Since the first draft of human genome was published in February 2001, many new discoveries have been made which have elucidated the complexity of the human genome and subsequently the human proteome. In the past decade, application of genomics and proteomics technologies for early detection of diseases have demonstrated that many types of diseases can be diagnosed at an early stage which would be helpful in initiation of treatment protocols at an earlier time point in the clinic. We have previously reported the application of proteomics technologies for early detection of ovarian cancer (1, 2, 3), prostate cancer (4), lymphatic vascular system (5) and drug-induced cardiac toxicities (6). Other genomics and proteomics technologies have been employed in a variety of other diseases in the past decade (7, 8).

As a result of human genome studies and the discovery of less than 25,000 genes in the human genome, a shift has occurred in the focus of research from mRNAs to noncoding RNAs as a major regulator of human genome. The presence of noncoding RNAs and its role in many human diseases make these molecules important mediators which have to be understood in medical research. We have recently reviewed the role of noncoding RNAs in cancer (9) and in the present article extend this review in a more comprehensive way to include many other types of diseases that are now known to occur in humans.

In early 90's, it was discovered that two small RNAs (instead of a protein) were the product of lin-4, a gene controlling the timing of larval development of Caenorhabditis elegans (C. elegans) (10). Later studies revealed that the longer RNA (70 nucleotides) was the precursor of the shorter RNA (22 nucleotides) which is now known as a member of the class of microRNA (miRNA) genes (11). By targeting specific mRNAs for degradation and/ or translational repression, microRNAs (miRNAs), a novel class of endo-genous, non-coding RNAs (ncRNAs) plays an important role in controlling gene expression (12). Originally it was thought that lin-4 gene expression was restricted to C. elegans, due to lack of homology with other species. However, in the year 2000 the miRNA gene (let-7) (product of lin-4 gene precursor) was discovered to target lin-41(a protein coding gene) in many species (13). Since then large amounts of microRNAs have been identified in mammals (14).

Members of ncRNAs include microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) that are known to have well preserved functions in various species. The conservation of ncRNAs’ activities in mediating the binding of RNA-enzymes to target RNA complexes results from their specific hybridization to other nucleic acids in the cell and their targeting ability of different cellular targets (15). Such specific functions are thought to limit sequence co-variation and tendency to evolution (16). As the human genome and its functions are rapidly being deciphered, the roles of miRNAs are becoming more evident in specific cellular functions. For example, miRNAs and a large set of ncRNAs including: Air, H19, Ipw, NTT, Tsix and XIST in mammals (known as ‘‘gene regulators’’) have been proposed to have different functions ranging from imprinting to inactivation of X-chromosome in mammals (17).

The biogenesis of miRNAs (Figure 1) involves multiple steps and specific cellular machinery (18). miRNAs are encoded as short inverted repeats having a double-stranded RNA (dsRNA) stem loop about 70 bp long and are found in both introns and intergenic clusters in the genome (18). RNA polymerase II is responsible for the synthesis of the introns and exons of both protein-coding and non-coding transcripts from where miRNAs are derived (19). In the nucleus, miRNAs are transcribed as primary pri-miRNA transcripts and then are processed to form the precursor pre-miRNA stem loop structure before transportation into the cytoplasm [where they are cleaved by the Dicer RNAase III endonu-clease and produce mature miRNA (21–23 nucleotides] (20).

Many major cellular functions such as development, differentiation, growth, and metabolism are regulated by miRNAs and approximately 2200 miRNA genes have been reported to exist in the mammalian genome (21). One third of the human genome is estimated to be regulated by miRNAs (22). The precise mechanisms involved in the miRNA transcription is not known but proximity to other genes in the genome and their locations in introns of coding genes, noncoding genes and exons are reported to influence their expression (23). In the genome, miRNAs are organized in clusters and share the same transcriptional regulatory units and are independently expressed if they have their own promoters (24, 25). It is estimated that about 50% of miRNAs expressed in the genome are transcribed from non-protein-coding genes and the remaining miRNAs are coded in the introns of coding genes (21).

