MicroRNA

This report demonstrates that introduction of physiologically relevant miRNAs can enhance somatic cell reprogramming. The mouse embryonic stem (ES) cell specific microRNAs (miRNA) miR-291-3p, miR-294, and miR-295 enhanced the efficiency of Klf4, Oct4 and Sox2 induced pluripotency. These miRNAs did not further enhance reprogramming in the presence of cMyc. cMyc binds the promoter of these miRNAs, suggesting that they are downstream effectors of cMyc promoted pluripotency. However, unlike exogenous cMyc, these miRNAs induced a homogeneous population of reprogrammed colonies suggesting overlapping and independent functions of cMyc and the miRNAs.

Techniques of molecular biology have improved diagnostic sensitivity, accuracy and validity in forensic medicine very much, especially in the field of identification (paternity testing, stain analysis). Since more than 10 years these techniques -meanwhile well established in clinical disciplines -are used also for other applications in forensic medicine: determination of cause and manner of death, tissue identification by mRNA and microRNA, examination of gene expression levels (survival time, time since death, cause of death), toxicogenetics.

The molecular pathogenesis of follicular lymphoma (FL) was partially revealed 3 decades ago, with the discovery of the translocation that brings BCL2 under the influence of immunoglobulin heavy chain en-hancers in a vast majority of cases. Despite the importance of this seminal observation, it has become increasingly clear that additional genetic alterations need to occur to trigger neoplastic transformation and disease progression. The evolution of FL involves developmental arrest and disruption of the normal function of one or more of epigenetic regulators including KMT2D/MLL2, EZH2 , CBP/ CREBBP , p300/ EP300 , and HIST1H1 in > 95% of cases. B-cells "arrested" in germinal centers acquire dozens of additional genetic aberrations that influence key pathways controlling their physiological development including B Cell Receptor (BCR) signaling, PI3K/AKT, TLR, mTOR, NF-κB, JAK/STAT, MAPK, CD40/CD40L, chemokine, and interleukin signaling. Additionally, most cases of FL do not result from linear accumulation of ge-nomic aberrations, but rather evolve from a common progenitor cell population by diverse evolution, creating multiple FL subclones in one patient. Moreover, one of the subclones might acquire a combination of aberrations involving genes controlling cell survival and proliferation including MDM2, CDKN2A/B, BCL6, MYC, TP53, β2M, FOXO1, MYD88, STAT3, or miR-17-92 , and this can lead to the transformation of an initially indolent FL to an aggressive lymphoma (2%-3% risk per year). The complexity of the disease is also underscored by the importance of its interactions with the microenvironment that can substantially influence disease development and prognosis. Interpreting individual aberrations in relation to their impact on normal processes, their frequency, position in the disease evolution, and the consequences of their (co)occurrence, are the basis for understanding FL pathogenesis. This is necessary for the identification of patients with risk of early progression or transformation, for the development of novel targeted therapies, and for personalized treatment approaches. In this review, we summarize recent knowledge of molecular pathways and microenvironmental components involved in FL biology, and discuss them in the context of physiological B-cell development, FL evolution, and targeted therapies.

We aim to examine the miR-1288 expression in cancer cell lines and a large cohort of patients with colorectal cancer. Two colon cancer cell lines (SW480 and SW48) and one normal colonic epithelial cell line (FHC) were recruited. The miRNA expressions of miR-1288 were tested on these cell lines by using quantitative real-time polymerase chain reaction (qRT-PCR). An exogenous miR-1288 (mimic) was used to detect cell proliferation and cell cycle changes in SW480 using MTT calorimetric assay and flow cytometry, respectively. In addition, tissues from 122 patients with surgical resection of colorectum (82 adenocarcinomas, 20 adenomas, and 20 non-neoplastic tissues) were tested for miR-1288 expression by qRT-PCR. The colon cancer cell lines showed reduced expression of miR-1288 compared to normal colonic epithelial cell line. Over expression of miR-1288 in SW480 cell line showed increased cell proliferation and increased G2-M phase cells. In tissues, reduced miR-1288 expression was noted in majority of colorectal adenocarcinoma compared to colorectal adenoma and non-neoplastic tissues. Reduced or absent expression of miR-1288 was noted in 76% (n ¼ 62/82) of the cancers. The expression levels of miR-1288 were higher in distal colorectal adenocarcinomas (P ¼ 0.013) and in cancers of lower T staging (P ¼ 0.033). To conclude, alternation of miR-1288 expression is important in the progression of colorectal cancer. The differential regulation of miR-1288 was found to be related to cancer location and pathological staging in colorectal cancers. ß

Sox2 has yet to be determined. Sox2 can act synergistically with Oct3/4 in vitro to activate Oct-Sox enhancers, which regulate the expression of pluripotent stem cellspecific genes, including Nanog, Oct3/4 and Sox2 itself. These findings suggest that Sox2 is required by ES cells for its Oct-Sox enhancer activity. Using inducible Sox2-null mouse ES cells, we show that Sox2 is dispensable for the activation of these Oct-Sox enhancers. In contrast, we demonstrate that Sox2 is necessary for regulating multiple transcription factors that affect Oct3/4 expression and that the forced expression of Oct3/4 rescues the pluripotency of Sox2-null ES cells. These results indicate that the essential function of Sox2 is to stabilize ES cells in a pluripotent state by maintaining the requisite level of Oct3/4 expression.

