Trypanosoma brucei dedicates ~30% of its genome to ~3,000 variant surface glycoprotein (VSG) genes, yet expresses only one at a time, a remarkable antigenic variation system that enables immune evasion. Understanding what alters this strict expression pattern is crucial for therapeutic development against African trypanosomiasis. To identify and rank factors that perturb VSG expression, we performed a comprehensive meta-analysis using a unified Snakemake pipeline (https://github.com/mtinti/myRna-seq) to reanalyze 454 RNA-seq runs (168 single-end, 280 paired-end, 6 nanopore datasets) from 31 publications, covering 35 experimental factors across 78 experiments.
Our standardized approach addressed two key aspects of VSG expression alteration: Which factors induce silent VSG expression? Which decrease active VSG expression? This generated the first systematic ranking of factors by their effect on VSG expression patterns. We also extracted quality control metrics that establish benchmarks for future T. brucei transcriptomics.
The provisional leaderboard and analysis results are available here: