小柯机器人

美国布罗德研究所Jesse S. Boehm、Aviv Regev等研究人员合作利用Perturb-seq对癌症中的编码变体进行大规模并行表征。2022年1月20日，《自然—生物技术》杂志在线发表了这项成果。

研究人员开发了一种方法，通过汇集的Perturb-seq对单细胞的变异影响进行功能评估。研究人员测量了200个TP53和KRAS变体对超过30万个单一肺癌细胞的RNA谱影响，并利用这些谱将变体归类为表型子集来区分功能获得型、功能丧失型和显性阴性变体，并且研究人员通过与正交检测的比较验证了这一点。

研究人员发现KRAS变异体不仅仅适合于离散的功能类别，而是跨越了功能增益表型的连续体，而且它们的功能影响不能仅仅通过它们在患者群中的频率来预测。这项工作为编码变异体影响表型提供了一种可扩展的、基因诊断的方法，并在多种疾病环境中具有潜在的应用。

据介绍，基因组测序研究已经确定了癌症中数以百万计的体细胞变异，但预测大多数变异的表型影响仍然具有挑战性。区分有影响的变异体的实验方法通常使用表型检测，这些方法报道了大量细胞群中预定义的基因特异性功能影响。

附：英文原文

Title: Massively parallel phenotyping of coding variants in cancer with Perturb-seq

Author: Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir, Fagre, Christian, Lo, April, McSharry, Maria, Giacomelli, Andrew O., Ly, Seav Huong, Rozenblatt-Rosen, Orit, Hahn, William C., Aguirre, Andrew J., Berger, Alice H., Regev, Aviv, Boehm, Jesse S.

Issue&Volume: 2022-01-20

Abstract: Genome sequencing studies have identified millions of somatic variants in cancer, but it remains challenging to predict the phenotypic impact of most. Experimental approaches to distinguish impactful variants often use phenotypic assays that report on predefined gene-specific functional effects in bulk cell populations. Here, we develop an approach to functionally assess variant impact in single cells by pooled Perturb-seq. We measured the impact of 200 TP53 and KRAS variants on RNA profiles in over 300,000 single lung cancer cells, and used the profiles to categorize variants into phenotypic subsets to distinguish gain-of-function, loss-of-function and dominant negative variants, which we validated by comparison with orthogonal assays. We discovered that KRAS variants did not merely fit into discrete functional categories, but spanned a continuum of gain-of-function phenotypes, and that their functional impact could not have been predicted solely by their frequency in patient cohorts. Our work provides a scalable, gene-agnostic method for coding variant impact phenotyping, with potential applications in multiple disease settings. The functional impact of somatic mutations in cancer genes is determined by pooled Perturb-seq.

DOI: 10.1038/s41587-021-01160-7

Source: https://www.nature.com/articles/s41587-021-01160-7

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex