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Identification of the gene expression changes and gene regulatory aspects in ELF3 mutant bladder cancer
Perihan Yagmur Guneri-Sozeri1,2, Serap Erkek-Ozhan3,4
1Izmir Biomedicine and Genome Center, 35340, Inciralti, Izmir, Turkey.
Background:
Recent genome-wide studies revealed the molecular subtypes and mutational landscape of bladder cancer, which is the 10th most common cancer causing many deaths. ELF3 is one of the frequently mutated genes in bladder cancer with 14% alteration rate. It mainly functions as an epithelial transcription factor and its proper function is critical for the urothelium development. However, the impact of ELF3 mutations in bladder cancer is currently unknown.
Methods And Results:
In this study, we analysed the gene expression data available for primary bladder cancer and bladder cancer cell lines according to the mutation status of ELF3. Our results show that de-regulated genes common in cell lines and primary tissue are primarily involved in ameboidal type cell migration and cell-cell junction organization. Additionally, we identify that ELF3-mutant cases in primary samples significantly overexpress PIK3C2B and ELF3 and PIK3C2B and ELF3 are significantly co-mutated in many cancer types. Our integrative analysis with existing Hi-C data further revealed the genes proximally located to ELF3, including PIK3C2B to be upregulated in ELF3 mutant cases, potentially as a result of truncated ELF3 protein product and subsequent changes in regulatory interactions.
Conclusions:
Our results provide important insights about how ELF3 mutation contributes to bladder tumorigenesis and uncover previously unknown dependencies.
Insights
Bladder cancer mutations in the ELF3 gene impact cell migration and organization. ELF3 mutations are linked to PIK3C2B overexpression, offering new insights into bladder cancer development.
Area of Science:
- Genitourinary oncology
- Cancer genomics
- Molecular biology
Background:
- Bladder cancer is a significant cause of cancer-related deaths, with recent studies elucidating its molecular subtypes and mutational landscape.
- ELF3, a critical epithelial transcription factor for urothelium development, is altered in 14% of bladder cancer cases, yet its functional impact remains unclear.
Purpose of the Study:
- To investigate the functional consequences of ELF3 mutations in bladder cancer.
- To identify molecular pathways and gene expression changes associated with ELF3 alterations in bladder tumors.
Main Methods:
- Analysis of gene expression data from primary bladder cancer tissues and cell lines stratified by ELF3 mutation status.
- Integrative analysis of gene expression data with Hi-C data to explore regulatory interactions.
- Examination of co-mutation patterns between ELF3 and other genes, including PIK3C2B.
Main Results:
- Genes commonly deregulated in ELF3-mutant bladder cancer are primarily involved in ameboidal cell migration and cell-cell junction organization.
- ELF3-mutant primary bladder tumors exhibit significant overexpression of PIK3C2B.
- ELF3 and PIK3C2B are frequently co-mutated across various cancer types.
- Integrative analysis suggests that ELF3 mutations may lead to PIK3C2B upregulation due to altered regulatory interactions caused by truncated ELF3 protein.
Conclusions:
- ELF3 mutations play a role in bladder cancer initiation and progression.
- The study reveals novel dependencies in ELF3-mutant bladder tumors, particularly the upregulation of PIK3C2B.
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