In higher eukaryotic organisms, almost the entire genome (97%) is transcribed as non-codingRNA (ncRNA) which consist of rRNA, tRNA, introns, 5’ and 3’ untranslated regions, transposable elements, intergenic regions, and microRNAs (12, 26). Recently, it has been suggested that mammalian miRNAs are derived from DNA repeats and transposons (27). Such reports have lead the scientific community to re-evaluate the functional role of transposons, especially because it appears that the specific sequences of transposons can play a major role in the developmental processes and epigenetic variations (28, 29). Furthermore, it has been recently demonstrated that miRNAs can be derived from processed pseudogenes (30), which were once believed to have no cellular functions (Figure 2).Most recent sequence analyses of the human genome demonstrates that the protein coding genes may be as low as 25,000 (31). Although the exact number of the protein coding genes in the human genome is not known, the 25,000 figure is at least 3-4 times lower than the figure believed in late 1980's. What these new data reveal is that a large segment of the human genome consists of non-coding protein genes. Further sequence analyses indicate that the Open Reading Frames (ORFs) comprise less than 2%, repetitive sequences around 46% (32, 33) and non-coding parts of protein-coding genes (introns, 5′ and 3′-UTRs) an estimated 25–27% (34) of the 3.2 billion bases in the human genome.

In addition to their major presence in the human genome, microRNAs have been shown to be involved in regulation of genes in higher eukaryotes (35). The rapid growth of research in the field of miRNAs is observed in the number of entries in the miRNA registry (version 1), with only 218 entries in 2002 and about 6500 entries in 2008 (version 11) (36, 37). The sequence analyses of genomes in eukaryotes indicate that simple unicellular organisms, invertebrates and mammals have 10-40%, 70–90% and 98% of their genomes composed of noncoding DNA regions, respectively (34).

The cellular functions of miRNAs appear to vary in eukaryotes, including regulation of leaf and flower development in plants (38) and modulation of differentiation of hematopoietic cells in mammals (39). The fact that many micro RNAs’ sequences are conserved among distantly related organisms indicates that miRNAs are involved in basic cellular processes (40).

MicroRNAs have been been demonstrated to play a major role in a wide range of developmental processes including metabolism, cell proliferation, apoptosis, developmental timing, and neuronal cell fate (15, 41–44). Other regulatory roles include neuronal gene expression (45), brain morphogenesis (46), muscle differentiation (47), and stem cell division (48).

The role of miRNAs as a major source in the development of cancer is still very much unappreciated (49). But altered patterns of miRNAs in cells have been shown to be responsible for changes that cause cells to make a decision to turn malignant (50).

MicroRNAs are now recognized to play a pivotal role in the regulation of certain processes related to development in all eukaryotes and because of their potential role as agents controlling cell growth and differentiation, they have been proposed to be good candidates for cancer therapy (51, 52).

MicroRNAs’ deficiencies or excesses have been linked to a number of other clinically important diseases ranging from myocardial infarction to autoimmune disease. Single point mutations in miRNA or its target or epigenetic silencing of miRNA transcription units is a mechanism by which the functions of miRNA in cell are affected (53). Great discoveries and rapid progress in the past few years on miRNAs provide the hope that miRNAs will in the near future have a great potential in the diagnosis and treatment of many diseases. In the following pages, the role of miRNAs as important new regulatory molecules in different human diseases will be reviewed (54).

It is now well documented that upregulation or down-regulation of miRNAs occurs in various human cancers (9). Over-expressed miRNAs may function as both oncogenes (through down-regulation of tumor-suppressor genes) and/ or regulator of cellular processes such as cell differentiation or apoptosis (55, 56).

