The diagnostic and prognostic significance of long non-coding RNA CRNDE in pan-cancer based on TCGA, GEO and comprehensive meta-analysis

Long noncoding RNA expression in acute lymphoblastic leukemia: A systematic review

Long noncoding RNAs (lncRNAs), as gene expression modulators, are potential players in Acute Lymphoblastic Leukemia (ALL) pathogenesis. We systematically explored current literature on lncRNA expression in ALL to identify lncRNAs consistently reported as differentially expressed (DE) either in ALL versus controls or between ALL subtypes. By comparing articles that provided global expression data for DE lncRNAs in the ETV6::RUNX1-positive ALL subtype, we identified four DE lncRNAs in three independent studies (two versus other subtypes and one versus controls), showing concordant expression of LINC01013, CRNDE and lnc-KLF7-1. Additionally, LINC01503 was consistently downregulated on ALL versus controls. Within RT-qPCR studies, twelve lncRNA were DE in more than one source. Thus, several lncRNAs were supported as DE in ALL by multiple sources, highlighting their potential role as candidate biomarkers or therapeutic targets. Finally, as lncRNA annotation is rapidly expanding, standardization of reporting and nomenclature is urgently needed to improve data verifiability and compilation.

Shifting the Cancer Screening Paradigm: The Rising Potential of Blood-Based Multi-Cancer Early Detection Tests

Cancer remains a leading cause of death worldwide, partly owing to late detection which entails limited and often ineffective therapeutic options. Most cancers lack validated screening procedures, and the ones available disclose several drawbacks, leading to low patient compliance and unnecessary workups, adding up the costs to healthcare systems. Hence, there is a great need for innovative, accurate, and minimally invasive tools for early cancer detection. In recent years, multi-cancer early detection (MCED) tests emerged as a promising screening tool, combining molecular analysis of tumor-related markers present in body fluids with artificial intelligence to simultaneously detect a variety of cancers and further discriminate the underlying cancer type. Herein, we aim to provide a highlight of the variety of strategies currently under development concerning MCED, as well as the major factors which are preventing clinical implementation. Although MCED tests depict great potential for clinical application, large-scale clinical validation studies are still lacking.

The lncRNA CRNDE is regulated by E2F6 and sensitizes gastric cancer cells to chemotherapy by inhibiting autophagy

Chemotherapy is an important treatment for gastric cancer (GC), but the primary and secondary drug resistance of tumours to chemotherapy seriously affects its curative effect. In recent years, the relationship between long noncoding RNAs (lncRNAs) and malignant tumours has received increasing attention. Based on accumulating evidence, lncRNAs are involved in the chemoresistance of GC, but the underlying mechanisms remain unclear. In this study, we identified the lncRNA colorectal neoplasia differentially expressed (CRNDE) as an important regulator of autophagy-associated chemoresistance in GC. Mechanistically, overexpression of CRNDE inhibits autophagy and induces apoptosis, thereby sensitizing GC cells to chemotherapy drugs. Moreover, E2F6, a classical transcriptional inhibitor, is confirmed to be upregulated in GC and represses the expression of CRNDE. The E2F6-CRNDE axis is clinically related to chemoresistant GC and poor outcomes in patients with advanced GC. Our findings suggest that the E2F6-CRNDE axis is a viable therapeutic target to protect against chemoresistance in GC.

CRNDE: A valuable long noncoding RNA for diagnosis and therapy of solid and hematological malignancies

Colorectal neoplasia differentially expressed (CRNDE) is an oncogenic long noncoding RNA (lncRNA). Increased CRNDE expression was initially discovered in colorectal cancer and then in a variety of solid tumors and hematological malignancies. CRNDE participates in multiple biological processes, such as cell proliferation, differentiation, migration, and apoptosis. CRNDE has been shown to modulate target gene expression through multiple mechanisms, including transcriptional regulation, post-transcriptional regulation, and competition for microRNA (miRNA) binding. In this review, we summarize the evidence that supports CRNDE in the diagnosis and prognosis predicting of cancers. The functional roles and molecular mechanisms of CRNDE are further described for major types of solid tumors and hematological malignancies. The therapeutic potential of CRNDE as a target for research and development is also discussed.

