Rigorous Comparison of Extracellular Vesicle Processing to Enhance Downstream Analysis for Glioblastoma Characterization.

Extracellular vesicles (EVs) are highly sought after as a source of biomarkers for disease detection and monitoring. Tumor EV isolation, processing, and evaluation from biofluids is convoluted by EV heterogeneity and biological contaminants and is limited by technical processing efficacy. This study rigorously compares common bulk EV isolation workflows (size exclusion chromatography, SEC; membrane affinity, MA) alongside downstream RNA extraction protocols to investigate molecular analyte recovery. EV integrity and recovery is evaluated using a variety of technologies to quantify total intact EVs, total and surface proteins, and RNA purity and recovery. A comprehensive evaluation of each analyte is performed, with a specific emphasis on maintaining user (n = 2), biological (n = 3), and technical replicates (n≥3) under in vitro conditions. Subsequent study of tumor EV spike-in into healthy donor plasma samples is performed to further validate biofluid-derived EV purity and isolation for clinical application. Results show that EV surface integrity is considerably preserved in eluates from SEC-derived EVs, but RNA recovery and purity, as well as bulk protein isolation, is significantly improved in MA-isolated EVs. This study concludes that EV isolation and RNA extraction pipelines govern recovered analyte integrity, necessitating careful selection of processing modality to enhance recovery of the analyte of interest.

Evaluation of RNA Isolation Methods in Human Adipose Tissue.

OBJECTIVE: Research has shown that RNA extraction from adipose tissue (AT) is challenging because of high lipid content and low RNA quantity. We compared a traditional RNA extraction with a column-based method in human AT to evaluate RNA quantity and quality. MATERIALS AND METHODS: Human subcutaneous AT (n = 9) was collected through needle biopsy, and RNA was extracted using the phenol-chloroform traditional method and the RNeasy Lipid Tissue Mini Kit column-based method. The RNA quantity, quality, integrity, and expression of key AT genes were assessed. RESULTS: We found that the RNA quantity and integrity were reduced by 40% and 15-20%, respectively, using the column-based method compared to the traditional method, but the findings were not statistically significant. The column-based method showed a higher 260/280 ratio (~2.0) compared to the traditional method (~1.8) (P <.05), suggesting lower amounts of contaminants. The expression of AT genes was comparable between methods. CONCLUSION: The traditional extraction method provides adequate RNA yield and integrity compared to the column-based method, which is an advantage when AT specimens are small.

Optimising total RNA quality and quantity by phenol-chloroform extraction method from human visceral adipose tissue: A standardisation study.

A multitude of challenges is faced during RNA extraction from human visceral adipose tissue (VAT) due to its atypical nature and a dearth of existing literature. Our study provides a convenient and inexpensive manual method using TRIzol reagent for the reproducible recovery of intact RNA from sparse human VAT samples. Fifty-two (52) samples were grouped and tested for the effect of different factors viz. initial VAT amount, TRIzol volume per unit tissue mass, residual fat following homogenisation and first centrifugation, an additional chloroform wash, and an additional ethanol wash on the extraction process. We found that increasing initial tissue mass and decreasing TRIzol volume simultaneously improved RNA yield and purity. A fat layer removal step and additional ethanol wash further propel the A260/280 and A260/230 to their desired values. Our modifications in the isolation protocol were combined and tested through reverse transcriptase quantitative PCR, which yielded consistent results, upholding our optimisation.

Optimised isolation method for RNA extraction suitable for RNA sequencing from feline teeth collected in a clinical setting and at post mortem.

Advanced next generation sequencing approaches have started to reveal the cellular and molecular complexity of the microenvironment in many tissues. It is challenging to obtain high quality RNA from mineralised tissues. We developed an optimised method of RNA extraction from feline teeth collected in a clinical setting and at post mortem. Teeth were homogenised in phenol-guanidinium solution at near-freezing temperatures and followed by solid-phase nucleic acid extraction utilising a commercially available kit. This method produced good RNA yields and improved RNA quality based on RNA integrity numbers equivalent (RINe) from an average of 3.6 to 5.6. No correlation was found between RNA purity parameters measured by A260:280 or A230:260 ratios and degree of RNA degradation. This implies that RNA purity indicators cannot be reliably used as parameters of RNA integrity. Two reference genes (GAPDH, RPS19) showed significant changes in expression levels by qPCR at low and moderate RINe values, while RPL17 was stable at all RINe values tested. Furthermore, we investigated the effect of quantity and quality of RNA on the quality of the resultant RNA sequencing (RNA-Seq) data. Thirteen RNA-seq data showed similar duplication and mapping rates (94 to 95%) against the feline genome regardless of RINe values. However one low yield sample with a high RINe value showed a high duplication rate and it was an outlier on the RNA-seq multidimensional scaling plot. We conclude that the overall yield of RNA was more important than quality of RNA for RNA-seq quality control. These results will guide researchers who wish to perform RNA extractions from mineralised tissues, especially if collecting in a clinical setting with the recognised restraints that this imposes.

