Differential Expression Profiles Of miRNAs Research Articles

Global identification and analysis of microRNAs involved in salt stress responses in two alfalfa (Medicago sativa ‘Millennium’) lines

Alfalfa is an important economic crop; a mutant (M) strain was identified during planting and production. M plants consistently had better relative water content and relative electrical conductivity under higher salt conditions compared with the wild type (WT) plants, suggesting that M plants have higher tolerance for salt. To understand the microRNAs (miRNAs) involved in salt stress response in alfalfa, 128 miRNAs were identified from the WT and M alfalfa plants under normal and saline conditions. Of the 128 miRNAs, 29 and 23 differentially expressed miRNAs were identified in the M vs. WT control (M-CK vs. WT-CK) and salt-stressed M vs. WT (M-salt vs. WT-salt) comparison, respectively. These miRNAs responded to salt stress and showed different expression patterns after salt treatment. Their potential target genes were predicted and further analysed by GO classification and KEGG pathway analysis, where the majority of target genes were associated with plant growth and development, and exhibited significant changes in WT and M plants. In addition, compared with the WT plants, miR172-CNGC, miR319-CAX2, miR408-NHX and miR2590-CHX14/15 showed significant upregulation in M alfalfa plants, suggesting that M plants have higher ion transport levels. The differential expression profiles of miRNAs and putative target genes were further validated by quantitative real-time polymerase chain reaction. It is speculated that these miRNAs are involved in the increased salt tolerance of the M alfalfa plants.

Variability in Cerebrospinal Fluid MicroRNAs Through Life.

The development of the human brain starts in the first weeks of embryo differentiation. However, there are many relevant neurodevelopmental processes that take place after birth and during lifespan. Such a fine and changing scenario requires the coordinated expression of thousands of genes to achieve the proper specialization and inter-connectivity. In this context, microRNAs (miRNAs), which can modulate mRNA stability and translation, are gaining recognition for their involvement in both brain development and neurodevelopmental disorders. Therefore, cerebrospinal fluid (CSF) miRNAs should be perfectly differentiated in relevant age periods. In this study, we aimed to highlight the biological variability of miRNA expression in the CSF throughout life, which is also crucial for biomarker discovery in CNS pathologies, especially in children, where they are desperately needed. We analyzed the CSF microRNAome of 14 healthy children (aged 0-7.4years) by smallRNA-Seq and compared it with previously published data in adults (N = 7) and elders (N = 11). miR-423-5p and miR-22-3p were overexpressed in the < 1 and > 3years groups, respectively. Additionally, we detected 18 miRNAs that reached their highest peak of expression at different time-points during the lifespan and sets of miRNAs that were exclusively expressed in a specific age group. On the contrary, miR-191-5p showed stable expression in CSF from the first year of life. Our results remark the complex differential miRNA expression profile that can be observed through life, which underlines the need for including appropriate age-matched controls when the expression of CSF miRNAs is analyzed in different pathological contexts. Graphical abstract.

Comprehensive Analysis of lncRNA Expression Pattern and lncRNA–miRNA–mRNA Network in a Rat Model With Cavernous Nerve Injury Erectile Dysfunction

