Comprehensive Pan-cancer Gene Signature Assessment through the Implementation of a Cascade Machine Learning System

Author:

Castillo-Secilla Daniel12ORCID,Galvez Juan Manuel2ORCID,Carrillo-Perez Francisco2ORCID,Prieto-Prieto Juan Carlos3ORCID,Valenzuela Olga4ORCID,Javier Herrera Luis2ORCID,Rojas Ignacio2ORCID

Affiliation:

1. Fujitsu Technology Solutions S.A., CoE Data Intelligence, Camino del Cerro de los Gamos, 1, Pozuelo de Alarcón, 28224, Madrid, Spain

2. Department of Computer Architecture and Technology, University of Granada. C.I.T.I.C., Periodista Rafael Gómez Montero, 2, 18014. Granada, Spain

3. Nuclear Medicine Department, IMIBIC, University Hospital Reina Sofia, Menéndez Pidal Avenue, 14004, Córdoba, Spain

4. Department of Applied Mathematics, University of Granada. Facultad de Ciencias, Campus de Fuentenueva, 18071, Granada, Spain

Abstract

Background: Despite all the medical advances introduced for personalized patient treatment and the research supported in search of genetic patterns inherent to the occurrence of its different manifestations on the human being, the unequivocal and effective treatment of cancer, unfortunately, remains as an unresolved challenge within the scientific panorama. Until a universal solution for its control is achieved, early detection mechanisms for preventative diagnosis increasingly avoid treatments, resulting in unreliable effectiveness. The discovery of unequivocal gene patterns allowing us to discern between multiple pathological states could help shed light on patients suspected of an oncological disease but with uncertainty in the histological and immunohistochemical results. Methods: This study presents an approach for pan-cancer diagnosis based on gene expression analysis that determines a reduced set of 12 genes, making it possible to distinguish between the main 14 cancer diseases. Results: Our cascade machine learning process has been robustly designed, obtaining a mean F1 score of 92% and a mean AUC of 99.37% in the test set. Our study showed heterogeneous over-or underexpression of the analyzed genes, which can act as oncogenes or tumor suppressor genes. Upregulation of LPAR5 and PAX8 was demonstrated in thyroid cancer samples. KLF5 was highly expressed in the majority of cancer types. Conclusion: Our model constituted a useful tool for pan-cancer gene expression evaluation. In addition to providing biological clues about a hypothetical common origin of cancer, the scalability of this study promises to be very useful for future studies to reinforce, confirm, and extend the biological observations presented here. Code availability and datasets are stored in the following GitHub repository to aim for the research reproducibility: https://github.com/CasedUgr/PanCancerClassification.

Funder

Spanish Ministry of Sciences, Innovation and Universities

Government of Andalusia

Publisher

Bentham Science Publishers Ltd.

Subject

Computational Mathematics,Genetics,Molecular Biology,Biochemistry

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