Cross validated serum exosomal microRNAs for the detection of oropharyngeal squamous cell carcinoma
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PROVIDER: PRJNA564555 | ENA |
REPOSITORIES: ENA
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Project description:Exosomes were purified from 250 ul serum using ExoQuickTm. The presence of particles consistent in size with exosomes (60-150nm) was confirmed using a Nanosight LM10. miRNA was extracted from exosomes using an miRNeasy Serum/Plasma kit (Qiagen, #217184). miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a custom high throughput TaqMan® OpenArray® Human microRNA panel (Life technologies). The panel consisted of probes for 110 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v20. The poor prognosis and rising incidence of HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) highlight the need for improved methods for detection of this cancer. Molecular biomarkers offer potential for this. The potential for circulating miRNAs as biomarkers in some other cancers has been shown, but circulating miRNAs have not been well validated in OPSCC. This study therefore used stabilised nested cross validation to investigate whether circulating miRNAs could be used to differentiate OPSCCs from healthy controls and patients with gastro-oesophageal reflux disease.
2020-07-15 | GSE137109 | GEO
Project description:Primary outcome(s): Prediction of malignant phenotype of colorectal cancer by serum and exosomal CEA family and detection of circulating tumor cells.
| 2629030 | ecrin-mdr-crc
Project description:The aim of this study was to identify and evaluate exosomal miRNAs in serum as early diagnostic markers for gastric cancer (GC). Methods: Using next-generation sequencing (NGS) and bioinformatics, we identified candidate serum exosomal miRNA markers for early detection of GC in patients. The candidates were further validated by qRT-PCR in 50 newly recruited early-stage GC patients and matched healthy individuals. Results: NGS revealed that the average mappable reads in the RNA libraries were about 6.5 million per patient. A total of 66 up and 13 down-regulated exosomal miRNAs were found in the screened cohort after removal of log2 transformed read counts <5 and p >0.05. In the validation cohort, by comparing candidate exosomal miRNAs levels in early-stage GC patients and healthy individuals, higher levels of miR-92b-3p, let-7g-5p, miR-146b-5p and miR-9-5p were found to be significantly associated with GC. Diagnostic power of the combined panels of the exosomal miRNAs or the combination of exosomal miRNAs and CEA outperformed that of single exosomal miRNA marker for establishing a diagnosis of early-stage GC. In addition, serum levels of exosomal miR-92b-3p were significantly associated with low adhesion, let-7g-5p and miR-146b-5p were significantly correlated with nerve infiltration, and miR146b-5p was statistically correlated with tumor invasion depth in early-stage GC. Conclusions: Serum exosomal miR-92b-3p, -146b-5p, -9-5p, and let-7g-5p may serve as potential noninvasive biomarkers for early diagnosis of GC. Further validation of these candidate exosomal miRNAs in larger experimental cohorts are required in order to confirm the diagnostic values.
2020-02-21 | GSE130654 | GEO
Project description:Preoperative prediction of lymph node (LN) metastasis is accepted as an important independent risk factor for treatment decision-making for esophageal squamous cell carcinoma (ESCC) patients. This study aimed to develop a non-invasive biomarker to identify LN metastasis preoperatively in ESCC patients with serum exosomal RNA-seq.
2020-07-30 | GSE155360 | GEO
Project description:Objective: The expression pattern of exosomal miRNAs derived from parathyroid tumor is still unknown. In the present work, we aimed to examine the differences on microRNA (miRNA) expression, present in serum exosomes, by comparing parathyroid carcinoma (PC) and parathyroid adenoma (PA). Methods: MiRNA expression profile of serum exosomes, derived from 4 PC patients and 4 PA patients, were analyzed by next-generation sequencing technology. The differential expressions of target miRNAs were further verified in both serum exosomes and tissues of PC/PA patients by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Lastly, receiver operating characteristic (ROC) curves were plotted to investigate the efficiency of target exosomal miRNAs in distinguishing PC patients from PA controls. Results: Multiple differentially expressed miRNAs of serum exosomes were screened out by sequencing. Based on this screening, hsa-miR-146b-5p (p=0.0846), hsa-miR-27a-5p (p=0.0412), hsa-miR-93-5p (p=0.73), hsa-miR-381-3p (p=0.1239) and hsa-miR-134-5p (p=0.0694) were up-regulated in the serum exosomes of PC patients. These results were validated by qPCR, where the trend on differential miRNA expression was consistent with the sequencing results. Specifically, the expression of exosomal hsa-miR-27a-5p was able to clearly distinguish PC patients from PA controls, and related analysis indicated that the area under the ROC curve was 0.8594 (p=0.0157). Conclusion: Here we present, for the first time, the miRNA expression profile of serum exosomes derived from PC patients. Based on this result, we presently suggest that the exosomal hsa-miR-27a-5p may serve as a putative tumor marker for preoperative identification of PC and PA subjects.
