Establishing a three-miRNA signature as a prognostic model for colorectal cancer through bioinformatics analysis

Wang, Yiming; Huang, Lumi; Shan, Nan; Ma, Huiqin; Lu, Songmei; Chen, Xingyue; Long, Heng

doi:10.18632/aging.203400

Cited by 12 publications

(11 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For instance, Li et al assessed the prognostic value of methylation regions in CRC and detected four differentially methylated regions, namely MUC12, TBX20, CHN2, and B3GNT7, as potential prognostic indicators for CRC and created a prognostic prediction score on their basis 34 . Moreover, many other reports have focused on transcriptional-level analysis, including research on mRNAs, long non-coding RNAs (lncRNAs), or miRNAs 35 – 37 .…”

Section: Discussionmentioning

confidence: 99%

Alternative polyadenylation associated with prognosis and therapy in colorectal cancer

Zhang

Wang

2022

Sci Rep

View full text Add to dashboard Cite

Colorectal cancer (CRC) is among the most widely spread cancers globally. Aberrant alternative polyadenylation (APA) plays a role in cancer onset and its progression. Consequently, this study focused on highlighting the role of APA events and signals in the prognosis of patients with CRC. The APA events, RNA sequencing (RNA-seq), somatic mutations, copy number variants (CNVs), and clinical information of the CRC cohort were obtained from The Cancer Genome Atlas (TCGA) database and UCSC (University of California-Santa Cruz) Xena database. The whole set was sorted into two sets: a training set and a test set in a ratio of 7:3. 197 prognosis-related APA events were collected by performing univariate Cox regression signature in patients with CRC. Subsequently, a signature for APA events was established by least absolute shrinkage and selection operator (LASSO) and multivariate Cox analysis. The risk scores were measured for individual patients on the basis of the signature and patients were sorted into two groups; the high-risk group and the low-risk group as per their median risk scores. Kaplan–Meier curves, principal component analysis (PCA), and time-dependent receiver operator characteristic (ROC) curves revealed that the signature was able to predict patient prognosis effectively and further validation was provided in the test set and the whole set. The high-risk and low-risk groups displayed various distributions of mutations and CNVs. Tumor mutation burden (TMB) alone and in combination with the signature predicted the prognosis of CRC patients, but the gene frequencies of TMBs and CNVs did not change in the low- and high-risk groups. Moreover, immunotherapy and chemotherapy treatments showed different responses to PD-1 inhibitors and multiple chemotherapeutic agents in the low and high-risk groups based on the tumor immune dysfunction and exclusion (TIDE) and genomics of drugs sensitivity in cancer (GDSC) databases. This study may help in understanding the potential roles of APA in CRC, and the signature for prognosis-related APA events can work as a potential predictor for survival and treatment in patients with CRC.

show abstract

Section: Discussionmentioning

confidence: 99%

Alternative polyadenylation associated with prognosis and therapy in colorectal cancer

Zhang

Wang

2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The 14 miRNAs were correlated with the prognosis of patients with carcinoma of colon. However, other researchers have reported that upregulation of hsa-miR-194-3p was associated with the early T-stages [41].Studies have shown that high levels of mir-21-3p are associated with short survival time, poor prognosis, pathological features and positive lymph nodes [42]. Its overexpression in breast tumors is a sign of disease deterioration.…”

Section: Discussionmentioning

confidence: 98%

A novel N7-methylguanosine(m7G) methylation-associated miRNA signature for prognostic value in patient with carcinoma of colon

