Clinical significance of C/D box small nucleolar RNA U76 as an oncogene and a prognostic biomarker in hepatocellular carcinoma

Wu, Long; Chang, Lei; Wang, Haitao; Ma, Weijie; Qin, Peng; Yuan, Yufeng

doi:10.1016/j.clinre.2017.04.018

Cited by 37 publications

(38 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Multivariate analysis number of cases in their study (only 30 HCC tissues) may be the major reason for this difference. Wu et al (20) reported that the overexpression of SNORD76 is associated with decreased survival of HCC patients. In vitro and in vivo functional studies consistently indicated that SNORD76 promoted HCC cell growth and tumorigenicity.…”

Section: Univariate Analysismentioning

confidence: 99%

Genomic analysis of small nucleolar RNAs identifies distinct molecular and prognostic signature in hepatocellular carcinoma

Yang

Lin

et al. 2018

Oncol Rep

View full text Add to dashboard Cite

As one of the most lethal malignancies worldwide, hepatocellular carcinoma (HCC) has a high mortality rate, which is mainly due to the complex and multi-step aberrations in gene expression associated with it. Small nucleolar RNAs (snoRNAs), non-coding RNAs that are 60-300 nucleotides in length, have been proposed to be closely associated with numerous human diseases, including HCC. However, the current knowledge regarding their clinical significance and mechanistic roles in HCC is limited. The present study comprehensively analyzed the snoRNA expression profiles in HCC and identified several ones that were dysregulated. The potential regulatory mechanisms of these snoRNAs were assessed via gene functional enrichment analyses. Univariate and multivariate Cox regression analyses were performed to identify snoRNAs that are independently associated with the risk of mortality. Subsequently, a prognostic index (PI) for survival prediction was established, which may serve as a prognostic biomarker for patients with HCC (hazard ratio, 3.023; 95% confidence interval: 1.785-5.119; P<0.001). In addition, a series of bioinformatics analyses were performed to identify potential differences in the perturbation of pathways between high-and low-risk groups. The PI developed in the present study was determined to have a moderate predictive value regarding the clinical outcome for HCC patients.

show abstract

Section: Univariate Analysismentioning

confidence: 99%

Genomic analysis of small nucleolar RNAs identifies distinct molecular and prognostic signature in hepatocellular carcinoma

Yang

Lin

et al. 2018

Oncol Rep

View full text Add to dashboard Cite

show abstract

“…However, exceRpt had 39 unique snoRNAs but 32 (82%) of them existed in one sample. snoRNAs were stable in circulation and they have been validated as biomarkers in some disease studies 32,33 . Compared with exceRpt, COMPSRA may have a more robust results in snoRNAs detection.…”

