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Updated: May 29, 2025
Parallel Measurement of Circadian Clock Gene Expression and Hormone Secretion in Human Primary Cell Cultures
Published on: November 11, 2016
Single-cell RNA sequencing integrated with bulk RNA sequencing analysis of clock circadian regulator with prognostic
Zhen Shen1, Yuelei Zhao2, Xinxin Xu2
1Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, PR China.
Background:
Disruption of circadian rhythm was found to be associated with immune infiltration and thyroid cancer. However, the role of clock circadian regulator (CLOCK) in the progression of thyroid cancer and its immune microenvironment remains largely unexplored. Therefore, our aim was to explore the role and potential mechanism of CLOCK in thyroid cancer.
Methods:
Single cell sequencing analysis and bulk RNA sequencing analysis was used for LASSO regression and Kaplan-Meier survival estimates. Potential mechanism analysis were gained through KEGG/GO analysis, GSEA analysis and PPI network. In vivo and in vitro experiment was used for further validation.
Results:
The result showed CLOCK protein was overexpressed in thyroid cancer compared with normal tissue in both thyroid specific mouse model and human sample. A prognostic model incorporating CLOCK and other related genes (FAT4, OR6K2, STK40, TMEM63A, HRCT1, SUPT5H, and OR2C3) was developed using LASSO regression. Functional assay and bioinformatics analysis indicated that CLOCK knockdown hindered tumor growth and the activity of MAPK signaling. Besides, analyses of gene enrichment, signaling pathways, and immune checkpoints suggested that CLOCK might inhibit immune infiltration within the tumor microenvironment. Confirmatory in vitro experiments and immunohistochemical assays in human samples further linked high CLOCK expression to reduced T cell cytotoxicity and infiltration.
Conclusion:
These findings underscore the pivotal role of CLOCK in thyroid cancer prognosis and immune suppression, highlighting its potential as a target for therapeutic intervention and prognostic assessment in thyroid cancer management.
Insights
Clock circadian regulator (CLOCK) is overexpressed in thyroid cancer, hindering anti-tumor immunity and progression. Targeting CLOCK may offer new therapeutic strategies for thyroid cancer management.
Area of Science:
- Oncology
- Molecular Biology
- Immunology
Background:
- Circadian rhythm disruption is linked to thyroid cancer and immune infiltration.
- The specific role of the clock circadian regulator (CLOCK) in thyroid cancer progression and its immune microenvironment is largely unknown.
Purpose of the Study:
- To investigate the role and underlying mechanisms of CLOCK in thyroid cancer development and progression.
- To explore CLOCK's impact on the tumor immune microenvironment.
Main Methods:
- Utilized single-cell and bulk RNA sequencing, LASSO regression, and Kaplan-Meier survival analysis.
- Performed KEGG/GO analysis, GSEA, and PPI network analysis for mechanism exploration.
- Validated findings through in vivo and in vitro experiments and immunohistochemical assays.
Main Results:
- CLOCK protein is overexpressed in thyroid cancer tissues compared to normal tissues.
- A prognostic model including CLOCK and other genes (FAT4, OR6K2, STK40, TMEM63A, HRCT1, SUPT5H, OR2C3) was developed.
- CLOCK knockdown inhibited tumor growth, MAPK signaling, and suppressed immune infiltration, reducing T cell cytotoxicity.
Conclusions:
- CLOCK plays a critical role in thyroid cancer prognosis and immune suppression.
- CLOCK represents a potential therapeutic target and prognostic biomarker for thyroid cancer.
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