microRNAs (miRNAs) are intracellular and circulating molecular components contributing to genome expression control through binding mRNA targets, which generally results in downregulated mRNA expression. One miRNA can target several mRNAs, and one transcript can be targeted by several miRNAs, resulting in complex fine-tuning of regulation of gene networks and signaling pathways. miRNAs regulate metabolism, adipocyte differentiation, pancreatic development, β-cell mass, insulin biosynthesis, secretion, and signaling, and their role in diabetes and obesity is emerging. Their pathophysiological effects are essentially dependent on cellular coexpression with their mRNA targets, which can show tissue-specific transcriptional responses to disease conditions and environmental challenges. Current knowledge of miRNA biology and their impact on the pathogenesis of diabetes and obesity is based on experimental data documenting miRNA expression generally in single tissue types that can be correlated with expression of target mRNAs to integrate miRNA in functional pathways and gene networks. Here we present results from the most significant studies dealing with miRNA function in liver, fat, skeletal muscle, and endocrine pancreas and their implication in diabetes and obesity.
microRNAs (miRNAs or miRs) are endogenous single-stranded 20–24 long noncoding RNAs present in all multicellular organs. They are synthesized and matured through an ubiquitous enzymatic machinery involving the nuclear DROSHA and the cytoplasmic DICER ribonucleases III (39). These two endonucleolytic enzymes play complementary roles in miRNA maturation resulting in cleavage of pri-miRNAs into pre-miRNAs, which are cleaved by DICER for eventual release of active miRNAs (6). The specific function of DICER in the final stage of miRNA biogenesis made its inactivation a prime target for studying the global biological role of miRNA at the organism and organ levels. miRNAs can be encoded by specific miRNA genes, as well as by introns of protein-coding genes through independent promoters (5), and often modulate the same biological mechanisms as the protein encoded by the host gene (73). miRNAs regulate gene expression through mRNA decay and translational repression (28). They are incorporated into an RNA-induced silencing complex with Argonaute proteins that have RNase H activity (28) and can cleave interacting mRNA targets following imperfect base pairing (61).
Typically, one miRNA can target several mRNAs (Fig. 1A), and one transcript can be targeted by several miRNAs. This process results in massively increased complexity of transcriptional regulation of gene networks and signaling pathways. However, binding of an miRNA seed region to its mRNA targets can translate into biological effects only if miRNAs and target RNAs are present simultaneously in the same cells of a tissue at a given time. Whether the miRNAs are synthesized locally or transported into cells of a tissue, their biological functions are essentially dependent on tissue-specific expression patterns of target mRNAs present in the tissue at a given time and in specific biological conditions. Adaptive genome transcription patterns in response to a stimulus can result in miRNA pairing to different collections of transcripts and subsequently in altered miRNA biological function (Fig. 1B).
miRNA research has highlighted unexpectedly complex systems that regulate the expression of groups of genes that do not necessarily share biological functions. Growing evidence supports crucial roles of miRNAs in metabolism regulation, adipocyte differentiation, pancreatic development, and insulin biosynthesis, secretion, and signaling, which we address in this review. We do not cover details of molecular mechanisms involved in miRNA synthesis and maturation and mediation of their function, which are reviewed elsewhere (5, 28, 39, 61). Here, we discuss the most significant studies dealing with biological function in liver, fat, muscle, and endocrine pancreas of miRNAs, as summarized in Table 1. We underline the importance of paralleled genome-wide profiling of miRNAs and mRNAs in multiple organs to address miRNA-mediated whole body regulation of biological processes.
Regulation of β-Cell Development and Insulin Secretion by miRNAs
Investigating genome expression in pancreatic β-cells is central to our understanding of molecular mechanisms that regulate insulin secretion and compensate for insulin resistance in the pathogenesis of Type 2 diabetes. The global impact of miRNAs on the development of the pancreas was evidenced in pancreas-specific DICER-null mouse embryos, which exhibit increased apoptosis resulting in dramatic loss (79–95%) in all endocrine cell types, with a predominant effect on β-cells, and die shortly after birth (47). However, when Dicer is inactivated in β-cells of adult mice, islet architecture and differentiation markers remain unchanged, but insulin content, insulin mRNA levels, and glucose-induced insulin secretion are decreased, resulting in hyperglycemia and glucose intolerance (52).
