ABSTRACT: We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.
Project description:We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.
Project description:Despite improvements in capabilities of proteomics technologies, the introduction of new plasma-based protein biomarkers for clinical use remains low. One reason is the cumbersome requirement to test thousands of protein candidates in follow-up quantitative verification studies. We sought to evaluate internal standard triggered parallel reaction monitoring (IS-PRM) in the context of biomarker verification by developing a method to quantify 5,176 peptides (1,314 proteins) as candidate biomarkers for early detection of breast cancer. Method performance was characterized in a response curve showing large linear range (4 orders of magnitude) and good repeatability (median CV 7.7%). The method was applied to pools of cancer and control human plasma, detecting 893 proteins and qualifying 164 candidates to advance for further evaluation. The method shows good quantitative performance, greatly expanding the capabilities for quantification of large numbers of proteins, and is well suited for large scale relative quantification of protein sets.
Project description:Rat has been treated with different compounds with the purpose of investigating toxicological mechanisms. But toxic and non-toxic compounds has been administered. 3 toxic (ANIT, DMN, NMF) 3 non-tox (Caerulein, dinitrophenol(DNP), Rosiglitazone) in 5-plicates (30 arrays in all) and 9 untreated (control), 39 samples in all. The array data was used to identify genes with biomarker potential for detecting toxic properties of compounds. Keywords: other
Project description:Rat has been treated with different compounds with the purpose of investigating toxicological mechanisms. But toxic and non-toxic compounds has been administered. 3 toxic (ANIT, DMN, NMF) 3 non-tox (Caerulein, dinitrophenol(DNP), Rosiglitazone) in 5-plicates (30 arrays in all) and 9 untreated (control), 39 samples in all. The array data was used to identify genes with biomarker potential for detecting toxic properties of compounds. Keywords: other Rats was treated with different compounds and RNA from liver was extracyed after 48 hours. Microarrays (GeneChip Rat230 version 2) was run on the RNA
Project description:EVP miRNAs levels were measured in 54 plasma samples collected approximately 24-28 weeks gestation from individuals in New Hampshire using the NanoString nCounter Human v3 miRNA expression panel
Project description:MicroRNAs are a family of 19- to 25-nucleotides noncoding small RNAs that primarily function as gene regulators. Aberrant microRNA expression has been described for several human malignancies, and this new class of small regulatory RNAs has both oncogenic and tumor suppressor functions. Despite this knowledge, there is little information regarding microRNAs in blood especially because microRNAs in blood, if exist, were thought to be digested by RNase. Recent studies, however, have revealed that microRNAs exist and escape digestion in serum and plasma. Thus, we performed microRNA microaray to obtain insight into microRNA deregulation in the plasma of a leukemia patient. Here, we have revealed that microRNA-638 (miR-638) is stably present in human plasmas, and miR-92a dramatically decreased in the plasmas of acute leukemia patients. Our data indicate that the ratio of miR-92a/miR-638 in plasma has strong potential for clinical application as a novel biomarker for detection of leukemia. Seven normal samples and two acute leukemia samples ware profiled and compared.
Project description:This study demonstrated that there were a number of dysregulated circRNAs in exosomes from OSA with AMI patients, which might be effectively served as a promising diagnostic biomarker and therapeutic targets. Objectives: Circular RNAs (circRNAs) are recently identified as a class of non-coding RNAs that participate in the incidence of acute myocardial infarction(AMI)
Project description:Methylation-based liquid biopsies show promise in detecting cancer from circulating cell-free DNA, but current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here we report LABS (Linear Amplification based Bisulfite Sequencing), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.
Project description:Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. The numbers of up- and down-regulated circRNAs during tumorigenesis are almost equal. In addition, we discovered that the expression of different circRNA isoforms from the same linear RNA also different. Strikingly, as much as ~18,000 circRNAs could be robustly detected in plasmas, and ~8,000 circRNAs show different expression after surgery of tumor removal. Altogether, taking advantage of the huge number of circRNAs detected in tumor and plasma, we provide strong evidence for circRNA expression, regulation and potential clinical application as non-invasive biomarkers.
