Profile of microRNA in Blood Plasma of Healthy Humans

Clo-miR-14: a medicinally valued spice-derived miRNA with therapeutic implications in rheumatoid arthritis

Plant microRNAs (miRNA) are regularly consumed orally along with diet, gaining attention for their RNA-based drug potential because of their ability to regulate mammalian gene expression specifically at the post-transcriptional level. Medicinally valued plants are well known for their anti-inflammatory property; however, the contribution of their miRNA in managing inflammation has been less studied. We investigated miRNA from four medicinally valued regularly consumed spices, and validated one of the most potential miRNA 'Clo-miR-14' for its thermal stability, and absorption in the plasma samples of RA patient's by RT-PCR. In vitro and in vivo studies were performed to investigate the effect of Clo-miR-14 in ameliorating rheumatoid arthritis (RA) like symptoms. Our results suggest that 'Clo-miR-14,' an exogenous miRNA present in Curcuma longa, absorbed through regular diet, has robust thermal stability at 100°C in humans. It significantly reduced pro-inflammatory cytokines (TNF, IL-1β, IL-6) and RA-like symptoms, suggesting that plant-based miRNA could be a promising candidate as an RNA-based drug for RA pathogenesis.

Frequency shift Raman-based sensing of serum MicroRNA for ultrasensitive cervical cancer diagnosis

Cervical cancer is the most common gynaecological tumor. The development of a sensor for the ultrasensitive detection of cervical cancer is significant in guaranteeing its prognosis. Herein, we proposed a novel surface-enhanced Raman scattering (SERS) analysis platform using a frequency shifts-based sensing model for rapid and ultrasensitive microRNA (miRNA) assay. During the analysis process, miR-21 can be captured by the single-stranded DNA (ssDNA) modified on the platform which is complementary pairing with miR-21. The connection of miR-21 can lead to the variation of the molecular weight and result in the deformation extent of the Raman report molecule 6Thioguanine (6TG); thus, the peak at 1301 cm-1 due to the ring C-N stretches of 6TG shifts to lower frequency. The detection limit (LOD) of the proposed SERS analysis platform is as low as 8.32 aM. Moreover, the platform also has excellent specificity and repeatability, with the relative standard deviation (RSD) value of 6.53 %. Serum samples of cervical cancer patients and healthy subjects were analyzed via the platform and the accuracy of the detection results was verified by qRT-PCR, revealing that SERS results and qRT-PCR results have high homogeneity. Thus, the platform can serve as a potential tool for clinical diagnosis of cervical cancer.

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer

MOTIVATION

One of the standard methods of high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to the standard differential expression analysis, differential co-expression one aims to detect pairs or clusters whose mutual expression changes between two conditions.

RESULTS

We developed Differential Co-expression Network Analysis (DCoNA)-an open-source statistical tool that allows one to identify pair interactions, which correlation significantly changes between two conditions. Comparing DCoNA with the state-of-the-art analog, we showed that DCoNA is a faster, more accurate and less memory-consuming tool. We applied DCoNA to prostate mRNA/miRNA-seq data collected from The Cancer Genome Atlas (TCGA) and compared predicted regulatory interactions of miRNA isoforms (isomiRs) and their target mRNAs between normal and cancer samples. As a result, almost all highly expressed isomiRs lost negative correlation with their targets in prostate cancer samples compared to ones without the pathology. One exception to this trend was the canonical isomiR of hsa-miR-93-5p acquiring cancer-specific targets. Further analysis showed that cancer aggressiveness simultaneously increased with the expression level of this isomiR in both TCGA primary tumor samples and 153 blood plasma samples of P. Hertsen Moscow Oncology Research Institute patients' cohort analyzed by miRNA microarrays.

AVAILABILITY AND IMPLEMENTATION

Source code and documentation of DCoNA are available at https://github.com/zhiyanov/DCoNA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Chemical Induction of Trophoblast Hypoxia by Cobalt Chloride Leads to Increased Expression of DDIT3

Choriocarcinoma cells BeWo b30 are used to model human placental trophoblast hypoxia using cobalt (II) chloride and hydroxyquinoline derivative (HD) as chemical inducers of hypoxia-inducible factor (HIF). In this study, it was shown that both substances activate the hypoxic pathway and the epithelial-mesenchymal transition and inhibit the pathways of cell proliferation. However, CoCl2 caused activation of the apoptosis pathway, increased the activity of effector caspases 3 and 7, and increased the expression of the unfolded protein response target DDIT3. The mTORC1 pathway was activated upon exposition to CoCl2, while HD suppressed this pathway, as it happens during real trophoblast hypoxia. Thus, effect of CoCl2 on BeWo cells can be a model of severe hypoxia with activation of apoptosis, while HD mimics moderate hypoxia.

Levels of miR-374 increase in BeWo b30 cells exposed to hypoxia

In humans, trophoblast hypoxia during placental development can be a cause of serious pregnancy complications, such as preeclampsia and fetal growth restriction. The pathogenesis of these conditions is not fully clear and may be associated with changed expression of some genes and regulatory molecules, including miRNA, in trophoblast cells. The aim of this study was to analyze miRNA profiles and measure the expression of their target genes in a model of trophoblast hypoxia. Human choriocarcinoma BeWo b30 cells were used as a trophoblast model. Hypoxia was induced by cobalt chloride (CoCl2) and an oxyquinoline derivative. MRNA and miRNA expression profiles were evaluated by means of next generation sequencing (NGS); the expression of individual genes was analyzed by PCR. We studied the secondary structure of mRNAs of target genes for those miRNAs whose expression had changed significantly and analyzed potential competition between these miRNAs for the binding site. The observed changes in the expression of the key genes involved in the response to hypoxia confirmed the feasibility of using CoCl2 and the oxyquinoline derivative as hypoxia inducers. The analysis revealed an increase in miR-374 levels following the activation of the hypoxia pathway in our trophoblast model. The changes were accompanied by a reduction in FOXM1 mRNA expression; this mRNA is a target for hsa-miR-374a-5p and hsa-miR374b-5p, which can compete with hsa-miR-21-5p for the binding sites on FOXM1 mRNA. The involvement of FOXM1 in the regulation of the invasive cell potential suggests the role of miR-374 and FOXM1 in the pathogenesis of disrupted trophoblast invasion during placental development as predisposing for fetal growth restriction and preeclampsia.

