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. mRNA profiles of TNBC tumors from mice treated with EGFR-targetd CAR-T therapy or radiotherapy alone and in combination