Cell-free RNAs (cfRNAs) are promising analytes as non-invasive biomarkers and have even greater potential if tied in with metabolomics. Plasma is an optimal source for cfRNAs but is often derived from a variety of anticoagulants. Plasma obtained in heparin is suitable for metabolomics but is difficult to utilize for qPCR-based downstream analysis. In the present study, we aimed to develop a simple, time-efficient, and cost-effective heparinase protocol, followed by library preparation and sequencing of human plasma cfRNAs drawn and stored in heparin at -80 °C for several years. Blood was collected in CPT™ sodium heparin tubes from patients with chronic HCV infection (NCT02400216) at the National Institutes of Health (NIH) Clinical Center. Plasma cfRNAs were treated with heparinase I and used for library preparation and next-generation sequencing (NGS). Heparinase treatment maintained RNA integrity and allowed for successful library preparation for all the study subjects even with 7 ng of cfRNAs as starting material. The classification report derived from Pavian R package v1.2.0 showed no artificial reads. The abundance of chordate over microbial reads suggests no addition of experimental error through heparinase I treatment. We report a novel and practical approach to heparinase treatment for human plasma collected and frozen in sodium heparin for several years. This is an effective demonstration of utilizing heparin plasma for NGS and downstream transcriptomic research, which could then be integrated with metabolomics from the same samples, maximizing efficiency and minimizing blood draws.

Quantitative real-time PCR (qRT-PCR) is a highly sensitive and reliable method for detection and quantification of DNA. When combined with a prior stage of RNA reverse transcription to generate complementary DNA (cDNA), this is a powerful approach to determine and analyze gene transcriptional expression. Real-time quantitative reverse transcription PCR has become the gold standard method in studying genes expression and virulence regulation under various genetic backgrounds (e.g., in the absence of regulators) or environmental conditions. Here we demonstrate the utilization of this approach to study the transcriptional regulation of the conjugation pilus of the Salmonella enterica serovar Infantis virulence plasmid (pESI).

Acute phase proteins (APPs) determination in different fluids like serum, saliva and meat juice measured with ultrasensitive assays can be used to evaluate the disease status of porcine populations under field conditions. Liver is the main production site of serum APPs, but the origin of APPs that can be determined in body fluids different from blood remains unknown. The objective of this study was to clarify the origin of three APPs: C-reactive protein (CRP), serum amyloid A (SAA) and haptoglobin (Hp) in saliva and meat juice. The mRNA expression of these proteins was measured in liver, salivary gland and diaphragmatic muscle by quantitative PCR and compared with the protein levels in serum, saliva and meat juice, respectively in healthy and naturally diseased animals. As expected, concentrations of all APP were significantly higher in all body fluids from diseased animals. Levels of all APPs mRNA were very low in diaphragmatic muscle tissue, and the expression was independent of the disease status. In contrast, we found higher expression levels of SAA and Hp mRNA in the salivary gland of diseased animals, while CRP mRNA was not detected. Our data indicate that the APP present in meat juice derived predominantly from serum. This assumption is also supported by the good correlation of the levels of both proteins in meat juice with those in serum. Further, the lower variability of the APP levels within the two groups of animals, suggests meat juice as an alternate sampling material. The APP levels that are determined in saliva, however, appear to result from an increased local production except for CRP, indicating that the salivary gland responds to disease. These findings are relevant for the establishment of saliva as the preferred diagnostic sample for health monitoring programmes, due to the technical and ethical advantages of the collection.