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Regulatory RNAs in the Nervous System

Opinion ARTICLE

Front. Cell. Neurosci., 15 November 2013 | https://doi.org/10.3389/fncel.2013.00208

MicroRNAs: fundamental regulators of gene expression in major affective disorders and suicidal behavior?

Gianluca Serafini1*, Maurizio Pompili1, Katelin F. Hansen2, Karl Obrietan2, Yogesh Dwivedi3, Mario Amore4, Noam Shomron5 and Paolo Girardi1
  • 1Department of Neurosciences, Mental Health and Sensory Organs – Sant'Andrea Hospital, Sapienza University of Rome, Rome, Italy
  • 2Department of Neurosciences, Ohio State University, Columbus, OH, USA
  • 3Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
  • 4Section of Psychiatry, Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health University of Genova, Genova, Italy
  • 5Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

Introduction

Major affective disorders are one of the foremost causes of morbidity worldwide; such disabling conditions are also frequently associated with suicidal behavior (Innamorati et al., 2011; Gonda et al., 2012; Serafini et al., 2012). Although many psychopharmacological agents are currently available, in particular for the treatment of major depressive disorder (MDD) (Serafini et al., 2013), our knowledge concerning the molecular and cellular mechanisms underlying this complex condition is still limited. Indeed, even minor alterations in the expression of genes regulating neural and structural plasticity may be crucial to understanding the pathogenesis of major affective disorders (Dwivedi et al., 2009a,b; Serafini et al., 2011, 2012).

MiRNAs are gene expression regulators critically affecting brain development that have been investigated as potential biomarkers for the diagnosis, management, treatment, and progression of neuropsychiatric disorders (Machado-Vieira et al., 2010; Saugstad, 2010; Dwivedi, 2011). Several facets of miRNA expression alterations are currently under investigation to gain insight into the pathology of neuronal disorders (Hansen et al., 2007; Lopez et al., 2013): miRNA expression alterations in pathophysiological models of disease (Ziu et al., 2011; Brandenburger et al., 2012); miRNA expression alterations in the blood of patients, most of which represent further downstream or compensatory effects (Schipper et al., 2007; Gallego et al., 2012); and miRNAs and their effectors acting as targets for the action of psychoactive drugs such as antidepressants and mood stabilizers (Zhou et al., 2009; Baudry et al., 2010; Oved et al., 2012).

Several miRNAs have emerged as potential mediators of depressive pathophysiology. The existence of polymorphisms in pre-miR-30e (Xu et al., 2010) and pre-miR-182 (Saus et al., 2010) has been associated with an increased risk of major depression. Depressive behavioral responses have been induced by miR-16 up-regulation in the raphe nuclei and hippocampus, with the latter associated with subsequent down-regulation of BNDF (Bai et al., 2012). MiR-16 down-regulation within the locus coeruleus was also induced in depressive mouse models (Launay et al., 2011). Smalheiser et al. (2012) investigated the expression of miRNAs in the prefrontal cortex (specifically in Brodmann Area 9) of 18 antidepressant-free depressed suicide victims, and 17 well-matched non-psychiatric controls, whose information was collected using the psychological autopsy method. In this study, global miRNA expression was significantly down-regulated by 17%, and 24 miRNAs were down-regulated by at least 30%. The authors also found significant down-regulation in an extensive inter-connected network of 21 miRNAs involved in cellular growth and differentiation. Notably, both the global decrease of miRNA expression, as well as its decreased variability, are consistent with hypo-activation of the frontal cortex in depressed subjects. Interestingly, the noted miRNAs have been suggested to be down-regulated in the frontal cortex of rats treated with corticosterone, and therefore, might be crucial in regulating stress-mediated miRNA expression in depressed subjects (Dwivedi et al., unpublished data). Hence, alterations in miRNA expression may be a fundamental event underlying gene network reorganization associated with major depression.

Nevertheless, a comprehensive understanding of miRNA networks dysregulated in major depression and induced by antidepressant medications as a function of brain region is currently unknown (Mouillet-Richard et al., 2012). It is also generally poorly understood how miRNA regulation affects cellular signaling networks in these biological processes. Here we provide an overview and critical review of the published work, particularly examining the role of miR-185 in major depression and suicidal behavior.

