Cell-type-specific signatures of microRNAs on target mRNA expression

Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we show that predicted human mRNA targets of several highly tissue-specific miRNAs are typically expressed in the same tissue as the miRNA but at significantly lower levels than in tissues where the miRNA is not present. Conversely, highly expressed genes are often enriched in mRNAs that do not have the recognition motifs for the miRNAs expressed in these tissues. Together, our data support the hypothesis that miRNA expression broadly contributes to tissue specificity of mRNA expression in many human tissues. Based on these insights, we apply a computational tool to directly correlate 3' UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown. We show that this tool can identify functionally important 3' UTR motifs without cross-species comparison.     

MicroRNAs in platelet production and activation

MicroRNAs are small RNA molecules that modulate protein expression by degrading mRNA or repressing translation. They have been shown to play important roles in hematopoiesis, including embryonic stem cell differentiation, erythropoiesis, granulocytopoiesis/monocytopoiesis, lymphopoiesis, and megakaryocytopoiesis. miR-150 and miR-155 play divergent roles in megakaryocytopoiesis, with the former promoting development of megakaryocytes at the expense of erythrocytes and the latter causing a reduction in megakaryocyte colony formation. Platelets also contain fully functional miRNA machinery, and certain miRNA levels in platelets have been found to coordinate with reactivity to specific agonists and to pathologic states. This review will cover the current state of knowledge of miRNAs in megakaryocytes and platelets and the exciting possibilities for future research.     

Regulated expression of microRNAs in normal and polycythemia vera erythropoiesis

OBJECTIVE: Polycythemia vera (PV) is a myeloproliferative disorder, arising from the acquired mutation(s) of a hematopoietic stem cell. The JAK2 V617F somatic mutation is found in most PV patients; however, it is not the disease-initiating mutation. Because microRNAs (miRNAs) play a regulatory role in hematopoiesis, we studied miRNA expressions in PV and normal erythropoiesis. METHODS: Peripheral blood mononuclear cells were cultured in a three-phase liquid system resulting in synchronized expansion of erythroid progenitors. Using gene-expression profiling by CombiMatrix MicroRNArray, we searched for PV-specific changes at days 1, 14, and 21. Twelve miRNA candidates were then reevaluated by quantitative real-time polymerase chain reaction in a larger number of samples obtained from progenitors at the same stage of differentiation. RESULTS: A significant difference in miR-150 expression was found in PV. In normal erythropoiesis, three expression patterns of miRNAs were observed: progressive downregulation of miR-150, miR-155, miR-221, miR-222; upregulation of miR-451, miR-16 at late stages of erythropoiesis; and biphasic regulation of miR-339, miR-378. The miR-451 appears to be erythroid-specific. CONCLUSIONS: We identified the miRNAs with regulated expression in erythropoiesis; one appeared to be PV-specific. Their miRNA expression levels define early, intermediate, and late stages of erythroid differentiation. The validity of our findings was confirmed in nonexpanded peripheral blood cells.     

Evaluation of plasma microRNA expressions in patients with juvenile idiopathic arthritis

Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease of childhood, yet its etiology is unknown. It is known that microribonucleic acids (miRNAs) play a role in immunoregulation. We aimed to evaluate the plasma expression of some candidate miRNAs that are associated with the pathogenesis of autoimmunity. Thirty-one patients diagnosed with JIA and age-sex-matched 31 healthy children were enrolled for the study. The plasma levels of four candidate miRNAs (miRNA-16, miRNA-155, miRNA-204, and miRNA-451), which are known to be associated with autoimmunity, were examined in all the subjects. The plasma levels of miRNAs were measured with real-time PCR in the patients in active and inactive periods and in the healthy controls. The groups were compared with each other. The plasma miRNA-155 levels were found to increase in the JIA patients compared to the healthy controls, and it was statistically more significant in the inactive period. We found that the JIA patients had the higher levels of miRNA-16 and the lower levels of miRNA-204/miRNA-451 expressions compare with the control group, but there was no statistically significant difference. A statistically significant decrease in the plasma levels of miRNA-204 was found in the patients that were in inactive disease with only methotrexate therapy. The plasma miRNA expressions were compared in the JIA subtypes, and it was observed that miRNA-204 levels were higher in polyarticular JIA and miRNA-451 levels were higher in enthesitis-related arthritis without statistical significance. The significant alterations in the plasma expression of miRNA-155 and miRNA-204 suggest to us that these molecules may be related to the pathogenesis of JIA. More comprehensive and functional researches about the role of these molecules are needed in this regard.     

