Lipid metabolic rewiring in cancer: A proteomic insight into new axis of therapeutic vulnerability

Lipid metabolism plays a pivotal role in cancer progression, influencing cellular energy balance, membrane synthesis, and signaling pathways that drive proliferation and survival. Our previous findings state that in neuroblastoma (NB), a lethal pediatric tumor, loss of retinal degeneration protein 3 (RD3) leads to increased lipid droplet accumulation. Importantly, our studies also found out that RD3 loss in NB results in increased tumor aggressiveness and metastasis, consequent poor clinical outcome of patients. However, the molecular mechanisms underlying the metabolic shift and tumor progression in NB remain unclear. Herein, we investigated the mechanism behind the RD3-dependent metabolic reprogramming in NB by assessing the directed proteomics shift. Proteomic profiling was performed using NB patient-derived clones during diagnosis (CHLA-15, CHLA-42) those harbor high RD3, and in their reverse-engineered (RD3 stably knockdown) counterparts. Global proteomics was performed using DIA on an Orbitrap Exploris 480 (Ideaproteomics) applying statistical (log₂ fold change, -log₁₀(Padj) FDR correction) considerations. Functional mapping was performed, and differential expression was realized using Omics Playground V4 (BigOmics analytics). Our findings demonstrate that RD3 knockdown induces a pronounced adipogenic signature in NB. Among the proteins altered, 71 were strongly linked to lipid metabolic pathways, including 47 that were upregulated and 24 that were downregulated. Notably, the upregulation of GPAT1 reflects RD3-dependent control of glycerophospholipid synthesis; increased levels of ACOX1, ECH1 and ACADM indicate RD3-mediated fatty acid beta-oxidation; and elevated GPAT4 and DGAT1 expression supports a role for RD3 in modulating triglyceride biosynthesis. In addition, ESYT1 upregulation highlights RD3 involvement in lipid trafficking. PLIN2 downregulation underscores RD3-dependent regulation of lipid droplet dynamics, while reduced SCP2 and APOE expression points to RD3-associated control of cholesterol transport. Our study for the first time recognized that RD3 deficiency dysregulates lipid metabolic activity. This RD3-dependent metabolic disruption of lipid homeostasis leads to the aggressiveness of NB tumors, resulting in poor patient survival. Therefore, harnessing the mechanism of this unrecognized axis of metabolic reprogramming in NB could lead to promising avenues for novel targeted interventions and improve patient survival. Funding: Kerr Foundation 28-34200; Department of Defense, DoD CA-210339; OCAST-HR19-045; NIH P20GM103639; and supported by P30CA225520, P30GM154635 and R23-03.