Section: Resultsmentioning

confidence: 99%

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis

Jiang

Kho

Chase

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Small RnA-Seq is a common means to interrogate the small RnA'ome or the full spectrum of small RnAs (<200 nucleotide length) of a biological system. A pivotal problem in NGS based small RNA analysis is identifying and quantifying the small RnA'ome constituent components. for example, small RNAs in the circulatory system (circulating RNAs) are potential disease biomarkers and their function is being actively investigated. Most existing nGS data analysis tools focus on the microRnA component and a few other small RNA types like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate the full small RnA'ome, a prerequisite for downstream data analysis. We present coMpSRA, a comprehensive modular stand-alone platform for identifying and quantifying small RnAs from small RnA sequencing data. coMpSRA contains prebuilt customizable standard RnA databases and sequence processing tools to enable turnkey basic small RNA analysis. We evaluated COMPSRA against comparable existing tools on small RNA sequencing data set from serum samples of 12 healthy human controls, and COMPSRA identified a greater diversity and abundance of small RNA molecules. coMpSRA is modular, stand-alone and integrates multiple customizable RnA databases and sequence processing tool and is distributed under the GnU General public License free to non-commercial registered users at https://github.com/cougarlj/coMpSRA. Small RNA sequencing (RNA-seq) technology was developed successfully based on special isolation methods and the RNA-seq technique, which facilitates the investigation of a comprehensive profile of small RNAs 1,2. One of the most important applications is to quantify small RNAs in the circulatory system (circulating RNAs). The human circulatory system contains various types of RNA molecules, including fragmental mRNA, miRNA, piRNA, snRNA, snoRNA, and some other non-coding sequences 3,4. Studies have shown the biomarker potential of circulating RNAs in cancer 5 , cardiovascular disease 6 , and asthma 7. Moreover, other types of DNA and RNA fragments discovered in the human circulating system have been implicated as potential causes of chronic disease 8,9. In anticipation of a continued growing number of circulating RNAs studies, a comprehensive and stable platform is needed to identify the RNA classification, RNA read counts, differential expression between case and control samples, including both human and non-human (e.g. microbiome) small RNAs (<200 nucleotide length). Previous efforts to characterize small RNAs have focused primarily on microRNAs (miRNAs). For instance, sRNAnalyzer is a comprehensive and customizable pipeline for the small RNA-seq data centred on microRNA (miRNA) profiling 10. sRNAtoolbox is a web-based small RNA research toolkit 11 and SeqCluster has started to focus on non-miRNAs by comparing the sequence similarity 12. Some efforts have begun to characterize the full spectrum of small RNAs of a biological system (the small RNA' ome), such as Oasis2, miRMaster and exceRpt 13-15. Oasis2 and miRMaster are...

show abstract

“…However, exceRpt had 39 unique snoRNAs but 32 (82%) of them existed in one sample. snoRNAs were stable in circulation and they have been validated as biomarkers in some disease studies [30, 31]. Compared with exceRpt, COMPASS may have a more robust results in snoRNAs detection.…”

Section: Resultsmentioning

confidence: 99%

COMPASS: a COMprehensive Platform for smAll RNA-Seq data analySis

Kho

Chase

et al. 2019

Preprint

View full text Add to dashboard Cite

25Background 26Circulating RNAs are potential disease biomarkers and their function is being actively 27 investigated. Next generation sequencing (NGS) is a common means to interrogate 28 the small RNA'ome or the full spectrum of small RNAs (<200 nucleotide length) of a 29 biological system. A pivotal problem in NGS based small RNA analysis is identifying 30 and quantifying the small RNA'ome constituent components. Most existing NGS data 31 analysis tools focus on the microRNA component and a few other small RNA types 32 like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate 33 the full small RNA'ome, a prerequisite for down-stream data analysis. 34 35 Results 36 We present COMPASS, a comprehensive modular stand-alone platform for 37 identifying and quantifying small RNAs from small RNA sequencing data. 38 COMPASS contains prebuilt customizable standard RNA databases and sequence 39 processing tools to enable turnkey basic small RNA analysis. We evaluated 40 COMPASS against comparable existing tools on small RNA sequencing data set from 41 serum samples of 12 healthy human controls, and COMPASS identified a greater 42 diversity and abundance of small RNA molecules. 43 44 Conclusion 45 COMPASS is modular, stand-alone and integrates multiple customizable RNA 46 databases and sequence processing tool and is distributed under the GNU General 47 Li Page 3 COMPASS https://regepi.bwh.harvard.edu/circurna/ and the source code is available at 49 https://github.com/cougarlj/COMPASS. 50 51 Keywords 52 Small RNA-Seq, circulating RNA, extracellular RNA, miRNA, RNA identification, 53 RNA quantification 54 55

show abstract

Clinical significance of C/D box small nucleolar RNA U76 as an oncogene and a prognostic biomarker in hepatocellular carcinoma

Cited by 37 publications

References 32 publications

Genomic analysis of small nucleolar RNAs identifies distinct molecular and prognostic signature in hepatocellular carcinoma

Genomic analysis of small nucleolar RNAs identifies distinct molecular and prognostic signature in hepatocellular carcinoma

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis

COMPASS: a COMprehensive Platform for smAll RNA-Seq data analySis

Contact Info

Product

Resources

About