Phospholipase D3 regulates lysosomal morphology, biogenesis, and function in neurons.

Phospholipase D3 (PLD3) is a lysosomal protein in neurons and is linked to an Alzheimers disease (AD) risk through coding variants. Its role in lysosomal abnormalities observed in AD remains unclear. We conducted a comprehensive study integrating transcriptomic, proteomic, and cell biology approaches to investigate PLD3s role in lysosome function in neurons. PLD3 undergoes aberrant ubiquitination in AD brain tissue, leading to altered protein abundance and subcellular location. We assessed the lysosomal proteome in SH-SY5Y cells with PLD3 knockout and found PLD3-/- cells had higher levels of proteins related to lysosomal biogenesis, endocytosis, and calcium signaling. Loss of PLD3 caused an enlargement in neuronal lysosome size, increased endocytic activity and a decline in lysosomal clearance of aggregated human {beta}-amyloid or -synuclein, despite increased expression level and activity of cathepsin B. PLD3-deficiency increase the level and transcriptional activity of transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3), suggesting a role for PLD3 in regulating lysosomal biogenesis. In summary, we found that PLD3 is required to maintain neuronal lysosomal function.