Proximity labeling of Snx14 reveals a functional interaction with delta-9 desaturase SCD1 to maintain ER homeostasis

Fatty acids (FAs) are central cellular metabolites that contribute to lipid synthesis, and can be stored or harvested for metabolic energy. Dysregulation in FA processing and storage causes toxic FA accumulation or altered membrane compositions and contributes to metabolic and neurological disorders. Saturated lipids are particularly detrimental to cells, but how lipid saturation levels are maintained remains poorly understood. Here, we identify the cerebellar ataxia SCAR20-associated protein Snx14, an endoplasmic reticulum (ER)-lipid droplet (LD) tethering protein, as a novel factor required to maintain the lipid saturation balance of cellular membranes. We show that Snx14-deficient cells and SCAR20 disease patient-derived cells are hypersensitive to saturated FA (SFA)-mediated lipotoxic cell death that compromises ER integrity. Using APEX2-based proximity labeling, we reveal the protein composition of Snx14-associated ER-LD contacts and define a functional interaction between Snx14 and Δ-9 FA desaturase SCD1. We show that SCD1 is upregulated in SNX14KO cells, and SNX14KO-associated SFA hypersensitivity can be rescued by ectopic SCD1 overexpression. The hydrophobic PXA domain of Snx14 and its interaction with SCD1 are required for Snx14-mediated SFA protection function. Lipidomic profiling reveals that SNX14KO cells exhibit increased membrane saturation, and mimics the lipid profile of SCD1-inhibited cells. Altogether these mechanistic insights reveal a functional interaction between Snx14 and SCD1 in the ER network to maintain FA homeostasis and membrane saturation, defects in which may underlie the neuropathology of SCAR20.