Associations Among PCSK9 Levels, Atherosclerosis-Derived Extracellular Vesicles, and Their miRNA Content in Adults With Obesity

Background: Extracellular vesicles (EV) concentration is generally increased in patients with cardiovascular diseases, although the protective role of EVs in atherosclerosis has been reported. Among the specific cargo of EVs, miRNAs contribute to different stages of atherosclerosis. Aim of the present report has been to investigate, in individuals with obesity, the interplay among EVs derived from cells relevant for the atherosclerotic process (i.e., platelets, endothelium, monocytes/macrophages, and neutrophils), their miRNA content and proprotein convertase subtilisin/kexin type 9 (PCSK9), one of the main regulators of low-density lipoprotein receptor (LDLR).Methods and Results: EVs have been isolated from 936 individuals with obesity (body mass index = 33.6 ± 5.6 Kg/m2) and a raised cardiovascular risk (e.g., LDL-C = 131.6 ± 36.4 mg/dL, HOMA-IR = 3.1, and roughly 50% on anti-hypertensive medications). PCSK9 levels were negatively associated with EV count in the range 150–400 nm and with those derived from macrophages (CD14+), endothelium (CD105+), and neutrophils (CD66+). The association between PCSK9 and platelet-derived EVs (CD61+) was modified by platelet counts. PCSK9 was significantly associated with five EV-derived miRNAs (hsa-miRNA−362−5p,−150,−1244,−520b-3p,−638). Toll-like receptor 4 and estrogen receptor 1 were targeted by all five miRNAs and LDLR by four. The effect on LDLR expression is mainly driven by hsa-miR-150. Considering the implication of EV in atherosclerosis onset and progression, our findings show a potential role of PCSK9 to regulate EV-derived miRNAs, especially those involved in inflammation and expression of low-density lipoprotein receptor (LDLR) receptor.

163 DNA Methylation Across Generation in Bovine

Scientists are starting to realize that some effects from the animal environment may affect their progeny’s phenotype. These epidemiological evidences of early life programming are very well described in humans and rodents but less documented in bovines, especially in relation to the peri-conceptual period. In fact, as other species the bovine gametes may carry non-genetic information that will impact the survival, the fitness and the phenotype of the embryo-fetus-offspring. Using a peri-pubertal age model we have compared the semen of bulls that we obtained at different ages just after puberty for whole genome DNA methylation, miRNA content and open DNA access regions to identify mechanistic relation to gene expression and DNA methylation in embryos created with the same bulls compared to themselves and mated by IVF to the same heifer several times. A similar experiment was also done with pre-peri and post puber heifers using the same adult bull for repetitive IVF. The overall results indicate that the same pathways are affected in embryos from immature parents. The targeted processes are overwhelmingly associated with cellular metabolism involving mitochondria function and the mTOR pathways amongst others. A very similar conclusion was also observed with embryos obtained from adult mothers under negative energy balance and the resulting calves obtained by surrogate gestations using blood DNA methylation to assess the intergenerational legacy. These results support a metabolic programming across generation associated with an energy deficient status of the parent.

Regulation of miRNA content. Part 2. Degradation of miRNAs

The scientific review presents the process of regulation of microRNA content — microRNA degradation. To write the article, information was searched using databases Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka. The article presents the characteristics of the most important process of RNA metabolism — degradation of 3'→5' RNA. Degradation of microRNA is inherent in organisms of all kingdoms of life and is involved in the regulation of RNA representation, elimination of dysfunctional or incorrectly constructed RNA molecules and processing of RNA precursors. Exoribonucleases that affect the stability of mature forms of miRNA are presented. It is emphasized that XRN exoribonucleases degrade various RNA substrates during total RNA degradation and are involved in specific processes such as nonsense-mediated degradation, gene silencing, rRNA maturation, and transcription termination. It is shown that exoribonuclease XRN2 plays a crucial role in the termination of transcription during viral infection, namely it has cytoplasmic antiviral activity against hepatitis C virus. The role of RNA-degrading exosome in microRNA degradation is presented. RNA-degrading exosome is a ubiquitous complex and 3'-5'-endo- and exoribonucleases of eukaryotes, which interacts with several processing cofactors and degrades almost all classes of cytoplasmic RNA. The article reflects the function of evolutionarily conserved phosphorolytic 3'-5'-exoribonuclease — polynucleotide phosphorylase. The role of exoribonuclease 1, which is an evolutio­narily conserved 3'-5'-exoribonuclease of the DEDDh family, is involved in the final processing of 5.8S rRNA, replication-dependent histone mRNA, siRNA, and miRNA. Eri1 exoribonuclease has been shown to regulate global microRNA homeostasis in lymphocytes and to participate in NK cell development and antiviral response. Thus, one of the mechanisms of regulation of miRNA content is the most important process of RNA metabolism, which is inherent in organisms of all kingdoms of life, namely the degradation of miRNAs.

