Molecular profiling of SV-BR-1-GM, a clinically effective GM-CSF-secreting human breast cancer cell line

The SV-BR-1 cell line was derived from a chest wall lesion of a breast cancer patient. SV-BR-1 cells were stably transfected with CSF2 (encoding GM-CSF), resulting in the SV-BR-1-GM cell line. Following irradiation to prevent cell replication, both SV-BR-1 (Wiseman and Kharazi, The Open Breast Cancer Journal, 2010, 2, 4-11) and SV-BR-1-GM (Wiseman and Kharazi, Breast J. 2006 Sep-Oct;12(5):475-80) cells have been applied as whole-cell therapeutics in clinical trial settings for advanced breast cancer. Molecular profiles of non-irradiated SV-BR-1-GM cells have been established from various manufacturing lots via Illumina HumanHT-12 V4.0 expression beadchip arrays (GPL10558). A key finding from the study is the identification of an immune signature expressed in SV-BR-1-GM cells which includes the MHC class II factors HLA-DMA, HLA-DMB, HLA-DRA, and HLA-DRB3. Since tumor regressions were apparent in clinical trial subjects matching at an HLA-DRB3 allele with SV-BR-1-GM we hypothesize that (partial) HLA matching is needed for maximal tumor-directed clinical responses to occur. Total RNA was extracted via RNeasy Mini kit (Qiagen) from cultured SV-BR-1-GM cells or from cryopreserved SV-BR-1-GM cells obtained directly from cryovials. RNA was amplified as antisense RNA and biotinylated using the Illumina™ TotalPrep™-96 RNA Amplification Kit (Thermo Fisher Scientific). The biotinylated antisense RNA was then hybridized onto HumanHT-12 v4 Expression BeadChip arrays (Illumina, San Diego, CA) and thereafter stained with Cy3-streptavidin. Fluorescent signal intensities were acquired on an iScan array scanner (Illumina). Average signal intensities and detection p-values were calculated using GenomeStudio (Illumina).