Project description:Circulating plasma miRNAs profiling in platelets-free plasma samples from Behçet's disease patients compared with healthy subjects, aimed to both pathogenesis elucidation and candidate non-invasive biomarkers identification.
Project description:The experiment is for demonstrating the miRNA profiles in plasma exosomes derived from mild cognitive impairment and Alzheimer's disease patients and healthy donors.
Project description:Genome wide DNA methylation profiling of tumor and normal samples with esophageal squamous cell carcinoma patients. The Illumina GolodenGate methylation cancer panel I was used to obtain DNA methylation profiles across approximately 1,505 CpGs in esophageal squemous cell carcinoma samples. Samples included normal, tumors and plasma samples with esophageal squamous cell carcinoma, also inculding the plasma samples with cancer-free individual.
Project description:Cell-free RNAs in biofluids provide opportunities to monitor cancer in a non-invasive manner. Although extracellular microRNAs are extensively characterized, fragmented cell-free long RNAs are not well investigated. Here, we developed Detector-seq (depletion-assisted multiplexing cell-free total RNA sequencing) to enable the deciphering of the cell-free transcriptome. After demonstrating the superior performance of detecting fragmented cell-free long RNAs, we applied Detector-seq to compare cell-free RNAs in human plasma and its extracellular vesicle (EV). Distinct human and microbial RNA signatures were revealed. Structured circular RNA, tRNA, and Y RNA were enriched in plasma, while mRNA and srpRNA were enriched in EV. Meanwhile, cell-free RNAs derived from the virus were more enriched in plasma than in EV. We identified RNAs that showed a selective distribution between plasma and EV and uncovered their distinct functional pathways, that is RNA splicing, antimicrobial humoral response enriched in plasma and transcriptional activity, cell migration, and antigen receptor-mediated immune signals enriched in EV. Although distinctive cancer-relevant RNA signals were identified in plasma and EV, a comparable performance of distinguishing cancer patients from normal individuals could be achieved. Compared to human RNAs, microbe-derived RNA features enabled better classification between colorectal and lung cancer. And for these microbial RNAs, plasma RNAs outperformed EV RNAs for the discrimination of cancer types. Overall, our work provides insights into the unexplored difference of cell-free RNA signals between plasma and EV, thus offering practical guidance for proper selection (with/without EV enrichment) when launching an RNA-based liquid biopsy study. Furthermore, with the ability to capture understudied cell-free long RNA fragments, Detector-seq offers new possibilities for transcriptome-wide characterization of cell-free RNAs to facilitate the understanding of extracellular RNA biology and clinical advances of liquid biopsy.
Project description:Cell-free RNA (cfRNA) in plasma reflects gene expression profiles of both localized sites of cancer and at the systemic host response. Here we explore the diagnostic potential of cell-free transcriptomes by mRNA sequencing. We sequenced total cell-free plasma RNA from 90 plasma samples from two independent sample cohorts representing two cancer types, two pre-cancerous conditions and non-cancer donors. We identified distinct gene sets and built classification models that could distinguish cancer patients with specific cancer types from premalignant conditions and non-cancer individuals with high accuracy. Determination of multiple myeloma from its pre-cancerous monoclonal gammopathy of undetermined significance (MGUS) yielded an accuracy of 90% (17/19). Detection of primary liver cancer from its premalignant condition cirrhosis yielded an accuracy of 100% (12/12). This work lays the foundation for developing low cost assays by measuring mRNA transcript levels in plasma using a small panel of genes for detection that can distinguish the presence of cancer from pre-cancerous conditions and non-cancer individuals.
