Differential gene expression in either CD3+ lymphocytes or CD11b+ myeloid cells due to Class IIa HDAC inhibitor treatment

The aim of this study was to identify differential gene expression resulting from the inhibition of class IIa HDACs in the CD3+ or CD11b+ cells residing in MMTV-PyMT tumors. Prior to necropsy and collection of tumors from MMTV-PyMT mice, 5 mice were treated with either vehicle (DMSO) or 50 mg/kg TMP195 for 5 days. Tumors from these 5 mice were pooled to generate the single cell suspensions taken to EPCAM depletion and FACS sorting. Cells were sorted from the single cell populations based on viability (7-AAD negative) and the presence/absence of cell-surface antigens assess by flow cytometry (BD FACS Aria II). CD3+ lymphocyte populations were 7-AAD-/CD45+/CD19-/CD3+/CD11b-; and CD11b+ myeloid cells were 7-AAD-/CD45+/CD19-/CD3-/CD11b+. This was repeated 6 times (n=3 vehicle-treatment groups, n=3 TMP195 treatment groups). All samples were immediately processed for RNA extraction, and stored at -80 C until labeling and hybridization to Affymetrix arrays.