Magez, S. et al. The role of B-cells and IgM antibodies in parasitemia, anemia, and VSG switching in Trypanosoma brucei-infected mice. PLoS Pathog. 4, e1000122 (2008).
Cross, G. A. M., Kim, H. S. & Wickstead, B. Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427. Mol. Biochem. Parasitol. 195, 59â73 (2014).
Müller, L. S. M. et al. Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature 563, 121â125 (2018).
Hertz-Fowler, C. et al. Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS ONE 3, e3527 (2008).
Cosentino, R. O., Brink, B. G. & Nicolai Siegel, T. Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay. NAR Genom. Bioinform. 3, lqab082 (2021).
Hall, J. P. J., Wang, H. & David Barry, J. Mosaic VSGs and the scale of Trypanosoma brucei antigenic variation. PLoS Pathog. 9, e1003502 (2013).
Mugnier, M. R., Cross, G. A. M. & Papavasiliou, F. N. The in vivo dynamics of antigenic variation in Trypanosoma brucei. Science 347, 1470â1473 (2015).
Jayaraman, S. et al. Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Negl. Trop. Dis. 13, e0007262 (2019).
Capewell, P. et al. The skin is a significant but overlooked anatomical reservoir for vector-borne African trypanosomes. eLife 5, e17716 (2016).
Camara, M. et al. Extravascular dermal trypanosomes in suspected and confirmed cases of gambiense human African trypanosomiasis. Clin. Infect. Dis. 73, 12â20 (2021).
Trindade, S. et al. Trypanosoma brucei parasites occupy and functionally adapt to the adipose tissue in mice. Cell Host Microbe https://doi.org/10.1016/j.chom.2016.05.002 (2016).
Carvalho, T. et al. Trypanosoma brucei triggers a marked immune response in male reproductive organs. PLoS Negl. Trop. Dis. https://doi.org/10.1371/journal.pntd.0006690 (2018).
De Niz, M. et al. Organotypic endothelial adhesion molecules are key for Trypanosoma brucei tropism and virulence. Cell Rep 36, 109741 (2021).
Control and Surveillance of Human African Trypanosomiasis: Report of a WHO Expert Committee. WHO Technical Report Series (WHO, 2013).
Crilly, N. P. & Mugnier, M. R. Thinking outside the blood: perspectives on tissue-resident Trypanosoma brucei. PLoS Pathog. 17, e1009866 (2021).
Kamper, S. M. & Barbet, A. F. Surface epitope variation via mosaic gene formation is potential key to long-term survival of Trypanosoma brucei. Mol. Biochem. Parasitol. 53, 33â44 (1992).
Seed, J. R. & Effron, H. G. Simultaneous presence of different antigenic populations of Trypanosoma brucei gambiense in Microtus montanus. Parasitology 66, 269â278 (1973).
Seed, J. R., Edwards, R. & Sechelski, J. The ecology of antigenic variation. J. Protozool. 31, 48â53 (1984).
Barry, J. D. & Emery, D. L. Parasite development and host responses during the establishment of Trypanosoma brucei infection transmitted by tsetse fly. Parasitology 88, 67â84 (1984).
Tanner, M., Jenni, L., Hecker, H. & Brun, R. Characterization of Trypanosoma brucei isolated from lymph nodes of rats. Parasitology 80, 383â391 (1980).
Vickerman, K. Trypanosome sociology and antigenic variation. Parasitology 99, S37âS47 (1989).
Barry, J. D. & Turner, C. M. R. The dynamics of antigenic variation and growth of African trypanosomes. Parasitol. Today 7, 207â211 (1991).
Engstler, M. & Boshart, M. Cold shock and regulation of surface protein trafficking convey sensitization to inducers of stage differentiation in Trypanosoma brucei. Genes Dev. 18, 2798â2811 (2004).
Turner, C. M., Hunter, C. A., Barry, J. D. & Vickerman, K. Similarity in variable antigen type composition of Trypanosoma brucei Rhodesiense populations in different sites within the mouse host. Trans. R. Soc. Trop. Med. Hyg. 80, 824â830 (1986).
