Circulating MicroRNA as Potential Source for Neurodegenerative Diseases Biomarkers

Evaluation of RNA isolation methods for microRNA quantification in a range of clinical biofluids

BACKGROUND

Extracellular microRNAs (miRNAs), released from cells into biofluids, have emerged as promising biomarkers for diagnostic and prognostic purposes. Several RNA isolation methods are available for the analysis of these cell-free miRNAs by RT-qPCR. Not all methods, however, are equally suitable for different biofluids. Here, we extracted total RNA from four very diverse biofluids: serum, urine, bile, and graft preservation fluid (perfusate). Four different protocols were used: a phenol-chloroform extraction and alcohol precipitation in combination with a precipitation carrier (QP) and three different column-based isolation methods, one with phenol-chloroform extraction (RN) and two without (NG and CU). For this range of clinical biofluid samples, we evaluated the potential of these different RNA isolation methods assessing recovery efficiency and the co-purification of RT-qPCR inhibiting compounds.

RESULTS

Differences were observed between each of the RNA isolation methods in the recovery of cel-miR-39, a synthetic miRNA spiked in during the workup procedure, and for endogenous miRNAs. Co-purification of heparin, a known RT-qPCR inhibitor, was assessed using heparinase I during cDNA synthesis. RT-qPCR detection of synthetic miRNAs cel-miR-39, spiked in during RNA workup, cel-miR-54, spiked in during cDNA synthesis, and endogenous miRNAs was strongly improved in the presence of heparinase I for some, but not all, isolation methods. Other, co-isolated RT-qPCR inhibitors were not identified, except for biliverdin, which co-isolated from some bile samples with one of the methods. In addition, we observed that serum and urine contain compounds that enhance the binding of heparin to certain solid-phase columns.

CONCLUSIONS

For reliable measurements of miRNA-based biomarkers in biofluids, optimization of RNA isolation procedures is recommended as methods can differ in miRNA detection and in co-purification of RT-qPCR inhibitory compounds. Heparinase I treatment confirmed that heparin appeared to be the major RT-qPCR inhibiting compound, but also biliverdin, co-isolated from bile, could interfere with detection.

MicroRNAs as potential biomarkers for the diagnosis of Traumatic Brain Injury: A systematic review and meta-analysis

Background: Traumatic brain injury (TBI) is a sudden trauma on the head, in which severe TBI (sTBI) is usually associated with death and long-term disability. MicroRNAs (miRNAs) are potential biomarkers of diverse diseases, including TBI. However, few systematic reviews and meta-analyses have been conducted to determine the clinical value of miRNAs expression in TBI patients. Methods: We conducted this systematic review and meta-analysis study according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched PubMed, Embase, the Cochrane Library, Web of Science, from inception to August 26, 2020. We included articles written in English that have reported on the diagnostic value of miRNAs expression in TBI patients. We excluded studies that did not provided sufficient information to construct the 2×2 contingency table. Results: Eight studies investigating the diagnostic value of miRNA in TBI were analyzed in this study. The overall sensitivity, specificity and area under the curve (AUC) of miRNAs in diagnosis of TBI were 89% [95% confidence interval (CI): 0.84-0.93], 92% (95% CI 0.82-0.97) and 95% (95% CI 0.93-0.97). We found that panels of multiple miRNAs could improve the diagnostic accuracy of TBI. Samples from blood and brain tissue have significantly enhanced diagnostic accuracy, when compared with saliva. The AUC of miRNAs in severe TBI was 0.97, with 91% sensitivity and 92% specificity. Conclusion: This systematic review and meta-analysis demonstrated that miRNAs could be potential diagnostic markers in TBI patients. MiRNAs detected in blood and brain tissue display high accuracy for TBI diagnosis.

Wide Profiling of Circulating MicroRNAs in Spinocerebellar Ataxia Type 7

Spinocerebellar ataxia type 7 (SCA7), a neurodegenerative disease characterized by cerebellar ataxia and retinal degeneration, is caused by a CAG repeat expansion in the ATXN7 gene coding region. Disease onset and progression are highly variable between patients, thus identification of specific/sensitive biomarkers that can improve the monitoring of disease progression is an immediate need. Because altered expression of circulating microRNAs (miRNAs) has been shown in various neurological diseases, they could be useful biomarkers for SCA7. In this study, we showed, to our knowledge for the first time, the expression profile of circulating miRNAs in SCA7. Using the TaqMan profiling low density array (TLDA), we found 71 differentially expressed miRNAs in the plasma of SCA7 patients, compared with healthy controls. The reliability of TLDA data was validated independently by quantitative real-time polymerase chain reaction in an independent cohort of patients and controls. We identified four validated miRNAs that possesses the diagnostic value to discriminate between healthy controls and patients (hsa-let-7a-5p, hsa-let7e-5p, hsa-miR-18a-5p, and hsa-miR-30b-5p). The target genes of these four miRNAs were significantly enriched in cellular processes that are relevant to central nervous system function, including Fas-mediated cell-death, heparansulfate biosynthesis, and soluble-N-ethylmaleimide-sensitive factor activating protein receptor pathways. Finally, we identify a signature of four miRNAs associated with disease severity that discriminate between early onset and adult onset, highlighting their potential utility to surveillance disease progression. In summary, circulating miRNAs might provide accessible biomarkers for disease stage and progression and help to identify novel cellular processes involved in SCA7.

