Trypanosome Antigenic Variation

As disease-causing pathogens face a cutthroat battle against the human immune system, they have evolved different ways to counter attacks from our cells. One of these is the parasite Trypanosoma brucei, cause of African sleeping sickness.

Trypanosomes are eukaryotes (a category which includes plants and animals) made of a single cell and a flagellum that allows it to move throughout the human bloodstream. They primarily use evasion over singular parasite lifetimes, riding out the innate (first, non-specific) immune response and then tricking the body’s adaptive (specific) immunity that kicks in afterward. While innate immunity is immediate, the adaptive response takes time to recognize a specific pathogen and raise levels of cells necessary to combat it. Recognition occurs primarily via surface molecules (antigens) on pathogen's outside.

For trypanosomes, those antigens take the form of a variant surface glycoprotein (VSG) coat that covers the outer surface of each organism. As the immune system attacks trypanosomes, some members of the parasite population switch to express a different variety of the glycoprotein coat which the immune system has not yet recognized. This cycle of antigenic variation repeats, with adaptive immunity continually lagging behind those trypanosomes that take advantage of the lull before immunity response to vary the glycoproteins on their cell membranes.

Current knowledge of the antigenic variation process in trypanosomes is rather lacking, but available evidence points to two methods of switching: transcriptional modification and recombination.The former involves silencing the currently transcribed VSG expression site and activating another of approximately 15 expression sites located near telomeres in the trypanosome genome. On the other hand, the latter involves splicing together either a full or fragments of a VSG gene into an expression site. A trove of thousands of such genes and pseudogenes lies outside the expression sites in 11 large chromosomes as well as 50 to 100 smaller ones.

Inside the cell, VSG genes on silent expression sites (i.e. not in use) in the cell nucleus are physically located on the periphery. These sites also show formation of heterochromatin, the tightly-packed, downregulated form of DNA. On the other hand, the active expression site is enveloped in an “expression-site body” located in the center adjacent to the nucleolus and to a reservoir of RNA polymerase I.

Although all expression sites undergo transcription initiation, in which RNA polymerase binds to a promoter, only the active expression site undergoes elongation (the addition of complementary nucleotides to transcribe DNA into mRNA) and maturation (intron splicing and the addition of a 5’ cap and 3’ poly-A tail). Trypanosome cells additionally assemble a “production line” of proteins that activate expression sites and serve as molecular bridges to boost VSG production.

Recombination, being the more complex process, occurs in two different ways: the trypanosome either recombines a complete VSG gene or pseudogene through double-stranded DNA breaks into the active expression site, or it splices together parts of multiple genes to produce a “mosaic” VSG that is completely novel. Where or how specifically the cell performs this recombination is currently unknown.

Three different theories exist as to how recombination is initiated. The first is that T. brucei actively generates double-stranded breaks in the expression site, perhaps due to an unidentified endonuclease that recognizes certain structures in the VSG gene. The second is that random telomere loss induces single-ended breaks in DNA to result in recombination. Opposing these two is a third viewpoint theorizing that rather than forming directly, the breaks result from unrelated lesions like stalled DNA replication forks (the result of a failed cell cycle checkpoint).

After decades of research, still little is known about the parasite that causes African sleeping sickness, frequently the top cause of mortality in many rural villages in the Democratic Republic of the Congo, Angola, and South Sudan. The lack of understanding of trypanosome-specific pathways has hampered the identification of targets for the development of treatments. The quest to decipher the process of antigen switching not only in trypanosomes but in other neglected tropical diseases thus continues on.