BackgroundLong noncoding RNAs (lncRNAs) are differentially expressed in erectile dysfunction (ED) associated with aging and diabetes mellitus; however, the lncRNA expression profile in cavernous nerve (CN) injury–related ED (CNI-ED) is unknown. AimTo investigate the dysregulated lncRNAs, microRNAs (miRNAs), and mRNA expression in CNI-ED and construct a potential lncRNA–miRNA–mRNA network. Methods22 male Sprague–Dawley (SD) rats were divided into bilateral CN crush (BCNC) and Sham groups. Using second-generation high-throughput sequencing technology, we analyzed the expression profiles of lncRNA, miRNA, and mRNA of the 2 groups. 17 differentially expressed lncRNAs were selected and further validated by quantitative real-time polymerase chain reaction (RT-qPCR). The lncRNA–miRNA–mRNA network, Gene Ontology (GO) term enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using Cytoscape. OutcomesIntra-cavernosal pressure, mean arterial pressure, smooth muscle content, and the expression of miRNA, mRNA, and lncRNA were measured. ResultsThe BCNC group showed decreased intra-cavernosal/mean arterial pressure as well as decreased smooth muscle/collagen ratios compared with the Sham group. The RNA sequencing results revealed dysregulated expressions of 65 lncRNA, 14 miRNA, and 750 mRNA in the BCNC group based on the following criteria: fold change >2 and P < .05. Among the 17 lncRNAs further selected based on mean count number >4 in both groups, 3 lncRNAs (TCONS_00028173, TCONS_00049985, and TCONS_00058429) were further validated for differential expression by RT-qPCR. GO analysis suggests that these 3 lncRNAs could regulate various processes such as myotube differentiation and muscle cell differentiation. Furthermore, the KEGG pathway analysis showed that the mRNAs in the competing endogenous RNA (ceRNA) network are involved in pathways, including axon guidance and vascular endothelial growth factor signaling pathway. Clinical TranslationOur findings may provide new information on molecular pathophysiology of CNI-ED and suggest further research to find a more effective therapy for CNI-ED. Strengths & LimitationsThis study is the first to identify the lncRNA expression pattern and propose a ceRNA network in a rat model with cavernous nerve injury–related erectile dysfunction. However, analogous studies are needed to confirm these findings in humans. In addition, we constructed the network by only confirming the lncRNA. ConclusionOur study reveals differential expression profiles of lncRNAs, miRNAs, and mRNAs between the BCNC and Sham groups and suggests that these differentially expressed lncRNAs may play critical roles in CNI-ED by regulating apoptosis and fibrosis in the corpus cavernosum via targeting mRNAs or miRNAs.Cong R, Wang Y, Wang Y. Comprehensive Analysis of lncRNA Expression Pattern and lncRNA–miRNA–mRNA Network in a Rat Model With Cavernous Nerve Injury Erectile Dysfunction. J Sex Med 2020;17:1603–1617.

Key miRNAs associated with memory and learning disorder upon exposure to sevoflurane determined by RNA sequencing.

The study aimed to identify differentially expressed microRNAs (miRNAs/miRs) and explore the mechanisms governing impaired memory and learning ability in developing brains exposed to sevoflurane. A total of six 7-day-old male ICR mice were randomly assigned into the sevoflurane anesthesia group (treated with 2.4% sevoflurane) or control group (treated with normal saline solution at the same dose). After 14 days, the mice were subjected to a Morris water maze experiment. Then, the animals were sacrificed and hippocampus tissues were isolated. RNAs in hippocampus tissues were sequenced and the differential miRNA expression profiles were identified by a bioinformatics approach. The learning and memory function of mice were significantly affected by sevoflurane exposure. A total of 18 miRNAs were found to be significantly affected by sevoflurane administration. Their target genes clustered into different functional groups, such as ‘dephosphorylation’, ‘vesicle localization’ and the ‘Wnt signaling pathway’. miR-101b-3p was closely related with ‘chromatin binding’ and ‘protein serine/threonine kinase activity’. The most represented pathways for miRNAs included ‘neuroactive ligand-receptor interaction’ (miR-1187), ‘long-term depression’ (miR-425-5p), ‘FoxO signaling pathway’ (miR-425-5p) and the ‘neurotrophin signaling pathway’ (miR-467a-3p). miR-467a-3p (degree=89), miR-101b-3p (degree=59), and miR-1187 (degree=51) were the hub nodes in the miRNA regulatory network. The Wnt signaling pathway, miR-467a-3p, miR-1187 and miR-101b-3p may be therapeutic targets for preventing cognitive impairments induced by sevoflurane.

