Abstract 1899: Metabolic vulnerability of breast cancer based on shifts in the expression of metabolic enzyme isoforms

Background & Purpose: Isoforms of metabolic enzymes share similar catalytic activities. Most cells express several isoforms that likely represent redundancy and contribute robustness to biochemical processes. The distribution of isoforms varies by tissue and differentiation stage and may be altered during neoplastic transformation. Our hypothesis is iosenzyme expression changes in neoplastic cells, particularly the loss of isoenzyme diversity, can render cancer cells more vulnerable to metabolism targeted therapies. Our goal was to identify isoenzyme expression shifts in breast cancer compared to normal breast tissue to define metabolic processes in the cancer that rely on the expression of only one or a few enzyme isoforms due to loss of isoenzyme diversity. Methods: Metabolic enzymes (n=1,267) were identified in the KEGG database and we established pair-wise isoform expression distributions in breast cancer gene expression data sets (n=1,081 cancers) and in 40 normal breast samples. We looked for isoenzyme pairs that showed loss of expression in one isoform in cancer compared to normal while the other isoform was preserved or overexpressed. We assessed the isoform expression relationships in breast cancer cell lines (n=18) to identify experimental models for functional studies and used siRNAs to knock down the preserved isoform in cell lines that showed loss of the other isoform. Results: We identified 98 pairs of isoenzymes that showed reduced expression in one isoform in at least 20% of cancer patients compared to normal tissue (< 3 standard deviations below the mean of normal expression, the lower boundary of the same gene in normal tissues), while the expression of the second, larger than its lower boundary in normal tissues. These included PAPP2B/PAPP2C, COX7A1/COX7A2, ALDOC/ALDOA, LDHB/LDHA, and ME3/ME2 where the first member of the pair showed reduced expression in 83.7%, 48.2%, 33.0%, 49.4%, and 46.9% of cancers, respectively. Overall cancers shifted towards expressing isoforms that are normally high in muscle for many energy metabolism related enzymes. We tested the functional implication of knocking down ME2 (malic enzyme 2) expression in MDA435 cells that showed reduced ME3 expression but high ME2 levels. We observed a 54.0%, growth inhibition compared to scrambled siRNA control. In the control cell lines, MDA231 and MDA 468 that have preserved ME3 and ME2 expression, ME2 knockdown had no significant growth inhibitory effect. Conclusions: We d