Piwi-interacting Ribonucleic acids(piRNAs)molecule is a wellknown subclass of small non-codingRNAmolecules that are mainly responsible for maintaining genome integrity,regulating gene expression,and germline stem cell...Piwi-interacting Ribonucleic acids(piRNAs)molecule is a wellknown subclass of small non-codingRNAmolecules that are mainly responsible for maintaining genome integrity,regulating gene expression,and germline stem cell maintenance by suppressing transposon elements.The piRNAs molecule can be used for the diagnosis of multiple tumor types and drug development.Due to the vital roles of the piRNA in computational biology,the identification of piRNAs has become an important area of research in computational biology.This paper proposes a two-layer predictor to improve the prediction of piRNAs and their function using deep learning methods.The proposed model applies various feature extraction methods to consider both structure information and physicochemical properties of the biological sequences during the feature extraction process.The outcome of the proposed model is extensively evaluated using the k-fold cross-validation method.The evaluation result shows that the proposed predictor performed better than the existing models with accuracy improvement of 7.59%and 2.81%at layer I and layer II respectively.It is anticipated that the proposed model could be a beneficial tool for cancer diagnosis and precision medicine.展开更多
Hepatocellular carcinoma(HCC)is the most common and deadliest subtype of liver cancer worldwide and,therefore,poses an enormous threat to global health.Understanding the molecular mechanisms underlying the development...Hepatocellular carcinoma(HCC)is the most common and deadliest subtype of liver cancer worldwide and,therefore,poses an enormous threat to global health.Understanding the molecular mechanisms underlying the development and progression of HCC is central to improving our clinical approaches.PIWIinteracting RNAs(piRNAs)are a class of small non-coding RNAs that bind to PIWI family proteins to regulate gene expression at transcriptional and posttranscriptional levels.A growing body of work shows that the dysregulation of piRNAs plays a crucial role in the progression of various human cancers.In this editorial,we report on the current knowledge of HCC-associated piRNAs and their potential clinical utility.Based on the editorial by Papadopoulos and Trifylli,on the role and clinical evaluation of exosomal circular RNAs in HCC,we highlight this other emerging class of non-coding RNAs.展开更多
The relevance of genetic mechanism to the phenotype of hypoxic adaptation remains elusive.Tibetan chickens typically used to investigate the mechanism for the adaptation of hypoxia and the recognition of hypoxia-relat...The relevance of genetic mechanism to the phenotype of hypoxic adaptation remains elusive.Tibetan chickens typically used to investigate the mechanism for the adaptation of hypoxia and the recognition of hypoxia-related piRNA remains an open issue.The purpose of this study was to illustrate whether the piRNAs were related to hypoxic adaptation.First of all,the differentially expressed piRNAs(DEpiRNAs)were identified through RNA sequencing between the Tibetan chickens and Daheng broilers.Subsequently,the target genes of DEpiRNAs were predicted and annotated by software.The network was constructed by Cytoscape.In our study,a total of 277 DEpiRNAs(33 down-regulated,244 up-regulated)were identified in the Tibetan chickens compared with the Daheng broilers.All of the 277 DEpiRNAs predicted 36658 targeted genes.Gene Ontology(GO)analysis showed that the target genes were significantly enriched in the biological process correlated with proliferation and apoptosis of cells,including cell cycle,mitochondrial outer membrane permeabilization,and positive regulation of stress-activated mitogen-activated protein kinase cascade.Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis implicated that the DEpiRNAs were mainly involved in immune and metabolism,including natural killer cell-mediated cytotoxicity,toll-like receptor signaling pathway and fatty acid metabolism.Furthermore,a predicted network with four piRNAs acted on 11 pathways via interacting with 22 target genes,in which piR-gga-1368839 regulated metabolic pathways by acting on DHCR24.In conclusion,we determined the DEpiRNAs in the Tibetan chickens and found that these piRNAs were associated with metabolism,which may be favorable for researching the biological adaptation to hypoxic stress.展开更多
PIWI-interacting RNAs(pi RNAs)are a class of small noncoding RNA molecules that specifically bind to piwi protein family members to exert regulatory functions in germ cells.Recent studies have found that pi RNAs,as ti...PIWI-interacting RNAs(pi RNAs)are a class of small noncoding RNA molecules that specifically bind to piwi protein family members to exert regulatory functions in germ cells.Recent studies have found that pi RNAs,as tissue-specific molecules,both play oncogenic and tumor suppressive roles in cancer progression,including cancer cell proliferation,metastasis,chemoresistance and stemness.Additionally,the atypical manifestation of pi RNAs and PIWI proteins in various malignancies presents a promising strategy for the identification of novel biomarkers and therapeutic targets in the diagnosis and management of tumors.Nonetheless,the precise functions of pi RNAs in cancer progression and their underlying mechanisms have yet to be fully comprehended.This review aims to examine current research on the biogenesis and functions of pi RNA and its burgeoning importance in cancer progression,thereby offering novel perspectives on the potential utilization of pi RNAs and piwi proteins in the management and treatment of advanced cancer.展开更多
基金This research was supported by the Ministry of Higher Education(MOHE)of Malaysia through Fundamental Research Grant Scheme(FRGS/1/2020/ICT02/UPM/02/3).