Expression characteristics of long non-coding RNA in colon adenocarcinoma and its potential value for judging the survival and prognosis of patients: bioinformatics analysis based on The Cancer Genome Atlas database

Background

To investigate the expression characteristics of long non-coding RNA (lncRNA) in colon adenocarcinoma (COAD) and its potential value in predicting the prognosis of patient survival.

Methods

We downloaded COAD-related RNA sequencing (RNA-seq) data and patient survival data from The Cancer Genome Atlas (TCGA). The data were analyzed for lncRNA expression differences, subjected to Cox regression analysis for survival rate, and Kaplan-Meier (KM) survival curves were plotted to analyze the role of the key genes related to prognostic survival by pathway enrichment analysis.

Results

The data of 494 COAD clinical samples from TCGA were analyzed; 204 lncRNAs were differentially expressed, 156 were up-regulated, and 48 were down-regulated. The 10 genes with the most significant expression differences were Linc02418, Blacat1, ELFN1-AS1, CRNDE, AC002384.1, AL353801.1, LINC01645, AC073283.2, AC087379.1, and LINC00484. Cox regression analysis of 204 lncRNA genes showed that 23 lncRNA genes with significant effects on the prognosis and survival rate of COAD patients were obtained when P<0.05 was used as the threshold. With P≤0.001 as the threshold, the KM curves of 4 genes (Linc02257, Linc02474, Ac010789.1, Ac083967.1) were statistically significant (P<0.05). The gene Linc02257 was selected for Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and it was revealed that the inheritance of Linc02257-regulated gene expression was closely related to tumor development, such as collagen-containing extracellular matrix, organogenesis, activity of membrane protein receptors, and ion channel activity. The signaling pathways regulated by Linc02257 were also closely related to tumors, such as neuroactive ligand-receptor interaction, the PI3K-AKT signaling pathway, calcium signaling pathway, and protein digestion and absorption.

Conclusions

In COAD, lncRNA is differentially expressed and plays an important role in the disease regulation. It has potential application value in the diagnosis, targeted therapy, and prognosis of COAD patients.

Analysis of Multiple Human Tumor Cases Reveals the Carcinogenic Effects of PKP3

Plakophilins (PKPs) act as a key regulator of different signaling programs and control a variety of cellular processes ranging from transcription, protein synthesis, growth, proliferation, and tumor development. The function and possible mechanism of PKP3 in ovarian cancer (OC) remain unknown. It is extremely important to investigate the expression and prognostic values of PKP3, as well as their possible mechanisms, and immune infiltration in OC. Therefore, in this paper we explored the potential oncogenic role of PKP3 in 33 tumors based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. The result outcomes showed that PKP3 is highly expressed in most cancers, and the expression level and prognosis of PKP3 showed little significance in cancer patients. Moreover, oncologists have found that members of the plakophilin family have different degrees of abnormality in ovarian cancer. PKP3 played a key part in carcinogenesis and aggressiveness of OC as well as malignant biological activity and can be used as a biomarker for early diagnosis and prognosis evaluation in OC.

RPARP-AS1/miR125a-5p Axis Promotes Cell Proliferation, Migration and Invasion in Colon Cancer

Background

It was reported that long-noncoding RNAs (lncRNAs) had been identified as a novel class of regulators related to various cancers. RPARP-AS1, a differentially-expressed gene, was found in analysis of the gene expression profile of CRC from GEO database. However, its function has not been clear.

Methods

RPARP-AS1 expression was determined by qPCR and Startbase3 analysis. Knockdown of RPARP-AS1 in CRC cell lines was performed by RNAi technology, named si-RPARP-AS1 HCT116 and si-RPARP-AS1 LoVo. Cell proliferation was examined by CCK8 and colony formation assay. RNA pull-down and Luciferase reporter assay were performed to confirm the interaction between RPARP-AS1 and miR-125a-5p.

Results

In the study, we found that the expression of RPARP-AS1 was significantly up-regulated in CRC tissues and multiple CRC cell lines, which was closely related to poor prognosis of CRC patients. Loss-of-function studies indicated that knockdown of RPARP-AS1 inhibited CRC cell proliferation, migration and invasion in HCT116 and LoVo cell lines. Results of research on the mechanisms showed that RPARP-AS1 functioned as a competitive endogenous RNA (ceRNA) to sponge miR-125a-5p, therefore promoting CRC procession.

Conclusion

In summary, these results indicated that RPARP-AS1/miR-125a-5p axis played a positive role in promoting cell proliferation, migration and invasion in CC. It may be as a biomarker used to evaluate CRC prognosis.

