PO.BCS01.14 · 生物信息与计算
通过功能模块预测和in4mer enCas12a平台绘制癌症相关的遗传相互作用图谱
Mapping cancer-relevant genetic interactions with functional module prediction and in4mer enCas12a platform
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
遗传相互作用（GI），尤其是合成致死，对功能基因组学和癌症治疗至关重要。在酵母中，系统性的GI图谱绘制已产生了覆盖约90%基因的近乎完整的网络，确立了GI网络架构的核心原则并定义了主要功能模块。然而，由于人类基因组更大、复杂性更高且细胞异质性广泛，将这一成功转化到人类细胞中要困难得多。即使是百万规模的CRISPR Cas9组合筛选也仅采样了可能搜索空间的约0.1%，凸显了对预测模型和更高效的多重扰动技术的需求。为应对这一挑战，我们利用从酵母GI网络中获得的洞见，优先选择预测富集遗传相互作用的人类基因模块。通过这一策略，我们识别出五个基因密集的模块，包括受体酪氨酸激酶（RTK）信号通路和DNA损伤反应（DDR）通路，为系统性GI图谱绘制提供了可操作的搜索空间。使用我们优化的基于CRISPR enCas12a的in4mer平台（可实现紧凑、高保真的多重扰动），我们在这些模块内进行了全对全GI筛选。使用单个88k构建体文库，我们对206个RTK基因、167个DDR基因和4,435个精选旁系同源基因对的所有成对组合，连同阳性和阴性对照，在12个癌细胞系中进行了筛选。一致地，旁系同源基因在各筛选中仍是强遗传相互作用的主要来源，而整合的多细胞系分析揭示了较弱但一致的合成致死和抑制相互作用。值得注意的是，我们在内质网定位的蛋白质糖基化通路中识别出一个密集的GI网络，并在3D类器官和患者来源异种移植中验证了关键相互作用，表明2D GI筛选是更具生理相关性系统中GI依赖性的稳健预测因子。总之，将功能模块优先排序与enCas12a多重筛选相结合，为揭示人类GI图谱中有意义的子集提供了高效策略，并支持在规模上发现具有治疗相关性的脆弱点。
查看英文原文 English abstract
Genetic interaction (GI), particularly synthetic lethality, is essential to functional genomics and cancer therapy. In yeast, systematic GI mapping has produced a near-complete network covering ~90% of genes, establishing core principles of GI network architecture and defining major functional modules. However, translating this success to human cells has been far more challenging due to the larger genome, greater complexity, and extensive cellular heterogeneity. Even the million-scale CRISPR Cas9 combinatorial screens sample only ~0.1% of the possible search space, highlighting the need for predictive models and more efficient multiplex perturbation technologies. To address this challenge, we leveraged insights from the yeast GI network to prioritize human gene modules predicted to be enriched for genetic interactions. Through this strategy, we identified five densely gene modules, including receptor tyrosine kinase (RTK) signaling and the DNA damage response (DDR) pathway, providing a tractable search space for systematic GI mapping. Using our optimized CRISPR enCas12a-based in4mer platform, which enables compact, high-fidelity multiplex perturbations, we performed all-by-all GI screens within these modules. With a single 88k construct library, we performed all pairwise combinations of 206 RTK genes, 167 DDR genes, and 4,435 curated paralog pairs, along with positive and negative controls, across 12 cancer cell lines. Consistently, paralogs remained the dominant source of strong genetic interactions across screens, while integrated multi-line analysis revealed weaker but consistent synthetic lethal and suppressor interactions. Notably, we identified a dense GI network within the ER-localized protein glycosylation pathway and validated key interactions in 3D organoid and patient-derived xenograft, demonstrating that 2D GI screens are robust predictors of GI dependencies in more physiologically relevant systems. In conclusion, combining functional-module prioritization with enCas12a multiplex screening provides an efficient strategy for uncovering meaningful subsets of the human GI landscape and supports discovery of therapeutically relevant vulnerabilities at scale.
利益披露 Disclosure
C. Lin, None..
V. Gheorghe, None..
S. Alibai, None..
S. Kim, None..
Y. Xu, None..
X. Ma, None..
L. L. Wilson, None..
R. Moser, None.