Topographically and chemically modified titanium implants are recognized to have improved osteogenic properties; however, the molecular regulation of this process remains unknown. This study aimed to determine the microRNA profile and the potential regulation of osteogenic differentiation following early exposure of osteoprogenitor cells to sand-blasted, large-grit acid-etched (SLA) and hydrophilic SLA (mod-SLA) surfaces. Firstly, the osteogenic characteristics of the primary osteoprogenitor cells were confirmed using ALP activity and Alizarin Red S staining. The effect of smooth (SMO), SLA and modSLA surfaces on the TGF-b/BMP (BMP2, BMP6, ACVR1) and non-canonical WNT/Ca 2+ (WNT5A, FZD6) pathways, as well as the integrins ITGB1 and ITGA2, was determined. It was revealed that the modified titanium surfaces could induce the activation of TGF-b/BMP and non-canonical WNT/Ca 2+ signaling genes. The expression pattern of microRNAs (miRNAs) related to cell differentiation was evaluated. Statistical analysis of the differentially regulated miRNAs indicated that 35 and 32 miRNAs were down-regulated on the modSLA and SLA surfaces respectively, when compared with the smooth surface (SMO). Thirty-one miRNAs that were down-regulated were common to both modSLA and SLA. There were 10 miRNAs up-regulated on modSLA and nine on SLA surfaces, amongst which eight were the same as observed on modSLA. TargetScan predictions for the down-regulated miRNAs revealed genes of the TGF-b/BMP and non-canonical Ca 2+ pathways as targets. This study demonstrated that modified titanium implant surfaces induce differential regulation of miRNAs, which potentially regulate the TGF-b/BMP and WNT/Ca 2+ pathways during osteogenic differentiation on modified titanium implant surfaces.

In this review, the pathways involving small RNAs are provided followed by a new and updated network that illustrates their interplay with diverse cellular mechanisms in Caenorhabditis elegans. The RNA silencing pathways are now recognized as key factors that connect together the many variations in biological processes, including transcriptional gene regulation, post-transcriptional gene silencing, translational gene silencing, apoptosis, meiosis, and antiviral defense. The utilization of small RNAs represents a specific, energy conserving, and fast mechanism of gene regulation via a core system known as RNA interference.

Background: Cervical cancer is the second most common malignancy of women worldwide. Recently, aberrant miRNA expression has been demonstrated in human cervical cancer, however the functional role of miRNAs in cervical cancer remains unclear. We previously observed a significant overexpression of miR-205 in human cervical cancer tissues as compared to their matched normal cervical tissues in a sequencing-based miRNA profiling analysis. In this study, we further explore the role of miR-205 in cervical cancer.

nAture methods | VOL.9 NO.4 | APRIL 2012 | 403 understanding the function of individual micrornA (mirnA) species in mice would require the production of hundreds of loss-of-function strains. to accelerate analysis of mirnA biology in mammals, we combined recombinant adenoassociated virus (rAAV) vectors with mirnA 'tough decoys' (tuds) to inhibit specific mirnAs. intravenous injection of rAAV9 expressing anti-mir-122 or anti-let-7 tuds depleted the corresponding mirnA and increased its mrnA targets. rAAV producing anti-mir-122 tud but not anti-let-7 tud reduced serum cholesterol by >30% for 25 weeks in wild-type mice. high-throughput sequencing of liver mirnAs from the treated mice confirmed that the targeted mirnAs were depleted and revealed that tuds induced mirnA tailing and trimming in vivo. rAAV-mediated mirnA inhibition thus provides a simple way to study mirnA function in adult mammals and a potential therapy for dyslipidemia and other diseases caused by mirnA deregulation.

MicroRNAs (miRNAs) are a group of small, ∼21 nt long, riboregulators inhibiting gene expression at a post-transcriptional level. Their most distinctive structural feature is the foldback hairpin of their precursor pre-miRNAs. Even though each pre-miRNA deposited in miRBase has its secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures.

Hyperphosphorylated forms of the microtubule-associated protein (MAP) tau accumulate in Alzheimer's disease and related tauopathies and are thought to have an important role in neurodegeneration. However, the mechanisms through which phosphorylated tau induces neurodegeneration have remained elusive. Here, we show that tau-induced neurodegeneration is associated with accumulation of filamentous actin (F-actin) and the formation of actin-rich rods in Drosophila and mouse models of tauopathy. Importantly, modulating F-actin levels genetically leads to dramatic modification of tau-induced neurodegeneration. The ability of tau to interact with F-actin in vivo and in vitro provides a molecular mechanism for the observed phenotypes. Finally, we show that the Alzheimer's disease-linked human β-amyloid protein (Aβ) synergistically enhances the ability of wild-type tau to promote alterations in the actin cytoskeleton and neurodegeneration. These findings raise the possibility that a direct interaction between tau and actin may be a critical mediator of tau-induced neurotoxicity in Alzheimer's disease and related disorders.

MicroRNAs (miRNAs) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. miRNAs are most often identified through computational prediction from genome sequences. The rainbow trout genome sequence is not available yet, which does not allow miRNA prediction for this species which is of great economic interest for aquaculture and sport fisheries, and is a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. To identify miRNAs from rainbow trout, we constructed a miRNA library from a pool of nine somatic tissues. Analysis of the library identified 210 unique sequences representing 54 distinct miRNAs; 50 with conserved sequences matching previously identified miRNAs and four novel miRNAs. In addition, 13 miRNAs were computationally predicted from the rainbow trout transcriptome. Real-time PCR was used to measure miRNA expression patterns in adult somatic tissues and unfertilized eggs. The majority of the miRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. Potential miRNA-target interactions were computationally predicted and single nucleotide polymorphisms (SNPs) were identified in the miRNAs and their target sites in the rainbow trout transcripts. The rainbow trout miRNAs identified and characterized in this study provide a new tool for functional genome research in salmonids. Tissue-specific miRNAs may serve as molecular markers, predictive of specific functional and diagnostic implications. The data on genetic polymorphisms in miRNA-target interactions is particularly useful for rainbow trout breeding programs.

Introduction: Amyotrophic Lateral Sclerosis is a group of sporadic or familial disorders, characterized by upper and lower motor neuron involvement, with variable progression. Areas covered: The authors present the role of exercise in counteracting muscle disuse, particularly on limb weakness, that might antagonize denervation. The persistence of inactivity can affect many systems and the patient can develop deconditioning, muscle joint tightness, which causes contractures and pain. The main area of the review is the evaluation of the studies done on ALS exercise rehabilitation protocols, this was done by the evaluation of outcome function and patient independence exerting a positive psychological impact on both patients and caregivers. A second target is underlying differences between endurance and resistance exercise protocols, which may throw light on the biological mechanism of skeletal muscle repair, functional performance, and metabolism. The authors present not only exercise trials but also molecular biomarkers that might help define changes induced by physical rehabilitation. Our findings might help to achieve the best rehabilitation program. A standardized rehabilitation protocol is important: the instructed patients may continue therapy at home or be followed by telemedicine. Expert opinion: This review evaluates exercise rehabilitation, a controversial issue, evidence is weak and non-conclusive but represents the art status.

Collagen remodelling by fibroblasts has a crucial role in organizing tissue structures that are essential to motility during wound repair, development and regulation of cell growth. However, the mechanism of collagen fibre movement in threedimensional (3D) matrices is not understood. Here, we show that fibroblast lamellipodia extend along held collagen fibres, bind, and retract them in a 'hand-over-hand' cycle, involving α2β1 integrin. Wild-type fibroblasts move collagen fibres three to four times farther per cycle than fibroblasts lacking myosin II-B (myosin II-B −/−). Similarly, myosin II-B −/− fibroblasts contract 3D collagen gels threefold less than controls. On twodimensional (2D) substrates, however, rates of collagen bead and cell movement are not affected by loss of myosin II-B. Green fluorescent protein (GFP)-tagged myosin II-B, but not II-A, restores normal function in knockout cells and localizes to cell processes, whereas myosin II-A is more centrally located. Additionally, GFP-myosin II-B moves out to the periphery and back during handover hand fibre movement, whereas on 2D collagen, myosin II-B is more centrally distributed. Thus, we suggest that cyclic myosin II-B assembly and contraction in lamellipodia power 3D fibre movements. Remodelling of extracellular matrix proteins is critical to the organization of tissues and organs; therefore, it is important to understand the cellular and molecular steps in single collagen fibre movement. Surprisingly, cell motility on glass and other 2D substrates is not necessarily relevant to the movement of fibres in 3D matrices. There is limited overlap between the proteins localized to 3D matrix contacts and those at 2D adhesions 1,2. Furthermore, the morphology of fibroblasts in a 3D collagen matrix bears little resemblance to their morphology on a 2D collagen-coated surface 3,4. Thus, there is a fundamentally different mode of motility on 3D fibres compared with 2D surfaces 5. Carefully orchestrated movements of actin and myosin underlie most cellular motile processes 6-8. This motile machinery forms the cortical cytoskeleton. Upon binding extracellular matrix proteins, integrin receptors initiate a complex signalling cascade culminating in the