Turner, C. M. R. & Barry, J. D. High frequency of antigenic variation in Trypanosoma brucei rhodesiense infections. Parasitology 99, 67â75 (1989).
Salanti, A. et al. Evidence for the involvement of VAR2CSA in pregnancy-associated malaria. J. Exp. Med. 200, 1197â1203 (2004).
Duffy, P. E. & Fried, M. Plasmodium falciparum adhesion in the placenta. Curr. Opin. Microbiol. 6, 371â376 (2003).
Jonsson, A. âB., Ilver, D., Falk, P., Pepose, J. & Normark, S. Sequence changes in the pilus subunit lead to tropism variation of Neisseria gonorrhoeae to human tissue. Mol. Microbiol. 13, 403â416 (1994).
Nassif, X. et al. Antigenic variation of pilin regulates adhesion of Neisseria meningitidis to human epithelial cells. Mol. Microbiol. 8, 719â725 (1993).
Rudel, T., van Putten, J. P. M., Gibbs, C. P., Haas, R. & Meyer, T. F. Interaction of two variable proteins (PilE and PilC) required for pilus-mediated adherence of Neisseria gonorrhoeae to human epithelial cells. Mol. Microbiol. 6, 3439â3450 (1992).
Virji, M. & Heckels, J. E. The role of common and type-specific pilus antigenic domains in adhesion and virulence of gonococci for human epithelial cells. J. Gen. Microbiol. 130, 1089â1095 (1984).
Dean, S., Marchetti, R., Kirk, K. & Matthews, K. R. A surface transporter family conveys the trypanosome differentiation signal. Nature 459, 213â217 (2009).
McWilliam, K. R. et al. High-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes. Preprint at bioRxiv https://doi.org/10.1101/2024.03.22.586247 (2024).
Smith, J. E. et al. DNA damage drives antigen diversification through mosaic VSG formation in Trypanosoma brucei. Preprint at bioRxiv https://doi.org/10.1101/2024.03.22.582209 (2024).
Calvo-Alvarez, E., Cren-Travaillé, C., Crouzols, A. & Rotureau, B. A new chimeric triple reporter fusion protein as a tool for in vitro and in vivo multimodal imaging to monitor the development of African trypanosomes and Leishmania parasites. Infect. Genet. Evol. 63, 391â403 (2018).
Hutchinson, S. et al. The establishment of variant surface glycoprotein monoallelic expression revealed by single-cell RNA-seq of Trypanosoma brucei in the tsetse fly salivary glands. PLoS Pathog. 17, e1009904 (2021).
Savage, A. F. et al. Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts. PLoS Negl. Trop. Dis. 6, 1708 (2012).
Schopf, L. R., Filutowicz, H., Bi, X. J. & Mansfield, J. M. Interleukin-4-dependent immunoglobulin G1 isotype switch in the presence of a polarized antigen-specific Th1-cell response to the trypanosome variant surface glycoprotein. Infect. Immun. 66, 451 (1998).
Liu, G. et al. Distinct contributions of CD4+ and CD8+ T cells to pathogenesis of trypanosoma brucei infection in the context of gamma interferon and interleukin-10. Infect. Immun. 83, 2785â2795 (2015).
Reinitz, D. M. & Mansfield, J. M. T-cell-independent and T-cell-dependent B-cell responses to exposed variant surface glycoprotein epitopes in trypanosome-infected mice. Infect. Immun. 58, 2337â2342 (1990).
Radwanska, M. et al. Comparative analysis of antibody responses against HSP60, invariant surface glycoprotein 70, and variant surface glycoprotein reveals a complex antigen-specific pattern of immunoglobulin isotype switching during infection by Trypanosoma brucei. Infect. Immun. 68, 848â860 (2000).
Robbiani, D. F. et al. AID is required for the chromosomal breaks in c-myc that lead to c-myc/IgH translocations. Cell 135, 1028â1038 (2008).
