PMID- 35606755 OWN - NLM STAT- MEDLINE DCOM- 20220525 LR - 20220716 IS - 1477-7819 (Electronic) IS - 1477-7819 (Linking) VI - 20 IP - 1 DP - 2022 May 24 TI - Construction and validation of immune-related LncRNAs classifier to predict prognosis and immunotherapy response in laryngeal squamous cell carcinoma. PG - 164 LID - 10.1186/s12957-022-02608-z [doi] LID - 164 AB - BACKGROUND: Rapid advances in transcriptomic profiles have resulted in recognizing IRLs (immune-related long noncoding RNAs), as modulators of the expression of genes related to immune cells that mediate immune inhibition as well as immune stimulatory, indicating LncRNAs play fundamental roles in immune modulation. Hence, we establish an IRL classifier to precisely predict prognosis and immunotherapeutic efficiency in laryngeal squamous cell carcinoma (LSCC). METHODS: LSCC RNA-seq (RNA sequencing) datasets, somatic mutation data, and corresponding clinicopathologic information were acquired from TCGA (the Cancer Genome Atlas) and Gene Expression Omnibus (GEO) databases. Spearman correlation analysis identified LncRNAs associated with immune-related genes (IRG). Based on Lasso penalized regression and random forest (RF), we constructed an IRL classifier associated with prognosis. GEO database was utilized to validate the IRL classifier. The predictive precision and clinical application of the IRL classifier were assessed and compared to clinicopathologic features. The immune cell infiltration of LSCC was calculated via CIBERSORTx tools and ssGSEA (single-sample gene set enrichment analysis). Then, we systematically correlated the IRL classifier with immunological characteristics from multiple perspectives, such as immune-related cells infiltrating, tumor microenvironment (TME) scoring, microsatellite instability (MSI), tumor mutation burden (TMB), and chemokines. Finally, the TIDE (tumor immune dysfunction and exclusion) algorithm was used to predict response to immunotherapy. RESULTS: Based on machine learning approach, three prognosis-related IRLs (BARX1-DT, KLHL7-DT, and LINC02154) were selected to build an IRL classifier. The IRL classifier could availably classify patients into the low-risk and high-risk groups based on the different endpoints, including recurrence-free survival (RFS) and overall survival (OS). In terms of predictive ability and clinical utility, the IRL classifier was superior to other clinical characteristics. Encouragingly, similar results were observed in the GEO databases. Immune infiltration analysis displayed immune cells that are significantly richer in low-risk group, CD8 T cells and activated NK cells via CIBERSORTx algorithm as well as activated CD8 T cell via ssGSEA. Additionally, compared with the high-risk group, immune score, CD8 T effector was higher in the low-risk group, yet stromal score, score of p53 signaling pathway and TGFher in the Tx algorithm, was lower in the low-risk group. Corresponding results were confirmed in GEO dataset. Finally, TIDE analysis uncovered that the IRL classifier may be effectually predict the clinical response of immunotherapy in LSCC. CONCLUSION: Based on BARX1-DT, KLHL7-DT, and LINC02154, the IRL classifier was established, which can be used to predict the prognosis, immune infiltration status, and immunotherapy response in LSCC patients and might facilitate personalized counseling for immunotherapy. CI - (c) 2022. The Author(s). FAU - Wang, Xiaofeng AU - Wang X AD - Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China. FAU - Pan, Ya AU - Pan Y AD - Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China. FAU - Ou, Yangpeng AU - Ou Y AD - Department of Oncology, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, 516000, Guangdong Province, People's Republic of China. FAU - Duan, Tingting AU - Duan T AD - Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China. denieceduan@163.com. FAU - Zou, Yuxia AU - Zou Y AD - Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China. zouyuxiazzz@163.com. FAU - Zhou, Xuejun AU - Zhou X AD - Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China. xuejunzhouent@hainmc.edu.cn. LA - eng PT - Journal Article DEP - 20220524 PL - England TA - World J Surg Oncol JT - World journal of surgical oncology JID - 101170544 RN - 0 (Biomarkers, Tumor) RN - 0 (RNA, Long Noncoding) SB - IM MH - Biomarkers, Tumor/genetics MH - *Head and Neck Neoplasms MH - Humans MH - Immunotherapy MH - Prognosis MH - *RNA, Long Noncoding/genetics MH - Squamous Cell Carcinoma of Head and Neck/genetics/therapy MH - Tumor Microenvironment PMC - PMC9128282 OTO - NOTNLM OT - IRL classifier OT - Immune infiltration OT - Immunotherapy response OT - LSCC OT - Prognosis COIS- The authors declare that they have no competing interests. EDAT- 2022/05/24 06:00 MHDA- 2022/05/26 06:00 PMCR- 2022/05/24 CRDT- 2022/05/23 23:47 PHST- 2022/02/13 00:00 [received] PHST- 2022/04/19 00:00 [accepted] PHST- 2022/05/23 23:47 [entrez] PHST- 2022/05/24 06:00 [pubmed] PHST- 2022/05/26 06:00 [medline] PHST- 2022/05/24 00:00 [pmc-release] AID - 10.1186/s12957-022-02608-z [pii] AID - 2608 [pii] AID - 10.1186/s12957-022-02608-z [doi] PST - epublish SO - World J Surg Oncol. 2022 May 24;20(1):164. doi: 10.1186/s12957-022-02608-z.