The differential expression of micro-RNAs 21, 200c, 204, 205, and 211 in benign, dysplastic and malignant melanocytic lesions and critical evaluation of their role as diagnostic biomarkers

Overlapping histological features between benign and malignant lesions and a lack of firm diagnostic criteria for malignancy result in high rates of inter-observer variation in the diagnosis of melanocytic lesions. We aimed to investigate the differential expression of five miRNAs (21, 200c, 204, 205, and 211) in benign naevi (n = 42), dysplastic naevi (n = 41), melanoma in situ (n = 42), and melanoma (n = 42) and evaluate their potential as diagnostic biomarkers of melanocytic lesions. Real-time PCR showed differential miRNA expression profiles between benign naevi; dysplastic naevi and melanoma in situ; and invasive melanoma. We applied a random forest machine learning algorithm to classify cases based on their miRNA expression profiles, which resulted in a ROC curve analysis of 0.99 for malignant melanoma and greater than 0.9 for all other groups. This indicates an overall very high accuracy of our panel of miRNAs as a diagnostic biomarker of benign, dysplastic, and malignant melanocytic lesions. However, the impact of variable lesion percentage and spatial expression patterns of miRNAs on these real-time PCR results was also considered. In situ hybridisation confirmed the expression of miRNA 21 and 211 in melanocytes, while demonstrating expression of miRNA 205 only in keratinocytes, thus calling into question its value as a biomarker of melanocytic lesions. In conclusion, we have validated some miRNAs, including miRNA 21 and 211, as potential diagnostic biomarkers of benign, dysplastic, and malignant melanocytic lesions. However, we also highlight the crucial importance of considering tissue morphology and spatial expression patterns when using molecular techniques for the discovery and validation of new biomarkers.

The differential pathological outcome between Chlamydia infection and vaccination is mediated by microRNA dysregulation

Abstract Previous studies found that in contrast to immunization with an IL-10 knockout dendritic cell (DC)-based cellular or Vibrio cholerae ghost (VCG)-based subunit vaccine, immunization with live chlamydial elementary bodies does not protect against upper genital tract pathology following Chlamydia genital infection. The molecular mechanism regulating live Chlamydia- and vaccine-induced immunity is currently incompletely understood. To elucidate the mechanisms underlying this intriguing outcome, we examined the characteristic miRNA expression profiles in the upper genital tract (UGT) tissues of mice after immunization with live, subunit and DC-based Chlamydia vaccines using the NanoString nCounter Mouse miRNA assay. There were notable differences in miRNA expression profiles after immunization with the different vaccine formulations, with the DC vaccine-immunized group showing the highest number of uniquely differentially expressed (DE) miRNAs. Only 2 miRNAs, miR-146a and miR-2140 were commonly expressed in the genital tracts of the 3 immunization groups. Pathway analysis showed that the DE miRNAs regulate a number of pathways involved in disease and biological functions and targeted genes regulating immune response and inflammation. A number of central focus molecules associated with the miRNAs, including E2F Transcription Factor 1 (E2F1), Peroxisome Proliferator Activated Receptor Alpha (PPARA), and Interferon gamma (IFNG) were identified. Taken together, the results suggest that miRNA dysregulation plays an important role in the pathological outcome associated with chlamydial infection versus vaccination.

Extracellular Vesicles isolated from Mesenchymal Stromal Cells Modulate CD4+ T Lymphocytes Toward a Regulatory Profile.

Mesenchymal stromal cells (MSCs) can generate immunological tolerance due to their regulatory activity in many immune cells. Extracellular vesicles (EVs) release is a pivotal mechanism by which MSCs exert their actions. In this study, we evaluate whether mesenchymal stromal cell extracellular vesicles (MSC-EVs) can modulate T cell response. MSCs were expanded and EVs were obtained by differential ultracentrifugation of the supernatant. The incorporation of MSC-EVs by T cells was detected by confocal microscopy. Expression of surface markers was detected by flow cytometry or CytoFLEX and cytokines were detected by RT-PCR, FACS and confocal microscopy and a miRNA PCR array was performed. We demonstrated that MSC-EVs were incorporated by lymphocytes in vitro and decreased T cell proliferation and Th1 differentiation. Interestingly, in Th1 polarization, MSC-EVs increased Foxp3 expression and generated a subpopulation of IFN-γ+/Foxp3+T cells with suppressive capacity. A differential expression profile of miRNAs in MSC-EVs-treated Th1 cells was seen, and also a modulation of one of their target genes, TGFbR2. MSC-EVs altered the metabolism of Th1-differentiated T cells, suggesting the involvement of the TGF-β pathway in this metabolic modulation. The addition of MSC-EVs in vivo, in an OVA immunization model, generated cells Foxp3+. Thus, our findings suggest that MSC-EVs are able to specifically modulate activated T cells at an alternative regulatory profile by miRNAs and metabolism shifting.

