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

Rizzo, Francesca; Rinaldi, Antonio; Marchese, Giovanna; Coviello, Elena; Sellitto, Assunta; Cordella, Angela; Giurato, Giorgio; Nassa, Giovanni; Ravo, Maria; Tarallo, Roberta; Milanesi, Luciano; Destro, Annarita; Torzilli, Guido; Roncalli, Massimo; Tommaso, Luca Di; Weisz, Alessandro

doi:10.18632/oncotarget.10567

Cited by 65 publications

(52 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…By definition, piRNAs interact with PIWIL proteins, which we found in prostate . Recent small‐RNA sequencing studies of human somatic tissues have also detected hundreds of annotated or predicted piRNAs in ovary, liver, brain, and cell lines . The piRNAs identified in other human tissues share characteristics with the piRNAs we identified in prostate epithelium, such as a large portion mapping to introns and a weak or absent secondary piRNA biogenesis signature.…”

Section: Discussionsupporting

confidence: 56%

High levels of PIWI‐interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens

et al. 2019

View full text Add to dashboard Cite

Background Vitamin D, a hormone that acts through the nuclear vitamin D receptor (VDR), upregulates antitumorigenic microRNA in prostate epithelium. This may contribute to the lower levels of aggressive prostate cancer (PCa) observed in patients with high serum vitamin D. The small noncoding RNA (ncRNA) landscape includes many other RNA species that remain uncharacterized in prostate epithelium and their potential regulation by vitamin D is unknown. Methods Laser capture microdissection (LCM) followed by small‐RNA sequencing was used to identify ncRNAs in the prostate epithelium of tissues from a vitamin D‐supplementation trial. VDR chromatin immunoprecipitation‐sequencing was performed to identify vitamin D genomic targets in primary prostate epithelial cells. Results Isolation of epithelium by LCM increased sample homogeneity and captured more diversity in ncRNA species compared with publicly available small‐RNA sequencing data from benign whole prostate. An abundance of PIWI‐interacting RNAs (piRNAs) was detected in normal prostate epithelium. The obligate binding partners of piRNAs, PIWI‐like (PIWIL) proteins, were also detected in prostate epithelium. High prostatic vitamin D levels were associated with increased expression of piRNAs. VDR binding sites were located near several ncRNA biogenesis genes and genes regulating translation and differentiation. Conclusions Benign prostate epithelium expresses both piRNA and PIWIL proteins, suggesting that these small ncRNA may serve an unknown function in the prostate. Vitamin D may increase the expression of prostatic piRNAs. VDR binding sites in primary prostate epithelial cells are consistent with its reported antitumorigenic functions and a role in ncRNA biogenesis.

show abstract

Section: Discussionsupporting

confidence: 56%

High levels of PIWI‐interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens

et al. 2019

View full text Add to dashboard Cite

show abstract

“…As a methylation inducer, the impact of piRNAs during cancer development could be a consistent question. These later years, some works have profiled piRNA expression and explored their biological functions in cancer, including liver cancer [47,48]. In particular, piR-Hep1 was found to be upregulated in half of HCC tumors and piR-Hep1 silencing inhibited cell viability, motility, and invasiveness via a reduction of AKT phosphorylation.…”

Section: Piwirnasmentioning

confidence: 99%

Non-coding RNAs open a new chapter in liver cancer treatment

Gougelet

Desbois-Mouthon

2019

Clinics and Research in Hepatology and Gastroenterology

View full text Add to dashboard Cite

Despite the intensive efforts to identify the molecular events responsible for the emergence of liver cancer, hepatocellular carcinoma (HCC) remains a major health problem in the world. Thus, the identification of new therapeutic opportunities is a short-term necessity. These last few decades, non-coding RNAs appeared as interesting therapeutic strategies with their pleiotropic inhibitory action in the cell itself but also in recipient cells via their secretion into extracellular vesicles. This short review recapitulates recent advancements concerning non-coding RNAs and their deregulations in liver cancer.

show abstract

“…In addition, piRNA is directly or indirectly involved in the formation of liver cancer. In 2016, Rizzo et al found that hsa_piR_013306 accumulates only in hepatocellular carcinomas (Rizzo, et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Inferring Disease-Associated Piwi-Interacting RNAs via Graph Attention Networks

Zheng

You

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Motivation: PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and somatic tissues, and correlates with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes out gradually, new bioinformatics methods for large-scale identification and prioritization of potential associations are therefore of interest. However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining. This study aims to make preliminary attempts on bionetwork based graph mining. Results: In this study, we present a method based on graph attention network to identify potential and biologically significant piRNA-disease associations (PDAs), called GAPDA. The attention mechanism can calculate a hidden representation of an association in the network based on neighbor nodes and assign weights to the input to make decisions. In particular, we introduced the attention-based Graph Neural Networks to the field of bio-association prediction for the first time, and proposed an abstract network topology suitable for small samples. Specifically, we combined piRNA sequence information and disease semantic similarity with piRNA-disease association network to construct a new attribute network. In the experiment, GAPDA performed excellently in five-fold cross-validation with the AUC of 0.9038. Not only that, but it still has superior performance compared to methods based on collaborative filtering and attribute features. The experimental results show that GAPDA ensures the prospect of the graph neural network on such problems and can be an excellent supplement for future biomedical research.

show abstract

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

Cited by 65 publications

References 56 publications

High levels of PIWI‐interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens

High levels of PIWI‐interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens

Non-coding RNAs open a new chapter in liver cancer treatment

Inferring Disease-Associated Piwi-Interacting RNAs via Graph Attention Networks

Contact Info

Product

Resources

About