Objective: To identify microRNAs (miRNAs) differentially expressed at early stages of gestation (12e14 weeks) in the serum of pregnant women, who later developed severe preeclampsia (sPE) in the third trimester of pregnancy (n ¼ 24) compared to women with normal pregnancy (n ¼ 24). Materials and Methods: Sera from 12e14-week-gestation whole blood were subjected to microarray analysis with TaqMan Low Density Array chips (human microRNA panel V3.0), and to quantitative realtime polymerase chain reaction. Results: By using the TaqMan Low Density Array chip technology, 19 mature miRNAs appeared differentially expressed in the group of women who later developed sPE as compared to normal women. The expression of four miRNAs (miR-1233, miR-520, miR-210, miR-144) was validated by quantitative realtime polymerase chain reaction analysis. MiR-1233 was the most overexpressed in the serum of women who later developed sPE. Conclusion: Circulating miRNAs deserve further investigation in order to explore their potential role in the pathogenesis of preeclampsia. In particular, miR-1233 might represent a potential marker of early sPE.

Dendritic cells (DCs) exposed to tumor antigens followed by treatment with T h 1-polarizing differentiation signals have paved the way for the development of DC-based cancer vaccines. Critical parameters for assessment of the optimal functional state of DCs and prediction of the vaccine potency of activated DCs have in the past been based on measurements of differentiation surface markers like HLA-DR, CD80, CD83, CD86, and CCR7 and the level of secreted cytokines like interleukin-12p70. However, the level of these markers does not provide a complete picture of the DC phenotype and may be insufficient for prediction of clinical outcome for DC-based therapy. We therefore looked for additional biomarkers by investigating the differential expression of microRNAs (miRNAs) in mature DCs relative to immature DCs. A microarray-based screening revealed that 12 miRNAs were differentially expressed in the two DC phenotypes. Of these, four miRNAs, hsa-miR-155, hsa-miR-146a, hsa-miR-125a-5p, and hsa-miR-29a, were validated by real-time polymerase chain reaction and northern blotting. The matured DCs from 12 individual donors were divided into two groups of highly and less differentiated DCs, respectively. A pronounced difference at the level of miRNA induction between these two groups was observed, suggesting that quantitative evaluation of selected miRNAs potentially can predict the immunogenicity of DC vaccines. ᭧

rescuing collapsed replication forks. In contrast, uncontrolled HR can lead to chromosome translocations, loss of heterozygosity, and deletion of repetitive sequences. Controlled HR is particularly important for the preservation of repetitive sequences of the ribosomal gene (rDNA) cluster. Here we show that recombinational repair of a DSB in rDNA in Saccharomyces cerevisiae involves the transient relocalization of the lesion to associate with the recombination machinery at an extranucleolar site. The nucleolar exclusion of Rad52 recombination foci entails Mre11 and Smc5-Smc6 complexes and depends on Rad52 SUMO (small ubiquitin-related modifier) modification. Remarkably, mutations that abrogate these activities result in the formation of Rad52 foci within the nucleolus and cause rDNA hyperrecombination and the excision of extrachromosomal rDNA circles. Our study also suggests a key role of sumoylation for nucleolar dynamics, perhaps in the compartmentalization of nuclear activities.

Background: Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far.

Cancer metastasis is a multistep process characterised by local invasion, transport by the circulation, and survival and proliferation of metastasising cells in distant tissues. Similarities have been observed between the invasive and metastatic behaviour of cancer cells on the one hand and the long-distance migration of cells during development on the other. Epithelial cells usually form a mono-or multilayer on top of a basement membrane, and by lining the cavities and surfaces of the body, they form a protective barrier. Th ese cells are tightly connected to each other by adhesion proteins (for example, E-cadherin), they express epithelial markers (for example, cytokera-tins), and they are apico-basally polarised. Together with the extracellular matrix (ECM), mesen chymal cells fi ll the interstitial spaces and are a source of growth factors. Mesenchymal cells lack cell-cell contacts, express mesenchymal markers such as vimentin, and exhibit migratory behaviour. During epithelial-to-mesenchymal transition (EMT), epithelial cells lose their epithelial features and acquire a fi broblast-like morphology, with cytoskeletal reorganisation, upregu lation of mesenchymal markers, and enhancement of motility, invasiveness and metastatic capabilities . Th erefore, reactivation of an embryonic EMT program could be the underlying mechanism of tumour invasion. At distant sites, cancer cells can under go the reverse process, a mesenchymal-to-epithelial transi tion (MET). Th is is a transient phenomenon in which cancer cells reacquire epithelial characteristics once the invasion step is fi nished . Understanding these processes is crucial because metastasis is a prominent cause of cancer-related death.