文摘Piwi-interacting Ribonucleic acids(piRNAs)molecule is a wellknown subclass of small non-codingRNAmolecules that are mainly responsible for maintaining genome integrity,regulating gene expression,and germline stem cell maintenance by suppressing transposon elements.The piRNAs molecule can be used for the diagnosis of multiple tumor types and drug development.Due to the vital roles of the piRNA in computational biology,the identification of piRNAs has become an important area of research in computational biology.This paper proposes a two-layer predictor to improve the prediction of piRNAs and their function using deep learning methods.The proposed model applies various feature extraction methods to consider both structure information and physicochemical properties of the biological sequences during the feature extraction process.The outcome of the proposed model is extensively evaluated using the k-fold cross-validation method.The evaluation result shows that the proposed predictor performed better than the existing models with accuracy improvement of 7.59%and 2.81%at layer I and layer II respectively.It is anticipated that the proposed model could be a beneficial tool for cancer diagnosis and precision medicine.
文摘Hepatocellular carcinoma(HCC)is the most common and deadliest subtype of liver cancer worldwide and,therefore,poses an enormous threat to global health.Understanding the molecular mechanisms underlying the development and progression of HCC is central to improving our clinical approaches.PIWIinteracting RNAs(piRNAs)are a class of small non-coding RNAs that bind to PIWI family proteins to regulate gene expression at transcriptional and posttranscriptional levels.A growing body of work shows that the dysregulation of piRNAs plays a crucial role in the progression of various human cancers.In this editorial,we report on the current knowledge of HCC-associated piRNAs and their potential clinical utility.Based on the editorial by Papadopoulos and Trifylli,on the role and clinical evaluation of exosomal circular RNAs in HCC,we highlight this other emerging class of non-coding RNAs.
基金Supported by Science and Technology Support Planning Project of Sichuan Province(2021YFYZ00312020YFN0146+1 种基金SASA2022CZYX002)National Modern Agricultural Technology System Construction of China(CARS-41-G04)。
文摘The relevance of genetic mechanism to the phenotype of hypoxic adaptation remains elusive.Tibetan chickens typically used to investigate the mechanism for the adaptation of hypoxia and the recognition of hypoxia-related piRNA remains an open issue.The purpose of this study was to illustrate whether the piRNAs were related to hypoxic adaptation.First of all,the differentially expressed piRNAs(DEpiRNAs)were identified through RNA sequencing between the Tibetan chickens and Daheng broilers.Subsequently,the target genes of DEpiRNAs were predicted and annotated by software.The network was constructed by Cytoscape.In our study,a total of 277 DEpiRNAs(33 down-regulated,244 up-regulated)were identified in the Tibetan chickens compared with the Daheng broilers.All of the 277 DEpiRNAs predicted 36658 targeted genes.Gene Ontology(GO)analysis showed that the target genes were significantly enriched in the biological process correlated with proliferation and apoptosis of cells,including cell cycle,mitochondrial outer membrane permeabilization,and positive regulation of stress-activated mitogen-activated protein kinase cascade.Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis implicated that the DEpiRNAs were mainly involved in immune and metabolism,including natural killer cell-mediated cytotoxicity,toll-like receptor signaling pathway and fatty acid metabolism.Furthermore,a predicted network with four piRNAs acted on 11 pathways via interacting with 22 target genes,in which piR-gga-1368839 regulated metabolic pathways by acting on DHCR24.In conclusion,we determined the DEpiRNAs in the Tibetan chickens and found that these piRNAs were associated with metabolism,which may be favorable for researching the biological adaptation to hypoxic stress.
基金supported by the Basic and Applied Basic Research Foundation of Guangdong Province(2022A1515220184)the Natural Science Foundation of Guangdong Province(2021A1515010547)。
文摘PIWI-interacting RNAs(pi RNAs)are a class of small noncoding RNA molecules that specifically bind to piwi protein family members to exert regulatory functions in germ cells.Recent studies have found that pi RNAs,as tissue-specific molecules,both play oncogenic and tumor suppressive roles in cancer progression,including cancer cell proliferation,metastasis,chemoresistance and stemness.Additionally,the atypical manifestation of pi RNAs and PIWI proteins in various malignancies presents a promising strategy for the identification of novel biomarkers and therapeutic targets in the diagnosis and management of tumors.Nonetheless,the precise functions of pi RNAs in cancer progression and their underlying mechanisms have yet to be fully comprehended.This review aims to examine current research on the biogenesis and functions of pi RNA and its burgeoning importance in cancer progression,thereby offering novel perspectives on the potential utilization of pi RNAs and piwi proteins in the management and treatment of advanced cancer.