MicroRNA-212-5p Prevents Dopaminergic Neuron Death by Inhibiting SIRT2 in MPTP-Induced Mouse Model of Parkinson's Disease

Recently, emerging evidences show that sirtuins (SIRTs) modulate aging progress and affect neurodegenerative diseases. For example, inhibition of SIRT2 has been recognized to exert neuroprotective effects in Parkinson’s disease (PD). However, current SIRT2 inhibitors are lack of selective property distinguished from its homolog. In this study, we found that SIRT2 protein level was highly increased in PD model, which was negatively regulated by miR-212-5p. In detail, miR-212-5p transfection reduced SIRT2 expression and inhibited SIRT2 activity. In vivo study, miR-212-5p treatment prevented dopaminergic neuron loss and DAT reduction by targeting SIRT2, which means miR-212-5p shows neuroprotective effect in PD. Mechanismly, we found nuclear acetylated p53 was up-regulation according to p53 is a major deacetylation substrate of SIRT2. Furthermore, decreased cytoplasmic p53 promoted autophagy in PD model, which was showed as autophagosomes, autophagic flux, LC3 B and p62 expression. Meanwhile, we also found miR-212-5p treatment somehow alleviated apoptosis in PD model, which might have some underlying mechanisms. In conclusions, our study provides a direct link between miR-212-5p and SIRT2-mediated p53-dependent programmed cell death in the pathogenesis of PD. These findings will give us an insight into the development of highly specifically SIRT2 inhibitor of opening up novel therapeutic avenues for PD.

Improved Detection of Circulating miRNAs in Serum and Plasma Following Rapid Heat/Freeze Cycling

BACKGROUND

The measurement of circulating miRNAs has proven to be a powerful biomarker tool for several disease processes. Current protocols for the detection of miRNAs usually involve an RNA extraction step, requiring a substantial volume of patient serum or plasma to obtain sufficient input material.

OBJECTIVE

Here, we describe a novel methodology that allows detection of a large number of miRNAs from a small volume of serum or plasma without the need for RNA extraction.

METHODS

Three μl of serum or plasma was subjected to three cycles of high and low temperatures (heat/freeze cycles) followed by miRNA arrays.

RESULTS

Our results indicate that miRNA detection following this process is highly reproducible when comparing multiple samples from the same subject. Moreover, this protocol increases the reproducibility of miRNA detection in samples that were previously subjected to multiple freeze-thaw cycles. Importantly, the detection of miRNAs from serum vs. plasma following heat/freeze cycling are highly comparable, indicating that this heat/freeze process effectively eliminates differences in detection between serum and plasma samples that have been reported using other sample preparation methodologies.

CONCLUSION

We propose that this method is a potent alternative to current RNA extraction protocols, substantially reducing the amount of sample necessary for miRNA detection while simultaneously improving miRNA detection and reproducibility.

Genetic and epigenetic alterations in meningiomas

Meningiomas originate from the arachnoid layer of the meninges and divided histologically into three grades: benign (grade I), atypical (grade II), and malignant meningiomas (grade III). Genetic alterations in grade I meningiomas include frequent deletions of chromosomal locus 22q12 and NF2 gene mutations and uncommon somatic SMARCB1 and SMARCE1gene mutations; In grade II meningiomas, chromosomal losses occur on 1p, 22q, 14q, 18q, 10, and 6q, and gains on 20q, 12q, 15q, 1q, 9q, and 17q; In grade III meningiomas, losses have been recognized on 6q, 10, and 14q and alterations of PTEN, CDKN2A and CDKN2B genes. Epigenetic alterations in meningiomas include hypermethylation of the tumor suppressor genes p73 in grade I meningiomas and TIMP3 GSTP1, MEG3, HOXA6, HOXA9, PENK, WNK2 and UPK3A genes with an increasing frequency according to grade. Abnormal expression of IGF signaling family genes and Wnt signaling pathway is associated with meningioma progression. MiRNA expression profiling of meningiomas show downregulation of miR-29c-3p, miR-200a, miR-145 and miR- 219-5p and upregulation of miR-21 miR-335 and miR-190a levels. In conclusion, extensive genetic and epigenetic alterations exist in meningiomas that may help assessing prognosis. In addition, since miRNA expression may be modified by artificial miRNAs, new effective therapeutic strategies may be developed especially for resistant or high grade meningiomas.

Genome-wide identification of microRNA-related variants associated with risk of Alzheimer's disease

MicroRNAs (miRNAs) serve as key post-transcriptional regulators of gene expression. Genetic variation in miRNAs and miRNA-binding sites may affect miRNA function and contribute to disease risk. Here, we investigated the extent to which variants within miRNA-related sequences could constitute a part of the functional variants involved in developing Alzheimer’s disease (AD), using the largest available genome-wide association study of AD. First, among 237 variants in miRNAs, we found rs2291418 in the miR-1229 precursor to be significantly associated with AD (p-value = 6.8 × 10⁻⁵, OR = 1.2). Our in-silico analysis and in-vitro miRNA expression experiments demonstrated that the variant’s mutant allele enhances the production of miR-1229-3p. Next, we found miR-1229-3p target genes that are associated with AD and might mediate the miRNA function. We demonstrated that miR-1229-3p directly controls the expression of its top AD-associated target gene (SORL1) using luciferase reporter assays. Additionally, we showed that miR-1229-3p and SORL1 are both expressed in the human brain. Second, among 42,855 variants in miRNA-binding sites, we identified 10 variants (in the 3′ UTR of 9 genes) that are significantly associated with AD, including rs6857 that increases the miR-320e-mediated regulation of PVRL2. Collectively, this study shows that miRNA-related variants are associated with AD and suggests miRNA-dependent regulation of several AD genes.