High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes. However, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR interference1 perturbations across the full spectrum of gene regulation, from chromatin remodelling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled more than 300,000 cultured melanoma cells to characterize multimodal phenotypic and gene regulatory responses to perturbations in more than 140 vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent cooperative transcription factor activities across diverse genetic perturbations. We further dissected phenotypic responses to perturbations in Mediator complex components, linking module-specific biochemical properties to convergent transcriptional activations. We identified common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineated how perturbations in functionally unrelated genes reshape cell state. Thus, PerturbFate establishes a versatile platform for identifying key molecular regulators by anchoring multimodal regulatory dynamics to disease-relevant phenotypes.
高通量基因组研究已揭示多种遗传变异与疾病表型之间的关联。然而，阐明功能迥异的基因扰动如何导致趋同的细胞状态仍然具有挑战性。在此，我们提出PerturbFate——一个高通量、高成本效益、基于组合索引的单细胞平台，能够系统性地探究大规模平行CRISPR干扰扰动在全谱系基因调控（从染色质重塑、新生转录到稳态转录组表型）中的作用。利用PerturbFate，我们分析了超过30万个培养的黑色素瘤细胞，以表征对140余个维莫非尼耐药相关基因扰动的多模式表型及基因调控响应。我们发现了跨多种遗传扰动的共享去分化细胞状态，其标志为趋同的合作性转录因子活性。我们进一步解析了对中介体复合物组分扰动的表型响应，将模块特异性生化特性与趋同的转录激活相关联。我们识别出在不同遗传扰动中驱动相似表型结果的共同调控节点，并描绘了功能无关基因的扰动如何重塑细胞状态。因此，PerturbFate建立了一个通用平台，通过将多模式调控动态与疾病相关表型锚定，从而识别关键分子调控因子。
Mapping convergent regulators of melanoma drug resistance by PerturbFate
肿瘤(癌症)患者之家