Extracellular Vesicle Separation Techniques Impact Results from Human Blood Samples: Considerations for Diagnostic Applications

Extracellular vesicles (EVs) are reminiscent of their cell of origin and thus represent a valuable source of biomarkers. However, for EVs to be used as biomarkers in clinical practice, simple, comparable, and reproducible analytical methods must be applied. Although progress is being made in EV separation methods for human biofluids, the implementation of EV assays for clinical diagnosis and common guidelines are still lacking. We conducted a comprehensive analysis of established EV separation techniques from human serum and plasma, including ultracentrifugation and size exclusion chromatography (SEC), followed by concentration using (a) ultracentrifugation, (b) ultrafiltration, or (c) precipitation, and immunoaffinity isolation. We analyzed the size, number, protein, and miRNA content of the obtained EVs and assessed the functional delivery of EV cargo. Our results demonstrate that all methods led to an adequate yield of small EVs. While no significant difference in miRNA content was observed for the different separation methods, ultracentrifugation was best for subsequent flow cytometry analysis. Immunoaffinity isolation is not suitable for subsequent protein analyses. SEC + ultracentrifugation showed the best functional delivery of EV cargo. In summary, combining SEC with ultracentrifugation gives the highest yield of pure and functional EVs and allows reliable analysis of both protein and miRNA contents. We propose this combination as the preferred EV isolation method for biomarker studies from human serum or plasma.

Regulation of miRNA content. Part 1. Editing miRNA. Тailing miRNA

This scientific review presents the processes of regulation of miRNA content. To write the article, information was searched using Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka databases. The article presents the characteristics of the processes of microRNA editing and microRNA tailing, which regulate the content of microRNA through the transcription control. It is emphasized that editing is the most important mechanism of posttranscriptional regulation of microRNA that occurs with the help of RNA-specific adenosine deaminase. The article shows that editing leads to a change in the secondary structure of the microRNA mo­lecule and the deviation of the process of microRNA maturation. It is shown that microRNA tailing is a posttranscriptional elongation of the tail of the molecule by adding nucleotides to the 3’-end of RNA. It has been found that uridinylation is a very common posttranscriptional process that regulates gene expression. The effect of uridinylation on microRNA biogenesis has been demonstrated on the example of the miR let-7 family, which inhibits proliferation and promotes cell differentiation. It has been established that another type of microRNA tailing, namely adeny­lation, most often contri­butes to the stabilization of the molecule, but in some cases can lead to microRNA degradation. Thus, the regulation of miRNA content is carried out by editing miRNA, microRNA tailing. Due to editing, the secondary structure of the microRNA molecule changes and the microRNA maturation process deviates. MicroRNA tailing is a post-transcriptional elongation of the tail of the molecule by ad­ding nucleotides to the 3’-end of RNA by polyuridinylation or poly­a­denylation. Uridinylation affects the processing and degradation of miRNA precursors with different molecular effects, which in some cases contribute to the development of diseases.

Urinary miRNA profiles discriminate between obstruction-induced bladder dysfunction and healthy controls

Urgency, frequency and incomplete emptying are the troublesome symptoms often shared between benign prostatic obstruction-induced (BLUTD) and neurogenic (NLUTD) lower urinary tract dysfunction. Previously, using bladder biopsies, we suggested a panel of miRNA biomarkers for different functional phenotypes of the bladder. Urine is a good source of circulating miRNAs, but sex- and age-matched controls are important for urinary metabolite comparison. In two groups of healthy subjects (average age 32 and 57 years old, respectively) the total protein and RNA content was very similar between age groups, but the number of secreted extracellular vesicles (uEVs) and expression of several miRNAs were higher in the young healthy male volunteers. Timing of urine collection was not important for these parameters. We also evaluated the suitability of urinary miRNAs for non-invasive diagnosis of bladder outlet obstruction (BOO). A three urinary miRNA signature (miR-10a-5p, miR-301b-3p and miR-363-3p) could discriminate between controls and patients with LUTD (BLUTD and NLUTD). This panel of representative miRNAs can be further explored to develop a non-invasive diagnostic test for BOO. The age-related discrepancy in the urinary miRNA content observed in this study points to the importance of selecting appropriate, age-matched controls.