Unique miRNA expression profilings have been demonstrated for many types of cancer. A list of such profiles for reproductive cancers (breast, ovary, and endometrioid adenocarcinoma) and colon, hematological cancers (AML, ALL, CML, CLL), esophagus, gastro-intestinal, lung, bladder, and thyroid tumors are shown in Tables 1 and 2, respectively (9). It has been predicted that microRNAs will have a great potential to be used in diagnosis and treatment of cancer in the near future (Tables 1–3).

Endothelial cells are known to play a major role in the angiogenesis process. In recent studies (57–59) the mirRNA expression pattern (known for its tissue and cell type specificity) in endothelial cells has been demonstrated to include let-7b, miR-16, miR-21, miR-23a, miR-29, miR-100, miR-221, and miR-222. The regulation of miRNAs during patho-physiological processes has been suggested to help uncovering the role of miRNAs in vascular cells. For example in two recent reports (60, 61), the regulation of miRNAs in vascular cells in response to serum and hypoxia have been studied. In one study (60) the pro-angiogenic miR-130a is expressed at low levels in quiescent HUVEC and is upregulated in response to foetal bovine serum. In another study (61) hypoxia was shown to induce miR-210 expression in endothelial cells. The overexpression of miR-210 was reported to be associated with the enhanced formation of capillary-like structures whereas inhibition of miR-210 expression was linked to decreased tube formation and migration (62).

miR-221 and miR-222 are among the highly expressed miRNAs in HUVEC that exhibit anti-angiogenic effects (59). Similar observations were reported (57) for the anti-angiogenic function of miR-221 miR-222 in endothelial cells. This study also showed that the overexpression of miR-221 and miR-222 also indirectly reduces the expression of the endothelial Nitric Oxide Synthase (eNOS) (57) Nitric oxide (NO) is an important molecule in regulating endothelial cell growth (63), migration (64), vascular remodeling (65), and angiogenesis (66) and its impaired bioavailability is the cause of diseases including: atherosclerosis and ischemic cardiomyopathy (67). Recently it was demonstrated that eNOS also plays a major role in the mobilization and functional activity of stem cells (68–70); therefore, designing miRNAs to target eNOS is thought to regulate vasculogenesis (62).

The homoeostasis of the vascular system depends on the functionality of endothelial cells and coordinated regulation of angiogenesis, vasculogenesis, and vessel regression. Little is known about the regulatory machinery at the gene expression level during neovascularization and vascular remodeling (62). However, the discovery of microRNAs in recent years has made it evident that these RNA molecules have an important function in regulation of heart function (71) and mammalian cardiovascular system in general (72).

The miRNA expression levels have been linked to deregulation of developmental processes and disease states, such as cardiac hypertrophy and failure. Many miRNAs are expressed in a tissue-cell-specific manner (73) and in adult cardiac tissue, miR-1, miR-16, miR-27b, miR-30d, miR-126, miR-133, miR-143, and the let-7 family are abundantly expressed (74). Studies have shown that three mirRNAs (miR-1, miR-133, and miR-208) are highly expressed in the heart (23, 75) and are important regulators of heart development and myocyte differentiation (72, 76–78). Recently, deregulated expression of miR-1 and miR-133 were reported in human heart failure (71, 79, 80).

Severe cardiac remodeling with detrimental outcomes can result from disturbances in the physiological stimuli to the heart (81). One of the major responses of the heart to such stimuli is an extensive tissue remodeling known as pathological hypertrophic growth. Although the precise mechanisms involved in cardiovascular biological functions are not known, an increasing number of studies suggest that miRNAs are important regulators of cardiovascular growth, proliferation, cell differentiation, and apoptosis.

Cardiac hypertrophy in humans is a major determinant of mortality and morbidity in cardiovascular diseases. Because miRNAs are important regulators for the differentiation and growth of cardiac cells, they are hypothesized to have an important role in cardiac hypertrophy and heart failure (82). Indeed, several recent reports have found aberrant expression of miRNAs in diseased hearts and vessels. miR-23a, miR-23b, miR-24, miR-195, miR-199a, and miR-214 were upregulated during cardiac hypertrophy (Table 4), and their over-expression in cardiomyocytes in vitro caused an induction of hypertrophic growth. Interestingly, miR-24, miR-125b, miR-195, miR-199a, and miR-214 were similarly upregulated in the tissue of patients with end-stage failing human hearts (74).