The Cancer Genome Atlas (TCGA) project has analyzed mRNA expression, miRNA expression, promoter methylation, and DNA copy number in 489 high-grade serous ovarian adenocarcinomas (HGS-OvCa) and the DNA sequences of exons from coding genes in 316 of these tumors. These results show that HGS-OvCa is characterized by TP53 mutations in almost all tumors (96%); low prevalence but statistically recurrent somatic mutations in 9 additional genes including NF1, BRCA1, BRCA2, RB1, and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three miRNA subtypes, four promoter methylation subtypes, a transcriptional signature associated with survival duration and shed new light on the impact on survival of tumors with BRCA1/2 and CCNE1 aberrations. Pathway analyses suggested that homologous recombination is defective in about half of tumors, and that Notch and FOXM1 signaling are involved in serous ovarian cancer pathophysiology.

Endometriosis, defined as the presence of endometrial tissue outside the uterus, is a common gynecological disease with poorly understood pathogenesis. MicroRNAs are members of a class of small noncoding RNA molecules that have a critical role in posttranscriptional regulation of gene expression by repression of target mRNAs translation. We assessed differentially expressed microRNAs in ectopic endometrium compared with eutopic endometrium in 3 patients through microarray analysis. We identified 50 microRNAs differentially expressed and the differential expression of five microRNAs was validated by real-time RT-PCR in other 13 patients. We identified in silico their predicted targets, several of which match the genes that have been identified to be differentially expressed in ectopic versus eutopic endometrium in studies of gene expression. A functional analysis of the predicted targets indicates that several of these are involved in molecular pathways implicated in endometriosis, thus strengthening the hypothesis of the role of microRNAs in this pathology.

The importance of high quality sample material, i.e. non-degraded or fragmented RNA, for classical gene expression profiling is well documented. Hence, the analysis of RNA quality is a valuable tool in the preparation of methods like RT-qPCR and microarray analysis. For verification of RNA integrity, today the use of automated capillary electrophoresis is state of the art. Following the recently published MIQE guidelines, these pre-PCR evaluations have to be clearly documented in scientific publication to increase experimental transparency. RNA quality control may also be integrated in the routine analysis of new applications like the investigation of microRNA (miRNA) expression, as there is little known yet about factors compromising the miRNA analysis. Agilent Technologies is offering a new lab-on-chip application for the 2100 Bioanalyzer making it possible to quantify miRNA in absolute amounts [pg] and as a percentage of small RNA [%]. Recent results showed that this analysis met...

The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, nextgeneration sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.

The Rho family of small GTPases (RhoA, Rac1 and Cdc42) controls signal-transduction pathways that influence many aspects of cell behaviour, including cytoskeletal dynamics 1-3 . At the leading edge, Rac1 and Cdc42 promote cell motility through the formation of lamellipodia and filopodia, respectively. On the contrary, RhoA promotes the formation of contractile actin−myosin-containing stress fibres in the cell body and at the rear 1,2,4 . Here, we identify synaptopodin, an actinassociated protein, as a novel regulator of RhoA signalling and cell migration in kidney podocytes. We show that synaptopodin induces stress fibres by competitive blocking of Smurf1mediated ubiquitination of RhoA, thereby preventing the targeting of RhoA for proteasomal degradation. Gene silencing of synaptopodin in kidney podocytes causes the loss of stress fibres and the formation of aberrant non-polarized filopodia and impairment of cell migration. Together, these data show that synaptopodin is essential for the integrity of the podocyte actin cytoskeleton and for the regulation of podocyte cell migration.

It is due to the advances in high-throughput omics data generation that RNA species have re-entered the
focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE
projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with
various but primarily regulatory roles. Many of these are linked to the emergence and progression of
human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and
biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers.
These efforts led to the identification of a new tool-kit for cancer diagnosis, monitoring, and treatment,
which is now starting to enter and impact on clinical practice. This chapter is to elaborate on the state
of the art in RNA systems biology, including a review and perspective on clinical applications toward an
integrative RNA systems medicine approach. The focus is on the role of ncRNAs in cancer.

MicroRNAs (miRNAs) are short ~18-22 nucleotide, single-stranded, non-coding RNA molecules playing a crucial role in regulating diverse biological processes and are frequently dysregulated during disease pathogenesis. Thus, targeting miRNA could be a potential candidate for therapeutic invention. This systemic review aims to summarize our current understanding regarding the role of miRNAs associated with Th2-mediated immune disorders and strategies for therapeutic drug development and current clinical trials.

