Computational Methods for Structure-to-Function Analysis of Diet-Derived Catechins-Mediated Targeting of In Vitro Vasculogenic Mimicry. (April 2021)

• Record Type: Journal Article
• Authors: Uthamacumaran, Abicumaran; Suarez, Narjara Gonzalez; Baniré Diallo, Abdoulaye; Annabi, Borhane
• Is Part Of: Cancer informatics. Volume 20(2021)
• Publication Date: 2021-04
• Subjects: Computational analysis -- machine learning -- vasculogenic mimicry -- ovarian cancer -- epithelial-mesenchymal transition -- green tea catechins; Bioinformatics -- Periodicals; Biology -- Data processing -- Periodicals; Cancer -- Periodicals; Cancer -- Research -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1177/11769351211009229
• Languages: English
• ISSNs: 1176-9351

Abstract

Background: Vasculogenic mimicry (VM) is an adaptive biological phenomenon wherein cancer cells spontaneously self-organize into 3-dimensional (3D) branching network structures. This emergent behavior is considered central in promoting an invasive, metastatic, and therapy resistance molecular signature to cancer cells. The quantitative analysis of such complex phenotypic systems could require the use of computational approaches including machine learning algorithms originating from complexity science. Procedures: In vitro 3D VM was performed with SKOV3 and ES2 ovarian cancer cells cultured on Matrigel. Diet-derived catechins disruption of VM was monitored at 24 hours with pictures taken with an inverted microscope. Three computational algorithms for complex feature extraction relevant for 3D VM, including 2D wavelet analysis, fractal dimension, and percolation clustering scores were assessed coupled with machine learning classifiers. Results: These algorithms demonstrated the structure-to-function galloyl moiety impact on VM for each of the gallated catechin tested, and shown applicable in quantifying the drug-mediated structural changes in VM processes. Conclusions: Our study provides evidence of how appropriate 3D VM compression and feature extractors coupled with classification/regression methods could be efficient to study in vitro drug-induced perturbation of complex processes. Such approaches could be exploited in the development and characterization of drugs targeting VM.