RNA profiling of CSF resident macrophages and monocyte-macrophages from leptomeningeal metastasis mice

We investigated the functional effect of dura-derived leptomeningeal matastasis (LM)-associated macrophages (dLAMs) on the cerebrospinal fluid (CSF) niche during LM outgrowth. Using lung cancer leptomeningeal metastasis models of Cx3cr1CreER:mTmG mice with tamoxifen administration, we achieved dLAMs and monocyte-macrophages via fluorescence-activated cell sorting (FACS). Then we performed bulk RNAseq analysis for these two cell populations. At day12 of LLC-LeptoM cell inoculation for LM models in Cx3cr1CreER:mTmG mice, CSF cells were collected and sorted for dLAMs and monocyte-macrophages (mono-MΦs). During FACS, dLAMs were sorted by CD45+CD11b+F4/80+Ly6C-GFP+, and mono-MΦs were sorted by CD45+CD11b+F4/80+GFP- and CD45+CD11b+F4/80lowLy6C+GFP-. We then performed gene expression profiling analysis using data obtained from bulk RNAseq of dLAMs and mono-MΦs.Total 10 samples were analyzed using RNAseq, including three dLAMs samples and three mono-MΦs samples.