RNA Sequencing-based Transcriptome Profiling of TNBC Tumors from Mice Treated with EGFR-targetd CAR-T Therapy or Radiotherapy Alone and in Combination

We performed RNA-seq experiments on TNBC tumor tissues from mice treated with EGFR targeted CAR-T therapy or radiotherapy alone and in combination. In brief, we established E0771-EGFR TNBC cell line and inoculated the E0771-EGFR cells orthotopically into the 4th inguinal mammary fat pads of C57BL/6 mice. When the average tumor volume reached 100 mm3 on day 14, tumor bearing mice were divided to 4 groups (3 mice per group). Tumor bearing mice were given tail vein injection of 5×106 UT cells (group 1) or CAR-T cells (group 2), or exposed to 10 Gy local irradiation first then followed by tail vein injection of UT cells (group 3) or CAR-T cells (group 4). Tumor tissues were collected on day 21. Tumor tissues collected from group 1 to group 4 were named as T1, T2, T3 and T4. Total RNA from tumor was prepared using the RNeasy Plus Universal Mini Kit (QIAGEN). RNA-Seq libraries were constructed after oligo dT-based mRNA enrichment using a NEBNext mRNA Magnetic Isolation Module (New England Biolabs). The RNA-Seq Library Prep Kit (Illumina) was then used according to the manufacturer’s instructions and the cDNAs were sequenced with the Illumina Hiseq 4000.