The Challenges of miRNA:mRNA Target Prediction in Modeling Pathology

Expression profiling and RNA sequencing of miRNAs have increased our understanding of which miRNAs are present in specific tissues, and how they may change under pathological conditions (Oved et al., 2012). However, once identified, linking a miRNA to its mRNA targets can be a challenging task, and the authenticity of functional miRNA:mRNA target pairs should be validated. A very small fraction of software-predicted miRNA targets are validated in vivo. As suggested by Kuppers et al. (2011), only a subset of predicted targets are consistently reduced in phenotypes that overexpress some miRNAs. Validation could be provided by showing a direct interaction between the miRNA and mRNA target. Further, miRNA silencing, overexpression, and luciferase reporter based assays are commonly used as supporting evidence for a functional interaction (Kuhn et al., 2008).

Many databases for miRNA target prediction have been created using an array of interrogation approaches. Considering varying degrees of sequence similarity, conservation, site accessibility, and variation in the targeted regions of the mRNA, the numerous databases can provide a surprising level of divergent results. This divergence speaks to the difficulty that scientists have had in developing a clear and concise set of rules underlying miRNA:mRNA interaction: clearly target prediction software should only be viewed as a tool to guide bench science.

Table 1 Provides a summary of current miRNA target prediction software that may be used to guide in silico investigations into miRNA and their putative targets. The analytical paradigms for each database are describes as well as advantages of each mode of inquiry.

TABLE 1
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Table 1. Comprehensive list of miRNA target databases and software.

MiR-185: A Role in Major Affective Disorders and Suicidal Behavior?

Preliminary studies have suggested the importance of miR-185 and miR-491-3p in the pathogenesis of major depression and suicidal behavior. MiR-185 is expressed in several brain regions such as the hippocampus and cortex, predominantly in synapses (Lugli et al., 2008; Xu et al., 2013). Earls et al. (2012) reported that miR-185 regulates cognitive and psychiatric symptoms of patients with the 22q11 deletion syndrome. Recently, Xu et al. (2013) suggested that miR185 controls the expression of Golgi-apparatus related genes including a new inhibitor of neuronal maturation. In particular, a reduction of miR-185 altered dendritic and spine development resulting in structural alterations of the hippocampus.

With respect to MDD and suicidality, miR-185 was shown to be upregulated in patients who completed suicide (Maussion et al., 2012). These increases in expression were correlated with reduced TrkB-T1, a truncated TrkB transcript whose downregulation has been associated with suicide (Ernst et al., 2009). The downregulation of TrkB-T1was associated with suicidal behavior in a sample of 38 suicide completers (60.5% having been previously diagnosed with MDD). Of note, five putative binding sites for miR-185 were found in the 3′ UTR of TrkB-T1 (using an in silico investigation). Array findings were confirmed with RT-PCR investigation and three of the five potential binding sites for miR-185 in the TrkB-T1 3′ UTR were demonstrated to be functional by luciferase assay. The authors did not find any confounding effect of age, pH, PMI, or suicide method. Through Pearson correlation and subsequent in vitro functional analyses (using silencing or exogenous expression of miR-185), TrkB-T1 levels and hsa-miR-185 levels were reported to be inversely correlated.

A few notes of caution should be mentioned with regard to the Maussion et al. (2012) study. The authors acknowledge that the underlying mechanism of increased miR-185 expression remains unclear. The study used HEK293 cells that yielded TrkB-T1 expression levels that were 10-fold greater than neuronal cell lines. Furthermore, RNA binding proteins, such as ELAVL1 or PABPC1, may be expressed in HEK293 cells (Drury et al., 2010) and potentially bind TrkB mRNA (Jain et al., 2011). Therefore, despite disproportionate increases in TrkB-T1 expression, the functional effect of hsa-miR-185 on TrkB-T1 observed in HEK293 cells might have been attenuated by the expression of these genes and their binding activity (George and Tenenbaum, 2006). Further, the study is limited by the small sample size and the negative findings in other brain regions, such as the cerebellum. Indeed, presumably only a limited part of the total variability in miRNAs that might regulate TrkB-T1 has been identified.

