Project description:The extracellular RNAs (exRNAs) from human biofluid have recently been systematically characterized. However, the correlations of biofluid exRNA levels and human diseases remain largely untested. Here, considering the unmet need for presymptomatic biomarkers of sporadic Alzheimer’s disease (AD), we leveraged the recently developed SILVER-seq (small-input liquid volume extracellular RNA sequencing) technology to generate exRNA profiles from a longitudinal collection of human plasma samples. These 164 plasma samples were collected from research subjects 70 years or older with up to 15 years of clinical follow-up prior to death and whose clinical diagnoses were confirmed by pathological analysis of their post mortem brains. The exRNAs of AD-activated genes and transposons in the brain exhibited a concordant trend of increase in AD plasma in comparison with age-matched control plasma. However, when we required statistical significance with multiple testing adjustments, phosphoglycerate dehydrogenase (PHGDH) was the only gene that exhibited consistent upregulation in AD brain transcriptomes from 3 independent cohorts and an increase in AD plasma as compared to controls. We validated PHGDH’s serum exRNA and brain protein expression increases in AD by using 5 additional published cohorts. Finally, we compared the time-course exRNA trajectories between “converters” and controls. Plasma PHGDH exRNA exhibited presymptomatic increases in each of the 11 converters during their transitions from normal to cognitive impairment but remained stable over the entire follow-up period in 8 out of the 9 control elderly subjects. These data suggest the potential utilities of plasma exRNA levels for screening and longitudinal exRNA changes as a presymptomatic indication of sporadic AD.
Project description:Study to detect possible interactions between blood collection tubes and RNA purification methods on extracellular RNA (exRNA) sequencing. Different combinations of blood collection tubes (3 in total), time intervals between blood draw and downstream processing (immediate (T0), after 4 hours (T4), after 16 hours (T16)), and RNA purification kits (2 in total) were evaluated by applying mRNA capture sequencing (Illumina) to exRNA from human healthy donor plasma or serum.
Project description:Study to detect possible interactions between blood collection tubes and RNA purification methods on extracellular RNA (exRNA) sequencing. Different combinations of blood collection tubes (3 in total), time intervals between blood draw and downstream processing (immediate (T0), after 4 hours (T4), after 16 hours (T16)), and RNA purification kits (2 in total) were evaluated by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma or serum.
Project description:To evaluate the impact of blood collection tubes on extracellular RNA (exRNA) sequencing, 10 different blood collection tubes were compared by applying RNA Exome sequencing (Illumina) to exRNA from human healthy donor plasma or serum. Three time spans between blood draw and downstream processing were evaluated for each of the tubes. Preservation tubes were processed immediately upon blood collection (T0), after 24 hours (T24), or after 72 hours (T72). Non-preservation plasma and serum tubes were processed immediately upon blood collection (T0), after 4 hours (T4), or after 16 hours (T16). Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.
Project description:To evaluate the impact of blood collection tubes on extracellular RNA (exRNA) sequencing, 10 different blood collection tubes were compared by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma or serum. Three time spans between blood draw and downstream processing were evaluated for each of the tubes. Preservation tubes were processed immediately upon blood collection (T0), after 24 hours (T24), or after 72 hours (T72). Non-preservation plasma and serum tubes were processed immediately upon blood collection (T0), after 4 hours (T4), or after 16 hours (T16). Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.
Project description:Large cohort: exRNA composition of platelet-depleted plasma from a cohort of 173 female and 63 male healthy volunteers of diverse races and ages, collected at two visits spaced two weeks apart; 4 formerly-collected aliquots from study subject P12, who displayed a stable neuroendocrine miRNA signature in plasma; 20 plasma samples of pregnant women spanning all trimesters T1 to T3 of pregnancy, with an expected placenta miRNA contribution. P12 Family: exRNA from two replicates of platelet-depleted plasma from three unstudied P12 family members and a sample from P12 collected four years after the initial discovery of the phenotype, along with samples of two healthy volunteers. Plasma subfractions: exRNA of samples from P12 and his family, two healthy male volunteers, two non-pregnant, and nine pregnant women, separated by differential ultracentrifugation into 10,000 × g and 100,000 × g pellets, and corresponding 10,000 × g and 100,000 × g supernatants.
Project description:Plasma contains several bioactive molecules (RNA, DNA, proteins, lipids, and metabolites), which are well preserved in extracellular vesicles, that are involved in many types of cell-to-cell interactions, and are capable of modifying biological processes in recipient cells. To obtain information about the source of mRNA molecules present in the plasma, we analyzed the plasma extracellular RNA (exRNA) of healthy individuals using RNA-sequencing and compared it to that of the peripheral blood mononuclear cell (PBMCs) of the same individual. The resultant data indicates that large proportion of the transcripts in plasma are derived from cell types other than PBMCs. To assess aging-associated changes in the plasma exRNA composition, gene ontology enrichment analysis was performed, revealing a functional decline in biological processes as a result of aging. Additionally, plasma RNA levels were analyzed with differential expression analysis, revealing 10 transcripts with significant aging-associated changes. Thus, it seems that the plasma exRNA is not fully derived from the PBMCs. Instead, other cell types supply RNAs to constitute the plasma exRNA compartment. This was true in both the young and elderly individuals that were tested. Furthermore, the RNA content of the plasma showed significant changes due to aging, affecting important biological processes.
Project description:To evaluate the impact of the RNA purification method on extracellular RNA (exRNA) sequencing, 8 different RNA purification kits were compared by applying RNA Exome sequencing (Illumina) to exRNA from human healthy donor plasma. Minimum and maximum plasma input volumes recommended by the manufacturers were tested in triplicate.
