SPACE: multimodal spatial CRISPR screening with whole-transcriptome readout at subcellular resolution in 3D models

作者：Mengwei Hu, Yi Cui, Qianhui Huang, Khoi Chu, Sierra Mckinzie, Michael Patrick, Sharanya Iyengar, Maerjianghan Abuduli, Marianne Spatz, Nandita Joshi, Brendan Miller, Shamsudheen Karuthedath Vellarikkal, Timothy Riordan, Danny A. Bitton, Jan Lubojacky, Iya Khalil, Federica Piccioni, Michael Rhodes, Alex M. Tamburino, Shanshan He, Joseph Beechem, Vanessa M. Peterson · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2025 · DOI：10.1101/2025.09.14.675819 · 被引用次数：3 · 研究领域：Environmental DNA in Biodiversity Studies

Abstract Current spatial CRISPR screening technologies are limited by targeted readouts and high costs, restricting the scope of biological discovery. Here we present SPA tial C ell E xploration (SPACE), a spatial CRISPR screening platform that integrates whole-transcriptome profiling (∼18,000 genes), multiplexed protein detection (∼68 markers), and CRISPR perturbation mapping at subcellular resolution. SPACE significantly reduces whole-transcriptome profiling costs compared to sequencing methods while preserving spatial context. We demonstrate SPACE by screening 43 CRISPR knockouts (KOs) across ∼100,000 cells in hundreds of cancer-associated fibroblast (CAF)-tumor spheroids, obtaining whole-transcriptome and multiplexed protein readout from the same exact cells. SPACE revealed previously unknown regulatory mechanisms on tumor extracellular matrix (ECM) remodeling, and identified spatially-resolved ligand-receptor interactions and perturbation-specific spatial gene signatures that are not detectable with dissociation-based methods. This scalable, cost-effective platform provides a transformative framework for high-throughput spatial perturbation studies in complex tissue models.