Optimization of phenol-chloroform RNA extraction.

Accurate and reliable analysis of gene expression depends on the extraction of pure and high-quality RNA. However, while the conventional phenol-chloroform RNA extraction is preferable over silica-based columns, particularly when cost is a concern or higher RNA yield is desired, it can result in significant RNA contamination. Contaminants including excess phenol, chloroform, or salts, can have significant impacts on downstream applications, including RNA quantification and reverse transcription, that can skew data collection and interpretation. To overcome the issue of RNA contamination in the conventional phenol-chloroform based RNA extraction method, we have optimized the protocol by adding one chloroform extraction step, and several RNA washing steps. Importantly, RNA quality and purity and accuracy in the quantification of RNA concentration were significantly improved with the modified protocol, resulting in reliable data collection and interpretation in downstream gene expression analysis. •Our protocol is customized by the addition of a second chloroform extraction step. Chloroform is carefully pipetted so as to not disturb the interphase layer. Any contaminants accidentally removed from interphase will be present in subsequent steps and can result in RNA contaminated with protein or phenol. The additional chloroform step increases RNA purity.•Additionally, the addition of 2 additional ethanol washes, initially intended to remove any residual salts from the isopropanol RNA precipitation step, also removed residual phenol contamination, enhancing RNA purity.•In summary, these modifications serve to enhance not only the purity of the RNA but, also increase the accuracy and reliability of RNA quantification.

Recovery of cell-free mRNA and microRNA from human semen based on their physical nature.

Cell-free seminal mRNA (cfs-mRNA) and microRNA (cfs-miRNA) have been found in human ejaculate and reported as promising noninvasive biomarkers for disorders of male reproductive organs and forensic identification. However, seminal plasma is particularly challenging for RNA extraction due to its complicated composition and high content of protein, DNA, and polysaccharide. Here, we report a novel, simple, and reliable method for the isolation of cfs-mRNA and cfs-miRNA from human semen based on our previous findings of their physical nature. Seminal microvesicles (0.1-0.5 µm in diameter), which contain the majority of cfs-mRNA, were enriched by a microfilter. Protein complexes, which most cfs-miRNA is bound with, were enriched by an ultrafilter. Harvesting the complexes or microvesicles, in which RNAs exist, avoided the influence of other components in human semen, thus favoring RNA isolation and purification. This new method can efficiently isolate cfs-mRNA and cfs-miRNA separately based on their physical nature, with high RNA purity, and low DNA contamination. It may also be applied or modified to isolate cell-free RNAs in other fluids.

Effects of different processing methods of human amniotic membrane on the quality of extracted RNA

The aim of this study was to determine the efficiency of different human amniotic membrane (HAM) processing methods on the concentration, purity and integrity of RNA. Two different techniques (Technique 1 and Technique 2) were employed for the processing of HAM, which differed in terms of washing solution, sample storage conditions and processing time. Based on preservation of HAM, three groups were formed under each technique. In Technique 1, the groups were fresh frozen 1 (F1), glycerol preserved (GP) and gamma irradiated glycerol preserved (IGP); where else in Technique 2, the groups were fresh frozen 2 (F2), 50% glycerol/Dulbecco’s modified Eagle medium (DMEM) cryopreserved HAM diluted with phosphate buffered saline (GB) and 50% glycerol/DMEM cryopreserved HAM diluted with diethylprocarbonate water (GD). Total RNA was extracted from the samples and their concentration, purity and integrity were examined. The F2 sample of which there was no pre-washing step and involved direct sample storage at -80ºC, shorter processing time and chilled processing conditions had yielded better quality of RNA compared to the others.