Fatty Acids Modify the MicroRNA Content of Exosomes Released by Hypothalamic Astrocytes and the Response of POMC Neurons to These Exosomes

It is now clear that hypothalamic astrocytes participate in maintaining metabolic homeostasis. Both nutrients and metabolic hormones can directly impact on these glial cells to modify their release of gliotransmitters, metabolic factors, growth factors, etc, as well as their physical interaction with neighboring neurons. Another mechanism by which astrocytes could communicate with neurons is through their release of exosomes. We have previously shown (by RNAseq analysis) that exposure to palmitic acid (PA) dramatically modifies the miRNA content of exosomes released by hypothalamic astrocytes. Here our objectives were: 1) To determine if the miRNA changes in hypothalamic astrocyte-derived exosomes in response to oleic acid (OA) differ from those seen in response to PA and 2) Analyze the response of POMC neurons to exosomes derived from astrocytes exposed to either PA or OA. Primary hypothalamic astrocyte cultures were treated with PA (0.5 mM), OA (0.5 mM) or vehicle (V) for 24 hours. Exosomes were purified from the media and used for miRNA analysis and to treat a POMC neuronal cell line (mHypoA-POMC/GFP-1). Both OA and PA modified miRNA levels in exosomes compared to those detected in V exosomes, but these modifications differed between the two fatty acids. Furthermore, the response of POMC neurons to exosomes from vehicle (E-V), OA (E-OA) and PA (E-PA) treated astrocytes for 24 hours differed significantly. The expression of POMC mRNA was significantly decreased in response to E-V and increased in response to both E-OA and E-PA, although the increase in POMC mRNA was significantly greater in E-PA treated neurons. These results suggest that hypothalamic astrocytes can directly communicate with neurons involved in metabolic control through exosomes and that the messages contained within these exosomes are modulated by the nutrient environment.

Diurnal Variation of Plasma Extracellular Vesicle Is Disrupted in People Living with HIV

Background: Several types of extracellular vesicles (EVs) secreted by various immune and non-immune cells are present in the human plasma. We previously demonstrated that EV abundance and microRNA content change in pathological conditions, such as HIV infection. Here, we investigated daily variations of large and small EVs, in terms of abundance and microRNA contents in people living with HIV (PLWH) receiving antiretroviral therapy (HIV+ART) and uninfected controls (HIV−). Methods: Venous blood samples from n = 10 HIV+ART and n = 10 HIV− participants were collected at 10:00 and 22:00 the same day. Large and small plasma EVs were purified, counted, and the mature miRNAs miR-29a, miR-29b, miR-92, miR-155, and miR-223 copies were measured by RT-PCR. Results: Large EVs were significantly bigger in the plasma collected at 10:00 versus 22:00 in both groups. There was a significant day–night increase in the quantity of 5 miRNAs in HIV− large EVs. In HIV+ART, only miR-155 daily variation has been observed in large EVs. Finally, EV-miRNA content permits to distinguish HIV− to HIV+ART in multivariate analysis. Conclusion: These results point that plasma EV amount and microRNA contents are under daily variation in HIV− people. This new dynamic measure is disrupted in PLWH despite viral-suppressive ART. This study highlights a significant difference concerning EV abundance and their content measured at 22:00 between both groups. Therefore, the time of blood collection must be considered in the future for the EV as biomarkers.

Extracellular Vesicles Analysis in the COVID-19 Era: Insights on Serum Inactivation Protocols towards Downstream Isolation and Analysis

Since the outbreak of the COVID-19 crisis, the handling of biological samples from confirmed or suspected SARS-CoV-2-positive individuals demanded the use of inactivation protocols to ensure laboratory operators’ safety. While not standardized, these practices can be roughly divided into two categories, namely heat inactivation and solvent-detergent treatments. These routine procedures should also apply to samples intended for Extracellular Vesicles (EVs) analysis. Assessing the impact of virus-inactivating pre-treatments is therefore of pivotal importance, given the well-known variability introduced by different pre-analytical steps on downstream EVs isolation and analysis. Arguably, shared guidelines on inactivation protocols tailored to best address EVs-specific requirements will be needed among the analytical community, yet deep investigations in this direction have not yet been reported. We here provide insights into SARS-CoV-2 inactivation practices to be adopted prior to serum EVs analysis by comparing solvent/detergent treatment vs. heat inactivation. Our analysis entails the evaluation of EVs recovery and purity along with biochemical, biophysical and biomolecular profiling by means of a set of complementary analytical techniques: Nanoparticle Tracking Analysis, Western Blotting, Atomic Force Microscopy, miRNA content (digital droplet PCR) and tetraspanin assessment by microarrays. Our data suggest an increase in ultracentrifugation (UC) recovery following heat treatment; however, it is accompanied by a marked enrichment in EVs-associated contaminants. On the other hand, solvent/detergent treatment is promising for small EVs (<150 nm range), yet a depletion of larger vesicular entities was detected. This work represents a first step towards the identification of optimal serum inactivation protocols targeted to EVs analysis.