Transcriptomic profiling of tumor-infiltrating and lymph node-derived Treg and B cells in Foxp3-Cre-YFP and Foxp3-Cre-YFP Appl2f/f melanoma-bearing Mice

Tregs are a critical target for developing anti-tumor immunotherapy, however, they are also critical for maintaining systemic immune tolerance and homeostasis. It remains a formidable challenge to specifically disable Tregs in the tumor microenvironment without compromising systemic immune tolerance. An ideal target is that barely expressed or dispensable in peripheral Tregs but significantly increased and critical for the immunosuppressive activity of tumor infiltrated Tregs (TIL-Tregs). In an attempt to search for specific targets that mediate TIL-Tregs fitness in the tumor microenvironment, we performed RNA-seq of TIL-Tregs and Tregs from the draining lymph nodes (dLN-Tregs) of mice bearing B16-F0 melanoma. Overall design: For bulk RNA-sequencing, Treg cells or B cells in the tumor infiltrated lymphocytes (TILs) or draining lymph nodes (dLNs) were sorted from Foxp3-Cre or Foxp3-Cre Appl2f/f mice bearing B16-F0 melanoma. RNA was extracted and used for RNA-Sequencing analysis.