IDENTIFICATION OF SIGNIFICANT RNA-BINDING PROTEINS IN THE PROCESS OF CD44 SPLICING USING THE BOOSTED BETA REGRESSION ALGORITHM

V. O. Novosad; Новосад В. О.

doi:10.31857/S2686738922601023

IDENTIFICATION OF SIGNIFICANT RNA-BINDING PROTEINS IN THE PROCESS OF CD44 SPLICING USING THE BOOSTED BETA REGRESSION ALGORITHM

Authors: Novosad V.O.¹^,2
Affiliations:
1. Faculty of Biology and Biotechnology, National Research University Higher School of Economics,
2. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Issue: Vol 510, No 1 (2023)
Pages: 316-321
Section: Articles
URL: https://journals.rcsi.science/2686-7389/article/view/135704
DOI: https://doi.org/10.31857/S2686738922601023
EDN: https://elibrary.ru/QFUIKM
ID: 135704

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Abstract

The expression of RNA-binding proteins and their interaction with the spliced pre-mRNA are the key factors in determining the final isoform profile. Transmembrane protein CD44 is involved in differentiation, invasion, motility, growth and survival of tumor cells, and is also a commonly accepted marker of cancer stem cells and epithelial-mesenchymal transition. However, the functions of the isoforms of this protein differ significantly. In this paper, we developed a method based on the boosted beta regression algorithm for identification of the significant RNA-binding proteins in the splicing process by modeling the isoform ratio. The application of this method to the analysis of CD44 splicing in colorectal cancer cells revealed 20 significant RNA-binding proteins. Many of them were previously shown as EMT regulators, but for the first time presented as potential CD44 splicing factors.

Keywords

alternative splicing, CD44, CRC, boosted beta regression, RNA-binding proteins, RNA-seq, TCGA

About the authors

V. O. Novosad

Faculty of Biology and Biotechnology, National Research University Higher School of Economics, ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Author for correspondence.
Email: vnovosad@hse.ru
Russian Federation, Moscow; Russian Federation, Moscow

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