Wang¹,

Liu²

2022

Preprint

View full text Add to dashboard Cite

Background:m7G methylation-associated genes were selected as the main research perspectives in this study, establishing a novel m7G methylation-associated miRNA risk signature for prognostic value in patient with carcinoma of colon. Methods:We identified two genes that are m7G methylation-associated and have been validated by searching in the PubMed database.The m7G methylation-associated miRNAs were screened via estimating the differentially expressed of miRNAs in 457 carcinoma of colon patient samples and 8 matched samples from a database named The Cancer Genome Atlas (TCGA). SelectingSingle-factor Cox analyses as well as multi-factor Cox analyses constructed the risk signature of 12 m7G methylation-associated miRNAs.Nomograms was adopted to predict the potential impact of m7G methylation-associated miRNAs on occurrence, development.The functions of DEGs that deserving to be noticed were classified and analyzed by functional enrichment analysis.Disease ontology analysis was used to explore the potential connection various diseases and carcinoma of colon.The outcome of associated analysis about immunocyte or immunological functioning revealed that what role does immunocyte or immunological functioning play in the development of carcinoma of colon.Finally, the relationship between high or low expression of significantly DEGs and immune cells and immune function was analyzed. Results:The results of nomogram analysis were as follows that the risk signature might predict the prognosis and the overall cumulative probability of survival（1-,3-,5-year） effectively about patients with carcinoma of colon. Through the analysis of Kaplan-Meier curve outcomes, we can draw a conclusion that depressedly expressed of hsa-miR-21-3p might be significantly relevant with decreased survival of patients.What the analyses of Gene ontology (GO) , Kyoto Encyclopedia of Genes and Genomes (KEGG) and Disease ontology（DO）,taking advantage of the common DEGs about risk score and immune score,demonstrated that these common DEGs play a partial role in the occurrence and development of tumors.Through disease ontology analysis,we found that eating disorder might be associated with carcinoma of colon. Conclusions: m7G methylation-associated miRNAs were related to the prognosis of patients with carcinoma of colon. A risk signature established based on these miRNAs could effectively predict the survival rate of later period in patients with carcinoma of colon.According to the displayed outcom from Our research that m7G methylation-associated miRNA regulators can serve as reliable prognostic biomarkers of carcinoma of colon, which might Greater probably be applyed as potential targets of therapeutic strategies.

show abstract

“…The real-time quantitative PCR (qPCR) was conducted as previous report [ 30 ]. Extracted total RNA from tissues and cell lines by Triazole (Invitrogen).…”

Section: Methodsmentioning

confidence: 99%

A novel immune-related long non-coding RNAs risk model for prognosis assessment of lung adenocarcinoma

Shan

Chen

et al. 2021

Aging

Self Cite

View full text Add to dashboard Cite

Background: The abundant immune-related long non-coding RNA (IRLNRs) in immune cells and immune microenvironment have the potential to forecast prognosis and evaluate the effect of immunotherapy. IRLNRs analysis will provide a new perspective for LUAC research. Methods: We calculated the immune score of each sample according to the expression levels of immune-related genes (IRGs) and screened the survival-related IRLNRs (sIRLNRs) by Cox regression analysis. The expression levels of AC068338.3 and AL691432.2 in tissues and cell lines were confirmed by RT-qPCR. Results: 36 IRLNRs were selected by Pearson correlation analysis. Ten sIRLNRs were significantly correlated with the clinical outcomes of LUAC patients. Five sIRLNRs were identified by multivariate COX regression analysis to establish the immune-related risk score model (IRRS). The overall survival (OS) in the high-risk group was shorter than that in the low-risk group. IRRS could be an independent prognostic factor with significant survival correlation The distributions of immune gene concentrations were different between high-risk group and low-risk group. Furthermore, we further verified that the expression levels of AC068338.3 and AL691432.2 in different LUAC cell lines and tumor tissues were lower than that in Human bronchial epithelial cell (HBE) and adjacent tissues respectively. The lower expression levels of AC068338.3 and AL691432.2 were detected with the more advance T-stages. Conclusions: Our results highlighted some sIRLNRs with significant clinical correlations and demonstrated their monitored and prognostic values for LUAC patients. The results of this study may provide a new perspective for immunological research and immunotherapy strategies.

show abstract

Establishing a three-miRNA signature as a prognostic model for colorectal cancer through bioinformatics analysis

Cited by 12 publications

References 32 publications

Alternative polyadenylation associated with prognosis and therapy in colorectal cancer

Alternative polyadenylation associated with prognosis and therapy in colorectal cancer

A novel N7-methylguanosine(m7G) methylation-associated miRNA signature for prognostic value in patient with carcinoma of colon

A novel immune-related long non-coding RNAs risk model for prognosis assessment of lung adenocarcinoma

Contact Info

Product

Resources

About