MicroRNA regulation via DNA methylation during the morula to blastocyst transition in mice

DNMT1 maintains the methylation of miR-152-3p to regulate TMSB10 expression, thereby affecting the biological characteristics of colorectal cancer cells

Objective

DNA methyltransferases (DNMTs) take on a relevant role in epigenetic control of cancer proliferation and cell survival. However, the molecular mechanisms underlying the establishment and maintenance of DNA methylation in human cancer remain to be fully elucidated. This study was to investigate that how DNMT1 affected the biological characteristics of colorectal cancer (CRC) cells via modulating methylation of microRNA (miR)‐152‐3p and thymosin β 10 (TMSB10) expression.

Methods

DNMT1, miR‐152‐3p, and TMSB10 expression, and the methylation of miR‐152‐3p in CRC tissues and cells were detected. SW‐480 and HCT‐116 CRC cells were transfected with DNMT1 or miR‐152‐3p‐related sequences or plasmids to explore their characters in biological functions of CRC cells. The binding relationship between DNMT1 and miR‐152‐3p and the targeting relationship between miR‐152‐3p and TMSB10 were analyzed. The tumor growth was also detected in vivo.

Results

Upregulated DNMT1, TMSB10, reduced miR‐152‐3p, and methylated miR‐152‐3p were detected in CRC tissues and cells. Silenced DNMT1 or upregulated miR‐152‐3p reduced TMSB10 expression and suppressed CRC progression and tumor growth. Moreover, elevated DNMT1 could reverse the effect of miR‐152‐3p upregulation on CRC development and tumor growth. DNMT1 maintained methylation of miR‐152‐3p. TMSB10 was the direct target gene of miR‐152‐3p.

Conclusion

The study highlights that silenced DNMT1 results in non‐methylated miR‐152‐3p to depress TMSB10 expression, thereby inhibiting CRC development, which provides a new approach for CRC therapy.

Pleiotropic roles of tankyrase/PARP proteins in the establishment and maintenance of human naïve pluripotency

Tankyrase 1 (TNKS1; PARP-5a) and Tankyrase 2 (TNKS2; PARP-5b) are poly-ADP-ribosyl-polymerase (PARP)-domain-containing proteins that regulate the activities of a wide repertoire of target proteins via post-translational addition of poly-ADP-ribose polymers (PARylation). Although tankyrases were first identified as regulators of human telomere elongation, important and expansive roles of tankyrase activity have recently emerged in the development and maintenance of stem cell states. Herein, we summarize the current state of knowledge of the various tankyrase-mediated activities that may promote human naïve and 'extended' pluripotency'. We review the putative role of tankyrase and PARP inhibition in trophectoderm specification, telomere elongation, DNA repair and chromosomal segregation, metabolism, and PTEN-mediated apoptosis. Importantly, tankyrases possess PARP-independent activities that include regulation of MDC1-associated DNA repair by homologous recombination (HR) and autophagy/pexophagy, which is an essential mechanism of protein synthesis in the preimplantation embryo. Additionally, tankyrases auto-regulate themselves via auto-PARylation which augments their cellular protein levels and potentiates their non-PARP tankyrase functions. We propose that these non-PARP-related activities of tankyrase proteins may further independently affect both naïve and extended pluripotency via mechanisms that remain undetermined. We broadly outline a hypothetical framework for how inclusion of a tankyrase/PARP inhibitor in small molecule cocktails may stabilize and potentiate naïve and extended pluripotency via pleiotropic routes and mechanisms.

Amniotic microvesicles impact hatching and pregnancy percentages of in vitro bovine embryos and blastocyst microRNA expression versus in vivo controls

Embryo development and implantation are dynamic processes, responsive to external signals, and can potentially be influenced by many environmental factors. The aims of this study were to evaluate the effects of a culture medium supplemented with amniotic-derived microvesicles (MVs) on in vitro embryo hatching after cryopreservation, and pregnancy rate following embryo transfer. In addition, miRNA profiling of blastocysts produced in vitro, with or without (control; CTR) amniotic MV supplementation, was also evaluated using blastocysts produced in vivo. In vitro embryos were cultured with and without amniotic MV supplementation. In vivo blastocysts were obtained from superovulated cows. Samples for RNA isolation were obtained from three pools of 10 embryos each (in vivo, in vitro-CTR and in vitro + MVs). Our results show that the hatching percentage of cryopreserved in vitro + MVs embryos is higher (P < 0.05) than in vitro-CTR embryos and the pregnancy rate with fresh and cryopreserved in vitro + MVs embryos is higher than in vitro-CTR embryos. In addition, the analysis of differently expressed (DE) microRNAs showed that embryos produced in vivo are clearly different from those produced in vitro. Moreover, in vitro-CTR and in vitro + MVs embryos differ significantly for expression of two miRNAs that were found in higher concentrations in in vitro-CTR embryos. Interestingly, these two miRNAs were also reported in degenerated bovine embryos compared to good quality blastocysts. In conclusion, MV addition during in vitro production of embryos seems to counteract the adverse effect of in vitro culture and partially modulate the expression of specific miRNAs involved in successful embryo implantation.