Comparative profiling of exosomal miRNAs in human adult peripheral and umbilical cord blood plasma by deep sequencing.

Aim: To assess differential expression profiles of miRNAs in exosomes derived from human peripheral blood (PB) and umbilical cord blood (UCB). Materials & methods: Small RNA sequencing was performed to characterize the miRNA expression in plasma exosomes processed from UCB of five healthy newborns and PB of five normal adult volunteers, and differentially expressed miRNAs were further analyzed. Results: A total of 65 exosomal miRNAs, including 46 upregulated and 19 downregulated, showed differential expression between UCB and PB. Target genes of these miRNAs were mainly enriched in signaling pathways associated with pregnancy, cancers, cell mobility and nervous system. Conclusion: Exosomal miRNAs may have essential roles in the biological functions of UCB, suggesting the therapeutic and biomarker potentials of exosomes in UCB.

Identification of non-invasive biomarkers for predicting the radiosensitivity of nasopharyngeal carcinoma from serum microRNAs

Serum microRNAs (miRNAs) have been reported as novel biomarkers for various diseases. But circulating biomarkers for predicting the radiosensitivity of nasopharyngeal carcinoma (NPC) have not been used in clinical practice. To screen out of differently expressed serum miRNAs from NPC patients with different radiosensitivity may be helpful for its individual therapy. NPC patients with different radiosensitivity were enrolled according to the inclusion and exclusion criteria. RNA was isolated from serum of these NPC patients before treatment. We investigated the differential miRNA expression profiles using microarray test (GSE139164), and the candidate miRNAs were validated by reverse transcription-quantitative real time polymerase chain reaction (RT-qPCR) experiments. Receiver operating characteristic (ROC) analysis has been applied to estimate the diagnostic value. In this study, 37 serum-specific miRNAs were screened out from 12 NPC patients with different radiosensitivity by microarray test. Furthermore, RT-qPCR analysis confirmed that hsa-miR-1281 and hsa-miR-6732-3p were significantly downregulated in the serum of radioresistant NPC patients (P < 0.05), which was consistent with the results of microarray test. ROC curves demonstrated that the AUC for hsa-miR-1281 was 0.750 (95% CI: 0.574–0.926, SE 87.5%, SP 57.1%). While the AUC for hsa-miR-6732-3p was 0.696 (95% CI: 0.507–0.886, SE 56.3%, SP 78.6%). These results suggested that hsa-miR-1281 and hsa-miR-6732-3p in serum might serve as potential biomarkers for predicting the radiosensitivity of NPC.

MicroRNA and mRNA analysis of angiotensin II-induced renal artery endothelial cell dysfunction.

Continuous activation of angiotensin II (Ang II) induces renal vascular endothelial dysfunction, inflammation and oxidative stress, all of which may contribute to renal damage. MicroRNAs (miRs/miRNAs) play a crucial regulatory role in the pathogenesis of hypertensive nephropathy (HN). The present study aimed to assess the differential expression profiles of potential candidate genes involved in Ang II-induced rat renal artery endothelial cell (RRAEC) dysfunction and explore their possible functions. In the present study, the changes in energy metabolism and autophagy function in RRAECs were evaluated using the Seahorse XF Glycolysis Stress Test and dansylcadaverine/transmission electron microscopy following exposure to Ang II. Subsequently, mRNA-miRNA sequencing experiments were performed to determine the differential expression profiles of mRNAs and miRNAs. Integrated bioinformatics analysis was applied to further explore the molecular mechanisms of Ang II on endothelial injury induced by Ang II. The present data supported the notion that Ang II upregulated glycolysis levels and promoted autophagy activation in RRAECs. The sequencing data demonstrated that 443 mRNAs and 58 miRNAs were differentially expressed (DE) in response to Ang II exposure, where 66 mRNAs and 55 miRNAs were upregulated, while 377 mRNAs and 3 miRNAs were downregulated (fold change >1.5 or <0.67; P<0.05). Functional analysis indicated that DE mRNA and DE miRNA target genes were mainly associated with cell metabolism (metabolic pathways), differentiation (Th1 and Th2 cell differentiation), autophagy (autophagy-animal and autophagy-other) and repair (RNA-repair). To the best of the authors' knowledge, this is the first report on mRNA-miRNA integrated profiles of Ang II-induced RRAECs. The present results provided evidence suggesting that the miRNA-mediated effect on the ‘mTOR signaling pathway’ might play a role in Ang II-induced RRAEC injury by driving glycolysis and autophagy activation. Targeting miRNAs and their associated pathways may provide valuable insight into the clinical management of HN and may improve patient outcome.

