DNA Damage Drives Antigen Diversification Through Mosaic Variant Surface Glycoprotein (VSG) Formation in

Overview

Journal bioRxiv

Date 2024 Sep 10

PMID 39253459

Authors

Jaclyn E Smith

Kevin J Wang

Erin M Kennedy

Jill M C Hakim

Jaime So

Alexander K Beaver

Aishwarya Magesh

Shane D Gilligan-Steinberg

Jessica Zheng

Bailin Zhang

Dharani Narayan Moorthy

Elgin Henry Akin

Lusajo Mwakibete

Monica R Mugnier

Affiliations

Soon will be listed here.

Abstract

Antigenic variation, using large genomic repertoires of antigen-encoding genes, allows pathogens to evade host antibody. Many pathogens, including the African trypanosome , extend their antigenic repertoire through genomic diversification. While evidence suggests that depends on the generation of new variant surface glycoprotein (VSG) genes to maintain a chronic infection, a lack of experimentally tractable tools for studying this process has obscured its underlying mechanisms. Here, we present a highly sensitive targeted sequencing approach for measuring VSG diversification. Using this method, we demonstrate that a Cas9-induced DNA double-strand break within the VSG coding sequence can induce VSG recombination with patterns identical to those observed during infection. These newly generated VSGs are antigenically distinct from parental clones and thus capable of facilitating immune evasion. Together, these results provide insight into the mechanisms of VSG diversification and an experimental framework for studying the evolution of antigen repertoires in pathogenic microbes.

References

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

Wickstead B, Ersfeld K, Gull K . The small chromosomes of Trypanosoma brucei involved in antigenic variation are constructed around repetitive palindromes. Genome Res. 2004; 14(6):1014-24. PMC: 419779. DOI: 10.1101/gr.2227704. View

Hall N, Karras M, Raine J, Carlton J, Kooij T, Berriman M . A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science. 2005; 307(5706):82-6. DOI: 10.1126/science.1103717. View

Rico E, Jeacock L, Kovarova J, Horn D . Inducible high-efficiency CRISPR-Cas9-targeted gene editing and precision base editing in African trypanosomes. Sci Rep. 2018; 8(1):7960. PMC: 5962531. DOI: 10.1038/s41598-018-26303-w. View

Gkeka A, Aresta-Branco F, Triller G, Vlachou E, van Straaten M, Lilic M . Immunodominant surface epitopes power immune evasion in the African trypanosome. Cell Rep. 2023; 42(3):112262. DOI: 10.1016/j.celrep.2023.112262. View

Sheader K, Vaughan S, Minchin J, Hughes K, Gull K, Rudenko G . Variant surface glycoprotein RNA interference triggers a precytokinesis cell cycle arrest in African trypanosomes. Proc Natl Acad Sci U S A. 2005; 102(24):8716-21. PMC: 1150830. DOI: 10.1073/pnas.0501886102. View

Rice-Ficht A, Chen K, Donelson J . Point mutations during generation of expression-linked extra copy of trypanosome surface glycoprotein gene. Nature. 1982; 298(5875):676-9. DOI: 10.1038/298676a0. View

Conway C, Proudfoot C, Burton P, Barry J, McCulloch R . Two pathways of homologous recombination in Trypanosoma brucei. Mol Microbiol. 2002; 45(6):1687-700. DOI: 10.1046/j.1365-2958.2002.03122.x. View

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

10.

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

11.

Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W . Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. PLoS One. 2016; 11(1):e0146638. PMC: 4709065. DOI: 10.1371/journal.pone.0146638. View

12.

Gruszynski A, DeMaster A, Hooper N, Bangs J . Surface coat remodeling during differentiation of Trypanosoma brucei. J Biol Chem. 2003; 278(27):24665-72. DOI: 10.1074/jbc.M301497200. View

13.

McCulloch R, Morrison L, Hall J . DNA Recombination Strategies During Antigenic Variation in the African Trypanosome. Microbiol Spectr. 2015; 3(2):MDNA3-0016-2014. DOI: 10.1128/microbiolspec.MDNA3-0016-2014. View

14.

Niimura Y, Nei M . Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci U S A. 2003; 100(21):12235-40. PMC: 218742. DOI: 10.1073/pnas.1635157100. View

15.

So J, Sudlow S, Sayeed A, Grudda T, Deborggraeve S, Ngoyi D . VSGs Expressed during Natural T. b. gambiense Infection Exhibit Extensive Sequence Divergence and a Subspecies-Specific Bias towards Type B N-Terminal Domains. mBio. 2022; 13(6):e0255322. PMC: 9765701. DOI: 10.1128/mbio.02553-22. View

16.

Adam R, Nigam A, Seshadri V, Martens C, Farneth G, Morrison H . The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. BMC Genomics. 2010; 11:424. PMC: 2996952. DOI: 10.1186/1471-2164-11-424. View

17.

Tsai S, Zheng Z, Nguyen N, Liebers M, Topkar V, Thapar V . GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2014; 33(2):187-197. PMC: 4320685. DOI: 10.1038/nbt.3117. View

18.

Pays E, Van Assel S, Laurent M, Darville M, Vervoort T, VAN MEIRVENNE N . Gene conversion as a mechanism for antigenic variation in trypanosomes. Cell. 1983; 34(2):371-81. DOI: 10.1016/0092-8674(83)90371-9. View

19.

Bernards A, Van der Ploeg L, Gibson W, Leegwater P, Eijgenraam F, de Lange T . Rapid change of the repertoire of variant surface glycoprotein genes in trypanosomes by gene duplication and deletion. J Mol Biol. 1986; 190(1):1-10. DOI: 10.1016/0022-2836(86)90070-7. View

20.

Mirdita M, Schutze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M . ColabFold: making protein folding accessible to all. Nat Methods. 2022; 19(6):679-682. PMC: 9184281. DOI: 10.1038/s41592-022-01488-1. View