Cardiac arrhythmias are still considered a serious health problem because of their sudden, unpredictable and potentially fatal nature. In human hearts with coronary heart disease and the rat model of myocardial infarction, it has been shown that the muscle-specific miRNA (miR-1) is upregulated in ischaemic heart tissue (61). Furthermore, the results of this study show that the injection of mature miR-1 exacerbates arrhythmogenesis, whereas inhibition of miR-1 by an antisense inhibitor suppresses arrhythmias. When the genes for the ion channels GJA1 and KCNJ2 were silenced, these proteins were shown to be important in mediating the miR-1-induced arrhythmogenic effect (61). The investigation into the role of miRNAs as a novel class of gene regulators in cardiovascular disease is a new frontier for research and it is hoped that the next decade will bring a greater understanding to their functions in cardiovascular biology (82).

Inflammation is an essential component of host defense system and a major response to infection and injury, which is believed to contribute to multiple acute and chronic diseases (83, 84). Recently a number of studies have investigated the role of miRNAs in vascular inflammation and leukocyte activation and their infiltration into the vascular wall. Indeed, a recent study (85) provides the first evidence that miRNAs control vascular inflammation.

In this study, miR-126 was demonstrated to inhibit the expression of vascular cell adhesion molecule 1 (VCAM-1), which is required to mediate leukocyte adherence to endothelial cells. In macrophages, miR-155 has been shown to be induced by cytokines such as TNFα and IFN-β (86, 87) and contribute to physiological granulocyte/ monocyte expansion during inflammation (88). Furthermore, miR-155 is reported to be required for B and T lymphocyte and dendritic cell function (89, 90). At the gene level, the transcription factor Pu.1 has been identified as a direct target of miR-155 in B cells (62, 90).

Another study (91) has demonstrated that miR-181 is involved in regulation of haematopoietic lineage differentiation and several miRNAs have been reported to regulate B-cell differentiation, including the miR-17-92 cluster and miR-150 (92–94). During monocyte differentiation, the transcription of miR-424 has been shown to increase and regulate the translation of the transcription factor NFI-A involved in monocyte/ macrophage differentiation (95). Moreover, miR-146 is found to be induced in macrophages by several microbial components and proinflammatory cytokines (96). Finally, the myeloid-specific miR-223 is reported to be involved in regulation of granulocyte differentiation and activation during inflammation (62, 97). The role of miRNAs in regulation of every major cell type important in modulation of the immune system indicates that they can be potentially used in immune therapies.

MicroRNAs are highly expressed in human and other mammalian brains relative to other organs (98–100). The results of high-throughput sequencing experiments suggest that the number of miRNAs expressed in human brain should be over 1000, although currently this number stands at about 550 in all humans (101). The expression of miRNAs in brain changes during brain development. Therefore, some miRNAs are expressed more abundantly during early development in the mammalian brain, and some are expressed less during later development (102, 103). The changes in miRNA expression levels in brain during development may represent biochemical signals for cell fate determination, apoptosis and/or cell division programming (104). Studies (105) have shown that some miRNAs are differentially expressed in neuronal nuclei, and/or different cell populations in brain (106).

Because miRNAs are known to be dynamically regulated in neurogenesis and brain development (107, 108), it is believed that miRNAs are also involved in neural development and play an important role in mediating neuronal plasticity. One of the major common traits linking many of the neurodevelopmental disorders [e.g. intellectual disability, autism, Attention Deficit Hyperactivity Disorder (ADHD) and epilepsy] is that disease onset occurs during periods of maturation and development (109). Therefore, it is very likely that miRNAs contribute significantly to the pathogenesis of neurodevelopmental disorders at the molecular level (110).