miR-221 and miR-155 regulate human dendritic cell development, apoptosis, and IL-12 production through targeting of p27kip1, KPC1, and SOCS-1

Dendritic cells (DCs) are potent antigen-presenting cells derived from hematopoietic progenitor cells and circulating monocytes. To investigate the role of microRNAs (miRNAs) during DC differentiation, maturation, and function, we profiled miRNA expression in human monocytes, immature DCs (imDCs), and mature DCs (mDCs). Stage-specific, differential expression of 27 miRNAs was found during monocyte differentiation into imDCs and mDCs. Among them, decreased miR-221 and increased miR-155 expression correlated with p27(kip1) accumulation in DCs. Silencing of miR-221 or overexpressing of miR-155 in DCs resulted in p27(kip1) protein increase and DC apoptosis. Moreover, mDCs from miR-155(-/-) mice were less apoptotic than those from wild-type mice. Silencing of miR-155 expression had little effect on DC maturation but reduced IL-12p70 production, whereas miR-155 overexpression in mDCs enhanced IL-12p70 production. Kip1 ubiquitination-promoting complex 1, suppressor of cytokine signaling 1, and CD115 (M-CSFR) were functional targets of miR-155. Furthermore, we provide evidence that miR-155 indirectly regulated p27(kip1) protein level by targeting Kip1 ubiquitination-promoting complex 1. Thus, our study uncovered miRNA signatures during monocyte differentiation into DCs and the new regulatory role of miR-221 and miR-155 in DC apoptosis and IL-12p70 production.     

microRNA与心脏干细胞治疗

随着心血管病发病率的逐年增高,心脏干细胞(CSCs)治疗心血管病的研究已成为新的潮流。现已证实,microRNA(miRNA)是心血管的发育、病理生理过程和疾病发生中一类重要的调节因子。人们对心脏特异性miRNAs的研究已取得一定进展,如miR-1、miR-133、miR-208、miR-21、miR-499、miR-155、miR-146b及miR-126等在与CSCs协同治疗心血管病中起着不可或缺的作用。在此,本文对miRNAs在CSCs治疗中所起的作用做一综述。     

EBUS-TBNA标本检测6种miRNA对非小细胞肺癌诊断和分型的意义

目的 探讨非小细胞肺癌(NSCLC)患者在超声引导下经支气管针吸活检(EBUS-TBNA)获取标本检测6种微小RNA (miRNA)的临床意义.方法 收集2014年10月至2016年1月在佛山市顺德区第一人民医院住院的NSCLC患者32例,同期收集肺部良性病变患者20例作为对照组,获取EBUS-TBNA标本,用实时定量PCR方法检测miRNA-21、miRNA-126、miRNA-155、miRNA-200c、miRNA-205和miRNA-375的表达水平,并评价其临床意义.结果 NSCLC组EBUS-TBNA标本中miRNA-21、miRNA-155、miRNA-205和miRNA-375的相对表达量显著高于对照组(t值分别为6.69、2.71、7.98、8.86,P值均＜0.01);NSCLC组EBUS-TBNA标本中miRNA-126、miRNA-200c的相对表达量显著低于对照组(t值分别为10.37、13.04,P值均＜0.01).miRNA-21和miRNA-155在腺癌的表达水平显著高于鳞癌(t值分别为5.054、3.289,P＜0.01或P＜0.05);miRNA-205在鳞癌的表达水平显著高于腺癌(t=0.780,P＜0.01).作ROC曲线,miRNA-21取1.96为诊断腺癌的临界值时,其敏感度和特异度分别为65.00％和100.00％;miRNA-155取1.05为诊断腺癌的临界值时,其敏感度和特异度分别为80.00％和75.00％;miRNA-205取2.31为诊断鳞癌的临界值时,其敏感度和特异度为91.67％和100.00％.结论 检测EBUS-TBNA标本中6种miRNA对NSCLC的诊断有价值,miRNA-21、miRNA-155和miRNA-205可能还具有鉴别肺鳞腺癌的作用.     

