Association Between TWF2 Knockdown and Reduced SNCA Expression: A Screen of 300 CRISPRi Perturbations in Human Embryonic Stem Cells

Abstract

Elevated α-synuclein, encoded by SNCA, is central to Parkinson’s disease pathology, and lowering SNCA expression is an actively pursued therapeutic strategy. Genes whose inhibition reduces SNCA without broadly disturbing the transcriptome would be useful starting points for experimental follow-up. We analyzed the Arc Institute Virtual Cell Challenge 2025 dataset, a CRISPR interference (CRISPRi) screen of 300 target genes across 491,046 human embryonic stem cells including 114,528 non-targeting control cells distributed across 48 processing batches, and tested every perturbation for its effect on SNCA and on the transcriptome as a whole. Twenty-eight perturbations significantly altered SNCA; twelve reduced it, four by at least 50%, and only two by at least 75%: knockdown of SNCA itself (95.2%) and of TWF2 (92.4%). Under criteria fixed before analysis, TWF2 knockdown altered 14 genes against a median of 136 across all perturbations, whereas EP300 and DOT1L, the other perturbations reducing SNCA by at least half, altered 2,855 and 2,472 genes. TWF2 was the only perturbation of the 300 satisfying both prespecified criteria. The association was reproduced by a cell-level rank-sum test, a replicate-level analysis blocked on processing batch, and a negative-binomial model with batch as a covariate, and was observed in all 30 batches containing sufficient cells for an independent estimate. At matched cell number the difference in gene counts persisted, indicating it is not explained by statistical power. These transcript-level associations identify TWF2 as a candidate for experimental investigation; they do not establish mechanism or therapeutic suitability.