As for the role of non-coding RNAs (especially mirRNAs) in human brain, it is speculated that these molecules may help the generation of complexity required for brain functions from approximately 25, 000 human protein-coding genes (106, 111, 112).

Results from both cell culture and animal studies indicate that miRNAs have an important role in regulation of normal immune functions and prevention of autoimmunity. What is not clear yet is the precise mechanism(s) by which miRNA dysregulation could lead to pathogenesis in an autoimmune disease. In the following sections some possible roles for miRNAs in regulation of two of the most significant autoimmune diseases [i.e. rheumatoid arthritis (RA)] and Systemic Lupus Erythematosus (SLE) will be reviewed (153).

The liver is composed of many cell types and each cell type may have a distinct miRNA expression profile. In recent years, an increasing understanding of miRNA functions in liver physiology and disease and identification and validation of miRNA targets have gained a lot of attention (167).

The muscular dystrophies are a heterogeneous group of disorders involving degeneration of skeletal muscle. Recent studies provide evidence to support a role for miRNAs in the regulatortion of muscle development. The roles of miRNAs in myogenesis have been mainly from studies on muscle-specific miR-1, miR-133 and miR-206 (174). Recently unique miRNA signatures have been found in Duchenne muscular dystrophy (175, 176).

It has been demonstrated that diagnosis of Facioscapulohumeral muscular dystrophy (FSHD) could be distinguished from Duchenne muscular dystrophy based on the level of miRNAs-381 and miRNAs-382 expressions in FSHD patients (175). Other studies have also shown a significant up-regulation of miRNAs-100, 103 and 107 in certain myopathies (176).

The involvement of miRNAs in hair follicle morphogenesis, autoimmune and chronic inflammatory diseases affecting skin has been proposed (177–181). Dermal fibroblasts are important cells involved in the wound healing process (182). Analysis of the potential involvement of miRNAs in regulating the transition to proliferation has been performed and a cluster of 33 miRNAs were reported to be involved in regulation of expression of target genes required for the entry of fibro-blasts into the cell cycle and proliferation (178). A recent review has outlined the potential importance of miRNAs’ involvement in wound angiogenesis and abnormal healing sequence in chronic wounds (179, 183).

Psoriasis is a chronic inflammatory skin disease and genetic and environmental factors are thought to be involved in pathogenesis of the disease. It is widely accepted that psoriasis results from impaired communications between the immune system and the structural cells of the skin (180, 184, 185). The psoriasis-associated miRNAs have been identified in the skin and miR-203 was found to be expressed more than 100-fold higher in skin compared to other organs (Table 4). Expression analyses of psoriasis-associated miRNAs (miR-203, miR- 146a, miR-21, and miR-125b) in cells that present in healthy and psoriatic skin (keratinocytes, dermal fibro-blasts, melanocytes, and leukocyte/ immune cell subsets) have been shown to have a distinctive expression pattern (183). Such studies demonstrate that psoriasis-specific miRNA are involved in the the pathogenesis of psoriasis.

One of the most exciting findings of human genome project has been the discovery of a major class of non-coding protein RNA molecules. The findings of human genome project have demonstrated that the DNA molecules previously known as “junk DNA”, is now actively transcribed and code for miRNAs. Studies now provide evidence that miRNAs play a pivotal role in a variety of developmental processes and disease as reviewed in the present article.miRNAs as a special class of non-coding RNAs can post-transcriptionally regulate gene expression in a negative manner; therefore, it is predicted to have a great potential in diagnosis and treatment of diseases in the future. For instance, in the last few years, several techniques such as miRNA silencing, antisense blocking and miRNA modification have been considered for potential therapeutic treatment of several types of cancers. As the role of miRNAs are further clarified and established in each disease, we will surely see new methods developed to address the diagnosis and treatment of major human diseases. This new knowledge appears to have a major role in the practice of personalized medicine in the near future.