Plant miRNA profile from pooled human serum samples
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE117971 | GEO | 2018/08/02
REPOSITORIES: GEO
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Project description:From serum samples of non-dialyzed and dialyzed patients with ADPKD and healthy control total RNA was isolated and miRNA expression was evaluated. Circulating microRNAs (miRNA) are important intercellular communication compounds. We investigated the influence of ADPKD (autosomal dominant polycystic kidney disease) and hemodialysis on the profile of serum miRNAs. We found 37 significant circulating miRNA that differ between ADPKD patients (dialyzed and non-dialyzed) and healthy controls. Bioinformatic analysis revealed strongest connections between those miRNAs and KEGG pathway: MicroRNAs in cancer. We selected 3 miRNAs with highest and 3 with lowest fold change in comparison of dialyzed and non-dialyzed patients and compared their expression in paired pre-/post-dialysis samples. All up-regulated miRNAs (miR-532-3p, miR-320b, miR-144-5p) were not significantly altered by hemodialysis. From down-regulated miRNAs miR-27a-3p was shown to be significantly lower after dialysis in both total and exosomal fraction. MiR-20a-5p was down-regulated after dialysis only in the exosomal fraction whereas miR-16-5p was unaltered by hemodialysis. MiR-16-5p was selected as the best circulating biomarker of ADPKD with miR-22-3p, let-7i-5p and miR-24-3p as following best ones. Circulating representatives of miR-17 family (new drug target of ADPKD (Hajarnis et al. 2017)) sharing the same seed region (miR-20a-5p, miR-93-5p and miR-106a-5p) showed significantly lowered expressed in sera of dialyzed patients vs non-dialyzed ones and their exosomal fraction dropped after hemodialysis. We concluded that serum miRNA among ADPKD patients differ substantially depending on the stage of CKD. These alterations show possible links with cancer. The exosomal fraction of miRNA was more affected by dialysis than total fraction of miRNAs suggesting their dynamically changing functional role.
2018-06-30 | GSE101811 | GEO
Project description:High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecologic neoplasm, with five-year survival rate below 30%. Early disease detection is of utmost importance to improve the cure rate of HGSOC. Liquid biopsies are now becoming a new paradigm to develop novel biomarkers with diagnostic and prognostic purposes. The focus of this study was to detect the levels of circulating miRNAs in tissues and sera from patients with HGSOC and to evaluate their diagnostic value. To this end, an array-based discovery platform, followed by an innovative statistical approach of data normalization, was exploited, to identify miRNA species selectively expressed in serum of patients with HGSOC. Sera from 106 high grade serous ovarian carcinoma (HGSOC) and 24 healthy controls were used for profiling serum microRNA using a modified version of a commercially available microarray, with the aim of identifying differentially expressed microRNA between tumor patients and healthy controls.
2017-01-30 | E-MTAB-4667 | biostudies-arrayexpress
Project description:Abstract: Background: MiRNA signatures in human sera have been reported for various tumor diseases. Here we generated miRNA profiles analyzing 1205 mature miRNA transcripts of serum samples of Wilms tumor patients, taken prior and after chemotherapy according to SIOP protocol 2001. Using a feature subset selection filter approach we identified a minimal number of miRNAs with a maximum contribution for the classification between treated and untreated patients and between patients and controls. Results: Analyzing 1205 mature miRNAs, we separated controls and Wilms tumor patients prior chemotherapy with an accuracy of 0.81. We obtained a similar accuracy (0.82) for the separation between controls and sera of Wilms tumor patients after preoperative chemotherapy. We identified 23 miRNAs that were differentially expressed in both comparisons. Subset selection improved the overall classification accuracy between controls and Wilms tumor patients prior and after chemotherapy to 0.94 and 0.91, respectively. Subset selection also allowed separating between Wilms tumor patients prior and after chemotherapy with an accuracy of 0.98. Conclusion: Our analysis identified serum based miRNA signatures that allowed separating between controls, untreated Wilms tumor patients, and Wilms tumor patients after chemotherapy with high accuracy for each of these comparisons.
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Project description:To identify serum miRNAs for the diagnosis of HCC, the profiling of 754 human miRNAs was analyzed in sera from six histopathologically confirmed HCC patients and eight CHB controls, using TaqMan Array Human MicroRNA A+B Cards Set v3.0 (Applied Biosystems, Foster City, CA). Serum miRNAs with differential levels between HCC and CHB were identified by comparing serum miRNA profiling of HCC patients with that of CHB controls.
