Project description:In our study, we generated and sequenced small RNA libraries from blood plasma samples. These samples were obtained from patients undergoing colonoscopy and are balanced for age, sex, and self-identified ancestry. From the sequencing data, we derived small-RNA feature counts and performed an analysis for differential expression between patients with and without colorectal adenoma. We found numerous significant associations, including hsa-miR-335-5p and a RNA fragment of the theoretical transcript, AK126744.
Project description:Targeted proteomics data was acquired from plasma extracellular vesicles; two pooled colorectal cancer group and two pooled healthy volunteers group. Non-targeted protemics data (selected reaction monitoring: SRM) was acquired from plasma extracellular vesicles; 209 colorectal cancer patients and 109 healthy volunteers.
Project description:Background: Circulating miRNAs in pituitary adenoma would help patient care especially in non-functioning adenoma cases as minimally invasive biomarkers of tumor recurrence and progression. Aim: Our aim was to investigate plasma miRNA profile in patients with pituitary adenoma. Materials and Methods: 149 plasma and extracellular vesicle (preoperative, early- and late postoperative) samples were collected from 45 pituitary adenoma patients. Adenomas were characterized based on anterior pituitary hormones and transcription factors by immunostaining. MiRNA next generation sequencing was performed on 36 samples (discovery set). Individual TaqMan assay was used for validation on extended sample set. PA tissue miRNAs were evaluated by TaqMan array and literature data. Results: Global downregulation of miRNA expression was observed in plasma samples of pituitary adenoma patients compared to normal samples. Expression of 29 miRNAs and isomiR variants were able to distinguish preoperative plasma samples and normal controls. MiRNAs with altered expression in both plasma and different adenoma tissues were identified. 3, 7 and 66 miRNAs expressed differentially between preoperative and postoperative plasma samples in growth hormone secreting, FSH/LH+ and hormone-immunonegative groups, respectively. MiR-143-3p was downregulated in late- but not in early postoperative plasma samples compared to preoperative ones exclusively in FSH/LH+ adenomas. Plasma level of miR-143-3p discriminated these samples with 81.8% sensitivity and 72.3% specificity (AUC=0.79; p=0.02). Conclusions: Differentially expressed miRNAs in pituitary adenoma tissues have low abundance in plasma minimizing their role as biomarkers. Plasma miR-143-3p decreases in patients with FSH/LH+ adenoma indicated successful surgery, but its application for evaluating tumor recurrence needs further investigation.
Project description:Background: Screening for the early detection of colorectal cancer is important to improve patient survival. The aim of this study was to investigate the potential of circulating cell-free miRNAs as biomarkers of CRC, and their efficiency at delineating patients with polyps and benign adenomas from normal and cancer patient groups. Methods: The expression of 667 miRNAs was assessed in a discovery set of 48 plasma samples comprising normal, polyp, adenoma, and early and advanced cancer samples. Three miRNAs (miR-34a, miR-150, and miR-923) were further examined in a validation cohort of 97 subjects divided into the same five groups, and in an independent public dataset of 40 CRC samples and paired normal tissues. Results: High levels of circulating miR-34a and low miR-150 levels distinguished groups of patients with polyps from those with advanced cancer (AUC=0.904), and low circulating miR-150 levels separated patients with adenomas from those with advanced cancer (AUC=0.875). In addition, the altered expression of miR-34a and miR-150 in an independent public dataset of forty CRC samples and paired normal tissues was confirmed. Conclusion: We identified two circulating miRNAs capable of distinguishing patient groups with different diseases of the colon from each other, and patients with advanced cancer from benign disease groups.
Project description:Parallel proteomic and phosphoproteomic analyses were conducted on plasma-derived small extracellular vesicles (sEVs) obtained from healthy individuals with negative colonoscopy (N), patients with advanced precancerous polyps (high-risk adenoma; HRA), and patients with colorectal cancer (CRC). In the discovery cohort, plasma samples were processed for sEV isolation using size-exclusion chromatography. The sEV isolates were digested with mass spectrometry-grade trypsin, and the resulting peptides were quantified using the Pierce Quantitative Colorimetric Peptide Assay. Peptides from each group (n = 10) were pooled, and 100 µg of the pooled peptides were aliquoted for phosphopeptide enrichment using the ProteoExtract Phosphopeptide Enrichment TiO2 Kit. Both the enriched phosphopeptides and corresponding unenriched peptides were analyzed in parallel using label-free quantitative mass spectrometry in three technical replicates. Findings were validated in individual samples (n = 50) through immunoblot analysis in the validation cohort.
Project description:We report the RNA-seq data of 40 advanced colorectal adenoma patients form Dongguk University Ilsan International Hospital. The polyps with a diameter of 1cm or greater were regarded as advenced colorectal adenoma and obtained through colonoscopy. The data consist of 22 tublar adenoma, 6 tublovillous adenoma, 5 sessile serrated adenoma/polyp, 1 traditional serrated adenoma, intramucosal adenocarcinoma, neuroendocrine tumor, hyperplastic polyp, inflammatory polyp, high grade dysplasia, and atypical glands with adjacent hyperplastic mucosa.
Project description:We showed that a lot of genes were deregulated in colorectal adenocarcinomas in comparison with colorectal adenomas. 37 colorectal adenoma and 9 colorectal adenocarcinoma samples were analyzed. We generated a comparison between adenocarcinomas and adenomas.
Project description:Whole transcriptome expression levels of healthy colonic, colorectal adenoma and colorectal cancer biopsy samples were analyzed by HTA 2.0 microarrays