Preeclampsia is a disease of pregnancy characterized by the new onset of hypertension and proteinuria after 20 weeks of gestation. It has been estimated that preeclampsia affects 3–5% of pregnancies worldwide, and recently, preeclampsia complicates 3–8% of pregnancies and resulting in a very large disease burden. Several pathological mechanisms have been implicated in the development of preeclampsia. These include endothelial dysfunction, an inflammatory pathway, oxidative stress, activation of thrombosis, and the renin-angiotensin system. In addition, some experts believe that placenta have a central role in pathogenesis of preeclampsia. Recently, several studies have reported the differential expression of microRNAs either in placenta and serum from preeclamptic women. In 2007, it was the first report preeclampsia was associated with altered expression of microRNAs in placenta. Later on, studies also documented that individual microRNAs deregulation in placenta of preeclamptic women. Target genes of these differentially expressed microRNAs participated in diverse pathological processes including in reproductive system such as immunologic dysfunction, cell adhesion, cell cycle and signaling, antiapoptosis and regulation of transcription. Our analysis showed that deregulation of individual miRNAs linked with a pivotal role in endothelial dysfunction, maternal inflammatory respond, oxidative stress, activation of thrombosis, regulation of angiogenic factors, regulation of nitric oxide synthase, calcium metabolism and regulation of the renin-angiotensin system. It seems that RNAs fulfill “missing-link” in the pathogenesis of preeclampsia.

Cancer initiation and progression is controlled by both genetic and epigenetic events. Epigenetics refers to the study of mechanisms that alter gene expression without permanently altering the DNA sequence. Epigenetic alterations are reversible and heritable, and include changes in histone modifications, DNA methylation, and non-coding RNA-mediated gene silencing. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications occur at the earliest stages of neoplastic transformation and are now believed to be essential players in cancer initiation and progression. Recent advances in epigenetics have not only offered a deeper understanding of the underlying mechanism(s) of carcinogenesis, but have also allowed identification of clinically relevant putative biomarkers for the early detection, disease monitoring, prognosis and risk assessment of cancer patients. At this moment, DNA methylation and non-coding RNA including with microRNAs (miR-NAs) and long non-coding RNAs (lncRNAs) represent the largest body of available literature on epigenetic biomarkers with the highest potential for cancer diagnosis. Following identification of cell-free nucleic acids in systematic circulation, increasing evidence has demonstrated the potential of cell-free epigenetic biomarkers in the blood or other body fluids for cancer detection. In this article, we summarize the current state of knowledge on epigenetic biomarkers -primarily DNA methylation and non-coding RNAsas potential substrates for cancer detection in gastric and colorectal cancer, the two most frequent cancers within the gastrointestinal tract. We also discuss the obstacles that have limited the routine use of epigenetic biomarkers in the clinical settings and provide our perspective on approaches that might help overcome these hurdles, so that these biomarkers can be readily developed for clinical management of cancer patients.

Cardiovascular disease (CVD) is a major cause of morbidity and mortality
worldwide. Innovative, more stringent diagnostic and prognostic biomarkers
and effective treatment options are needed to lessen its burden. In
recent years, microRNAs have emerged as master regulators of gene
expression – they bind to complementary sequences within the mRNAs of
their target genes and inhibit their expression by either mRNA degradation
or translational repression. microRNAs have been implicated in all major
cellular processes, including cell cycle, differentiation and metabolism.
Their unique mode of action, fine-tuning gene expression rather than turning
genes on/off, and their ability to simultaneously regulate multiple elements
of relevant pathways makes them enticing potential biomarkers and
therapeutic targets. Indeed, cardiovascular patients have specific patterns
of circulating microRNA levels, often early in the disease process. This
article provides a systematic overview of the role of microRNAs in the
pathophysiology, diagnosis and treatment of CVD.

Macroautophagy (autophagy herein) is a cellular stress response and a survival pathway that is responsible for the degradation of long-lived proteins, protein aggregates, as well as damaged organelles in order to maintain cellular homeostasis. Consequently, abnormalities of autophagy are associated with a number of diseases, including Alzheimers's disease, Parkinson's disease, and cancer. According to the current view, autophagy seems to serve as a tumor suppressor in the early phases of cancer formation, yet in later phases, autophagy may support and/or facilitate tumor growth, spread, and contribute to treatment resistance. Therefore, autophagy is considered as a stage-dependent dual player in cancer. microRNAs (miRNAs) are endogenous non-coding small RNAs that negatively regulate gene expression at a post-transcriptional level. miRNAs control several fundamental biological processes, and autophagy is no exception. Furthermore, accumulating data in the literature indicate that dysregulation of miRNA expression contribute to the mechanisms of cancer formation, invasion, metastasis, and affect responses to chemotherapy or radiotherapy. Therefore, considering the importance of autophagy for cancer biology, study of autophagy-regulating miRNA in cancer will allow a better understanding of malignancies and lead to the development of novel disease markers and therapeutic strategies. The potential to provide study of some of these cancer-related miRNAs were also implicated in autophagy regulation. In this review, we will focus on autophagy, miRNA, and cancer connection, and discuss its implications for cancer biology and cancer treatment.