2016-02-01 | GSE65708 | GEO
Project description:Recently, extra-cellular components, such as serum and exosome, attract more and more attention as biomarker candidates for mammalian health. However, the contribution of different blood components to the signature of respective microRNAs (miRNAs) remains unknown, especially in cattle. In this study we aimed to investigate the miRNAs from bovine sera and exosomes, and to provide insights into their future applications. Blood collected from four healthy dairy cows were used for this study. The sera and exosomes RNAs were extracted using two commonly used commercial kits (Norgen and Invitrogen total RNA isolation kit), respectively. Sera showed higher complexity of miRNome consisting of 328 miRNAs, while significantly less miRNAs (260, p = 0.001) were detected in exosomes. The profile of total detected miRNAs in sera and exosomes was different, while exosomes represented about 78% of total miRNAs expressed in sera, suggesting that exosomes are the major miRNAs carriers in bovine sera. There were 24 and 3 miRNAs (RPM > 5) that exclusively expressed in sera and exosomes, respectively. In addition, 12 miRNAs were differentially expressed between sera and exosomes (FDR < 0.05). Moreover, functional analysis showed that uniquely and highly expressed miRNAs in sera targeted functions of diseases and disorders, while the functions of those in exosomes were enriched in tissue development and lipid metabolism. Our results provide evidence that bovine sera and exosomes miRNomes are different with regarding to miRNA numbers, types and expressions. Based on their distinct profiles, miRNAs from sera and exosomes may reflect different aspects of physiological and pathological conditions in cattle. The functional analysis suggest that sera may be preferable for the purpose of detecting inflammation in cattle, while exosomes may be a better choice for monitoring the status of muscle development and lipid metabolism.
2016-10-28 | GSE72643 | GEO
Project description:Plant miRNA profile from pooled human serum samples
| PRJNA483878 | ENA
Project description:Anthracnose, caused by Colletotrichum gloeosporioides is one of the most serious diseases of tea plant [Camellia sinensis (L.) O. Kuntze]. MicroRNAs are key modulators of gene expression in defense responses and plant immunity; although, foliar application of exogenous caffeine in anthracnose disease control management has proven to be effective, miRNA-mediated regulatory mechanisms underlying caffeine-induced plant defense response to C. gloeosporioides remain unexplored in tea plant. Using high-throughput-sequencing, 24 miRNA sequencing data sets and 8 degradome data sets were generated from the susceptible cultivar Longjing43 (LJ43) and the resistant cultivar Zhongcha108 (ZC108) leaves treated with CK (Water), C. gloeosporioides-inoculation (CgI), exogenous caffeine (CN) and CgI + CN. Using sRNA sequencing, 424 conserved miRNAs and 417 novel miRNAs were identified; of these, 146 and 130 miRNAs were differentially expressed under CgI + CN treatment in the LJ43 and ZC108, respectively. Degradome sequencing identified 599 targets predicted to be cleaved by 210 conserved and 70 novel miRNAs. Majority of the annotated targets were found to involve in regulation of transcription factors, oxidation-reduction and metabolic process for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. The expression pattern of eight miRNAs and their targets were validated by qRT-PCR, and correlation analysis of csn-miR164a_R+1_1ss21AG/NAC-17 and csn-miR396b-5p/GRF-1 showed highly significant negative R-value at 7th dpi under CgI + CN in the LJ43. This study provides important insights into the novel approach of exogenous caffeine-induced miRNAs dynamically exerts its fungicidal activity through regulating JA/ET signaling pathway, thereby accurately switch on LJ43 susceptibility nature to resistance activity against C. gloeosporioides infection.
2021-12-29 | GSE146713 | GEO
Project description:The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation specific PCR assay for a panel of ten genes, discovered through whole genome methylation array analysis of serum DNA. Cancer-specific methylated DNA was detected in training and test sets of recurrent Stage 4 patient sera with a sensitivity of >90% and a specificity of >96%. A core methylation signature was retained in serum, primary and metastatic tissues throughout the course of the disease, and the cMethDNA assay levels reflected patient response to chemotherapy. Together, our data suggest that the cMethDNA assay can provide a sensitive tool to detect minute levels of tumor DNA present in a vast excess of normal DNA in serum. Samples used: 11 cancer sera,,4 pools of normal leukocytes (5 donors per pool), 6 normal breast tissues microdissected, adjacent to tumor, 15 normal breast tissues, organoid preparations
2014-03-01 | E-GEOD-52621 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we profiled exosomal miRNAs in sera of colon cancer patients (n=88) at various TNM stages (I to IV) and healthy controls (n=11) and selected significantly higher microRNAs in serum exosomes of colorectal cancer patients than that of healthy controls. Moreover, we tried to detect their serum exosome levels of using samples from patients after surgical resection of primary tumors (n=24).
2014-04-01 | GSE39833 | GEO
Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we profiled exosomal miRNAs in sera of colon cancer patients (n=88) at various TNM stages (I to IV) and healthy controls (n=11) and selected significantly higher microRNAs in serum exosomes of colorectal cancer patients than that of healthy controls. Moreover, we tried to detect their serum exosome levels of using samples from patients after surgical resection of primary tumors (n=24).
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