Construction of competing endogenous RNA network and identification of novel molecular biomarkers in colon cancer

Gu, Xiaoqing; Xu, Zicheng; Liu, Yiting; Liu, Zonghang; Zheng, Lei

doi:10.1097/md.0000000000025369

Cited by 5 publications

(5 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…According to limited studies, miR-129-5p may be sponged by high motility group box protein 1 (HMGB1) and inhibit the HMGB1 signals ( 11 ). Besides, the miR-129-5p/NFAT5 axis and miR-129-5p/SEMA6A axis may represent a novel regulatory mechanism concerning the progression of colon cancer ( 12 , 13 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of Key Carcinogenic Genes in Colon Adenocarcinoma

Dai¹,

Z²,

Qiu³

et al. 2022

ijph

View full text Add to dashboard Cite

Background: We aimed to probe carcinogenic genes associated with colon adenocarcinoma (COAD) development. Methods: The gene expression profile of COAD were downloaded from TCGA. Differentially expressed genes (DEGs) were identified; GO and KEGG pathway enrichment were analyzed. Applying the up-mRNA-and-down-miRNA pairs and the down-mRNA-and-up-miRNA pairs, the miRNA target network was generated. The important genes were further analyzed towards the influence on overall survival and immune infiltration. In addition, essential miRNAs were selected for expression validation using real-time qPCR. Results: Together, from 2020-2021, in Central Laboratory of the Second Affiliated Hospital of Fujian Medical University, we found 3060 up-regulated transcripts and 2254 down-regulated transcripts in mRNA expression, with 235 up-regulated and 263 down-regulated miRNAs. We discovered 98 enriched GO terms using the upregulated DEGs and 315 enriched GO terms using downregulated DEGs. There were 14 enriched KEGG pathways based on the down-regulated DEGs and only one pathway based on the up-regulated DEGs. There were 61 up-mRNA-and-down-miRNA pairs, including 7 miRNAs and 41 carcinogenic targets, among which HOXC13, FOXL2NB, ALOXE3, and ZIC2 were found related to a poorer OS. ZIC2 located at the subnet with the most targets (the miR-129-5p subnet). ZIC2 expression was correlated with immune-cell infiltration. Conclusion: These risk genes, interaction networks, and enrichments may provide a better understanding of the complex molecular mechanisms in COAD development and potential therapeutic targets for clinical treatment of COAD.

show abstract

Section: Discussionmentioning

confidence: 99%

Identification of Key Carcinogenic Genes in Colon Adenocarcinoma

Dai¹,

Z²,

Qiu³

et al. 2022

ijph

View full text Add to dashboard Cite

show abstract

“…In summary, they were able to identify two new regulatory pathways as LINC00114/miR-107/PCKS5, UCA1/miR-107/PCKS5, and UCA1/miR-129-5p/SEMA6A. Therefore, two new lncRNAs (LINC00114 and UCA1) were identified by bioinformatics analysis [123]. Furthermore, LINC00114 could be linked to the overall survival of colon cancer patients [123].…”

Section: Transcriptomicsmentioning

confidence: 99%

“…All biomarkers are summarized in Table 6. In a more complex study, Xi et al performed a bioinformatic analysis to construct a competing endogenous RNA (ceRNA) network based on the differentially expressed lncRNA and RNAs in two colon cancer gene expression datasets [123]. In summary, they were able to identify two new regulatory pathways as LINC00114/miR-107/PCKS5, UCA1/miR-107/PCKS5, and UCA1/miR-129-5p/SEMA6A.…”

Section: Transcriptomicsmentioning

confidence: 99%

See 1 more Smart Citation

Use of Omics Technologies for the Detection of Colorectal Cancer Biomarkers

Alorda-Clara

Torrens‐Mas

Morla-Barcelo

et al. 2022

Cancers

View full text Add to dashboard Cite

Colorectal cancer (CRC) is one of the most frequently diagnosed cancers with high mortality rates, especially when detected at later stages. Early detection of CRC can substantially raise the 5-year survival rate of patients, and different efforts are being put into developing enhanced CRC screening programs. Currently, the faecal immunochemical test with a follow-up colonoscopy is being implemented for CRC screening. However, there is still a medical need to describe biomarkers that help with CRC detection and monitor CRC patients. The use of omics techniques holds promise to detect new biomarkers for CRC. In this review, we discuss the use of omics in different types of samples, including breath, urine, stool, blood, bowel lavage fluid, or tumour tissue, and highlight some of the biomarkers that have been recently described with omics data. Finally, we also review the use of extracellular vesicles as an improved and promising instrument for biomarker detection.

show abstract

“…Several bioinformatic approaches that analyze genomic or transcriptomic data can be used to identify lncRNAs with prognostic or therapeutic potential in CRC. One such approach is the “detecting lncRNA cancer association” (DRACA) method, which was developed to evaluate potential molecular biomarkers by predicting lncRNA-cancer associations [ 45 , 46 ]. DRACA uses matrix factorization to consider interactions between lncRNAs, cancer prognosis, and other factors, such as miRNAs and genes, to predict lncRNA-cancer association.…”

Section: Approaches To Identify Relevant Lncrnas In Crcmentioning

confidence: 99%

Discovery and Validation of Clinically Relevant Long Non-Coding RNAs in Colorectal Cancer

Snyder

Iraola-Guzmán

Saus

et al. 2022

Cancers

View full text Add to dashboard Cite

Colorectal cancer (CRC) is the third most prevalent cancer worldwide, with nearly two million newly diagnosed cases each year. The survival of patients with CRC greatly depends on the cancer stage at the time of diagnosis, with worse prognosis for more advanced cases. Consequently, considerable effort has been directed towards improving population screening programs for early diagnosis and identifying prognostic markers that can better inform treatment strategies. In recent years, long non-coding RNAs (lncRNAs) have been recognized as promising molecules, with diagnostic and prognostic potential in many cancers, including CRC. Although large-scale genome and transcriptome sequencing surveys have identified many lncRNAs that are altered in CRC, most of their roles in disease onset and progression remain poorly understood. Here, we critically review the variety of detection methods and types of supporting evidence for the involvement of lncRNAs in CRC. In addition, we provide a reference catalog that features the most clinically relevant lncRNAs in CRC. These lncRNAs were selected based on recent studies sorted by stringent criteria for both supporting experimental evidence and reproducibility.

show abstract

Construction of competing endogenous RNA network and identification of novel molecular biomarkers in colon cancer

Cited by 5 publications

References 29 publications

Identification of Key Carcinogenic Genes in Colon Adenocarcinoma

Identification of Key Carcinogenic Genes in Colon Adenocarcinoma

Use of Omics Technologies for the Detection of Colorectal Cancer Biomarkers

Discovery and Validation of Clinically Relevant Long Non-Coding RNAs in Colorectal Cancer

Contact Info

Product

Resources

About