Analysis of distinct long noncoding <scp>RNA</scp> transcriptional fingerprints in pancreatic ductal adenocarcinoma

Yu, Xiang; Yuan, Lin; Sui, Wu; Zou, Yanfen; Lv, Zhongchuan

doi:10.1002/cam4.1027

Cited by 44 publications

(37 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For further in‐depth analysis, the lncRNA CASC9 , whose knockdown by three different methods was consistently associated with a loss of cell viability, was selected. The link of CASC9 to viability and proliferation was further supported by data from other tumor entities . We showed that the impact of CASC9 depletion was caused by a mixed phenotype including loss of proliferation and induction of apoptosis.…”

Section: Discussionsupporting

confidence: 66%

The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling

et al. 2018

View full text Add to dashboard Cite

The identification of viability-associated long noncoding RNAs (lncRNAs) might be a promising rationale for new therapeutic approaches in liver cancer. Here, we applied an RNA interference screening approach in hepatocellular carcinoma (HCC) cell lines to find viability-associated lncRNAs. Among the multiple identified lncRNAs with a significant impact on HCC cell viability, we selected cancer susceptibility 9 (CASC9) due to the strength of its phenotype, expression, and up-regulation in HCC versus normal liver. CASC9 regulated viability across multiple HCC cell lines as shown by clustered regularly interspaced short palindromic repeats interference and single small interfering RNA (siRNA)-mediated and siRNA pool-mediated depletion of CASC9. Further, CASC9 depletion caused an increase in apoptosis and a decrease of proliferation. We identified the RNA binding protein heterogeneous nuclear ribonucleoprotein L (HNRNPL) as a CASC9 interacting protein by RNA affinity purification and validated it by native RNA immunoprecipitation. Knockdown of HNRNPL mimicked the loss-of-viability phenotype observed upon CASC9 depletion. Analysis of the proteome (stable isotope labeling with amino acids in cell culture) of CASC9-depleted and HNRNPL-depleted cells revealed a set of coregulated genes which implied a role of the CASC9:HNRNPL complex in AKT signaling and DNA damage sensing. CASC9 expression levels were elevated in patient-derived tumor samples compared to normal control tissue and had a significant association with overall survival of HCC patients. In a xenograft chicken chorioallantoic membrane model, we measured decreased tumor size after knockdown of CASC9. Conclusion: Taken together, we provide a comprehensive list of viability-associated lncRNAs in HCC; we identified the CASC9:HNRNPL complex as a clinically relevant viability-associated lncRNA/protein complex which affects AKT signaling and DNA damage sensing in HCC.

show abstract

Section: Discussionsupporting

confidence: 66%

The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Transcriptional fingerprint analysis in pancreatic ductal adenocarcinoma (PDAC) demonstrated that F11-AS1 is downregulated in PDAC tumor tissues and cell lines. These results suggest that dysregulated lncRNAs play important roles in PDAC development and progression [54]. A literature review revealed that the remaining prognostic DELs identified in the present study were not reported previously, and their function in HCC and other cancers needs to be further investigated and verified.…”

Section: Discussionmentioning

confidence: 81%

Identification of Potential Prognostic Long Non-Coding RNA Biomarkers for Predicting Survival in Patients with Hepatocellular Carcinoma

Liao

Yang

Huang

et al. 2018

Cell Physiol Biochem

View full text Add to dashboard Cite

Background/Aims: The aim of the current study was to identify potential prognostic long non-coding RNA (lncRNA) biomarkers for predicting survival in patients with hepatocellular carcinoma (HCC) using The Cancer Genome Atlas (TCGA) dataset and bioinformatics analysis. Methods: RNA sequencing and clinical data of HCC patients from TCGA were used for prognostic association assessment by univariate Cox analysis. A prognostic signature was built using stepwise multivariable Cox analysis, and a comprehensive analysis was performed to evaluate its prognostic value. The prognostic signature was further evaluated by functional assessment and bioinformatics analysis. Results: Thirteen differentially expressed lncRNAs (DELs) were identified and used to construct a single prognostic signature. Patients with high risk scores showed a significantly increased risk of death (adjusted P < 0.0001, adjusted hazard ratio = 3.522, 95% confidence interval = 2.307–5.376). In the time-dependent receiver operating characteristic analysis, the prognostic signature performed well for HCC survival prediction with an area under curve of 0.809, 0.782 and 0.79 for 1-, 3- and 5-year survival, respectively. Comprehensive survival analysis of the 13-DEL prognostic signature suggested that it serves as an independent factor in HCC, showing a better performance for prognosis prediction than traditional clinical indicators. Functional assessment and bioinformatics analysis suggested that the prognostic signature was associated with the cell cycle and peroxisome proliferator-activated receptor signaling pathway. Conclusions: The novel lncRNA expression signature identified in the present study may be a potential biomarker for predicting the prognosis of HCC patients.

show abstract

“…DNA tiling arrays contain oligonucleotide probes encompassing an entire length of a defined DNA regionto identify novel lncRNAs so that DNA tiling arrays are a major advantage to discover new lncRNA. Some companies developed their microarray chips to detect lncRNA such as Array star and Affymetrix with about 30,000 lncRNA expression panel assay [9] . RNA-seq is a very powerful technique to detect and quantify lncRNAs as Fig4B.…”

Section: Clinical Sample and Detectionmentioning

confidence: 99%

Clinical Analysis of Long Non-coding RNA (LncRNA): Therapeutic Targeting of Tumorigenesis and Tumor Disease

Li¹

2017

IJLSSR

View full text Add to dashboard Cite

ABSTRACT-Long non-coding RNAs (lncRNAs) are a group of longer than 200 nucleotides which are the largest and more diverse transcripts in the cells. After study from Functional Annotation of Mammalian cDNA, lncRNAs demonstrated some special characteristics such as lower quantity, higher tissue-specificity, higher stage specificity and higher cell subtype specificity. The current evidence from tumor diseases suggests that lncRNAs are an important regulatory RNA present at tumor cells, and therefore their alterations are associated with tumorigenesis and tumor diseases. Here we presented a clinical landscape of lncRNA including detection of lncRNA and their clinical application such as diagnosis biomarkers and therapeutic targets. We also discussed the challenges and resolving strategies for these clinical applications.

show abstract

Analysis of distinct long noncoding RNA transcriptional fingerprints in pancreatic ductal adenocarcinoma

Cited by 44 publications

References 28 publications

The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling

The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling

Identification of Potential Prognostic Long Non-Coding RNA Biomarkers for Predicting Survival in Patients with Hepatocellular Carcinoma

Clinical Analysis of Long Non-coding RNA (LncRNA): Therapeutic Targeting of Tumorigenesis and Tumor Disease

Contact Info

Product

Resources

About