Differences in the Drosha and Dicer Cleavage Profiles in Colorectal Cancer and Normal Colon Tissue Samples

Human colorectal adenocarcinoma cell line Caco-2 is often used as a model of healthy intestinal epithelium, in particular, in miRNA studies. The work of the enzymes Drosha and Dicer is an integral part of the process of miRNA formation. Inaccuracies in the work of these enzymes lead to a change in the nucleotide sequences of miRNAs with the formation of new isoforms, which, in turn, can change intracellular regulatory mechanisms. In the framework of this study, it was shown that the quantitative estimates of inaccuracies in Drosha and Dicer activity significantly differ between the specimens of normal colon tissue and malignant colorectal tumors.

Detection of Low-Abundant MicroRNAs with Hybridization Microchips

The effect of low concentrations of miRNA on the ability of GeneChip miRNA 4.0 hybridization chips to evaluate their representation in the sample was studied. It is shown that the evaluation of the expression of 61 miRNAs is statistically significantly associated with the multiplicity of plasma dilution. Only 12 miRNAs showed very high Pearson correlation coefficient (>0.95) and they all decreased in response to dilution. High abundance of has-miR-4532 miRNA in plasma was demonstrated. This miRNA was never detected during sequencing of similar samples. It was concluded that in case of miRNA expression <1.12±0.33 units in log2 scale, dilution was not followed by further decrease in the signal intensity in GeneChip miRNA 4.0 chips.

Comparison of Profiles of Extracellular MicroRNA Secreted by Caco-2 Cells from the Apical Side of the Membrane under Static and Microcirculation Conditions

Extracellular microRNA are one of the indicators of the functional state of cells. Culturing of Caco-2 cells under the conditions of microcirculation in a Homunculus microfluidic device allows better simulating natural environment of the body in comparison with static culturing. Impedance spectroscopy (BioClinicum Research Center) was used for non-invasive estimation of the monolayer quality and changes in the cell apical membrane due to the formation of microvilli. Under static conditions, Caco-2 cells release more microRNA from the apical membrane than under microcirculation conditions, while secretion of miR-320a, miR-24-3p, and miR-221-3p microRNA under static conditions can indicate stress of the cells and activation of inflammatory response. Under microcirculation conditions, the expression of laminin-α1 (LAMA1) was lower than under static conditions, which indicates deeper differentiation of cells.

Metabolic Reprogramming of Trophoblast Cells in Response to Hypoxia

Hypoxia of trophoblast cells is an important regulator of normal development of the placenta. However, some pathological states associated with hypoxia, e.g. preeclampsia, impair the functions of placental cells. Oxyquinoline derivative inhibits HIF-prolyl hydroxylase by stabilizing HIF-1 transcription complex, thus modeling cell response to hypoxia. In human choriocarcinoma cells BeWo b30 (trophoblast model), oxyquinoline increased the expression of a core hypoxia response genes along with up-regulation of NOS3, PDK1, and BNIP3 genes and down-regulation of the PPARGC1B gene. These changes in the expression profile attest to activation of the metabolic cell reprogramming mechanisms aimed at reducing oxygen consumption by enabling the switch from aerobic to anaerobic glucose metabolism and the respective decrease in number of mitochondria. The possibility of practical use of the therapeutic properties of oxyquinoline derivatives is discussed.

Plasma Level of hsa-miR-619-5p microRNA Is Associated with Prostatic Cancer Dissemination beyond the Capsule

Profiles of circulating microRNA in the plasma of patients with prostate cancer with pathomorphological stages pT2, pT3, and pT4 are analyzed. The level of circulating microRNA hsa-miR-619-5p is elevated in patients with extracapsular spreading of the tumor, increasing significantly from stage pT2 to stage pT4.

Plasma Levels of hsa-miR-619-5p and hsa-miR-1184 Differ in Prostatic Benign Hyperplasia and Cancer

Peripheral blood plasma profiles of circulating microRNA expression were analyzed in patients with prostatic cancer and benign hyperplasia. In prostatic cancer, significant increase in hsa-miR-619-5p and hsa-miR-1184 microRNA expression and significant decrease in hsalet-7b-5p and hsa-let-7c-5p microRNA expression were observed. The role of the relationship between the microRNA expression and the activities and functions of host genes with introns encoding these microRNA is discussed.

MicroRNA hsa-miR-4674 in Hemolysis-Free Blood Plasma Is Associated with Distant Metastases of Prostatic Cancer

We analyzed microRNA profile in hemolysis-free blood plasma of patients with prostatic cancer. The metastatic form of prostatic cancer was found to be associated with increased levels of hsa-miR-22-3p, hsa-miR-663a, and hsa-miR-4674 in comparison with non-metastatic form. Common candidate target genes of these microRNA include JUNB, KMT2A, and XPO6.