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Consistent Analysis of Differentially Expressed Genes Across 7 Cell Types in Papillary Thyroid Carcinoma8.48 MB
Published VersionCC BY V4.0, Open Access
Journal article
Consistent Analysis of Differentially Expressed Genes Across 7 Cell Types in Papillary Thyroid Carcinoma
Computational and Structural Biotechnology Journal, Vol.21, pp.5337-5349
2023
Appears in Cancer Research Cluster Research Collection
Abstract
Single-cell transcriptome sequencing (scRNA-seq) provides a higher resolution of cellular differences than bulk RNA-seq, enabling the dissection of cell-type-specific responses to perturbations in papillary thyroid carcinoma (PTC). However, cellular genomic features are highly heterogeneous and have a large number of genes without any expression signals, which hinders the statistical power to identify differentially expressed genes and may generate many false-positive results. To overcome this challenge, we conducted an integrative analysis on two PTC scRNA-seq datasets and cross-validated consistent differential expression. By combining results from 32 common cell types in the two studies, we identified 31 consistently differentially expressed genes (DEGs) across seven cell types, including B cells, endothelial cells, epithelial cells, monocytes, NK cells, smooth muscle cells, and T cells. Functional enrichment analysis revealed that these genes are important for the adaptive immune response and autoimmune thyroid diseases. The additional disease-free survival analysis also confirmed that these 31 genes significantly affected patient survival time in large scale thyroid cancer cohort. Furthermore, we experimentally validated one of the top consistent DEGs as a potential biomarker gene of PTC epithelial cells, KRT7, which may be a upstream gene for the NF-κB signaling pathway. The result shows that KRT7 may promote thyroid cancer metastasis through the epithelial-mesenchymal transition and NF-κB signaling pathway. In summary, our single-cell transcriptome integration-based approach may provide insights into the important role of NF-κB in the underlying biology of the PTC.
Details
- Title
- Consistent Analysis of Differentially Expressed Genes Across 7 Cell Types in Papillary Thyroid Carcinoma
- Authors
- Xianhui Ruan (Corresponding Author) - Tianjin Medical University Cancer Institute and HospitalYue Huang (Author) - Tianjin Medical University Cancer Institute and HospitalLin Geng (Author) - Tianjin Medical University Cancer Institute and HospitalMengran Tian (Author) - Tianjin Medical University Cancer Institute and HospitalYu Liu (Author) - Tianjin Medical University Cancer Institute and HospitalMei Tao (Author) - Tianjin Medical University Cancer Institute and HospitalXiangqian Zheng (Author) - Tianjin Medical University Cancer Institute and HospitalPeng Li (Author) - Nankai UniversityMin Zhao (Author) - University of the Sunshine Coast, Queensland, School of Science, Technology and Engineering
- Publication details
- Computational and Structural Biotechnology Journal, Vol.21, pp.5337-5349
- Publisher
- Research Network of Computational and Structural Biotechnology
- Date published
- 2023
- DOI
- 10.1016/j.csbj.2023.10.045
- ISSN
- 2001-0370
- Copyright note
- This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
- Data Availability
- Supplementary data associated with this article can be found in the online version at doi:10.1016/j.csbj.2023.10.045.
- Grant note
- 82103386, 32200588, 82172821 / National Natural Science Foundation of China 2021ZD033 / Tianjin Education Commission for Higher Education Central Universities 63231123 / Nankai University
- Organisation Unit
- Cancer Research Cluster; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99971185602621
- Output Type
- Journal article
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