MiRNA profiling in renal carcinoma suggest the existence of a group of pro-angionenic tumors in localized clear cell renal carcinoma.

Renal cell carcinoma comprises a variety of entities, the most common being the clear-cell, papillary and chromophobe subtypes. These subtypes are related to different clinical evolution; however, most therapies have been developed for clear-cell carcinoma and there is not a specific treatment based on different subtypes. In this study, one hundred and sixty-four paraffin samples from primary nephrectomies for localized tumors were analyzed. MiRNAs were isolated and measured by microRNA arrays. Significance Analysis of Microarrays and Consensus Cluster algorithm were used to characterize different renal subtypes. The analyses showed that chromophobe renal tumors are a homogeneous group characterized by an overexpression of miR 1229, miR 10a, miR 182, miR 1208, miR 222, miR 221, miR 891b, miR 629-5p and miR 221-5p. On the other hand, clear cell renal carcinomas presented two different groups inside this histological subtype, with differences in miRNAs that regulate focal adhesion, transcription, apoptosis and angiogenesis processes. Specifically, one of the defined groups had an overexpression of proangiogenic microRNAs miR185, miR126 and miR130a. In conclusion, differences in miRNA expression profiles between histological renal subtypes were established. In addition, clear cell renal carcinomas had different expression of proangiogenic miRNAs. With the emergence of antiangiogenic drugs, these differences could be used as therapeutic targets in the future or as a selection method for tailoring personalized treatments.

Current insight into the roles of microRNA in vitiligo.

Vitiligo is a common chronic depigmented skin disease characterized by melanocyte loss or dysfunction in the lesion. The pathogenesis of vitiligo has not been fully clarified. Most studies have suggested that the occurrence and progression of vitiligo are due to multiple factors and gene interactions in which noncoding RNAs contribute to an individual's susceptibility to vitiligo. Noncoding RNAs, including microRNAs (miRNAs), are a hot topic in posttranscriptional regulatory mechanism research. miRNAs are noncoding RNAs with a length of approximately 22 nucleotides and play a negative regulatory role by binding to the 3'-UTR or 5'-UTR of the target mRNA to inhibit translation or initiate mRNA degradation. Previous studies have screened the differential expression profiles of miRNAs in the skin lesions, melanocytes, peripheral blood mononuclear cells (PBMCs) and sera of patients and mouse models with vitiligo. Moreover, several studies have focused on miRNA-25, miRNA-155 and other miRNAs involved in melanin metabolism, oxidative stress, and melanocyte proliferation and apoptosis. These miRNAs and regulatory processes further illuminate the pathogenesis of vitiligo and provide hope for the application of small molecules in the treatment of vitiligo. In this review, we summarize miRNA expression profiles in different tissues of vitiligo patients and the mechanisms by which key miRNAs mediate vitiligo development.

MiR-346 Inhibited Apoptosis Against Myocardial Ischemia-Reperfusion Injury via Targeting Bax in Rats.

