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Keneskhanova, Z.* ; McWilliam, K.R.* ; Cosentino, R.O.* ; Barcons-Simon, A.* ; Dobrynin, A. ; Smith, J.E.* ; Subota, I.* ; Mugnier, M.R.* ; Colomé-Tatché, M. ; Siegel, T.N.*

Genomic determinants of antigen expression hierarchy in African trypanosomes.

Nature, DOI: 10.1038/s41586-025-08720-w (2025)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
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 mystery1,2. 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 sequencing 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 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 show the critical role of repair sequence availability in the antigen selection mechanism. Furthermore, our study demonstrates the power of highly sensitive single-cell RNA sequencing methods in detecting genomic rearrangements that drive transcriptional changes at the single-cell level.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Blood-stream Forms; Gene-expression
ISSN (print) / ISBN 0028-0836
e-ISSN 1476-4687
Journal Nature
Publisher Nature Publishing Group
Publishing Place London
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants
European Research Council (ERC) Starting
ERC Consolidator
MSCA ITN Cell2Cell
European Union
LMUexcellent - Federal Ministry of Education and Research (BMBF)
Free State of Bavaria under the Excellence Strategy of the German Federal Government
Laender
Wellcome Trust
German Research Foundation