PMID- 35715770
OWN - NLM
STAT- MEDLINE
DCOM- 20220621
LR  - 20220716
IS  - 1471-2407 (Electronic)
IS  - 1471-2407 (Linking)
VI  - 22
IP  - 1
DP  - 2022 Jun 17
TI  - Comprehensive analysis reveals COPB2 and RYK associated with tumor stages of 
      larynx squamous cell carcinoma.
PG  - 667
LID - 10.1186/s12885-022-09766-z [doi]
LID - 667
AB  - BACKGROUND: Laryngeal squamous cell carcinoma (LSCC) is one of the highly 
      aggressive malignancy types of head and neck squamous cell carcinomas; genes 
      involved in the development of LSCC still need exploration. METHODS: We 
      downloaded expression profiles of 96 (85 in advanced stage and 11 in early stage) 
      LSCC patients from TCGA-HNSC. Function enrichment and protein-protein 
      interactions of genes in significant modules were conducted. Univariate and 
      multivariate Cox regression analyses were performed to explore potential 
      prognostic biomarkers for LSCC. The expression levels of genes at different 
      stages were compared and visualized via boxplots. Immune infiltration was 
      examined by the CIBERSORTx web-based tool and depicted with ggplot2. Gene set 
      enrichment analysis (GSEA) was utilized to analyze functional enrichment terms 
      and pathways. Immunohistochemical staining (IHC) was used to verify the 
      expression of genes in the LSCC samples. RESULTS: We identified 25 modules, 
      including 3 modules significantly related to tumor stages of LSCC via weighted 
      gene co-expression network analysis (WGCNA). UIMC1, NPM1, and DCTN4 in the module 
      'cyan', TARS in the module 'darkorange', and COPB2 and RYK in the module 
      'lightyellow' showed statistically significant relation to overall survival. The 
      expression of COPB2, DCTN4, RYK, TARS, and UIMC1 indicated association with the 
      change of fraction of immune cells in LSCC patients; two genes, COPB2 and RYK, 
      indicated different expression in various tumor stages of LSCC. Finally, COPB2 
      and RYK showed high-expression in tumor tissues of advanced LSCC patients. 
      CONCLUSIONS: Our study provided a potential perceptive in analyzing progression 
      of LSCC cells and exploring prognostic genes.
CI  - (c) 2022. The Author(s).
FAU - Zhou, Guojin
AU  - Zhou G
AD  - Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, 
      College of Medicine, Zhejiang University, No.3 Qingchun East Road, Hangzhou, 
      310016, Zhejiang, China.
FAU - Zhang, Shoude
AU  - Zhang S
AD  - Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, 
      College of Medicine, Zhejiang University, No.3 Qingchun East Road, Hangzhou, 
      310016, Zhejiang, China.
FAU - Jin, Mao
AU  - Jin M
AD  - Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, 
      College of Medicine, Zhejiang University, No.3 Qingchun East Road, Hangzhou, 
      310016, Zhejiang, China.
FAU - Hu, Sunhong
AU  - Hu S
AD  - Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, 
      College of Medicine, Zhejiang University, No.3 Qingchun East Road, Hangzhou, 
      310016, Zhejiang, China. 3193146@zju.edu.cn.
LA  - eng
PT  - Journal Article
DEP - 20220617
PL  - England
TA  - BMC Cancer
JT  - BMC cancer
JID - 100967800
RN  - 0 (Biomarkers, Tumor)
RN  - 0 (COPB2 protein, human)
RN  - 0 (Coatomer Protein)
RN  - EC 2.7.10.1 (RYK protein, human)
RN  - EC 2.7.10.1 (Receptor Protein-Tyrosine Kinases)
SB  - IM
MH  - Biomarkers, Tumor/genetics/metabolism
MH  - *Coatomer Protein/genetics/metabolism
MH  - Humans
MH  - *Laryngeal Neoplasms/genetics/metabolism/pathology
MH  - Neoplasm Staging
MH  - Prognosis
MH  - *Receptor Protein-Tyrosine Kinases/genetics/metabolism
MH  - *Squamous Cell Carcinoma of Head and Neck/genetics/metabolism/pathology
PMC - PMC9206315
OTO - NOTNLM
OT  - GSEA
OT  - Immune infiltration
OT  - LSCC
OT  - Tumor stages
OT  - WGCNA
COIS- The authors declare there are no competing interests.
EDAT- 2022/06/18 06:00
MHDA- 2022/06/22 06:00
PMCR- 2022/06/17
CRDT- 2022/06/17 23:39
PHST- 2021/01/04 00:00 [received]
PHST- 2022/05/23 00:00 [accepted]
PHST- 2022/06/17 23:39 [entrez]
PHST- 2022/06/18 06:00 [pubmed]
PHST- 2022/06/22 06:00 [medline]
PHST- 2022/06/17 00:00 [pmc-release]
AID - 10.1186/s12885-022-09766-z [pii]
AID - 9766 [pii]
AID - 10.1186/s12885-022-09766-z [doi]
PST - epublish
SO  - BMC Cancer. 2022 Jun 17;22(1):667. doi: 10.1186/s12885-022-09766-z.