Optical pooled CRISPR screens have been widely adopted for functional genomic studies. Gu et al. present CRISPRmap, an optical pooled screening approach that integrates sequencing-free in situ barcode readout with cyclic immunofluorescence and RNA detection. The cyclical hybridization readout method improves the specificity and sensitivity of barcode detection through combinatorial hybridization of primer and padlock detection oligonucleotides. CRISPRmap enables readout of cellular barcodes and multimodal phenotyping of perturbed cell states in base-editing screening. When compared to conventional optical pooled screening protocols, CRISPRmap provides an optimized barcode detection method in cell types such as primary fibroblasts, induced pluripotent stem cells and motor neurons, and human embryonic stem cells. CRISPRmap was applied to a breast cancer cell line with ionizing radiation exposure, and yielded insights into DNA damage repair gene variants with treatment-specific optical signatures. CRISPRmap multiplexed phenotypic readout can be expanded for transcriptomic and proteomic detection, offering future opportunities for joint RNA and protein profiling as well as gene functional studies in different cell types and tissues.

Original reference: Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02386-x (2024)

光学混合 CRISPR 筛选已广泛用于功能基因组研究。Gu 等人提出了 CRISPRmap，这是一种光学混合筛选方法，将免测序原位条形码读出与循环免疫荧光和 RNA 检测相结合。循环杂交读出方法通过引物和挂锁检测寡核苷酸的组合杂交提高了条形码检测的特异性和灵敏度。CRISPRmap 能够在碱基编辑筛选中读取细胞条形码和扰动细胞状态的多模式表型。与传统的光学混合筛选方案相比，CRISPRmap 在原代成纤维细胞、诱导多能干细胞和运动神经元以及人胚胎干细胞等细胞类型中提供了一种优化的条形码检测方法。将 CRISPRmap 应用于具有电离辐射暴露的乳腺癌细胞系，并产生了对具有治疗特异性光学特征的 DNA 损伤修复基因变异的见解。CRISPRmap 多重表型读数可以扩展用于转录组学和蛋白质组学检测，为不同细胞类型和组织中的联合 RNA 和蛋白质分析以及基因功能研究提供未来机会。

原始参考：Nat. Biotechnol.https://doi.org/10.1038/s41587-024-02386-x （2024）