Aberrant expression of miR-29a/29b and methylation level of mouse embryos after in vitro fertilization and vitrification at two-cell stage

Proper epigenetic modifications during preimplantation embryo development are important for a successful pregnancy. We aim to investigate the putative influence of in vitro fertilization (IVF) and vitrification on DNA methylation in mouse preimplantation embryos. The study groups consisted of blastocyst-derived vitrified two-cell embryos, nonvitrified embryos, and a control group of in vivo derived blastocysts. We assessed developmental competence, global DNA methylation, relative expression levels of miR-29a/29b, and their target genes, Dnmt3a/3b. Vitrified embryos had a lower developmental rate as compared with nonvitrified embryos. There was no significant decrease in blastocyst cell numbers among studied groups, whereas there was a steady decline in DNA methylation after IVF and vitrification. The levels of miR-29a/29b upregulated in the experimental groups as compared with the control group. IVF and vitrification caused Dnmt3a/3b downregulations in blastocysts. The results of this study have suggested that a relationship exists between IVF and embryo vitrification with methylation interruptions in the blastocysts.

RFSMMA: A New Computational Model to Identify and Prioritize Potential Small Molecule-MiRNA Associations

More and more studies found that many complex human diseases occur accompanied by aberrant expression of microRNAs (miRNAs). Small molecule (SM) drugs have been utilized to treat complex human diseases by affecting the expression of miRNAs. Several computational methods were proposed to infer underlying associations between SMs and miRNAs. In our study, we proposed a new calculation model of random forest based small molecule-miRNA association prediction (RFSMMA) which was based on the known SM-miRNA associations in the SM2miR database. RFSMMA utilized the similarity of SMs and miRNAs as features to represent SM-miRNA pairs and further implemented the machine learning algorithm of random forest to train training samples and obtain a prediction model. In RFSMMA, integrating multiple kinds of similarity can avoid the bias of single similarity and choosing more reliable features from original features can represent SM-miRNA pairs more accurately. We carried out cross validations to assess predictive accuracy of RFSMMA. As a result, RFSMMA acquired AUCs of 0.9854, 0.9839, 0.7052, and 0.9917 ± 0.0008 under global leave-one-out cross validation (LOOCV), miRNA-fixed local LOOCV, SM-fixed local LOOCV, and 5-fold cross validation, respectively, under data set 1. Based on data set 2, RFSMMA obtained AUCs of 0.8456, 0.8463, 0.6653, and 0.8389 ± 0.0033 under four cross validations according to the order mentioned above. In addition, we implemented a case study on three common SMs, namely, 5-fluorouracil, 17β-estradiol, and 5-aza-2'-deoxycytidine. Among the top 50 associated miRNAs of these three SMs predicted by RFSMMA, 31, 32, and 28 miRNAs were verified, respectively. Therefore, RFSMMA is shown to be an effective and reliable tool for identifying underlying SM-miRNA associations.

Altered microRNome Profiling in Statin-Induced HepG2 Cells: A Pilot Study Identifying Potential new Biomarkers Involved in Lipid-Lowering Treatment

PURPOSE

Statins are widely prescribed drugs to manage hypercholesterolemia. Despite they are considered effective lipid-lowering agents, significant inter-individual variability has been reported in relation to drug response. Among the reasons explaining this variation, genetic factors are known to partially contribute. Nonetheless, poor evidence exists regarding epigenetic factors involved.

METHODS

We investigated if atorvastatin can modulate the cholesterol related miR-33 family. Furthermore, we analyzed the microRNA expression profiles in HepG2 cells treated for 24 hours with atorvastatin or simvastatin using a microarray platform.

RESULTS

Our results indicate that atorvastatin does not influence the expression of the miR-33 family. In addition, microarray examination revealed that atorvastatin modulated thirteen miRs, whilst simvastatin only affected two miRs. All significantly modulated miRs after simvastastin therapy were also modulated by atorvastatin. In addition, four novel miRs with previously unreported functions were identified as statin-modulated.

CONCLUSION

We identified several novel miRs affected by statin treatment. Additional research is needed to determine the biological significance of differentially expressed miRs identified in statins-induced HepG2 cells.

