2026年最火的双虚拟敲除：CellOracle 虚拟 KO + scTenifoldKnk 验证 → 锁定目标基因

TL;DR - A WeChat bioinformatics tutorial walks through a Cell Proliferation (2026 Apr 15) paper, "Single-Cell Virtual Perturbation Screening Identifies STAT3 as a Key Regulator of Dentinogenesis," which pairs CellOracle virtual knockout with scTenifoldKnk cross-validation to nominate a target gene before wet-lab work. It matters as a reusable "prediction-to-verification" template for in-silico gene screening from public scRNA-seq data.

• Pipeline: public dataset GSE146123 (7 human samples, 24,177 QC-passing cells) → Leiden/UMAP clustering into 9 cell types → sub-clustering of 10,353 odontogenic mesenchymal cells into 6 subsets.
• Target nomination: Slingshot pseudotime + CytoTRACE2 placed EFNB2+ mesenchymal cells as progenitors; intersecting CellRank fate-driver genes (STAT3 corr=0.102, p=1.86e-25) with SCENIC RSS rankings singled out STAT3.
• Dual virtual KO: CellOracle GRN simulation showed perturbed vector fields diverting cells away from pre-odontoblast fate (negative inner-product scores vs. pseudotime); scTenifoldKnk independently ranked SFRP1, GPX3, ADIRF, EFNB2, FOS highest by Manifold Alignment Distance — a network-perturbation metric, not fold change.
• Enriched pathways (Wnt, JAK-STAT, PI3K-Akt, TNF, ECM-receptor) generated the STAT3 → WNT2B → Wnt/β-catenin hypothesis later tested in vitro/in vivo; the post includes runnable Seurat/GEOquery code loading 41,673 initial cells, with later steps promised in a follow-up.