Les parties codantes des gènes de l'ADN, qui détiennent les codes de fabrication des protéines qui régulent notre corps, n'occupent que 1,3% environ de la totalité de l'ADN. Les zones non-codantes dans et entre les gènes intriguent les scientifiques par leur présence énigmatique. Ayant abandonné l'idée que ces zones sont inutiles, ils commencent à mettre en évidence leurs fonctions possibles. Ils ont des rôles de régulation et de contrôle. Les zones intergènes comportent des séquences caractéristiques pour chaque individu, au point qu'elles ont été retenues par la législation comme base de l'empreinte génétique. Il existe donc une architecture significative dans l'ADN. Par des méthodes d'analyse statistique, des mathématiciens ont mis en évidence un ordre fractal qui varie selon le type d'ADN.

Triple negative breast cancer is deprived of estrogen receptor alpha (ERa), progesterone receptor (PR) and HER-2 protein. It constitutes the most heterogeneous and aggressive group of breast carcinomas, for which identification of novel characteristics and characterization of putative targets becomes very demanding. In the present work we have assayed the expression of ERa36, a recently identified ERa variant of 36 kDa, in a series of triple negative breast cancers, in relation to the clinical behavior and other clinico-pathological features of the tumors. While widely expressed within the cytoplasm in almost all tumors, we found that exclusively the membrane/submembrane expression of the receptor exhibits a correlation with patient's survival. Moreover, membrane ERa36 correlates in an inverse manner with the expression of miRNA210, a pro-angiogenic miR, with high prognostic relevance in triple negative carcinomas. A thorough transcriptomic, pharmacological-based approach in breast cancer cell lines, revealed an early (direct) transcriptional signature of the receptor activation, related to immune system processes and T-cell differentiation, RNA biosynthesis, regulation of metabolism, VEGF signaling and regulation of the cell cycle, with a down-regulation of CREB, NFjB and STATs transcription factors. Finally, ERa36 expression is not limited within breast cancer epithelial linen, but is equally identified in tumor vasculature, peritumoral fat tissue, lymphocytic infiltrate and stromal fibroblasts. In light of the above, ERa36 could represent a major counterpart in triple negative breast cancer.

The interplay between abnormalities in genes coding for proteins and noncoding microRNAs (miRNAs) has been among the most exciting yet unexpected discoveries in oncology over the last decade. The complexity of this network has redefined cancer research as miRNAs, produced from what was once considered "genomic trash," have shown to be crucial for cancer initiation, progression, and dissemination. Naturally occurring miRNAs are very short transcripts that never produce a protein or amino acid chain, but act by regulating protein expression during cellular processes such as growth, development, and differentiation at the transcriptional, posttranscriptional, and/or translational level. In this review article, miRNAs are presented as ubiquitous players involved in all cancer hallmarks. The authors also describe the most used methods to detect their expression, which have revealed the identity of hundreds of miRNAs dysregulated in cancer cells or tumor microenvironment cells. Furthermore, the role of miRNAs as hormones and as reliable cancer biomarkers and predictors of treatment response is discussed. Along with this, the authors explore current strategies in designing miRNA-targeting therapeutics, as well as the associated challenges that research envisions to overcome. Finally, a new wave in molecular oncology translational research is introduced: the study of long noncoding RNAs.

microRNAs (miRNAs) are approximately 22-nucleotide noncoding RNA regulatory genes that are key players in cellular differentiation and homeostasis. They might also play important roles in shaping metazoan macroevolution. Previous studies have shown that miRNAs are continuously being added to metazoan genomes through time, and, once integrated into gene regulatory networks, show only rare mutations within the primary sequence of the mature gene product and are only rarely secondarily lost. However, because the conclusions from these studies were largely based on phylogenetic conservation of miRNAs between model systems like Drosophila and the taxon of interest, it was unclear if these trends would describe most miRNAs in most metazoan taxa. Here, we describe the shared complement of miRNAs among 18 animal species using a combination of 454 sequencing of small RNA libraries with genomic searches. We show that the evolutionary trends elucidated from the model systems are generally true for all miRNA families and metazoan taxa explored: the continuous addition of miRNA families with only rare substitutions to the mature sequence, and only rare instances of secondary loss. Despite this conservation, we document evolutionary stable shifts to the determination of position 1 of the mature sequence, a phenomenon we call seed shifting, as well as the ability to post-transcriptionally edit the 5 0 end of the mature read, changing the identity of the seed sequence and possibly the repertoire of downstream targets. Finally, we describe a novel type of miRNA in demosponges that, although shows a different pre-miRNA structure, still shows remarkable conservation of the mature sequence in the two sponge species analyzed. We propose that miRNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation.

