In silico analysis of RNA-based aptamers for interaction with CD19 receptor in CAR-positive T-cell enrichment and            monitoring

Abstract

The T cells of a cancer patient are extracted and genetically modified during a procedure called CAR T-cell therapy (chimeric antigen receptor T-cell therapy), which can detect a particular tumor-associated antigen. Short, single-stranded oligonucleotides called aptamers tend to have a high affinity and specific binding to target molecules, such as the CD19 receptor. Novel aptamers exhibiting this high affinity and specificity for the chimeric antigen receptor CD19 have been recently engineered. It is assumed that the involved aptamers interact with a particular epitope on the CD19 receptor. In this study, in silico techniques were utilized for the analysis of the interactions between the CD19 receptor and the aptamers. Previous research was used to obtain the nucleotide sequences of the aptamers and used to model their secondary and tertiary structures using VFold2D and VFold3D, respectively. These structures were then docked onto the CD19 receptor using the HDOCK software with its default parameters. The aptamers CARap9s and CARap18s, which bind to the active site of the CD19 receptor through hydrogen and hydrophobic bonding, were further validated by the comparison of the CD19 binding site using electrostatic surface potential analysis and machine learning, such as the Graph Attention Site Prediction (GrASP) web server. Additional experimental work done in a different investigation supported these results. By utilizing CAR-aptamers to enrich and monitor CAR-positive cells, this study aims to facilitate identifying and isolating these cells and offers promising prospects for the advancement of CAR T-cell therapy.