High-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes

Kirsty R. McWilliam, Zhibek Keneskhanova, Raúl O. Cosentino, Atai Dobrynin, Jaclyn E. Smith, Ines Subota, Monica R. Mugnier, Maria Colomé-Tatché, T. Nicolai Siegel (2024 Mar 22) High-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes. bioR_Xiv preprint https://doi.org/10.1101/2024.03.22.586247

Abstract cited directly from the preprint:

Antigenic variation is an immune evasion strategy used by many different pathogens. It involves the periodic, non-random switch in the expression of different antigens throughout an infection. How the observed hierarchy in antigen expression is achieved has remained a mystery. A key challenge in uncovering this process has been the inability to track transcriptome changes and potential genomic rearrangements in individual cells during a switch event. Here, we report the establishment of a highly sensitive single-cell RNA-seq (scRNA-seq) approach for the model protozoan parasite Trypanosoma brucei. This approach has revealed genomic rearrangements that occur in individual cells during a switch event. Our data show that following a double-strand break (DSB) in the transcribed antigen-coding gene – an important trigger for antigen switching – the type of repair mechanism and the resultant antigen expression depend on the availability of a homologous repair template in the genome. When such a template was available, repair proceeded through segmental gene conversion, creating new, mosaic antigen-coding genes. Conversely, in the absence of a suitable template, a telomere-adjacent antigen-coding gene from a different part of the genome was activated by break-induced replication. Our results reveal the critical role of available repair sequence in the antigen selection mechanism. Additionally, our study demonstrates the power of highly sensitive scRNA-seq methods in detecting genomic rearrangements that drive transcriptional changes at the single-cell level.