The emergence of dramatic morphological differences (disparity) and the ensuing bewildering increase in the number of species (diversity) documented in the fossil record at key stages of animal and plant evolution have defied, and still defy, the explanatory powers of Darwin's theory of evolution by natural selection. Among the best examples that have captured the imagination of the layman and the interest of scores of scientists for  years are the origins of land plants from aquatic green plants, of flowering plants from seed plants, of chordates from non-chordates and of tetrapod vertebrates from non-tetrapods; and the conquest of the land by amphibians; the emergence of endotherms from ectotherm animals; the recurrent invention of flight (e.g. in arthropods, birds and mammals) from non-flying ancestors; and the origin of aquatic mammals from fourlegged terrestrial ancestors.

The emergence of dramatic morphological differences (disparity) and the ensuing bewildering increase in the number of species (diversity) documented in the fossil record at key stages of animal and plant evolution have defied, and still defy, the explanatory powers of Darwin's theory of evolution by natural selection. Among the best examples that have captured the imagination of the layman and the interest of scores of scientists for  years are the origins of land plants from aquatic green plants, of flowering plants from seed plants, of chordates from non-chordates and of tetrapod vertebrates from non-tetrapods; and the conquest of the land by amphibians; the emergence of endotherms from ectotherm animals; the recurrent invention of flight (e.g. in arthropods, birds and mammals) from non-flying ancestors; and the origin of aquatic mammals from fourlegged terrestrial ancestors.

microRNAs (miRNA) are involved in cancer development and progression, acting as tumor suppressors or oncogenes. Here, we profiled the expression of 290 unique human miRNAs in 11 normal and 106 bladder tumor samples using spotted locked nucleic acid-based oligonucleotide microarrays. We identified several differentially expressed miRNAs between normal urothelium and cancer and between the different disease stages. miR-145 was found to be the most down-regulated in cancer compared with normal, and miR-21 was the most upregulated in cancer. Furthermore, we identified miRNAs that significantly correlated to the presence of concomitant carcinoma in situ. We identified several miRNAs with prognostic potential for predicting disease progression (e.g., miR-129, miR-133b, and miR-518c*). We localized the expression of miR-145, miR-21, and miR-129 to urothelium by in situ hybridization. We then focused on miR-129 that exerted significant growth inhibition and induced cell death upon transfection with a miR-129 precursor in bladder carcinoma cell lines T24 and SW780 cells. Microarray analysis of T24 cells after transfection showed significant miR-129 target downregulation (P = 0.0002) and pathway analysis indicated that targets were involved in cell death processes. By analyzing gene expression data from clinical tumor samples, we identified significant expression changes of target mRNA molecules related to the miRNA expression. Using luciferase assays, we documented a direct link between miR-129 and the two putative targets GALNT1 and SOX4. The findings reported here indicate that several miRNAs are differentially regulated in bladder cancer and may form a basis for clinical development of new biomarkers for bladder cancer. [Cancer Res 2009;69(11):4851-60]

Techniques of molecular biology have improved diagnostic sensitivity, accuracy and validity in forensic medicine very much, especially in the field of identification (paternity testing, stain analysis). Since more than 10 years these techniques -meanwhile well established in clinical disciplines -are used also for other applications in forensic medicine: determination of cause and manner of death, tissue identification by mRNA and microRNA, examination of gene expression levels (survival time, time since death, cause of death), toxicogenetics.

Prostate cancer is a commonly diagnosed cancer in men and a leading cause of cancer deaths. Whilst the underlying mechanisms leading to prostate cancer are still to be determined, it is evident that both genetic and epigenetic changes contribute to the development and progression of this disease. Epigenetic changes involving DNA hypo-and hypermethylation, altered histone modifications and more recently changes in microRNA expression have been detected at a range of genes associated with prostate cancer. Furthermore, there is evidence that particular epigenetic changes are associated with different stages of the disease. Whilst early detection can lead to effective treatment, and androgen deprivation therapy has a high response rate, many tumours develop towards hormone-refractory prostate cancer, for which there is no successful treatment. Reliable markers for early detection and more effective treatment strategies are, therefore, needed. Consequently, there is a considerable interest in the potential of epigenetic changes as markers or targets for therapy in prostate cancer. Epigenetic modifiers that demethylate DNA and inhibit histone deacetylases have recently been explored to reactivate silenced gene expression in cancer. However, further understanding of the mechanisms and the effects of chromatin modulation in prostate cancer are required. In this review, we examine the current literature on epigenetic changes associated with prostate cancer and discuss the potential use of epigenetic modifiers for treatment of this disease.