Cranioencephalic functional lymphoid units in glioblastoma

We used single cell RNA sequencing to profile the immune cell repertoire of tumor tissue, peripheral blood mononuclear cells (PBMC), bone marrow mononuclear cells (BMMC) from distal bone and cranial (skull) bone from human treatment-naive glioblastoma patients. For comparison, we obtained and analyzed control samples (cranial bone and PBMC) from human non-malignant intracranial disease. Overall design: CD45+ cells were derived by magnetic cell separation from fresh clinical samples (tumor tissue, cranial bone, PBMC, BMMC) and analyzed using the 10x Genomics Chromium Next GEM Single Cell 3´ Reagent Kits v3.1 or the 10x Genomics Chromium Next GEM Single Cell 5´ Reagent Kits v2. A second set of data was derived from CD45+ single cell suspensions that underwent additional magnetic depletion of myeloid cells (CD14 negative flowthrough) and were further analyzed using the 10x Genomics Chromium Next GEM Single Cell 5´ Reagent Kits v2.