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A statistically rigorous method for determining antigenic switching networks

Noble, R. ORCID: 0000-0002-8057-4252 & Recker, M. (2012). A statistically rigorous method for determining antigenic switching networks. PLoS One, 7(6), e39335. doi: 10.1371/journal.pone.0039335


Many vector-borne pathogens rely on antigenic variation to prolong infections and increase their likelihood of onward transmission. This immune evasion strategy often involves mutually exclusive switching between members of gene families that encode functionally similar but antigenically different variants during the course of a single infection. Studies of different pathogens have suggested that switching between variant genes is non-random and that genes have intrinsic probabilities of being activated or silenced. These factors could create a hierarchy of gene expression with important implications for both infection dynamics and the acquisition of protective immunity. Inferring complete switching networks from gene transcription data is problematic, however, because of the high dimensionality of the system and uncertainty in the data. Here we present a statistically rigorous method for analysing temporal gene transcription data to reconstruct an underlying switching network. Using artificially generated transcription profiles together with in vitro var gene transcript data from two Plasmodium falciparum laboratory strains, we show that instead of relying on data from long-term parasite cultures, accuracy can be greatly improved by using transcription time courses of several parasite populations from the same isolate, each starting with different variant distributions. The method further provides explicit indications about the reliability of the resulting networks and can thus be used to test competing hypotheses with regards to the underlying switching pathways. Our results demonstrate that antigenic switch pathways can be determined reliably from short gene transcription profiles assessing multiple time points, even when subject to moderate levels of experimental error. This should yield important new information about switching patterns in antigenically variable organisms and might help to shed light on the molecular basis of antigenic variation.

Publication Type: Article
Additional Information: © 2012 Noble, Recker. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Publisher Keywords: Antigenic Variation; Antigens, Protozoan; Gene Expression Profiling; Plasmodium falciparum; Promoter Regions, Genetic; Reproducibility of Results; Transcription, Genetic
Subjects: H Social Sciences > HA Statistics
Q Science > QA Mathematics
Q Science > QR Microbiology
Departments: School of Science & Technology > Mathematics
Text - Published Version
Available under License Creative Commons: Attribution International Public License 4.0.

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