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Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets
Dengyun Zhao, … , Zigang Dong, Kangdong Liu
Dengyun Zhao, … , Zigang Dong, Kangdong Liu
Published April 23, 2024
Citation Information: JCI Insight. 2024;9(10):e171916. https://doi.org/10.1172/jci.insight.171916.
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Research Article Oncology Therapeutics

Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets

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Abstract

Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer and is characterized by an unfavorable prognosis. To elucidate the distinct molecular alterations in ESCC and investigate therapeutic targets, we performed a comprehensive analysis of transcriptomics, proteomics, and phosphoproteomics data derived from 60 paired treatment-naive ESCC and adjacent nontumor tissue samples. Additionally, we conducted a correlation analysis to describe the regulatory relationship between transcriptomic and proteomic processes, revealing alterations in key metabolic pathways. Unsupervised clustering analysis of the proteomics data stratified patients with ESCC into 3 subtypes with different molecular characteristics and clinical outcomes. Notably, subtype III exhibited the worst prognosis and enrichment in proteins associated with malignant processes, including glycolysis and DNA repair pathways. Furthermore, translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1) was validated as a potential prognostic molecule for ESCC. Moreover, integrated kinase-substrate network analysis using the phosphoproteome nominated candidate kinases as potential targets. In vitro and in vivo experiments further confirmed casein kinase II subunit α (CSNK2A1) as a potential kinase target for ESCC. These underlying data represent a valuable resource for researchers that may provide better insights into the biology and treatment of ESCC.

Authors

Dengyun Zhao, Yaping Guo, Huifang Wei, Xuechao Jia, Yafei Zhi, Guiliang He, Wenna Nie, Limeng Huang, Penglei Wang, Kyle Vaughn Laster, Zhicai Liu, Jinwu Wang, Mee-Hyun Lee, Zigang Dong, Kangdong Liu

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Figure 5

Identification of kinases and their potency in ESCC.

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Identification of kinases and their potency in ESCC.
(A) Potential activ...
(A) Potential activated kinases predicted by a kinase-substrate phosphorylation network are depicted. Dots represent previously unstudied kinases in ESCC, and triangles represent kinases implicated in ESCC based on previous literature. The color denotes the calculated P value for each kinase, and the size of the shapes corresponds to their enrichment ratios. (B) Kinase-phosphosubstrate regulation networks are depicted for selected kinases and their substrates, with orange circles representing kinases and blue circles representing their corresponding substrates. (C) Cell proliferation at 72 hours was evaluated by MTT assay after knockdown of the indicated kinases in KYSE30 cell (n = 6 for each group). (D and E) Cell proliferation measured by MTT assay (n = 6 for each group) (D) and soft agar assay (n = 12 for each group) (E) after CSNK2A1 knockdown. Scale bar: 200 μm. (F and G) Cell proliferation measured by MTT (n = 6 for each group) (F) and soft agar (n = 12 for each group) (G) assays after CSNK2A1 overexpression. Scale bar: 200 μm. (H–K) KYSE30 and KYSE450 cells stably expressing scramble or shCSNK2A1 were s.c. injected into the right flank of each mouse (KYSE30: scramble, n = 12; sh1, n = 10; sh2, n = 10; KYSE450: scramble, n = 12; sh1, n = 11; sh2, n = 10). Tumors were excised at the end of the experiment. Images of xenograft tumors are shown in H, while I presents xenograft tumor growth curves data from mice experiments; J displays tumor weights; and K represents tumor inhibition ratios. In all statistical plots, data were expressed as the mean ± SD. Two-tailed Student’s t test (F and G) and 1-way ANOVA (C–E, I, and J) were used to determine statistical significance. *P < 0.05, **P < 0.01, ***P < 0.001. Representative results from at least 3 independent biological replicates (C–G) are shown.

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