Beyond the global role of DICER, individual miRNAs contribute to the regulation of endocrine pancreas development and β-cell function, and their key features have been reviewed in detail (22). An array of data has provided important insights into the central role of the evolutionary conserved miR-375, which is expressed specifically in pancreatic islets. It regulates β-cell proliferation (41) and insulin secretion through an effect on insulin exocytose, which involves proteins encoded by miR-375 targets, including myotrophin (MTPN) (63) and phosphoinositide-dependent protein kinase-1 (PDK1) (13). miR-375 is also expressed in pancreatic α-cells and plays an important role in pancreas organogenesis. Inactivation of miR-375 in mice is associated with reduced β-cell mass, increased α-cell number and plasma glucagon levels, hyperglycemia, reduced insulin secretion, and disrupted islets architecture (64). miR-483 also shows similar patterns of regulation of insulin and glucagon secretion (53). Downregulated expression of miR-375 in ob/ob mice results in reduced β-cell mass and plasma insulin levels and severe diabetes. Finally, miR-375 expression is downregulated in islets of Goto-Kakizaki (GK) rats, which are characterized by depleted β-cell mass and deteriorated islet structure (13).
Other miRNAs also selectively affect islet development, including miR-7 and miR-199b-5p, which regulate β-cell proliferation (41, 57), and miR-124a, which is expressed during pancreas organogenesis and targets transcription factors (FOXA2, PDX1) involved in β-cell differentiation (4). miR-124a and miR-33a, a potent regulatory component of cholesterol metabolism in the liver (see below), inhibit insulin release and stimulated insulin secretion (46, 85). miR-9 and miR-96 regulate insulin release through the RabGTPase effector granuphilin, a component of secretory granules in β-cells (46, 62). The protein deacetylase SIRT1 can mediate the effects of miR-9 on insulin secretion (68). miR-29 isoforms may regulate insulin release in mouse islets through the plasma membrane monocarboxylate transporter SLC16A1, which ensures coupling of glucose metabolism and insulin secretion (65).
Expression of these miRNAs in β-cells has been directly or indirectly linked to transcription factors (PDX1, FOXA2, ONECUT2, HNF6, NGN3, NEUROD1) that play crucial roles in β-cells (21). Conversely, miRNA expression in β-cells is reactive to elevated concentration of glucose in MIN6 cells (77) and in human islets (76). Transcriptional studies of miR-26, miR-182, miR-148, and miR-200/141 using a luciferase expression reporter assay driving the minimal insulin promoter in cultured islets showed that these miRNAs can stimulate the transcription of the insulin gene, a phenomenon that could be mediated by transcriptional repressors of the insulin gene (BHLHE22, SOX6) (52).
Unresolved questions remain regarding miRNA-driven regulation of gene expression in β-cells through local mechanisms eventually causing hyperglycemia and through miRNA-reactive regulatory systems of gene expression that adapt to insulin resistance. Islet miRNA expression profiling in db/db and high fat diet (HFD)-fed mice identified changes in miRNA expression that occurred before diabetes onset through altered β-cell activity and mass (miR-132, miR-184, miR-338-3p) and once diabetes has developed through β-cell apoptosis (miR-34a, miR-146a, miR-199a-3p, miR-203, miR-210, miR-383) (56).
Although growing evidence supports important roles of miRNAs in the development of the endocrine pancreas and the differentiation and function of β-cells, the fact that key transcription factors required in these processes are miRNA targets suggests strong temporal effects of miRNAs on the organogenesis of the endocrine pancreas. There are also obvious limitations in the analysis of genome expression in β-cells, arising from technical issues with the procedures used for islet isolation, which may profoundly alter metabolic regulations and transcriptome landscapes. Finally, interpretation of results from gene and miRNA expression data in β-cell lines can be problematic as glucose sensing and the general insulin production machinery can be very different to those in insular β-cells.
miRNA-Mediated Regulation of Insulin Sensitivity in Adipose Tissue
Adipose tissue is the central organ in the pathogenesis of obesity through its dual roles in the metabolism and storage of fat and in the secretion of adipokines and adipocytokines. DICER-mediated global regulation of miRNA expression plays a key role in adipose tissue biology. The effect of calorie restriction on age-dependent coordinated downregulation of DICER and miRNA processing in adipose tissue was demonstrated in mice and Caenorhabditis elegans (54). DICER knockout in mouse adipose tissue is associated with increased sensitivity to oxidative stress (54).
Microarray-based profiling of miRNA expression in adipose tissue in animal models and obese patients has provided information on collections of known miRNAs that are differentially expressed in obesity (25, 26, 51, 81), including miRNAs consistently differentially expressed in various rodent models (e.g., miR-27a, miR-103, miR-107) and in both models and humans (e.g., miR-15a, miR-30d). An miR-29 paralog (miR-29a) was differentially expressed in visceral adipose tissue between GK and control rats (26), and a series of experiments indicated altered expression of miR-125a in visceral adipose tissue of HFD mice and in 3T3-L1 adipocytes (10). In addition, expression of miR-125a was downregulated in subcutaneous adipose tissue of obese patients, regardless of their diabetes status. These changes correlated with obesity intermediate quantitative phenotypes (fat mass, serum leptin, adiponectin, and triglycerides) (10). Of note, this miRNA is structurally related to miR-125b, which showed evidence of decreased expression with age in visceral fat and in DICER knockout cells (54).
Transcription factors and coactivators (PPARG, PGC1A, PGC1B, C/EBPs, KLFs, SREBPs) that play key roles in adipogenesis are controlled by miRNAs. Binding of miR-27a and miR-27b to the 3′-untranslated region of PPARG downregulates its expression in 3T3-L1 preadipocytes and hampers differentiation into adipocyte (31, 45). PPARG transcripts are also repressed by miR-130, which affects human adipocyte differentiation (42). Downregulated expression of PPARA by miR-519d in humans leads to increased lipid accumulation during preadipocyte differentiation (51). KLF5 expression is repressed by miR-448, resulting in reduced expression of adipogenic genes, reduced triglyceride accumulation, and impaired adipocyte differentiation (35). Finally, the locus of the transcriptional coactivator PGC1B, which regulates thermogenesis, glucose and fatty acid metabolism, and mitochondrial biogenesis, encodes two miRNAs originating from the same miRNA hairpin (miR-378 and miR-378*) coexpressed with PGC-1β (12). Inactivation of miR-378/378* in mice is associated with resistance to HFD-induced obesity and enhanced mitochondrial fatty acid metabolism in liver (7). These effects are partly explained by the repression of transcription of genes encoding the carnitine O-acetyltransferase (CRAT), an enzyme controlling fatty acid metabolism, and MED13, involved in a transcriptional coactivator complex required for gene expression.
In addition to their role in adipocyte differentiation and maturation, miRNAs also affect insulin resistance and contribute to differentiation into brown fat. miR-143 regulates the differentiation of cultured human preadipocytes into adipocytes by targeting the mitogen-activated protein kinase MAPK7 (ERK5) (16), which belongs to a family of proteins involved in cellular proliferation, differentiation, and transcription regulation and development. It also regulates insulin sensitivity in obese mice through activation of AKT (30), which is required for insulin-stimulated glucose transport. Expression of structurally related miR-133a and miR-133b is negatively correlated with the expression of PRDM16, one of their direct targets, as well as that of UCP1, PPARG, and PPARA, and regulates brown adipose tissue differentiation specifically from subcutaneous adipocytes (80). This system of miR-133a/b-mediated downregulation of PRDM16 expression is also functional in skeletal muscles, where miR-133a/b and PRDM16 are very abundant and where they regulate myoblast proliferation.
Examples of physically linked and structurally similar miRNAs sharing similar function have been reported in adipose tissue. Expression of miR-103 and miR-107, which are located within the gene encoding pantothenate kinase (PANK), is stimulated in ob/ob and HFD-fed obese mice and regulate adipocyte differentiation and insulin sensitivity in vivo (81). These effects are mediated through direct interaction of these miRNAs with caveolin 1 (CAV1), a scaffold protein and a critical regulator of the insulin receptor. Inactivation of miRNA-103/107 in adipocytes is associated with increased CAV1 expression, which leads to stabilization of the insulin receptor, enhanced insulin signaling and insulin-stimulated glucose uptake, and reduced adipocyte size (81). These effects may be mediated by other miRNAs since miR-103 and miR-107 target DICER, thus resulting in inhibition of the overall miRNA-processing system (50). The regulation of another structural component of caveolae [caveolin 2 (CAV2)] by miR-29a and miR-29b underlines the importance of caveolins in cellular function (24).
