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Weusthof C, Burkart S, Semmelmayer K, Stögbauer F, Feng B, Khorani K, Bode S, Plinkert P, Plath K, Hess J. Establishment of a Machine Learning Model for the Risk Assessment of Perineural Invasion in Head and Neck Squamous Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24108938. [PMID: 37240283 DOI: 10.3390/ijms24108938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Perineural invasion is a prevalent pathological finding in head and neck squamous cell carcinoma and a risk factor for unfavorable survival. An adequate diagnosis of perineural invasion by pathologic examination is limited due to the availability of tumor samples from surgical resection, which can arise in cases of definitive nonsurgical treatment. To address this medical need, we established a random forest prediction model for the risk assessment of perineural invasion, including occult perineural invasion, and characterized distinct cellular and molecular features based on our new and extended classification. RNA sequencing data of head and neck squamous cell carcinoma from The Cancer Genome Atlas were used as a training cohort to identify differentially expressed genes that are associated with perineural invasion. A random forest classification model was established based on these differentially expressed genes and was validated by inspection of H&E-stained whole image slides. Differences in epigenetic regulation and the mutational landscape were detected by an integrative analysis of multiomics data and single-cell RNA-sequencing data were analyzed. We identified a 44-gene expression signature related to perineural invasion and enriched for genes mainly expressed in cancer cells according to single-cell RNA-sequencing data. A machine learning model was trained based on the expression pattern of the 44-gene set with the unique feature to predict occult perineural invasion. This extended classification model enabled a more accurate analysis of alterations in the mutational landscape and epigenetic regulation by DNA methylation as well as quantitative and qualitative differences in the cellular composition in the tumor microenvironment between head and neck squamous cell carcinoma with or without perineural invasion. In conclusion, the newly established model could not only complement histopathologic examination as an additional diagnostic tool but also guide the identification of new drug targets for therapeutic intervention in future clinical trials with head and neck squamous cell carcinoma patients at a higher risk for treatment failure due to perineural invasion.
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Affiliation(s)
- Christopher Weusthof
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Sebastian Burkart
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl Semmelmayer
- Department of Oral and Cranio-Maxillofacial Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Fabian Stögbauer
- Institute of Pathology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Bohai Feng
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karam Khorani
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Sebastian Bode
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Peter Plinkert
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karim Plath
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Section Experimental and Translational Head and Neck Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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