A New Light on Potential Therapeutic Targets for Colorectal Cancer Treatment

The development and progression of colorectal cancer (CRC) involve changes in genetic and epigenetic levels of oncogenes and/or tumor suppressors. In spite of advances in understanding of the molecular mechanisms involved in CRC, the overall survival rate of CRC still remains relatively low. Thus, more research is needed to discover and investigate effective biomarkers and targets for diagnosing and treating CRC. The roles of long non-coding RNAs (lncRNAs) participating in various aspects of cell biology have been investigated and potentially contribute to tumor development. Our recent study also showed that CRNDE was among the top 20 upregulated genes in CRC clinical tissues compared to normal colorectal tissues by analyzing a Gene Expression Omnibus (GEO) dataset (GSE21815). Although CRNDE is widely reported to be associated with different types of cancer, most studies of CRNDE were limited to examining regulation of its transcription levels, and in-depth mechanistic research is lacking. In the present study, CRNDE was found to be significantly upregulated in CRC patients at an advanced TNM stage, and its high expression was correlated with poor outcomes of CRC patients. In addition, we found that knocking down CRNDE could reduce lipid accumulation through the miR-29b-3p/ANGPTL4 axis and consequently induce autophagy of CRC cells.

CRNDE: an oncogenic long non-coding RNA in cancers

Colorectal neoplasia differentially expressed (CRNDE) is a long non-coding RNA which has been proved upregulated in various cancers. Meanwhile, CRNDE has been demonstrated to be involved in multiple biological processes of different cancers according to previous study. Moreover, recent studies suggested CRNDE might be a potential diagnostic biomarker and prognostic predictor due to its high sensitivity and specificity in cancer tissues and plasma. In this review, we summarize the biological function of CRNDE and the relevant mechanisms in cancers to establish a molecular basis for the clinical use of CRNDE in the future.

Proneural and mesenchymal glioma stem cells display major differences in splicing and lncRNA profiles

Therapy resistance and recurrence in high-grade gliomas are driven by their populations of glioma stem cells (GSCs). Thus, detailed molecular characterization of GSCs is needed to develop more effective therapies. We conducted a study to identify differences in the splicing profile and expression of long non-coding RNAs in proneural and mesenchymal GSC cell lines. Genes related to cell cycle, DNA repair, cilium assembly, and splicing showed the most differences between GSC subgroups. We also identified genes distinctly associated with survival among patients of mesenchymal or proneural subgroups. We determined that multiple long non-coding RNAs with increased expression in mesenchymal GSCs are associated with poor survival of glioblastoma patients. In summary, our study established critical differences between proneural and mesenchymal GSCs in splicing profiles and expression of long non-coding RNA. These splicing isoforms and lncRNA signatures may contribute to the uniqueness of GSC subgroups, thus contributing to cancer phenotypes and explaining differences in therapeutic responses.

Prognostic value of long non-coding RNA 01296 expression in human solid malignant tumours: a meta-analysis

Long intergenic non-coding RNA 01296 (LINC01296) has been reported to play an important role in many human malignancies, but a consistent perspective has not been established now. To explore the prognostic value of LINC01296 in different types of human solid malignant tumours, we performed this meta-analysis.An electronic search of PubMed, EMBASE, Web of Science, China National Knowledge Infrastructure, Cochrane Library, Chinese Biological Medical Literature database and WanFang database was applied to select eligible literatures. Pooled ORs or HRs with their 95% CIs were calculated to estimate the effects.A total of 559 patients from nine eligible studies were enrolled in this meta-analysis. The results revealed that high LINC01296 expression was significantly related to larger tumour size (OR 3.42, 95% CI 2.08 to 5.63), lymph node metastasis (OR 3.03, 95% CI 2.01 to 4.57) and advanced tumor-node-metastasis (TNM) stage (OR 4.41, 95% CI 2.65 to 7.34). Moreover, we found that elevated LINC01296 expression predicted a poor outcome for overall survival (HR 1.78, 95% CI 1.48 to 2.14) and recurrence-free survival (HR 4.00, 95% CI 1.04 to 15.67).High expression levels of LINC01296 were associated with unfavourable clinical outcomes of patients with cancer. Our results indicated that LINC01296 could serve as a prognostic predictor in human solid malignant tumours.