Of note, the subjects of the Maussion et al. (2012) study were not assessed for microduplications in the 22q11.2 region. This is of potential interest because the miR-185 locus maps to the 22q11.2 region, which has been associated with mood disorders such as depression and anxiety (Jolin et al., 2012; Weisfeld-Adams et al., 2012; Tang et al., 2013). Deletions of this region have also been consistently associated with schizophrenia (Karayiorgou et al., 2010) whereas duplications have been found in patients with autism (Lo-Castro et al., 2009). Alterations in the 22q11.2 region are also associated with morphological alterations in dendritic spines at glutamatergic synapses (Mukai et al., 2008), and abnormal maturation of miRNAs (Stark et al., 2008). Fénelon et al. (2013) have suggested that mice with a 22q11.2 microdeletion show significant alterations in high-frequency synaptic transmission, short- and long-term plasticity, and dendritic spine stability. The authors reported that variation in synaptic plasticity occurs by subtle changes in neuronal density and a reduction in inhibitory neuron. All of these alterations in neuronal function could play critical roles in depressive pathophysiology.

Understanding the Limitations of Studies Examining the Role of miRNAs in Major Affective Disorders

Since the first detection in Caenorhabditis elegans in 1993 (Lee et al., 1993), small interfering RNAs have raised great interest among neurobiologists for their potential role in neuropathological regulation. In line with this notion, large-scale analyses on post-mortem brains, as well as investigations in animal models of depression, have evaluated the impact of psychoactive medications on global miRNA expression. Transcriptome studies are now commonly used as a starting point to investigate the association between dysregulated miRNAs and major affective disorders. However, there are a number of conflicting studies with regard to the magnitude and direction of biologically-relevant miRNA expression changes in psychiatric disorders (Perkins et al., 2007; Beveridge et al., 2010). This could be due to tissue-specific variations in expression levels as well as heterogeneity in quantification and normalization procedures (Belzeaux et al., 2012). Furthermore, some studies on miRNAs and depression were conducted in peripheral blood despite uncertainties regarding how closely changes in peripheral miRNA expression reflect modifications in the central nervous system (e.g., Bocchio-Chiavetto et al., 2013). It is also worth noting that, “control” RNAs commonly used to normalize miRNA data (U6, U44, and U48) are very sensitive to post-mortem decay (Sadikovic et al., 2011) and thus, should be carefully matched among groups to prevent the emergence of artifactual shifts in miRNA expression. Finally, neuronal shrinkage, loss of glial cells, or loss of dendritic spines may also contribute to changes in miRNA levels. Clearly, changes in tissue composition or cellular compartments should be carefully taken into account when examining the available studies.

Conclusion

Our understanding of the molecular mechanisms underlying major affective disorders may be significantly enriched by the knowledge of miRNAs' mechanisms of action. MiRNA targets are critically involved in stress-related disorders, neuroplasticity, and neurodevelopmental disorders (Rogaev, 2005). Given that miRNAs have been hypothesized to modulate ~50% of protein-coding genes and hundreds of mRNAs (Krol et al., 2010), a new level of complexity regarding gene expression has emerged. The entire miRNA context (both mRNA networks and their cellular environments) should be critically investigated when interpreting the effects of changes in miRNA levels. Much remains to be examined in order to translate these investigations into novel therapeutics for the treatment of psychiatric conditions.

Acknowledgments

Part of the funding was provided by R01MH082802, R01MH 101890 to Dr. Dwivedi.

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Keywords: microRNAs, synaptic plasticity, major affective disorders, suicidal behavior, gene expression

Citation: Serafini G, Pompili M, Hansen KF, Obrietan K, Dwivedi Y, Amore M, Shomron N and Girardi P (2013) MicroRNAs: fundamental regulators of gene expression in major affective disorders and suicidal behavior?. Front. Cell. Neurosci. 7:208. doi: 10.3389/fncel.2013.00208

Received: 03 September 2013; Accepted: 21 October 2013;
Published online: 15 November 2013.

Edited by:

Tommaso Pizzorusso, CNR, Italy

Reviewed by:

Joseph A. Gogos, Columbia University, USA

Copyright © 2013 Serafini, Pompili, Hansen, Obrietan, Dwivedi, Amore, Shomron and Girardi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: gianluca.serafini@uniroma1.it