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Discovery of tumor immune infiltration-related snoRNAs for predicting tumor immune microenvironment status and prognosis in lung adenocarcinoma
- Source :
- Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 6386-6399 (2021), Computational and Structural Biotechnology Journal
- Publication Year :
- 2021
- Publisher :
- Elsevier, 2021.
-
Abstract
- Graphical abstract<br />Lung adenocarcinoma (LUAD) has a high mortality rate and is difficult to diagnose and treat in its early stage. Previous studies have demonstrated that small nucleolar RNAs (snoRNAs) play a critical role in tumor immune infiltration and the development of a variety of solid tumors. However, there have been no studies on the correlation between tumor-infiltrating immune-related snoRNAs (TIISRs) and LUAD. In this study, we filtered six immune-related snoRNAs based on the tissue specificity index (TSI) and expression profile of all snoRNAs between all LUAD cell lines from the Cancer Cell Line Encyclopedia and 21 types of immune cells from the Gene Expression Omnibus database. Further, we performed real-time quantitative polymerase chain reaction (RT-qPCR) to validate the expression status of these snoRNAs on peripheral blood mononuclear cells (PBMCs) and lung cancer cell lines. Next, we developed a TIISR signature based on the expression profiles of snoRNAs from 479 LUAD patients filtered by the random survival forest algorithm. We then analyzed the value of this TIISR signature (TIISR risk score) for assessing tumor immune infiltration, immune checkpoint inhibitor (ICI) treatment response, and the prognosis of LUAD between groups with high and low TIISR risk score. Further, we found that the TIISR risk score groups showed significant differences in biological characteristics and that the risk score could be used to assess the level of tumor immune cell infiltration, thereby predicting prognosis and responsiveness to immunotherapy in LUAD patients.
- Subjects :
- TIME, tumor immune microenvironment
Lung adenocarcinoma
RT-qPCR, Real-time Quantitative Polymerase Chain Reaction
medicine.medical_treatment
CCLE, Cancer Cell Line Encyclopedia
Biochemistry
GSVA, gene set variation analysis
PBMC, Peripheral Blood Mononuclear Cell
AUC, area under the curve
Structural Biology
TPM, transcripts per kilobase million
GEO, Gene Expression Omnibus
Small nucleolar RNAs
Small nucleolar RNA
Stage (cooking)
RSF, random survival forest
ICIs, immune checkpoints inhibitors
NK cell, natural killer cell
snoRNAs, small nucleolar RNAs
LUAD, lung adenocarcinoma
Computer Science Applications
Real-time polymerase chain reaction
medicine.anatomical_structure
Adenocarcinoma
Research Article
Biotechnology
Biophysics
Peripheral blood mononuclear cell
Tumor cell immune infiltration
HIC, immunohistochemistry
Immune system
TIISR signature
ssGSEA, single-sample gene set enrichment analysis
Genetics
medicine
IF, immunofluorescence
ComputingMethodologies_COMPUTERGRAPHICS
GO, gene ontology
Lung
business.industry
TIISR, tumor-infiltrating immune-related snoRNA
Immunotherapy
medicine.disease
HR, hazard ratio
ROC, receiver operating characteristic
Cancer research
Immune checkpoints
TCGA, The Cancer Genome Atlas
FPKM, fragments per kilobase of transcript per million
business
TSI, tissue specificity index
TP248.13-248.65
ncRNA, noncoding RNA
Subjects
Details
- Language :
- English
- ISSN :
- 20010370
- Volume :
- 19
- Database :
- OpenAIRE
- Journal :
- Computational and Structural Biotechnology Journal
- Accession number :
- edsair.doi.dedup.....3e2d4043c8554ee6af7977744fd1f51b