PurposeMyocardial ischemia-reperfusion injury (MIRI) is a common pathophysiological process after occlusion of the blood vessels to restore blood supply. Apoptosis is one of the ways of myocardial cell death in this process. MicroRNAs (miRNAs), a class of short and noncoding RNAs, are involved in multiple biological processes by post-transcriptionally targeting their downstream effectors. To date, whether miRNAs exert biological effects in myocardial ischemia-reperfusion (I/R) injury remains to be further studied.MethodsIn this study, we induced MIRI model by ligating rat left anterior descending artery (LAD) for 30 mins and reperfusion for 2 hrs. The differential expression profile of miRNAs in rat models of MIRI was analyzed by miRNAs sequencing.ResultsWe found that miRNAs sequencing analysis showed the expressions of 15 types of miRNAs, including miR-346, were downregulated and 29 types of miRNAs were elevated in the MIRI rat model. We observed the key regulator of apoptosis Bax was a predicted downstream target of miR-346 using online software TargetScan. And luciferase reporter assay was utilized to certify this prediction. Over-expression of miR-346 can attenuate myocardial injury and narrow infarct area by inhibiting myocardial cell apoptosis in rat models.ConclusionThis study revealed a novel pathway, miR-346/Bax axis, in the regulation of apoptosis in MIRI and which might be a new molecular mechanism and therapeutic target.

Signatures of circulating microRNA in four sarcoma subtypes.

Background: Sarcomas are rare malignant tumors of mesenchymal origin. The discovery of circulating biomarkers with high diagnostic value could supplement diagnosis of this heterogenous group of tumors. The aim of this study was to identify the profiles of circulating miRNA (c-miRNAs) in four groups of common bone and soft tissue sarcomas.Methods: At the time of diagnosis, blood samples were collected from 86 patients: 36 with locally advanced/unresectable/metastatic gastrointestinal stromal tumor (GIST) who received first-line treatment with imatinib; 16 with locally advanced osteosarcoma (OS); 26 with locally advanced synovial sarcoma (SS); and eight with locally advanced Ewing sarcoma (ES). In addition, samples were collected from 30 healthy controls. C-miRNAs were isolated using a miRCURY RNA Isolation Kit, followed by preparation of cDNA libraries and sequencing on the Ion Proton platform.Results: Pair-wise comparisons identified 156 unique c-miRNAs (adjusted P-value < 0.05) showing significant dysregulation between controls and patients; of these, 24, 36, 42, and 99 differentiated controls from pretherapeutic OS, SS, ES, and GIST, respectively. Ten c-miRNAs were commonly altered in at least three sarcoma types. Receiver operating characteristic curves and area under the curve (ROC-AUC) analyses revealed that a four-miRNA diagnostic classifier was able to differentiate controls from ES, GIST, OS, and SS, with AUC-ROC values of 1, 0.97, 0.95, and 0.94, respectively.Conclusions: Aberrant miRNA expression signatures were identified in serum from patients with four different sarcoma subtypes. Differences in miRNA expression profiles between sarcoma patients and healthy volunteers suggest that miRNAs may play a role in sarcoma development.

Differentially expressed microRNAs in exosomes of patients with breast cancer revealed by next‑generation sequencing.

MicroRNAs (miRNAs/miRs) in exosomes play crucial roles in the onset, progression and metastasis of cancer by regulating the stability of target mRNAs or by inhibiting translation. In the present study, differentially expressed miRNAs were identified in exosomes of 27 breast cancer patients and 3 healthy controls using RNA sequencing. The differentially expressed microRNAs were selected by bioinformatic analysis. Subjects were followed up for 2 years and exosomal miRNA profiles were compared between patients with and without recurrence of breast cancer. A total of 30 complementary DNA libraries were constructed and sequenced and 1,835 miRNAs were detected. There were no significant differences in the expression of miRNAs between the basal-like, human epidermal growth factor receptor-2+, luminal A, luminal B and healthy control (HC) groups. A total of 54 differentially expressed miRNAs were identified in triple-negative breast cancer (TNBC) patients vs. HCs, including 20 upregulated and 34 downregulated miRNAs. The results of the reverse transcription-quantitative PCR were consistent with this. Receiver operating characteristic curve analyses indicated that miR-150-5p [area under the curve (AUC)=0.705, upregulated], miR-576-3p (AUC=0.691, upregulated), miR-4665-5p (AUC=0.681, upregulated) were able to distinguish breast cancer patients with recurrence from those without recurrence. In conclusion, the present results indicated differences in miRNA expression profiles between patients with TNBC and healthy controls. Certain exosomal miRNAs were indicated to have promising predictive value as biomarkers for distinguishing breast cancer with recurrence from non-recurrence, which may be utilized for preventive strategies.

