Lysosomes have many roles, including degrading macromolecules and signalling to the nucleus¹. Lysosomal dysfunction occurs in various human conditions, such as common neurodegenerative diseases and monogenic lysosomal storage disorders (LSDs)^2,3,4. For most LSDs, the causal genes have been identified but, in some, the function of the implicated gene is unknown, in part because lysosomes occupy a small fraction of the cellular volume so that changes in lysosomal contents are difficult to detect. Here we develop the LysoTag mouse for the tissue-specific isolation of intact lysosomes that are compatible with the multimodal profiling of their contents. We used the LysoTag mouse to study CLN3, a lysosomal transmembrane protein with an unknown function. In children, the loss of CLN3 causes juvenile neuronal ceroid lipofuscinosis (Batten disease), a lethal neurodegenerative LSD. Untargeted metabolite profiling of lysosomes from the brains of mice lacking CLN3 revealed a massive accumulation of glycerophosphodiesters (GPDs)—the end products of glycerophospholipid catabolism. GPDs also accumulate in the lysosomes of CLN3-deficient cultured cells and we show that CLN3 is required for their lysosomal egress. Loss of CLN3 also disrupts glycerophospholipid catabolism in the lysosome. Finally, we found elevated levels of glycerophosphoinositol in the cerebrospinal fluid of patients with Batten disease, suggesting the potential use of glycerophosphoinositol as a disease biomarker. Our results show that CLN3 is required for the lysosomal clearance of GPDs and reveal Batten disease as a neurodegenerative LSD with a defect in glycerophospholipid metabolism.

溶酶体具有多种作用，包括降解大分子和向细胞核发出信号¹。溶酶体功能障碍发生在多种人类病症中，例如常见的神经退行性疾病和单基因溶酶体贮积症 (LSD) ^2,3,4。对于大多数LSD，致病基因已被确定，但在某些LSD中，相关基因的功能尚不清楚，部分原因是溶酶体只占细胞体积的一小部分，因此很难检测到溶酶体含量的变化。在这里，我们开发了 LysoTag 小鼠，用于完整溶酶体的组织特异性分离，与其内容物的多模式分析兼容。我们使用 LysoTag 小鼠来研究 CLN3，一种功能未知的溶酶体跨膜蛋白。在儿童中， CLN3的缺失会导致幼年神经元蜡质脂褐素沉着症（巴顿病），这是一种致命的神经退行性 LSD。对缺乏 CLN3 的小鼠大脑中的溶酶体进行非靶向代谢物分析显示，甘油磷酸二酯 (GPD) 大量积累，这是甘油磷脂分解代谢的最终产物。GPD 也在 CLN3 缺陷培养细胞的溶酶体中积累，我们表明 CLN3 是它们溶酶体出口所必需的。CLN3 的缺失还会扰乱溶酶体中的甘油磷脂分解代谢。最后，我们发现巴顿病患者脑脊液中甘油磷酸肌醇的水平升高，表明甘油磷酸肌醇作为疾病生物标志物的潜在用途。我们的结果表明，CLN3 是 GPD 溶酶体清除所必需的，并揭示 Batten 病是一种具有甘油磷脂代谢缺陷的神经退行性 LSD。