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Wan R, Bai L, Cai C, Ya W, Jiang J, Hu C, Chen Q, Zhao B, Li Y. Discovery of tumor immune infiltration-related snoRNAs for predicting tumor immune microenvironment status and prognosis in lung adenocarcinoma. Comput Struct Biotechnol J 2021; 19:6386-6399. [PMID: 34938414 PMCID: PMC8649667 DOI: 10.1016/j.csbj.2021.11.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
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.
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Key Words
- AUC, area under the curve
- CCLE, Cancer Cell Line Encyclopedia
- FPKM, fragments per kilobase of transcript per million
- GEO, Gene Expression Omnibus
- GO, gene ontology
- GSVA, gene set variation analysis
- HIC, immunohistochemistry
- HR, hazard ratio
- ICIs, immune checkpoints inhibitors
- IF, immunofluorescence
- Immune checkpoints
- LUAD, lung adenocarcinoma
- Lung adenocarcinoma
- NK cell, natural killer cell
- PBMC, Peripheral Blood Mononuclear Cell
- ROC, receiver operating characteristic
- RSF, random survival forest
- RT-qPCR, Real-time Quantitative Polymerase Chain Reaction
- Small nucleolar RNAs
- TCGA, The Cancer Genome Atlas
- TIISR signature
- TIISR, tumor-infiltrating immune-related snoRNA
- TIME, tumor immune microenvironment
- TPM, transcripts per kilobase million
- TSI, tissue specificity index
- Tumor cell immune infiltration
- ncRNA, noncoding RNA
- snoRNAs, small nucleolar RNAs
- ssGSEA, single-sample gene set enrichment analysis
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Affiliation(s)
- Rongjun Wan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Lu Bai
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Changjing Cai
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Wang Ya
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Juan Jiang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Chengping Hu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Qiong Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Bingrong Zhao
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
| | - Yuanyuan Li
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China, 410008
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. 410008
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China. 410008
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China. 410008
- National Clinical Research Center for Geriatric Disorders,Xiangya Hospital, Changsha, Hunan, P.R. China, 410008
- Corresponding author.
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Lin BB, Lei HQ, Xiong HY, Fu X, Shi F, Yang XW, Yang YF, Liao GL, Feng YP, Jiang DG, Pang J. MicroRNA-regulated transcriptome analysis identifies four major subtypes with prognostic and therapeutic implications in prostate cancer. Comput Struct Biotechnol J 2021; 19:4941-4953. [PMID: 34527198 PMCID: PMC8433071 DOI: 10.1016/j.csbj.2021.08.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNA (miRNA) deregulation plays a critical role in the heterogeneous development of prostate cancer (PCa) by tuning mRNA levels. Herein, we aimed to characterize the molecular features of PCa by clustering the miRNA-regulated transcriptome with non-negative matrix factorization. Using 478 PCa samples from The Cancer Genome Atlas, four molecular subtypes (S-I, S-II, S-III, and S-IV) were identified and validated in two merged microarray and RNAseq datasets with 656 and 252 samples, respectively. Interestingly, the four subtypes showed distinct clinical and biological features after comprehensive analyses of clinical features, multiomic profiles, immune infiltration, and drug sensitivity. S-I is basal/stem/mesenchymal-like and immune-excluded with marked transforming growth factor β, epithelial-mesenchymal transition and hypoxia signals, increased sensitivity to olaparib, and intermediate prognosis. S-II is luminal/metabolism-active and responsive to androgen deprivation therapy with frequent TMPRSS2-ERG fusion and a good prognosis. S-III is characterized by moderate proliferative and metabolic activity, sensitivity to taxane-based chemotherapy, and intermediate prognosis. S-IV is highly proliferative with moderate EMT and stemness, frequent deletions of TP53, PTEN and RB, and the poorest prognosis; it is also immune-inflamed and sensitive to anti-PD-L1 therapy. Overall, based on miRNA-regulated gene profiles, this study identified four distinct PCa subtypes that could improve risk stratification at diagnosis and provide therapeutic guidance.
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Key Words
- ADT, androgen deprivation therapy
- AR, androgen receptor
- AUC, Area under the dose-response curve
- BCR, biochemical recurrence
- CAFs, cancer-associated fibroblasts
- CCLs, cancer cell lines
- CTLA-4, cytotoxic T-lymphocyte associated protein-4
- DEmiRs, differentially expressed miRNAs
- DFS, disease-free survival
- EMT, epithelial-mesenchymal transition
- FDR, false discovery rate
- GEO, Gene Expression Omnibus
- GEP, gene expression profile
- GO, Gene Ontology
- GSEA, Gene Set Enrichment Analysis
- Heterogeneity
- ICB, immune checkpoint blockade
- IFN, interferon
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MDSCs, myeloid-derived suppressor cells
- MIRcor, miRNA-correlated
- Molecular subtypes
- NEPC, neuroendocrine prostate cancer
- NMF, non-negative matrix factorization
- NTP, Nearest template prediction
- OS, overall survival
- PCa, prostate cancer
- PD-1, programmed cell death protein-1
- PD-L1, programmed death-ligand 1
- Prostate cancer
- SCNAs, somatic copy number alterations
- SubMap, Subclass mapping
- TCGA, The Cancer Genome Atlas
- TGFβ, transforming growth factor β
- TMB, tumor mutation burden
- TNAs, tumor neoantigens
- Tregs, regulatory T cells
- k-NN, K-nearest neighbor
- mCRPC, metastatic castration-resistant prostate cancer
- miRNAs
- miRNAs, microRNAs
- ssGSEA, single-sample gene set enrichment analysis
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Affiliation(s)
- Bing-Biao Lin
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Han-Qi Lei
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Hai-Yun Xiong
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Xing Fu
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Fu Shi
- Department of Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
| | - Xiang-Wei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Ya-Fei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Guo-Long Liao
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Yu-Peng Feng
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Dong-Gen Jiang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Jun Pang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
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