Coessentiality mapping has been useful to systematically cluster genes into biological pathways and identify gene functions^1,2,3. Here, using the debiased sparse partial correlation (DSPC) method³, we construct a functional coessentiality map for cellular metabolic processes across human cancer cell lines. This analysis reveals 35 modules associated with known metabolic pathways and further assigns metabolic functions to unknown genes. In particular, we identify C12orf49 as an essential regulator of cholesterol and fatty acid metabolism in mammalian cells. Mechanistically, C12orf49 localizes to the Golgi, binds membrane-bound transcription factor peptidase, site 1 (MBTPS1, site 1 protease) and is necessary for the cleavage of its substrates, including sterol regulatory element binding protein (SREBP) transcription factors. This function depends on the evolutionarily conserved uncharacterized domain (DUF2054) and promotes cell proliferation under cholesterol depletion. Notably, c12orf49 depletion in zebrafish blocks dietary lipid clearance in vivo, mimicking the phenotype of mbtps1 mutants. Finally, in an electronic health record (EHR)-linked DNA biobank, C12orf49 is associated with hyperlipidaemia through phenome analysis. Altogether, our findings reveal a conserved role for C12orf49 in cholesterol and lipid homeostasis and provide a platform to identify unknown components of other metabolic pathways.

^{Coessentiality 映射对于系统地将基因聚类到生物通路和识别基因功能1,2,3}很有用。在这里，我们使用去偏稀疏偏相关 (DSPC) 方法³，构建了跨人类癌细胞系的细胞代谢过程的功能同性图。该分析揭示了与已知代谢途径相关的 35 个模块，并进一步将代谢功能分配给未知基因。特别是，我们确定了C12orf49作为哺乳动物细胞中胆固醇和脂肪酸代谢的重要调节剂。从机制上讲，C12orf49 定位于高尔基体，结合膜结合转录因子肽酶位点 1（MBTPS1，位点 1 蛋白酶）并且是切割其底物所必需的，包括固醇调节元件结合蛋白 (SREBP) 转录因子。该功能取决于进化上保守的未表征结构域 (DUF2054)，并在胆固醇耗尽的情况下促进细胞增殖。值得注意的是，斑马鱼中的c12orf49耗竭会阻碍体内饮食脂质清除，模仿mbtps1突变体的表型。最后，在电子健康记录 (EHR) 关联的 DNA 生物库中，C12orf49通过表型分析与高脂血症有关。总而言之，我们的研究结果揭示了C12orf49在胆固醇和脂质稳态中的保守作用，并提供了一个平台来识别其他代谢途径的未知成分。