Hector, R. F., Collins, M. S. & Pennington, J. E. Treatment of experimental Pseudomonas aeruginosa pneumonia with a human IgM monoclonal antibody. J. Infect. Dis. 160, 483â489 (1989).
Barth, W. F., Wochner, R. D., Waldmann, T. A. & Fahey, J. L. Metabolism of human gamma macroglobulins. J. Clin. Invest. 43, 1036 (1964).
Mehlitz, D. & Molyneux, D. H. The elimination of Trypanosoma brucei gambiense? Challenges of reservoir hosts and transmission cycles: expect the unexpected. Parasite Epidemiol. Control 6, e00113 (2019).
Larcombe, S. D., Briggs, E. M., Savill, N., Szoor, B. & Matthews, K. The developmental hierarchy and scarcity of replicative slender trypanosomes in blood challenges their role in infection maintenance. Proc. Natl Acad. Sci. USA 120, e2306848120 (2023).
Morrison, L. J., Majiwa, P., Read, A. F. & Barry, J. D. Probabilistic order in antigenic variation of Trypanosoma brucei. Int. J. Parasitol. 35, 961â972 (2005).
Pinger, J., Chowdhury, S. & Papavasiliou, F. N. Variant surface glycoprotein density defines an immune evasion threshold for African trypanosomes undergoing antigenic variation. Nat. Commun. 8, 828 (2017).
Trindade, S. et al. Slow growing behavior in African trypanosomes during adipose tissue colonization. Nat. Commun. 13, 7548 (2022).
Shimogawa, M. M. et al. Parasite motility is critical for virulence of African trypanosomes. Sci. Rep. 8, 9122 (2018).
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494â1512 (2013).
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644â652 (2011).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422â1423 (2009).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinf. 10, 421 (2009).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403â410 (1990).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841â842 (2010).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150â3152 (2012).
Li, W. & Godzik, A. CD-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658â1659 (2006).
Krueger, F. et al. FelixKrueger/TrimGalore: v.0.6.4 – add default decompression path. Zenodo https://doi.org/10.5281/zenodo.5127898 (2023).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
So, J. et al. VSGs expressed during natural T. b. gambiense infection exhibit extensive sequence divergence and a subspecies-specific bias towards type B N-terminal domains. mBio 13, e02553-22 (2022).
Gruszynski, A. E., DeMaster, A., Hooper, N. M. & Bangs, J. D. Surface coat remodeling during differentiation of Trypanosoma brucei. J. Biol. Chem. 278, 24665â24672 (2003).
Lee, J.-Y. & Kitaoka, M. A beginnerâs guide to rigor and reproducibility in fluorescence imaging experiments. Mol. Biol. Cell https://doi.org/10.1091/mbc.E17-05-0276 (2018).
Wirtz, E., Leal, S., Ochatt, C. & Cross, G. A. M. A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei. Mol. Biochem. Parasitol. 99, 89â101 (1999).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10â12 (2011).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15â21 (2013).
Shanmugasundram, A. et al. TriTrypDB: an integrated functional genomics resource for kinetoplastida. PLoS Negl. Trop. Dis. 17, e0011058 (2023).
RamÃrez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160âW165 (2016).
Song, Y. & Wang, J. ggcoverage: an R package to visualize and annotate genome coverage for various NGS data. BMC Bioinf. 24, 309 (2023).
Moloo, S. K. An artificial feeding technique for Glossina. Parasitology 63, 507â512 (1971).
MacLeod, E. T., Maudlin, I., Darby, A. C. & Welburn, S. C. Antioxidants promote establishment of trypanosome infections in tsetse. Parasitology 134, 827â831 (2007).
Beaver, A. mugnierlab/Beaver2022: Release for publication. Zenodo https://doi.org/10.5281/zenodo.13684001 (2024).
Barnett, S. A. The skin and hair of mice living at a low environmental temperature. Q. J. Exp. Physiol. Cogn. Med. Sci. 44, 35â42 (1959).