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Author Spotlight: Unlocking the Mysteries of Oral Potential Malignancies
Published on: August 11, 2023
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Long-read Sequencing Reveals Repeat Expansions and Large Structural Variants in Oral Squamous Cell Carcinoma
Li Hu1, Jiaxun Zhang1, Zhuoyuan Zhang2,3
1Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
Genomics, Proteomics & Bioinformatics
|December 27, 2025
Summary
This study reveals novel structural variants (SVs) in oral squamous cell carcinoma (OSCC), including repeat expansions impacting OBI1 gene expression and cell behavior. These findings enhance understanding of OSCC molecular pathogenesis.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Previous studies often grouped oral squamous cell carcinoma (OSCC) with other head and neck cancers, limiting OSCC-specific insights.
- Understanding structural variants (SVs) unique to OSCC is crucial for deciphering its molecular pathogenesis.
Purpose of the Study:
- To identify and characterize OSCC-specific somatic structural variants (SVs) using long-read whole-genome sequencing.
- To elucidate the functional impact of identified SVs on gene expression and cellular functions in OSCC.
Main Methods:
- Performed long-read whole-genome sequencing on 16 paired OSCC tumor and blood samples.
- Identified high-confidence somatic SVs and recurrent simple repeat expansions (SREs).
- Utilized gene knockout experiments to assess the functional consequences of SREs on gene expression and cell behavior.
Main Results:
- Discovered 5775 high-confidence somatic SVs, including five recurrent SREs.
- Identified an SRE in the OBI1 promoter present in 45% of OSCC samples, significantly reducing OBI1 expression and impairing cell proliferation and migration upon knockout.
- Confirmed that the 11q13 amplified region is susceptible to large SVs affecting ANO1, FADD, and CTTN expression, linking these SVs to OSCC development.
Conclusions:
- Somatic SVs, particularly SREs and large SVs in critical genomic regions, play a significant role in OSCC development.
- The OBI1 promoter SRE is a key driver in a subset of OSCC, affecting cell functions.
- This research provides a deeper understanding of the molecular mechanisms underlying OSCC.
Keywords:
Complex structural rearrangementsNanopore sequencingOral squamous cell carcinomaSimple repeat expansionSomatic structural variantsMore Related Videos
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