Inflammation is a hallmark of adipose tissue anomalies in obesity characterized by the release of adipokines and inflammatory cytokines [leptin, resistin, tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), adiponectin]. The role of miRNAs in inflammatory response in many diseases has been reviewed (49). Among miRNAs associated with inflammation, miR-155 is overexpressed in adipose tissue from obese patients (32), and miR-335 expression is stimulated by leptin, resistin, TNF-α, and IL-6 in human adipocytes (91). Investigations of miR-132 expression in human primary preadipocytes and in differentiated adipocytes established a relationship between overexpression of miR-132 and induction of nuclear factor-kappa B translocation, acetylation of p65, and production of IL-8 and monocyte chemoattractant protein-1 (MCP-1). These effects may be explained by downregulated expression of SIRT1, which contains a binding site for miR-132, resulting in the activation of inflammatory pathways (74).
Impact of miRNA on Insulin Sensitivity in Skeletal Muscles
Compared with other organs, relatively little is known about miRNA biology in skeletal muscles (58). Analysis of miRNA expression in gastrocnemius in db/db mice identified 41 differentially expressed miRNAs (2). Upregulated expression of miR-135a in this model was replicated in diabetic patients and coincided with reduced levels of transcripts encoding IRS2, a validated target for this miRNA. In vivo silencing of miR-135a in db/db mice was associated with improved glucose tolerance and increased levels of muscle IRS2 and p-Akt, suggesting a role of this miRNA in insulin signaling (2). In humans, microarray-based analysis of miRNA expression in skeletal muscle of diabetic patients identified differential expression of 62 miRNAs, including miR-106b and miR-133a (19). Further studies showed that miR-106b targets mitofusin-2 (Mfn2) and downregulates its expression and contributes to insulin resistance in C2C12 myotubes (88). miR-133a is, with miR-1, the most abundant miRNA in skeletal muscle (44). Differential expression of miR-133a in skeletal muscle was confirmed in humans in response to insulin stimulation and in streptozotocin (STZ)-induced diabetic mice (20). Insulin-induced downregulation of miR-133a expression is at least partly mediated by mechanisms involving a sterol regulatory element-binding protein (SREBP-1c) and a myocyte enhancer factor (MEF2C) (20).
Other important components of the insulin signaling pathway are influenced by specific miRNAs in muscle. For example, increased insulin sensitivity in muscle following global knockout of the Let-7 family may account for improved glucose homeostasis in HFD-fed obese mice (18). Anti-miRNA treatment in these mice results in increased lean and muscle mass (18), and muscle-specific overexpression of Let-7 in transgenic mice results in insulin resistance, which occurs through repression of multiple components of the insulin-PI3K-mTOR pathway (IGF1R, INSR, IRS2) (90).
Impact of miRNAs on Liver Insulin Sensitivity and in the Metabolism of Cholesterol
Strong experimental evidence supports the involvement of miRNAs in central insulin resistance through the regulation of the metabolism of cholesterol and free fatty acids in the liver (70). We and others have used microarray-based strategies to identify differentially expressed miRNAs in the liver in diabetes or obesity either occurring spontaneously in the GK rat (25, 26) and in ob/ob mice (81) or induced experimentally in response to HFD feeding (81). Novel hypotheses have emerged from these genome-wide miRNA expression studies, and subsequent investigations have focused on individual miRNAs. For example, pathway analysis of predicted mRNA targets of miR-125a, which is strongly overexpressed in the GK rat, pointed to the MAPK signaling pathway, thus providing clues to molecular mechanisms that mediate the effects of miR-125a and contribute to diabetes in this strain (26).
