Figure 6. In silico elucidation of the mechanisms of essentiality for the five genes selectively essential in ccRCC.

A) AGPAT6 is essential only in ccRCC because of loss of gene redundancy. In ccRCC, the repression of AGPAT9, GPAT2, and GPAM in glycerolipid metabolism renders the pathway solely dependent on AGPAT6 to produce essential lipids for biomass. B) GALT is selectively essential because of loss of pathway redundancy in ccRCC. Low or no expression of UGP2 forces the flux through GALT to produce glycogen in ccRCC. C) RRM2B, GCLC and GSS are essential only in ccRCC because of specific metabolic requirements of ccRCC cells that activate the corresponding pathway (flux rates are shown in fmol cell⁻¹ h⁻¹). Top: the measured secretion rate of 3-ureidopropionate in ccRCC cell lines is not matched by the observed uptake rate of its direct precursors, uracil and deoxyuridine. This forces a flux active in the catabolism of UDP (part of the pyrimidine degradation pathway) to compensate for the observed 3-ureidopropionate secretion rate. One of the pathway steps is uniquely catalyzed by RRM2B, given that the other genes associated to this reaction (RRM1 and RRM2) are not expressed in ccRCC. Bottom: ccRCC cell lines secrete glutamate at a high rate and the only flux distribution that fits glutamate secretion in the ccRCC metabolic network requires the cleavage of extracellular glutathione (GSH). Extracellular GSH is in turn derived from de novo GSH intracellular synthesis that is catalyzed by GSS and GCLC. Noteworthy, the reduction of reactive oxygen species like H₂O₂ by GSH is a metabolic function preserved in the predicted flux distribution. For each protein, the red shading represents the fraction of ccRCC samples in which the protein is expressed according to the Human Protein Atlas.