Abstract 2946: Perturb-seq analysis of TNFα-induced transcriptional response

Abstract

Abstract We performed a single-cell Perturb-seq screen on HEK293 cells with a ~100 sgRNA pooled library, aimed at identifying genes involved in TNFα-induced transcriptional response. As a reference, a parallel screen was performed with cells transduced in arrayed format with the same set of sgRNAs as the pooled library. For the pooled library screen, cells were transduced with the pooled sgRNA library, selected and expanded for 10 days, split into 2 samples for 72h TNFα treatment/mock-treatment. After treatment, cells were loaded on the 10X Genomics instrument according to manufacturer’s specifications at 2000, 7500 and 15,000 cells/sample/lane. For the arrayed screen, cells were transduced with individual sgRNAs in arrayed format, selected and expanded for 10 days, split into 2 samples for 72h TNFα treatment/mock treatment. After treatment ~10,000 from each sample were harvested for RNA purification. For both pooled library single-cell and arrayed screens, genome-wide transcriptome analysis was assayed using the DriverMap Targeted RNA-Seq assay. Both screens identified TNFRSF1A and IKBKG as top mediators of TFNα transcriptional response. Citation Format: Donato Tedesco, Alex Chenchik, Tianbing Liu, Dongfang Hu, Nadya Isachenko, Nadia Dolganov. Perturb-seq analysis of TNFα-induced transcriptional response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2946.