In parallel with these global genomic approaches, several miRNAs have been tested individually for their function in liver. Particular attention has focused on mechanisms associated with altered expression of miR-122, miR-33a, miR-33b, and Let-7, which illustrate specific aspects of miRNA biology (17, 71). Various experimental systems (antisense inhibitors, liver-specific knockout, locked nucleic acid) were used to inhibit liver miR-122 expression and to document its role on decreased biosynthesis of cholesterol and fatty acids in vitro, reduced plasma levels of triglycerides and both LDL and HDL cholesterol (15, 40), and increased in vitro fatty acid oxidation (reviewed in Ref. 17). These observations account for reduced HFD-induced nonalcoholic fatty liver disease (NAFLD) in mice inactivated for miR-122 (14, 15, 82).
Screening miRNA expression in liver of mouse models of obesity and diabetes (leptin-deficient ob/ob, leptin receptor-deficient db/db, HFD-fed mice), in obese patients, and in cellular systems revealed systematic overexpression of miR-143 (30), miR-802 (38), and miR-181a (89). These miRNAs target distinct sets of transcripts with different functions, including the oxysterol-binding-protein-related protein 8 (target of miR-143), which provides a link to mechanisms of energy metabolism and cell growth and differentiation mediated by the serine/threonine kinase AKT (protein kinase B, PKB), the transcription factor HNF1B (target of miR-802), and the NAD+-dependent deacetylase SIRT1 (target of miR-181a). These data underscore the breadth of hepatic functions that are dependent on the combined regulation of the expression of miRNAs and their mRNA targets.
Owing to the central role of the transcription factors sterol regulatory element-binding proteins (SREBP) in the regulation of cholesterol biogenesis, fatty acids, and phospholipids (67), the function of structurally related miR-33a and miR-33b, which are transcribed from intronic sequences of SREBP2 and SREBP1, respectively, and are coexpressed with their host genes, has been extensively studied (11, 48, 55, 69). In vivo and in vitro experimental systems have been used to demonstrate the role of these miRNAs on cholesterol and lipid homeostasis through a direct effect on the expression of genes encoding proteins regulating cholesterol efflux (ABCA1, ABCB11, ABCG1, ATP8B1, NPC1), fatty acid transport in mitochondria (CPT1A, CROT), fatty acid oxidation (HADHB), glucose metabolism and stress resistance (SIRT6), fatty acid and cholesterol synthesis (AMPKA1), and insulin signaling (IRS2). In addition, altered expression of these genes mediated by miR-33 can have knock-on effects on the expression of genes involved in the regulation of fatty acid production (ACC1, FASN, HMGCR, SCD1) and insulin sensitivity (through the activity of IRS2). Interestingly miR-33a downregulates ABCA1 also in islets and is associated with increased islet cholesterol accumulation (85).
The IRS and SREBP signaling pathways provide prime examples to illustrate the complexity of miRNA-mediated posttranscriptional control of gene networks, through combined effects of multiple miRNAs affecting functionally related target mRNAs and feedback regulatory loops of gene expression. For example, hepatic expression of IRS proteins is controlled by miRNAs as demonstrated by the direct regulation of IRS1 by miR-126 (72) and IRS2 by miR-33 and the Let-7 family, which also targets several other important genes downstream in this pathway (AKT2, IGF1R, INSR, PIK3IP, RICTOR, TISC1) (90). SREBP2 directly activates miR-182 and miR-96, which negatively regulate the expression of FBXW7 and INSIG-2, respectively. These genes affect nuclear SREBP levels and endogenous lipid synthesis (29), potentially leading to steatohepatitis (59). Furthermore, several miRNAs directly contribute to liver expression of miR-33 targets, including ABCA1 (target of miR-26, miR-128-2, miR-144) (1, 9, 27, 75), ABCG1 (target of miR-128-2) (1), and CPT1A (target of miR-370) (27).
Altered expression of miRNAs in liver can result in changes in expression of genes involved in the regulation lipid metabolism, ultimately leading to NAFLD and nonalcoholic steatohepatitis (NASH). We reported systematic upregulation of hepatic Srebp1 expression in response to HFD feeding in mice showing strong susceptibility (129S6, C57BL/6J) or resistance (BALB/c) to NAFLD and significantly perturbed expression of several direct and indirect miR-33 targets (ABCA1, ABCB11, CROT, FASN, HADHB, HMGCR, NPC1, SCD1) (79, 84). As miR-33b is not transcribed from the sequence of Srebp1 in mice, these effects are not directly caused by miR-33b-stimulated expression, but its absence may explain discordant patterns of gene expression changes in these strains and their susceptibility and resistance to NAFLD. Increased hepatic expression of miR-34a was reported in animal models of diabetes and obesity and in patients with NASH and NAFLD (8) and Type 2 diabetes (reviewed in Ref. 71). miR-34a may play a direct role in these disorders by targeting SIRT1, which controls key metabolic regulators (FOXO1, FXR, LXR, PGC1A, PPARG, P53, SREBP) (43).
Conservation and Specificity of miRNA Expression across Multiple Tissues
Our current understanding of the roles of miRNAs on glucose homeostasis and insulin secretion is based on investigations that often focused on a single tissue, thus providing limited information on the global biology of miRNAs at the organism level (Fig. 2). Abundance and tissue specificity of 345 miRNAs were tested in samples prepared from 40 human tissues and provided a global view of miRNA expression patterns with respect to tissue distribution and organ function (44). Results confirmed liver-specific expression of miR-122 but also showed that expression of miR-375 is not restricted to pancreatic islets, which limits its potential use as pharmacological target in diabetes. On the other hand miR-29b was ubiquitously expressed in all tested tissues. miR-375 and miR-483 are remarkable examples of differential miRNA-mediated intrapancreatic regulation, as they stimulate insulin secretion by β-cells and decrease glucagon secretion by α-cells (53, 64).
Evidence of conserved differential expression of miRNAs in diabetes in three insulin-sensitive tissues (liver, muscle, fat) was demonstrated by simultaneous genome-wide miRNA profiling in the diabetic GK strain and in normoglycemic strains (25, 26). The most significant example of coordinated miRNA expression was found for miR-29a and miR-29b, which were overexpressed in all three tissues in the GK rat (24). These miRNAs regulate insulin sensitivity by targeting proteins that contribute to insulin signaling, such as CAV2, a lipid raft-associated protein regulated by insulin, the insulin-induced gene 1, a negative regulator of SREBPs, and the insulin signaling intermediate phosphatidylinositol 3-kinase regulatory subunit-α (24, 60). However, these and other as-yet uncharacterized target genes may exhibit tissue-specific patterns of expression, thus leading to pleiotropic biological consequences of conserved miRNA expression. miRNA expression profiling in pancreas, liver, adipose tissue, skeletal muscle, and blood in a rat model of diabetes induced by HFD feeding and STZ revealed over 130 miRNAs differentially expressed in diabetic rats in at least one tissue and defined a core set of 84 miRNAs consistently differentially expressed in all tissues (33).
Detection and Impact of Circulating miRNAs on Insulin Signaling and Secretion
The presence of complexes of miRNAs and Argonaute proteins in extracellular fluids represents a novel system for cell-cell communication (22, 66). They mostly originate from neighboring tissues where they are secreted in exosomes. They are detected in blood where they can be taken up in their active form by recipient cells. Screening expression of over 700 miRNAs in plasma from Type 2 diabetic patients and in leptin-deficient ob/ob mice identified changes in the abundance of miRNAs (miR-15a, miR-29b, miR-126, miR-223, miR-28-3p) that may predict diabetes onset (86). Subsequent analyses of circulating miRNAs in Type 2 diabetic patients identified differences in serum concentrations of largely inconsistent series of miRNAs (34, 37). However, both studies reported an increase in the abundance of circulating miR-375 in patients that may be particularly relevant to diabetes pathogenesis. Further investigations are required to confirm prospects of applications of circulating miRNAs as diabetes-predictive biomarkers and to establish a catalog of circulating miRNAs and their impact in the cross talk between insulin-sensitive organs as well as between endocrine cells of pancreatic islets.
Causal Role of Altered miRNA Regulation in Diabetes and Obesity
Causality between altered miRNA expression and disease can be assessed when a system is challenged by treatment with an miRNA. On the other hand, changes in miRNA expression in disease models can either be a phenotype causative event or reflect phenotypic adaptations secondary to the disease. miRNA-mediated pathways may be involved in human genetic diseases through mutations and polymorphisms resulting in altered maturation of miRNAs, changes in their seed sequence, or modification of the conformation of hairpin structure that would affect binding to mRNA targets (Fig. 1, C and D). These could have broad-ranging consequences on the expression of large numbers of transcripts and on biological pathways that they regulate. Polymorphisms in the sequence of transcript targets, which would alter binding to miRNAs, may also affect mRNA-mediated function, with unpredictable pathophysiological consequences. However, reduction in the occurrence of genetic polymorphisms in predicted miRNA target sequences has been suggested, and there is evidence of association between sequence variants affecting these sites in cancer (87).
