Chromatin accessibility profiling of freshly isolated mouse lung cancer LLC- and breast cancer 4T1- derived leptomeningeal metastatic cancer cells from different anatomical locations [ATAC-Seq]

Cancer cells metastatic to the leptomeninges encounter a metabolically-challenging extreme microenvironment. To understand adaptations to this space, we subjected leptomeningeal-metastatic (LeptoM) mouse breast and lung cancers isolated from either the leptomeninges or orthotopic primary sites to ATAC- and RNA-sequencing. When inhabiting the leptomeninges, the LeptoM cells demonstrated transcription downstream of retinoid-X-receptors (RXRs). We found evidence of local retinoic acid (RA) generation in both human leptomeningeal metastasis and mouse models in the form of elevated spinal fluid retinol and expression of RA-generating dehydrogenases within the leptomeningeal microenvironment. Stimulating LeptoM cells with 9-cis RA induced expression of transcripts encoding de novo fatty acid synthesis pathway enzymes in vitro. In vivo, whereas knockout of Stra6 did not alter cancer cell leptomeningeal growth, knockout of Rxra/b/g interrupted cancer cell lipid biosynthesis and arrested cancer growth. These observations illustrate a mechanism whereby locally-generated developmental cues metabolically reprogram metastatic cancer cells and suggest novel therapeutic approaches. Overall design: We harvested LLC and 4T1 LeptoM cells from mouse leptomeningeal space, separating the CSF free-floating (floating) and pia mater-attached (adherent), or from orthotopic mouse lung (lung) or mammary fat pad (mfp). All cells were treated with the same enzymatic cocktail and prepared for flow cytometry-based sorting with fluorescent marker. Chromatin accessibilities were profiled by ATAC-sequencing.