A nomogram based on A-to-I RNA editing predicting overall survival of patients with lung squamous carcinoma.
Biomarkers, Tumor
/ genetics
Carcinoma, Non-Small-Cell Lung
/ genetics
Carcinoma, Squamous Cell
/ pathology
Chloride Channels
/ genetics
Endosomal Sorting Complexes Required for Transport
Gene Expression Regulation, Neoplastic
Humans
Lung
/ pathology
Lung Neoplasms
/ pathology
Nomograms
Prognosis
RNA Editing
RNA, Long Noncoding
/ genetics
A-to-I RNA editing
Lung squamous cell carcinoma
Nomogram
Overall survival
Journal
BMC cancer
ISSN: 1471-2407
Titre abrégé: BMC Cancer
Pays: England
ID NLM: 100967800
Informations de publication
Date de publication:
29 Jun 2022
29 Jun 2022
Historique:
received:
06
05
2021
accepted:
10
06
2022
entrez:
29
6
2022
pubmed:
30
6
2022
medline:
2
7
2022
Statut:
epublish
Résumé
Adenosine-to-inosine RNA editing (ATIRE) is characterized as non-mutational epigenetic reprogramming hallmark of cancer, while little is known about its predictive role in cancer survival. To explore survival-related ATIRE events in lung squamous cell carcinoma (LUSC), ATIRE profile, gene expression data, and corresponding clinical information of LUSC patients were downloaded from the TCGA database. Patients were randomly divided into a training (n = 134) and validation cohort (n = 94). Cox proportional hazards regression followed by least absolute shrinkage and selection operator algorithm were performed to identify survival-related ATIRE sites and to generate ATIRE risk score. Then a nomogram was constructed to predict overall survival (OS) of LUSC patients. The correlation of ATIRE level and host gene expression and ATIREs' effect on transcriptome expression were analyzed. Seven ATIRE sites that were TMEM120B chr12:122215052A > I, HMOX2 chr16:4533713A > I, CALCOCO2 chr17:46941503A > I, LONP2 chr16:48388244A > I, ZNF440 chr19:11945758A > I, CLCC1 chr1:109474650A > I, and CHMP3 chr2:86754288A > I were identified to generate the risk score, of which high levers were significantly associated with worse OS and progression-free survival in both the training and validation sets. High risk-score was also associated with advanced T stages and worse clinical stages. The nomogram performed well in predicting OS probability of LUSC. Moreover, the editing of ATIRE sites exerted a significant association with expression of host genes and affected several cancer-related pathways. This is the first comprehensive study to analyze the role of ATIRE events in predicting LUSC survival. The AITRE-based model might serve as a novel tool for LUSC survival prediction.
Sections du résumé
BACKGROUND
BACKGROUND
Adenosine-to-inosine RNA editing (ATIRE) is characterized as non-mutational epigenetic reprogramming hallmark of cancer, while little is known about its predictive role in cancer survival.
METHODS
METHODS
To explore survival-related ATIRE events in lung squamous cell carcinoma (LUSC), ATIRE profile, gene expression data, and corresponding clinical information of LUSC patients were downloaded from the TCGA database. Patients were randomly divided into a training (n = 134) and validation cohort (n = 94). Cox proportional hazards regression followed by least absolute shrinkage and selection operator algorithm were performed to identify survival-related ATIRE sites and to generate ATIRE risk score. Then a nomogram was constructed to predict overall survival (OS) of LUSC patients. The correlation of ATIRE level and host gene expression and ATIREs' effect on transcriptome expression were analyzed.
RESULTS
RESULTS
Seven ATIRE sites that were TMEM120B chr12:122215052A > I, HMOX2 chr16:4533713A > I, CALCOCO2 chr17:46941503A > I, LONP2 chr16:48388244A > I, ZNF440 chr19:11945758A > I, CLCC1 chr1:109474650A > I, and CHMP3 chr2:86754288A > I were identified to generate the risk score, of which high levers were significantly associated with worse OS and progression-free survival in both the training and validation sets. High risk-score was also associated with advanced T stages and worse clinical stages. The nomogram performed well in predicting OS probability of LUSC. Moreover, the editing of ATIRE sites exerted a significant association with expression of host genes and affected several cancer-related pathways.
CONCLUSIONS
CONCLUSIONS
This is the first comprehensive study to analyze the role of ATIRE events in predicting LUSC survival. The AITRE-based model might serve as a novel tool for LUSC survival prediction.
Identifiants
pubmed: 35768804
doi: 10.1186/s12885-022-09773-0
pii: 10.1186/s12885-022-09773-0
pmc: PMC9241197
doi:
Substances chimiques
Biomarkers, Tumor
0
CHMP3 protein, human
0
CLCC1 protein, human
0
Chloride Channels
0
Endosomal Sorting Complexes Required for Transport
0
RNA, Long Noncoding
0
Types de publication
Journal Article
Randomized Controlled Trial
Langues
eng
Sous-ensembles de citation
IM
Pagination
715Informations de copyright
© 2022. The Author(s).
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