CONCERT shows knockout location shapes tumor response, beats five baselines
marinkazitnik · x · 2026-10-25
Main results post of the CONCERT release thread: predicting how gene-knockout responses depend on where in a tumor they occur.
- Data: Perturb-Map uses CRISPR to knock out genes in mouse lung tumors with per-lesion tags, paired with spatial transcriptomics; the study covered Tgfbr2, Ifngr2 and Jak2 from the TGF-β and interferon pathways.
- Results: Placing a predicted Jak2 knockout patch into the tumor core or normal tissue moves predicted spots toward the measured Jak2 profile; CONCERT predicts Tgfbr2 responses depend most on the surrounding niche and Jak2 least, outperforming five baselines including scGEN, GEARS, Steamboat and CelComen.
- Implication: spatial models let researchers choose where in a tissue to perturb, not just which gene.
Authors: Xiang Lin, Kong, Boyang, Soumya Ghosh, Manolis Kellis, Marinka Zitnik (Harvard/Harvard Medical School).
Related event: Harvard's CONCERT Predicts Spatial Spread of Gene Perturbations in Tissue(4 posts)→
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