the proteins affected by the microRNA are involved (or not) in the...  Read more

Selbach et al. and Baek et al. present two nice papers that make an important methodological step forward, as both look directly to protein expression as it is modulated by miRNA. They both confirm that miRNA regulates large amounts of proteins, likely directly by binding to seeds in the 3’ ends of their target mRNA, but apparently also in a more indirect way by the regulation of the expression of some master regulators (e.g., Dicer in the Selbach paper). The big challenge is now to dissect the functional significance of this type of regulation and how the hundreds of microRNAs act together to regulate the overall expression pattern of proteins in cells and tissues in real life. There were already some hints in the past showing that specific microRNAs can reprogram cells in, for instance, a neuronal phenotype.

In vivo studies in the intact animals are now needed to correlate loss or gain of specific microRNAs to specific phenotypes, and those studies should be combined with a systematic analysis to see how the proteins affected by the microRNA are involved (or not) in the establishment of these phenotypes.

Concerning the medical use of microRNA: we are far away from any practical application (apart maybe from diagnostics). It is clear that we need to study this highly interesting novel dimension to the regulation of protein expression in much deeper detail. However, the relevance of the microRNA system for complex diseases can be easily extrapolated: dysregulation of this system could be involved in neurodegenerative disorders or psychiatric disorders, where multiple small problems ultimately could cause global brain failure.

View all comments by Bart De Strooper

MicroRNA and Proteome Change
In this study, Baek et al. used a quantitative proteomics approach (i.e., “conventional” SILAC method) to analyze the proteome changes induced by the overexpression and knockout of several miRNAs. Interestingly, authors happened to choose the “brain”-specific miR-124 (furthermore the most abundant miRNA in the brain) to investigate the effects of miRNA ectopic expression in HeLa cells. Since the data presented in the article were not interpreted from the neuroscience perspective, further analyses of supplementary data might provide some insight to neuroscientists interested in the role of miR-124 in the brain. (None of the top 20 hits appears to be previously linked with Alzheimer disease.)

To complement the overexpression experiments, authors also studied the role of endogenous miRNA by using specific mir gene knockout mice. Since the effects of knockout of endogenous mir gene on proteome were basically the reciprocal of those obtained by the ectopic overexpression, these data suggest that the miRNA overexpression experiments may be...  Read more

MicroRNA and Proteome Change
In this study, Baek et al. used a quantitative proteomics approach (i.e., “conventional” SILAC method) to analyze the proteome changes induced by the overexpression and knockout of several miRNAs. Interestingly, authors happened to choose the “brain”-specific miR-124 (furthermore the most abundant miRNA in the brain) to investigate the effects of miRNA ectopic expression in HeLa cells. Since the data presented in the article were not interpreted from the neuroscience perspective, further analyses of supplementary data might provide some insight to neuroscientists interested in the role of miR-124 in the brain. (None of the top 20 hits appears to be previously linked with Alzheimer disease.)

To complement the overexpression experiments, authors also studied the role of endogenous miRNA by using specific mir gene knockout mice. Since the effects of knockout of endogenous mir gene on proteome were basically the reciprocal of those obtained by the ectopic overexpression, these data suggest that the miRNA overexpression experiments may be physiologically relevant and an easy pilot study from which to get preliminary data.

From a technical point of view, it is of interest to know that TargetScan and PicTar performed the best, among several miRNA target prediction algorithms. This study is an exemplar of collaboration between proteomics lab (Dr. Gygi, the inventor of ICAT method) and microRNA lab (Dr. Bartel).

In a separate study by Selbach (Selbach et al., 2008), authors provided essentially similar data demonstrating that a single miRNA can regulate protein synthesis of hundreds or thousands of genes. The "variant" of the SILAC method described by authors (“Pulsed” SILAC) may be useful to apply to neurons, given the potential limitation of the conventional SILAC method to non-dividing cells (Spellman et al., 2008).

References:
Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N (2008) Widespread changes in protein synthesis induced by microRNAs. Nature. Abstract

Spellman DS, Deinhardt K, Darie CC, Chao MV, Neubert TA (2008) Stable Isotopic Labeling by Amino Acids in Cultured Primary Neurons: Application to Brain-derived Neurotrophic Factor-dependent Phosphotyrosine-associated Signaling. Mol Cell Proteomics 7:1067-1076. Abstract

View all comments by Jungsu Kim