Only a handful of miRNA loci are associated with a disease phenotype in human genome-wide association studies (GWAS), including Type 2 diabetes (miR-129) and body mass index (miR-148A) (http://www.ebi.ac.uk/gwas). A recent meta-analysis of circulating lipids identified 69 miRNAs in the vicinity of associated genetic variants, which may account for abnormal cholesterol regulation (83). However, analysis of computationally predicted genes regulated by Let-7 demonstrated significant enrichment of genes associated with risk single nucleotide polymorphisms for Type 2 diabetes and fasting glycemia (90), suggesting the involvement of regulatory mechanisms upstream of miRNAs. As very few GWAS hits are explained by variants affecting amino acid sequence of a protein, improved knowledge of regulatory elements of genome expression, including sequences that control miRNA biosynthesis and function, miRNA seed sequences, and miRNA-mRNA binding motifs, may provide clues to interpreting GWAS results.
Results from experiments discussed in this review underline the crucial regulatory roles of miRNA in the function of adipose tissue, liver, skeletal muscle, and pancreatic islets, and their impact in obesity and Type 2 diabetes. As illustrated in Table 1, knowledge of miRNA biological roles remains fragmentary as it is based on experiments of miRNA stimulation or inhibition in vivo or in vitro, which have been generally carried out in a single organ in rodent models and in cell systems. miRNA data are rapidly accumulating, but data integration at the systems level remains underdeveloped and requires advances in various areas. First, the apparent deficit of miRNAs in many species reflects underdeveloped structural and functional genome annotations. Even though they are detected in the genome of all sequenced species, the number of miRNAs varies substantially for large vertebrate genomes (Table 2). For genomes larger than 2.5 Gbp encoding over 20,000 genes, the number of annotated mature miRNA varies from 153 in sheep to 1,915 in mouse and 2,588 in human. Public repositories and specialized software tools have been developed to build miRNA inventories in many species and to assist in predicting transcript targets and analysis of evolutionary patterns of miRNAs (reviewed in Ref. 3). Even though software systems rely on consensus concepts of both structural features of miRNAs and molecular bases of miRNA-mRNA interaction, they apply different algorithms, which can give largely discordant results and should be addressed (3). Second, knowledge of the role of miRNAs in the regulation of insulin secretion and action is emerging mostly from experiments in animal models and will undoubtedly keep improving with paralleled genome-wide expression profiling data sets of miRNAs and mRNAs (36). However, a critical issue with miRNA studies in model systems lies in the potential conservation of DNA sequences of both miRNAs and their binding sites across species (23). Translation of regulatory mechanisms involving miRNAs between species relies on conservation of both miRNA catalogs and DNA sequences at the levels of miRNA seeds and target sites in mRNAs mainly localized in noncoding regions of genes, which may be more divergent between species than coding sequences. Translation of miRNA expression data in diabetes and obesity from rodent models to humans requires between-species comparisons of both miRNA catalogs across many organs, which is made possible by GTEx Consortium data (http://www.gtexportal.org/) and miRNA expression responsiveness to therapeutic options used in human diabetes and obesity and tested in rodents, including drugs (e.g., metformin) and surgical solutions (e.g., gastric sleeve). Finally, novel mechanisms of miRNA regulation are emerging, including competing endogenous RNA (ceRNA) (gene transcripts, pseudogenes, and long noncoding RNAs) that can interact with miRNA seed sequences and recruit miRNAs, thus limiting their availability to modulate gene expression (78).
M. R. Diawara was supported by a PhD studentship from the Ile de France region (CORDDIM).
No conflicts of interest, financial or otherwise, are declared by the author(s).
S.C. and D.G. prepared figures; S.C. and D.G. drafted manuscript; S.C., A.G., and D.G. edited and revised manuscript; S.C., M.R.D., A.G., and D.G. approved final version of manuscript.
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