Transcriptome analysis of leptomeningeal-metastatic cancer cells and FUS-deficient cancer cells

The prognosis of non-small cell lung cancer (NSCLC) with leptomeningeal metastases (LM) is dismal. The regulators of LM progression remain elusive, thus impeding effective clinical intervention. Here, we performed in vivo genome-wide CRISPR-based screens and discovered that Fused in sarcoma (FUS) ablation promoted LM in both PC9 and A549 cell lines. FUS repressed CD36 expression by directly interacting with and destabilizing PPARA mRNA. CD36 augmented fatty acid uptake and oxidative phosphorylation in NSCLC cells. Matrix metallopeptidase 2 (MMP2) was upregulated through CD36-mediated fatty acid metabolism, which enabled NSCLC cells to disrupt the endothelial barrier. FUS-deficient NSCLC cells increased the expression of neuroendocrine differentiation (NED) related markers, including SRY-box transcription factor 2 (SOX2), microtubule associated protein 2 (MAP2), enolase 2 (NSE) and synaptophysin (SYP), exhibited neurite-like extensions, and expanded robustly in cerebrospinal fluid-supplemented medium through a CD36-dependent manner. Mechanistically, fatty acid uptake increased acetyl-CoA and H3K27ac modifications to promote the expression of NED signature genes and MMP2 in NSCLC cells. Genetic or pharmacological inhibition of CD36, or inhibition of NED signature in NSCLC cells hindered LM and prolonged survival in mice. In patients with NSCLC, FUS downregulation and CD36 or SYP upregulation were associated with aggressive LM progression. Thus, CD36-mediated fatty acid metabolism and NED signature are crucial for LM progression in NSCLC, highlighting CD36 as a potential LM biomarker and a promising therapeutic target for LM treatment.