ROS functions as an upstream trigger for autophagy to drive hematopoietic stem cell differentiation

Background and objectives: We have recently described a mechanistic action of autophagy on hematopoiesis in which autophagy sustains hematopoietic stem cell multilineage differentiation by direct targeting of intracellular Notch. However, the upstream signal that triggers autophagy to degrade Notch during hematopoiesis remains elusive.

Methods: Conditional autophagy-essential gene Atg7 knockout mouse model is used for identifying signals regulating autophagy in the promotion of hematopoiesis.

Results: We find here that generation of reactive oxygen species (ROS) is progressively increased during hematopoietic stem cell differentiation, and inhibition of ROS production was found to attenuate the differentiation of hematopoietic stem cells. In hematopoietic stem and progenitor cells (HSPCs) of wild-type mice, inhibition of ROS production downregulated autophagy activity but upregulated intracellular Notch and its downstream effectors. In contrast, in the HSPCs of autophagy fully defective mice, ROS inhibition did not alter myeloid differentiation, and hematopoietic stem cell differentiation to multi-lineages no longer responded to ROS inhibition.

Discussion: The ROS-regulating hematopoiesis is mitochondrial origin, and this action depends on intact autophagy machinery capable of degrading intracellular Notch.

Conclusion: ROS functions as an upstream signal in the autophagic promotion of hematopoietic stem cell differentiation.     

Platelet microRNA-mRNA coexpression profiles correlate with platelet reactivity

MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'-untranslated regions of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5, and miR-107:CLOCK) were selected from this list, and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets.     

MicroRNA-repressed mRNAs contain 40S but not 60S components

MicroRNAs (miRNAs) are small noncoding RNAs that may target more than one-third of human genes, yet the mechanisms used by miRNAs to repress translation of target mRNAs are obscure. Using a recently described cell-free assay of miRNA function, we observe that miRNA-targeted mRNAs are enriched for 40S but not 60S ribosome components. Additionally, toeprinting analysis of miRNA-targeted mRNAs demonstrates that approximately 18 nt 3' relative to the initiating AUG are protected, consistent with 40S ribosome subunits positioned at the AUG codon. Our results suggest that miRNAs repress translation initiation by preventing 60S subunit joining to miRNA-targeted mRNAs.     

MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms

MicroRNAs (miRNAs) are endogenously encoded small noncoding RNAs, derived by processing of short RNA hairpins, that can inhibit the translation of mRNAs bearing partially complementary target sequences. In contrast, small interfering RNAs (siRNAs), which are derived by processing of long double-stranded RNAs and are often of exogenous origin, degrade mRNAs bearing fully complementary sequences. Here, we demonstrate that an endogenously encoded human miRNA is able to cleave an mRNA bearing fully complementary target sites, whereas an exogenously supplied siRNA can inhibit the expression of an mRNA bearing partially complementary sequences without inducing detectable RNA cleavage. These data suggest that miRNAs and siRNAs can use similar mechanisms to repress mRNA expression and that the choice of mechanism may be largely or entirely determined by the degree of complementary of the RNA target.