Involvement of MicroRNAs in Regulation of Radioresistance of HeLa and DU145 Cells

Using the method of massively parallel sequencing, differential miRNA expression profiles in the original and radioresistant variants of HeLa and DU145 cell lines after radiation exposure at the dose of 4 Gy were obtained. Comparative analysis made it possible to identify a group of miRNAs aberrant expression of which reflected the changes in cell metabolism of radioresistant variants that remained across a number of cell generations as compared to the original ones. The obtained results suggest that the role of miRNAs is associated with the maintenance of functional interaction between DNA methyltransferases, Myc transcription factor, and PTEN phosphatase in regulating the activity of PI3K/AKT and MAPK/ERK signaling pathways. This may underlie differences in realization of radioresistance of HeLa and DU145 cells.

Differential miRNAs profile and bioinformatics analyses in bone marrow mesenchymal stem cells from adolescent idiopathic scoliosis patients

BACKGROUND CONTEXTCoexistence of abnormal skeletal growth and reduced bone mineral density in the context of adolescent idiopathic scoliosis (AIS) suggests disturbed bone metabolism existing in such patients. Our previous study suggested increased proliferation ability and decreased osteogenic differentiation ability of bone marrow mesenchymal stem cells (BM-MSCs) of AIS. PURPOSETo explore the differential miRNA expression profile, Go (gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways in BM-MSCs of AIS and non-AIS controls were conducted using microarray approach and bioinformatics analyses. STUDY DESIGNmiRNA microarray approach and bioinformatics analysis. METHODSThe differentially expressed miRNAs (DEMs) of BM-MSCs from AIS patients compared with those from healthy individuals were analyzed using a microarray analysis. Comprehensive bioinformatics analyses were then used to enrich datasets for gene ontology and pathway. Based on the interaction network analysis of DEMs contained in significant pathways, 12 potential crucial miRNAs were selected for validation by RT-PCR. RESULTSThe study identified 54 previously unrecognized DEMs (12 upregulated, 42 downregulated) in BM-MSCs from AIS patients. These miRNAs are involved in multiple biological processes, including small GTPase-mediated signal transduction, DNA-dependent transcription, cytokinesis, cell adhesion, transmembrane transport, response to hypoxia, etc. Pathway analysis of these new identified miRNAs revealed dysregulated MAPK signaling pathway, PI3K-Akt signaling pathway, calcium signaling pathway, Notch signaling pathway, and ubiquitin-mediated proteolysis pathway, all of which have been reported to play important role in regulating the osteogenic or adipogenic differentiation of MSCs. Furthermore, interaction networks analysis indicated that seven most significant central miRNAs, including miR-17-5p, miR-106a-5p, miR-106b-5p, miR-16-5p, miR-93-5p, miR-15a-5p, and miR-181b-5p may play essential roles in AIS pathogenesis and accompanied osteopenia. CONCLUSIONThe current study reports the differential miRNAs expression profiles of BM-MSCs from AIS patients and related pathways for the first time. The identification of these candidate miRNAs provides a deep insight into the pathogenesis of AIS and the accompanying generalized osteopenia.

Differential MicroRNA Expression Profiles as Potential Biomarkers for Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a clinical challenge due to its poor prognosis. Therefore, the early diagnosis of PDAC is extremely important for achieving a cure. MicroRNAs (miRNAs) could serve as a potential biomarker for the early detection and prognosis of PDAC. In this work we analyzed plasma samples from healthy persons and PDAC patients to assess differential miRNA expression profiles by next generation sequencing technology and bioinformatics analysis. In this way, 165 mature miRNAs were found to be significantly deregulated in the patient group, of which 75 and 90 mature miRNAs were up- and down-regulated compared with healthy individuals, respectively. Furthermore, 1029 novel miRNAs were identified. In conclusion, plasma miRNA expression profiles are different between healthy individuals and patients with PDAC. These data provide a possibility for use of miRNA as diagnostic and prognostic biomarkers of PDAC.

