Transcriptomic profiling of the cancer-associated fibroblasts (CAFs) on murine MC38 liver metastasis sections by NanoString GeoMX DSP
To study how targeting Glut1 influences the transcriptome of cancer-associated fibroblasts (CAFs), the transcriptome of control CAFs and that of Glut1-deficient CAFs on murine MC38 liver metastasis sections were obtained and compared with the NanoString GeoMx DSP Overall design: Two months old Glut1F/F mice (control mice) and Glut1F/FPRß-CreERT2 mice (conditional Glut1 knockout mice) were received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-CD45 for immune cells, and SYTO 13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+ CD45-) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin- CD45-) within a same ROI were collected for transcriptomic profiling as well. Segments 17-20 were ROIs from Glut1F/FPRß-CreERT2 mice and 21-26 were from Glut1 F/F mice. 20 sequencing data were generated for the CAFs due to dual-indexing primers-based sequencing.