美国麻省理工学院Alex K. Shalek研究组利用混合扰动进行可扩展的压缩表型筛选。这一研究成果于2024年10月7日在线发表在国际学术期刊《自然—生物技术》上。

研究人员表示，利用生化扰动和高内涵读出的高通量表型筛选受到规模限制的约束。

为了解决这一问题，研究人员建立了一种将外源性扰动混合并通过计算去卷积的方法，从而减少所需的样本量、劳动量和成本。通过对生物活性小分子库和高内涵成像读出的基准测试，研究人员证明了压缩实验设计相比传统方法的效率提升。接着，研究人员在两个生物发现项目中应用了压缩筛选。

首先，研究人员利用早期传代的胰腺癌类器官，对肿瘤微环境重组蛋白配体库的转录响应进行绘图，发现了特定配体引发的表型变化。这些变化与经典参考特征不同，并且与临床结果相关。其次，研究人员识别出具有已知作用机制的化合物库对原代人外周血单个核细胞免疫反应的多效性调节作用。

总之，该方法赋能了信息丰富的表型筛选，有助于推进药物发现和基础生物学研究。

附：英文原文

Title: Scalable, compressed phenotypic screening using pooled perturbations

Author: Liu, Nuo, Kattan, Walaa E., Mead, Benjamin E., Kummerlowe, Conner, Cheng, Thomas, Ingabire, Sarah, Cheah, Jaime H., Soule, Christian K., Vrcic, Anita, McIninch, Jane K., Triana, Sergio, Guzman, Manuel, Dao, Tyler T., Peters, Joshua M., Lowder, Kristen E., Crawford, Lorin, Amini, Ava P., Blainey, Paul C., Hahn, William C., Cleary, Brian, Bryson, Bryan, Winter, Peter S., Raghavan, Srivatsan, Shalek, Alex K.

Issue&Volume: 2024-10-07

Abstract: High-throughput phenotypic screens using biochemical perturbations and high-content readouts are constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to reduce required sample size, labor and cost. We demonstrate the increased efficiency of compressed experimental designs compared to conventional approaches through benchmarking with a bioactive small-molecule library and a high-content imaging readout. We then apply compressed screening in two biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to a library of recombinant tumor microenvironment protein ligands, uncovering reproducible phenotypic shifts induced by specific ligands distinct from canonical reference signatures and correlated with clinical outcome. In the second, we identify the pleotropic modulatory effects of a chemical compound library with known mechanisms of action on primary human peripheral blood mononuclear cell immune responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts and basic biological inquiry.

DOI: 10.1038/s41587-024-02403-z

Source: https://www.nature.com/articles/s41587-024-02403-z