Comprehensive analysis of differentially expressed profiles and reconstruction of a competing endogenous RNA network in papillary renal cell carcinoma.

Long noncoding RNAs (lncRNAs) function as competing endogenous RNAs (ceRNAs). ceRNA networks may serve important roles in various tumors, as demonstrated by an increasing number of studies; however, papillary renal cell carcinoma (PRCC)-associated ceRNA networks mediated by lncRNAs remain unknown. Increased knowledge of ceRNA networks in PRCC may aid the identification of novel targets and biomarkers in the treatment of PRCC. In the present study, a comprehensive investigation of mRNA, lncRNA, and microRNA (miRNA) expression in PRCC was conducted using sequencing data from The Cancer Genome Atlas. Differential expression (DE) profiles of mRNAs, lncRNAs and miRNAs were evaluated, with 1,970 mRNAs, 1,201 lncRNAs and 96 miRNAs identified as genes with significantly different expression between PRCC and control paracancerous tissues. Based on the identified DEmRNAs, a protein-protein interaction network was generated using the STRING database. Furthermore, a ceRNA network for PRCC was determined using a targeted assay combined with the DE of miRNAs, mRNAs and lncRNAs, enabling the identification of important lncRNA-miRNA and miRNA-mRNA pairs. Analysis of the ceRNA network led to the extraction of a subnetwork and the identification of lncRNA maternally expressed 3 (MEG3), lncRNA PWRN1, miRNA (miR)-508, miR-21 and miR519 as important genes. Reverse transcription-quantitative polymerase chain reaction analysis was conducted to validate the results of the bioinformatics analyses; it was revealed that lncRNA MEG3 expression levels were downregulated in PRCC tumor tissues compared with adjacent non-tumor tissues. In addition, survival analysis was conducted to investigate the association between identified genes and the prognosis of patients with PRCC, indicating the potential involvement of 13 mRNAs, 15 lncRNAs and six miRNAs. In conclusion, the present study may improve understanding of the regulatory mechanisms of ceRNA networks in PRCC and provide novel insight for future studies of prognostic biomarkers and potential therapeutic targets.

Differential miRNA expression profile and proteome in plasma exosomes from patients with paroxysmal nocturnal hemoglobinuria

Paroxysmal Nocturnal Hemoglobinuria (PNH) is a clonal disease of blood cells caused by the lack of glycosyl phosphatidyl inositol anchored proteins bound to the cell membrane. In consequence, erythrocytes lead to intravascular hemolysis upon complement activation, which promotes high risk of thrombosis, intravascular hemolytic anemia, and bone marrow failure in patients. The mechanisms of thrombosis in PNH are still poorly understood. Treatment with eculizumab reduces intravascular hemolysis and thrombotic risk, but not in all cases. Exosomes are extracellular vesicles released by cells and whose secretion is closely related to the inflammatory status. They participate in cell communication by activating signaling pathways and transferring genetic material and proteins to host cells. In consequence, exosomes may serve as surrogate biomarkers for the prognosis and/or diagnosis of a disease. Isolation of exosomes was carried out from healthy controls and from three groups of PNH patients, i.e. i) with no eculizumab treatment; ii) under treatment with eculizumab that have not suffered thrombosis; and iii) under treatment with eculizumab but that have suffered thrombosis. The miRNAome and proteome was analyzed using plasma focus miRNAs PCR panel and LC-MS analysis respectively. We found differential expression of miRNAs miR-148b-3p, miR-423-3p, miR29b-3p, miR15b-5p, let-7e-5p, miR126-3p, miR-125b-5p and miR-376c-3p as well as hemoglobin, haptoglobin, protein S and C4-binding protein in healthy controls vs PNH patients. Our results warrant further research and provide new information on the content of exosomes that could play a role in the hypercoagulable state in this disease.