2020-11-13 | GSE161339 | GEO
Project description:Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin Lymphoma with complex clinical symptoms. Currently, the diagnosis of DLBCL depends largely on pathologic analysis of biopsy tissue, which is an invasive procedure and often poses some risk to patients. Exosomal miRNAs have emerged as promising noninvasive biomarkers for detecting tumor or monitoring disease progress. We aim to investigate the potential of circulating exosomal miRNAs to assist with diagnosis of DLBCL.In the present research, we used the miRCURY LNA™ microRNA Array to investgate the profiles of differentially expressed miRNAs in the exosomes of peripheral blood serum. As a result, circulating exosomal miRNA profiling yielded a total of 332 differentially expressed miRNAs (157 with up-expression and 175 with down-expression) between the DLBCL patients and healthy controls.
2021-12-06 | GSE171272 | GEO
Project description:Background/Aim: We investigated alterations in the expression of serum exosomal miRNAs with the progression of liver fibrosis and evaluated their clinical applicability as biomarkers. Methods: This study prospectively enrolled 71 patients who underwent liver biopsy at an academic hospital in Korea. Exosomes were extracted from serum samples, followed by next-generation sequencing (NGS) of miRNAs and targeted real-time quantitative polymerase chain reaction. A model was derived to discriminate advanced fibrosis based on miRNA levels and the performance of this model was evaluated. Validation of the effect of miRNA on liver fibrosis in vitro was followed. Methods: This study prospectively enrolled 71 patients who underwent liver biopsy at an academic hospital in Korea. Exosomes were extracted from serum samples, followed by next-generation sequencing (NGS) of miRNAs and targeted real-time quantitative polymerase chain reaction. A model was derived to discriminate advanced fibrosis based on miRNA levels and the performance of this model was evaluated. Validation of the effect of miRNA on liver fibrosis in vitro was followed. Results: NGS data revealed that exosomal miR-660-5p, miR-125a-5p, and miR-122 expression were changed significantly with the progression of liver fibrosis, of which miR-122 exhibited high read counts enough to be used as a biomarker. The level of exosomal miR-122 decreased as the pathologic fibrosis grade progressed and patients with biopsy-proven advanced fibrosis had significantly lower levels of exosomal miR-122 (P < 0.001) than those without advanced fibrosis. Exosomal miR-122 exhibited a fair performance in discriminating advanced fibrosis especially in combination with fibrosis-4 score and transient elastography. In a subgroup of patients with a non-viral etiology of liver disease, the performance of exosomal miR-122 as a biomarker was greatly improved. Inhibition of miR-122 expression increased the proliferation of the human hepatic stellate cell line, LX-2, and upregulated the expression of various fibrosis related proteins. Conclusion: Exosomal miR-122 may serve as a useful non-invasive biomarker for liver fibrosis, especially in patients with non-viral etiologies of chronic liver disease.
2021-07-15 | GSE179961 | GEO
Project description:Increased incidence of oropharyngeal squamous cell carcinoma (OPSCC) is mainly related to Human Papilloma Virus (HPV) infection. As OPSCCs are often diagnosed at an advanced stage, mortality and morbidity remain high. There are no diagnostic biomarkers for early stage detection of OPSCC. Serum from 25 patients with stage I-II OPSCC and 12 disease- individuals were studied with quantitative label-free proteomics using ultra-definition MSE. Statistical analyses were performed to identify proteins most reliably distinguishing early stage OPSCCs from controls. P16 was used as a surrogate marker for HPV. P16-positive and -negative tumours were also analysed separately. With two or more unique proteins per identification, 176 proteins were quantified. A clear separation between patients with early-stage tumours and controls was seen in principal component analysis. Latent structures discriminant analysis identified 96 proteins most reliably differentiating OPSCC patients from controls, with 13 upregulated and 83 downregulated in study cases. The set of proteins was studied further with network, pathway and protein-protein interaction analyses, and found to participate in e.g. lipid metabolism. We identified patients with early stage OPSCC from controls based on their serum proteome, and suggest a protein set for further evaluation as a diagnostic biomarker panel for OPSCC.
2018-07-11 | PXD008445 | Pride
Project description:To identify and assess exosomal miRNA signatures with potential to predict individuals with persistent organ failure (POF) at early phase of acute pancreatitis. We analyzed serum collected from 790 AP patients. In discovery cohort, we profiled exosomal miRNAs in sera sampled from AP patients with or without POF (5 vs. 5) using microarrays and identified a list of miRNAs with increased expression pattern. Of notes, 10 AP samples with/without POF are collected within 24 hours after AP onset and later did/didn’t develop POF. We further constructed a miRNA classifier (Cmi) through logistic regression and identified certain individual miRNAs (OR>2) as candidate predictive markers in the training cohort of 227 AP samples. Predictive performance of these markers were validated in three independent cohorts (255, 226 and 78 AP samples respectively).
2024-08-01 | GSE136030 | GEO
Project description:human oropharyngeal metagenome
| PRJNA428766 | ENA