In situ tumor arrays reveal early environmental control of cancer immunity [Whole Exome Sequencing]

We use a laser to implant tumor cells in a regular pattern on the ears of the animal. When GFP expressing tumor cells are implanted in a CD4-Cre Tdtomato mouse we can perform live imaging of red T Cells trafficking in and out of each micro-tumor of the array. Thanks to live imaging we were able to classified each of the implanted tumors as: 1-Rejected tumors (no GFP+ tumor cells anymore but lots of immune cells), 2- Inflamed tumors (GFP+ tumors infiltrated with lots of immune cells), 3-Excluded Tumors (GFP+ tumors with immune cells segregated around the tumor area) or Desert tumors (GFP+ tumor cells without any immune cells). As these tumors are implanted just under the epidermis, we were able to biopsy them out and pool them by categories (Rejected, Inflamed, Excluded and Desert). We froze down biopsies of pooled tumors for each category (Rejected, Inflamed, Excluded and Desert) and extracted DNA. We wish to characterize these 4 kinds of tumors (DNA seq) to evaluate how much tumors grown in the same animals from a clonal KPP tumor cell line differ from each other in terms of mutation load. Whole Exome Sequencing