近日，美国基因泰克公司Eric Lubeck等研究人员合作使用PerturbView在原代细胞和组织中进行多重、基于图像的汇合筛选。该项研究成果于2024年10月7日在线发表在《自然—生物技术》杂志上。

研究人员开发了PerturbView，这是一种光学汇合筛选（OPS）技术，利用体外转录在原位测序之前扩增条形码，从而使在多种系统中进行高度多重表型读取的筛选成为可能，包括原代细胞和组织。

研究人员在诱导多能干细胞来源的神经元、原代免疫细胞和动物模型的肿瘤组织切片中演示了PerturbView。在对原代骨髓来源的巨噬细胞进行免疫信号通路的筛选中，PerturbView发现了已知和新型的NF-κB信号调控因子。

此外，研究人员将PerturbView与来自小鼠异种移植模型的组织切片中的空间转录组学相结合，为原位筛选提供了丰富的光学和转录组表型。PerturbView扩大了OPS在广泛模型和应用中的适用范围。

据悉，OPS是一种可扩展的方法，用于将基于图像的表型与细胞干扰联系起来。然而，由于与干扰条形码的原位测序相关的限制，该方法迄今为止仅限于相对低通量的癌细胞系表型读取。

附：英文原文

Title: Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

Author: Kudo, Takamasa, Meireles, Ana M., Moncada, Reuben, Chen, Yushu, Wu, Ping, Gould, Joshua, Hu, Xiaoyu, Kornfeld, Opher, Jesudason, Rajiv, Foo, Conrad, Hckendorf, Burkhard, Corrada Bravo, Hector, Town, Jason P., Wei, Runmin, Rios, Antonio, Chandrasekar, Vineethkrishna, Heinlein, Melanie, Chuong, Amy S., Cai, Shuangyi, Lu, Cherry Sakura, Coelho, Paula, Mis, Monika, Celen, Cemre, Kljavin, Noelyn, Jiang, Jian, Richmond, David, Thakore, Pratiksha, Benito-Gutirrez, Elia, Geiger-Schuller, Kathryn, Hleap, Jose Sergio, Kayagaki, Nobuhiko, de Sousa e Melo, Felipe, McGinnis, Lisa, Li, Bo, Singh, Avtar, Garraway, Levi, Rozenblatt-Rosen, Orit, Regev, Aviv, Lubeck, Eric

Issue&Volume: 2024-10-07

Abstract: Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture due to limitations associated with in situ sequencing of perturbation barcodes. Here, we develop PerturbView, an OPS technology that leverages in vitro transcription to amplify barcodes before in situ sequencing, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF-κB signaling. Furthermore, we combine PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in situ screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.

DOI: 10.1038/s41587-024-02391-0

Source: https://www.nature.com/articles/s41587-024-02391-0