The Anti-Apoptotic Role of Berberine in Preimplantation Embryo In Vitro Development through Regulation of miRNA-21

Traditional Chinese medicinal herbs containing berberine have been historically used to prevent miscarriage. Here, we investigated whether the anti-apoptotic effects of berberine on pre-implantation embryonic development are regulated by miRNA-21. Mouse pronuclear embryos were cultured in medium with or without berberine, and some were then microinjected with a miRNA-21 inhibitor. The in vitro developmental rates of 2- and 4-cell embryos and blastocysts, blastocyst cell numbers, apoptotic rates, and apoptotic cell numbers were measured in each group. Furthermore, we examined the transcription levels of miRNA-21 and its target genes (caspase-3, PTEN, and Bcl-2) and their translation levels. Comparisons were made with in vivo-developed and untreated embryos. We found that berberine significantly increased the developmental rates and cell numbers of mouse blastocysts and decreased apoptotic cell rates in vitro. Berberine also significantly increased miRNA-21 and Bcl-2 transcription levels and significantly decreased caspase-3 and PTEN transcription levels. In embryos treated with a miRNA-21 inhibitor, the results followed the opposite trend; PTEN and caspase-3 transcription levels increased significantly, while the transcription level of Bcl-2 decreased significantly. Additionally, berberine treatment significantly increased the Bcl-2 protein level and significantly decreased the caspase-3 and PTEN protein levels in blastocysts, but there were no significant differences observed in the levels of these proteins in 2- and 4-cell embryos. This study revealed that miRNA-21 is important for pre-implantation embryonic development, especially blastocyst development in vitro. Berberine elevates miRNA-21 expression, decreases PTEN and caspase-3 levels, increases Bcl-2 levels, and exerts anti-apoptotic and pro-growth effects.

The role of DNA methylation: a challenge for the DOHaD paradigm in going beyond the historical debate

A heritage of considerable research into such phenomena as parental imprinting and carcinogenesis is an almost axiomatic association of the DNA methylation epigenetic mark with the silencing of gene expression. However, the increasing technical resolution afforded by burgeoning -omics technologies reveals that a more elaborate interaction may exist between DNA methylation, within sub-regions of gene structure and/or specific dinucleotide sites, and levels of gene activity. Furthermore, seminal observations from the field of DOHaD, which clearly define the alignment of sequential epigenetic modifications and gene activity appear not to support a strictly causal relationship between DNA methylation and gene silencing. The temporal element implicit within DOHaD studies provides a useful framework within which to further explore the role of epigenetic mechanisms and in particular perhaps, to address the question of ‘deterministic intent’ when implicating the epigenetic regulation of gene activity in the manifestation of phenotype.

Meeting the methodological challenges in molecular mapping of the embryonic epigenome

The past decade of life sciences research has been driven by progress in genomics. Many voices are already proclaiming the post-genomics era, in which phenomena other than sequence polymorphism influence gene expression and also explain complex phenotypes. One of these burgeoning fields is the study of the epigenome. Although the mechanisms by which chromatin structure and reorganization as well as cytosine methylation influence gene expression are not fully understood, they are being invoked to explain the now-accepted long-term impact of the environment on gene expression, which appears to be a factor in the development of numerous diseases. Such studies are particularly relevant in early embryonic development, during which waves of epigenetic reprogramming are known to have profound impacts. Since gametes and zygotes are in the process of resetting the genome in order to create embryonic stem cells that will each differentiate to create one of many specific tissue types, this phase of life is now viewed as a window of susceptibility to epigenetic reprogramming errors. Epigenetics could explain the influence of factors such as the nutritional/metabolic status of the mother or the artificial environment of assisted reproductive technologies. However, the peculiar nature of early embryos in addition to their scarcity poses numerous technological challenges that are slowly being overcome. The principal subject of this article is to review the suitability of various current and emerging technological platforms to study oocytes and early embryonic epigenome with more emphasis on studying DNA methylation. Furthermore, the constraint of samples size, inherent to the study of preimplantation embryo development, was put in perspective with the various molecular platforms described.

Downregulation of miR-452 promotes stem-like traits and tumorigenicity of gliomas

PURPOSE

miR-452 is reported to be required for neural crest stem cell differentiation during neural crest development. However, the biologic role of miR-452 in gliomas remains unclear. The aim of the present study was to evaluate the effect of miR-452 on the stem-like properties and tumorigenesis of glioma cells.

EXPERIMENTAL DESIGN

The expression of miR-452 was examined in glioma cells and glioma tissues using real-time PCR. The effects of miR-452 on stem-like traits and tumorigenesis were investigated in vitro and in vivo using patient-derived glioma cells and glioma cell lines. Western blotting and luciferase reporter assays were conducted to examine the negative regulation of Bmi-1, LEF1, and TCF4 by miR-452. The methylation of the miR-452 promoter region was examined by bisulfite genomic sequencing PCR.

RESULTS

miR-452 was markedly downregulated in glioma cells and clinical glioma tissues. miR-452 levels were inversely correlated with World Health Organization (WHO) grades and patient survival. miR-452 directly targeted and suppressed multiple stemness regulators, including Bmi-1, LEF1, and TCF4, resulting in reduced stem-like traits and tumorigenesis of glioma cells in vitro and in vivo. Furthermore, we showed that downregulation of miR-452 in gliomas was caused by hypermethylation of its promoter region.

CONCLUSIONS

Downregulation of miR-452 plays an important role in promoting the stem-like traits and tumorigenesis of gliomas and may represent a novel prognostic biomarker and therapeutic target for the disease.