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Characterisation of dysplastic liver nodules using low-pass sequencing and the proof of principle on liquid biopsies

ABSTRACT: Characterisation of dysplastic liver nodules using low-pass sequencing and the proof of principle on liquid biopsies

PROVIDER: PRJEB20592 | ENA |

REPOSITORIES: ENA

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P. vivax: proof-of-principle global transcription analysis from two wild isolates

Project description:The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented. To determine the extent of cross-hybridization of P. falciparum with P. vivax, and to determine overlaps in expression profiles of the P. vivax Sal1 monkey-adapted strain vs wild isolates, single dual hybridization analyses were performed.

2008-04-12 | E-GEOD-11075 | biostudies-arrayexpress

P. vivax: proof-of-principle global transcription analysis from two wild isolates

2008-04-12 | GSE11075 | GEO

P. vivax: proof-of-principle global transcription analysis from two wild isolates

Project description:P. vivax: proof-of-principle global transcription analysis from two wild isolates

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Specific patterns of PIWI-interacting small noncoding RNA expression changes in dysplastic liver nodules and hepatocellular carcinoma

Project description:Hepatocellular carcinoma (HCC) is considered the result of a stepwise carcinogenic process, more often beginning with development of premalignant lesions within a cirrhotic liver, morphologically characterized by low- (LGDN) and high-grade (HGDN) dysplastic nodules. Piwi-interacting RNAs (piRNAs) represent a large family of small noncoding (snc) RNAs, 23-35 nucleotide-long, first identified in fruitfly germline cells by their ability to interact with PIWI proteins and thereby exert epigenetic and post-transcriptional regulation of gene expression. The PIWI-piRNAs pathway is active also in human somatic tissues, including stem and cancer cells, where piRNAs and piRNA-like molecules have been shown to influence key cellular processes. We applied small RNA sequencing to search for human liver piRNAs and to profile their expression patterns in cirrhotic nodules (CNs), LGDN, HGDN, early HCC (eHCC) and progressed HCC (pHCC), aiming at identifying possible relationships between these sncRNAs and liver carcinogenesis. Analyzing 54 nodules (14 CN, 8 LGDN, 6 HGDN, 6 eHCC and 20 pHCC) from 17 patients, we identified a 125 piRNA expression signature that clearly discriminates HCC from matched CNs, correlating also to clinicopathological characteristics of HCC. This result was confirmed by functional analysis of predicted piRNA target mRNAs. Interestingly, 24 piRNAs showed specific expression patterns in dysplastic nodules, respect to cirrhotic liver and/or pHCC. These results demonstrate that the piRNA pathway is active in human liver, where it is likely to represent a new player in the molecular events that characterize hepatocellular carcinogenesis, from early stages to pHCC. Furthermore, they suggest that piRNAs might represent new disease biomarkers, potentially useful for differential diagnosis of dysplastic and neoplastic liver lesions.

2016-07-15 | E-MTAB-3973 | biostudies-arrayexpress

A new strategy for identifying mechanisms of drug-drug interaction using transcriptome analysis: Compound Kushen injection as a proof of principle

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Comparison of transcriptomic profiles between dysplastic stem cell subpopulations

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