Cancer cells adapt their metabolic processes to drive macromolecular biosynthesis for rapid cell growth and proliferation. RNA interference (RNAi)-based loss-of-function screening has proven powerful for the identification of new and interesting
cancer targets, and recent studies have used this technology in vivo to identify novel tumour suppressor genes. Here we developed a method for identifying novel
cancer targets via negative-selection RNAi screening using a human
breast cancer xenograft model at an orthotopic site in the mouse. Using this method, we screened a set of metabolic genes associated with aggressive
breast cancer and stemness to identify those required for in vivo
tumorigenesis. Among the genes identified,
phosphoglycerate dehydrogenase (PHGDH) is in a genomic region of recurrent copy number gain in
breast cancer and PHGDH
protein levels are elevated in 70% of oestrogen receptor (ER)-negative breast
cancers. PHGDH catalyses the first step in the
serine biosynthesis pathway, and
breast cancer cells with high PHGDH expression have increased
serine synthesis flux. Suppression of PHGDH in cell lines with elevated PHGDH expression, but not in those without, causes a strong decrease in cell proliferation and a reduction in
serine synthesis. We find that PHGDH suppression does not affect intracellular
serine levels, but causes a drop in the levels of α-ketoglutarate, another output of the pathway and a
tricarboxylic acid (TCA) cycle intermediate. In cells with high PHGDH expression, the
serine synthesis pathway contributes approximately 50% of the total anaplerotic flux of
glutamine into the TCA cycle. These results reveal that certain breast
cancers are dependent upon increased
serine pathway flux caused by PHGDH overexpression and demonstrate the utility of in vivo negative-selection RNAi screens for finding potential anticancer targets.