Project description:Circulating extracellular RNAs (exRNAs) are potential biomarkers of disease. We thus hypothesized that age-related changes in exRNAs can identify age-related processes. We profiled both large and small RNAs in human serum to investigate changes associated with normal aging. exRNA was sequenced in 13 young (30-32 yrs.) and 10 old (80-85 yrs.) African American women to identify all RNA transcripts present in serum. We identified age-related differences in several RNA biotypes, including mitochondrial transfer RNAs, mitochondrial ribosomal RNA, and unprocessed pseudogenes. Age-related differences in unique RNA transcripts were further validated in an expanded cohort. Pathway analysis revealed that EIF2 signaling, oxidative phosphorylation, and mitochondrial dysfunction were among the top pathways shared between young and old. Protein interaction networks revealed distinct clusters of functionally-related protein-coding genes in both age-groups. These data provide timely and relevant insight into the exRNA repertoire in serum and its change with aging.
Project description:Extracellular vesicles such as exosomes are selectively enriched in RNA that has potential for use as disease biomarkers. To systemically characterize circulating extracellular RNA profiles, we performed RNA sequencing analysis on plasma extracellular vesicles derived from 192 individuals including 100 colon cancer, 36 prostate cancer and 6 pancreatic cancer patients along with 50 healthy individuals. Of ~12.6 million raw reads for each of these subjects, the number of mappable reads aligned to RNA references was ~5.4 million including microRNAs(miRNAs) (~40.4%), piwi-interacting RNAs(piwiRNAs) (~40.0%), pseudo-genes (~3.7%), long noncoding RNAs (lncRNAs) (~2.4%), tRNAs (~2.1%), and mRNAs (~2.1%). To select the best candidates for potential extracellular RNA reference controls, we performed abundant level stability testing and identified a set of miRNAs showing relatively consistent expression. To estimate biological variations, we performed association analysis of expression levels with age and sex in healthy individuals. This analysis showed significant sex association with seven small noncoding RNAs (false discovery rate, or FDR<0.05), while no small noncoding RNAs were statistically associated with age. To identify disease-associated RNA transcripts, we performed analysis of covariance by including disease status, age, sex, RNA isolation and gel size selection dates. We observed a gradual increase of significantly associated RNAs (in particular, miRNAs) with disease advancement as denoted by cancer staging. We found significant association of miR-125a-5p and miR-1246-3p with all cancer types tested (FDR<0.05). Based on the disease associations, we developed cancer type-specific multivariate statistical models to predict disease status with an area under the ROC curve from 0.67 in stage I colon cancer to 0.92 in advanced prostate cancer. To date, this is the largest RNA-seq study to systematically profile extracellular RNA species, which has not only provided a baseline reference profile for circulating extracellular RNA, but also a set of RNA candidates for reference controls and disease biomarkers.
Project description:Human skeletal tissue contains an abundance of proteins some of which may be preserved over geological timescales. The profiling of proteins from ancient individuals — or palaeoproteomics —has begun to provide new information about the diseases suffered in past societies. We describe here the first dental palaeoproteomic profiles of Iron Age individuals, collected from the site of Long Long Rak rockshelter in northwest Thailand. We recovered amino acid sequences for thousands of proteins preserved in their dental tissue, however, it is evident that these palaeoproteomic profiles comprise a palimpsest of modifications that occurred both ante-mortem and post-mortem. Palaeoproteomic profiles are able to categorise disease and show the capacity of these individuals for harboring a variety of illnesses prior to death. Here we apply for the first time palaeoproteomic analysis to five prehistoric human teeth from Southeast Asia. We combine this method with stable isotope analysis using δ18O and δ13C values to broadly identify the diet of these individuals. The specimens were collected from log coffins contained within the Iron Age site of Long Long Rak (LLR) rockshelter in Pang Mapha district, Mae Hong Son Province, northwest Thailand.. Radiocarbon dating shows these log coffins to date within the range of 1,960±30 cal. yr BP to 1,636±44 cal. yr BP.
Project description:Alzheimer's disease (AD) is the most common neurodegenerative disorder. Extracellular vesicles (EVs) are carriers of nucleic acids, lipids and proteins, and are known to play a significant role in neurodegenerative pathogenesis. The goals of this study are to compare long RNA (exLR) profiling of EVs in normal human brains with which in AD human brain. EVs were isolated from frontal cortex of normal control (n=10) and AD (n=8) donors.