Evaluation of Diagnostic and Prognostic Value of hsa_circ_0084927 and Analysis of Associated ceRNA Network in Colorectal Cancer

Chen, Yi; Chen, Ling; Xu, Yali; Liu, Junjie; Tang, Weizhong

doi:10.2147/ijgm.s355043

Cited by 4 publications

(2 citation statements)

References 42 publications

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“…NcRNAs has been used as prognostic markers in colon cancer. A recent study found that has_circ_0084927 has prognostic value in colorectal cancer and has an endogenous competition mechanism [ 25 , 26 ]. The effect of KCNQ1OT1 on lncRNAs in the development of colon cancer has been confirmed in several studies [ 27 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

The noncoding RNAs regulating pyroptosis in colon adenocarcinoma were derived from the construction of a ceRNA network and used to develop a prognostic model

et al. 2022

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Background Noncoding RNAs (ncRNAs), pyroptosis and tumours are all hot topics in current research, but there are very limited studies on pyroptosis and its regulated ncRNAs in colon adenocarcinoma (COAD). Methods The COAD transcription profile dataset from TCGA was used for differential expression analysis. Pyroptosis-related genes (PRGs), the top 200 long noncoding RNAs (lncRNAs) and circular RNA (circRNAs) were selected from the results to construct an endogenous competitive RNA (ceRNA) network. Moreover, the expression of the ceRNAs was used for consensus cluster analysis of COAD and developing a risk model after combining clinical follow-up data by the least absolute shrinkage and selection operator method. The stability and independent prognostic ability of the risk model were evaluated. Finally, gene set enrichment analysis (GSEA) and immune score comparisons between the high-risk and low-risk groups were performed. Results There were 87 PRGs with significant differences, among which casp3/8, NLRP1/3, and IL-1α/1β were at the core of the interactions. The ceRNA network consisted of 58 lncRNAs, 6 circRNAs, 25 PRGs, and 55 microRNAs. We speculated that KCNQ1OT1-miRNAs-SQSTM1 and HSA_CIRC_0001495-miRNAs-PTEN have great potential and value in the pyroptosis mechanism of COAD. Nine RNAs were involved in the risk score, which had excellent independent prognostic ability. Survival analyses were significant between the high-risk (HR) and low-risk (LR) groups (training cohort: P < 0.001; test cohort: P = 0.037). GSEA was mainly enriched in tumour proliferation and metastasis related pathways, while differences in immune activity showed a bipolar distribution between the HR and LR groups. Conclusions The overall mechanism of pyroptosis in COAD was revealed. CeRNAs most closely related to the pyroptosis mechanism of COAD were selected and used to develop a prognostic model. The results may present new regulatory sites and potential targets for COAD pyroptosis mechanisms.

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Section: Discussionmentioning

confidence: 99%

The noncoding RNAs regulating pyroptosis in colon adenocarcinoma were derived from the construction of a ceRNA network and used to develop a prognostic model

et al. 2022

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“…This pattern is reversed in the HCT116 cell line samples from project PRJNA748887 [40], with the tRFs of lengths 29 and 31 nts now being more abundant. This pattern is absent in the cell line samples from projects PRJNA784982 [41], PRJNA595962 [42], and PRJNA789176 [43].…”

Section: The Abundances Of Different-length 5 -Trhs Depend On Contextmentioning

confidence: 91%

The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease

Akins,

Ostberg,

Cherlin

et al. 2023

ncRNA

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Transfer RNA-derived fragments (tRFs) are noncoding RNAs that arise from either mature transfer RNAs (tRNAs) or their precursors. One important category of tRFs comprises the tRNA halves, which are generated through cleavage at the anticodon. A given tRNA typically gives rise to several co-expressed 5’-tRNA halves (5′-tRHs) that differ in the location of their 3′ ends. These 5′-tRHs, even though distinct, have traditionally been treated as indistinguishable from one another due to their near-identical sequences and lengths. We focused on co-expressed 5′-tRHs that arise from the same tRNA and systematically examined their exact sequences and abundances across 10 different human tissues. To this end, we manually curated and analyzed several hundred human RNA-seq datasets from NCBI’s Sequence Run Archive (SRA). We grouped datasets from the same tissue into their own collection and examined each group separately. We found that a given tRNA produces different groups of co-expressed 5′-tRHs in different tissues, different cell lines, and different diseases. Importantly, the co-expressed 5′-tRHs differ in their sequences, absolute abundances, and relative abundances, even among tRNAs with near-identical sequences from the same isodecoder or isoacceptor group. The findings suggest that co-expressed 5′-tRHs that are produced from the same tRNA or closely related tRNAs have distinct, context-dependent roles. Moreover, our analyses show that cell lines modeling the same tissue type and disease may not be interchangeable when it comes to experimenting with tRFs.

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Investigating the biomarker value of circRNAs in the diagnosis of colorectal cancer: a systematic review

Latifi-Pakdehi,

Khezrian,

Doosti-Irani

et al. 2024

Discov Onc

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Circular RNAs (circRNAs) has recently been considered a class of endogenous RNAs that form a continuous closed loop with an ability to cancer development. Due to its properties, circRNAs has promising potential to be considered as non-invasive cancer biomarkers. The present review comprehensively and systematically assessed the role of circRNAs as diagnostic markers in blood or tissue samples of colorectal cancer (CRC) patients. Articles published until September 2022 were searched across Scopus, Web of Science (WoS), and PubMed databases to screen and find suitable circRNAs as diagnostic markers in CRC, Based on inclusion and exclusion criteria, 55 articles were selected as the final included articles. The sample size of the patients group ranged from 12 to 212. Among the circRNAs investigated in this study, 47 circRNAs were increased in patients and probably act as oncogenes and activate the downstream pathways in the initiation and exacerbation of cancer; 28 circRNAs were decreased, which probably acted as tumor suppressors and their decrease played a role in the progression of CRC, indicating that the aberrant expression of circRNAs are involved in the promotion of CRC and may associated with its clinicopathological features. Many pathological processes of cancer are regulated by the altered expression of circRNAs through the regulation of different signaling pathways. According to the results of this study, while circRNAs demonstrates promise as a biomarker for CRC diagnosis, it is necessary to conduct evaluative studies on a larger scale in future. Supplementary Information The online version contains supplementary material available at 10.1007/s12672-024-01602-z.

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Evaluation of Diagnostic and Prognostic Value of hsa_circ_0084927 and Analysis of Associated ceRNA Network in Colorectal Cancer

Cited by 4 publications

References 42 publications

The noncoding RNAs regulating pyroptosis in colon adenocarcinoma were derived from the construction of a ceRNA network and used to develop a prognostic model

The noncoding RNAs regulating pyroptosis in colon adenocarcinoma were derived from the construction of a ceRNA network and used to develop a prognostic model

The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease

Investigating the biomarker value of circRNAs in the diagnosis of colorectal cancer: a systematic review

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