br Another possible explanation for
Another possible explanation for associations of drug re-sponse to diverse antitumor agents with expression of OCM genes may involve common mechanisms of gene regula-tion or activation. For example, the role of the E2F family of transcriptional regulators as a possible common mechanism in co-regulation of OCM genes had been discussed previ-ously . The mammalian target of rapamycin, mTOR, is a common regulator of one-carbon metabolism that can in-fluence the expression of OCM genes and of components of the serine synthesis pathway thorough its action on tran-scriptional factors ATF4 (the activating transcription factor 4) and FOXK1, with additional feedback signaling from the OCM cycle affecting mTOR, as the mTORC1 complex is directly regulated by SAM, which is synthesized in the OCM path-way [2,7,20]. Another possible common mechanism could in-volve c-Myc and/or HIF-1, which regulate the components of various metabolic processes including the tricarboxylic MG-132 (TCA) cycle and OCM reactions and enhance cancer cell proliferation [1,17,28,104]. HIF-1 and c-Myc play important roles in regulation of glycolysis, in the control of multiple en-zymes involved in serine biosynthesis and catabolism, and in regulation of other metabolic processes in cancer cells that are connected with OCM reactions [2,28,77]. They promote SHMT2 expression, and c-Myc also regulates SHMT1 expres-sion and enhances expression of nucleotide biosynthesis-related genes [1,2,28]. While both c-Myc and HIF-1 upregu-late expression of certain OCM genes [2,28], expression lev-els of many OCM genes were correlated (Table 3), suggesting their possible concerted co-regulation. This could affect bio-logical processes that may be regulated by or interfere with the action of the targets of the drugs associated with OCM gene expression. A drug blocking the transcription or protein activ-ity of c-Myc and HIF-1 may be able to induce cell death, and cancer cells harboring higher OCM gene expression might be
more sensitive to such agents. For example, in addition to the role of mTOR in regulation of the OCM pathway, there have been multiple reports of c-Myc and HIF-1 activity and pro-tein stability being regulated by the PI3K/AKT/mTOR pathway [105–110]. In support of this hypothesis, SHMT2 expres-sion was weakly (r = 0.333, FDR adjusted p = 1.85 × 10−26) associated with expression of PDK1, the target of the PI3K/AKT/mTOR inhibitor BX-912 (Supplementary Table 4), and sensitivity to that agent was associated with expres-sion of both MTR and TYMS (r = −0.307 and −0.363, re-spectively; Table 1). c-Myc and HIF-1 may also be regulated by other targets of agents associated with OCM gene ex-pression (Table 1). For example, p38 MAPK signaling tar-geted by TAK-715 and VX-702 [25,39,47,58] was reported to be essential for HIF-1 activation . CaMK2 targeted by XMD15-27  induces c-Myc protein stabilization and ac-tivation of HIF-1 [112,113], whereas SIRT1 targeted by EX-
1 could affect folate metabolism levels in cancer cells with increased proliferation, and it may be possible to speculate that such cells may be sensitive to the drugs inhibiting the c-Myc and HIF-1 pathways. However, our analysis revealed only a small number of OCM genes which showed both statis-tically significant and modest correlations (Pearson r > 0.3) with MYC and HIF1A expression (Supplementary Table 4). For HIF1A, they included GART (r = −0.346, FDR adjusted p = 1.10 × 10−28) and NNMT (r = 0.330, p = 5.53 × 10−26). For
MYC, these genes were SHMT2 (r = 0.307, FDR adjusted p = 1.99 × 10−22) and SLC19A1 (r = 0.346, p = 1.08 × 10−28), with GART also showing a significant correlation with r close to 0.3 (r = 0.294, FDR p = 1.37 × 10−20). While c-Myc and HIF-1 protein activity may not be directly associated with the levels of expression of their genes, MYC and HIF1A, however, pos-itive associations of MYC expression with SHMT2 and GART expression may support the hypothesis of possible c-Myc in-volvement in associations between expression of these OCM genes and drug response. In contrast, a significant negative correlation between GART and HIF1A gene expression may indicate that HIF-1-induced transcriptional regulation of GART could be influenced only by post-transcriptional mechanisms, or that factors other than HIF-1 may have a direct positive effect on GART overexpression in tumors.
Among other possible contributors to drug sensitivity, cel-lular response could be affected via separate drug-specific mechanisms associated with OCM gene activity and func-tion, with possible contributions from the serine metabolism pathway and the pentose phosphate pathway, AMP-activated protein kinase activity, mTORC1 function, the effects of the OCM reactions and the methionine cycle on cellular methyla-tion processes, or via other mechanisms [1,8]. As discussed above, the activity of epigenetic factors and of epigenetic modifications and metabolic processes which are targeted by the HDAC inhibitors is directly linked to the OCM cycle [1,77,100]. TYMS and DHFR are among the most overex-pressed genes in tumor cells, and their upregulation, as well as overexpression and amplification of SHMT2 in cancer cells, are important contributors to the growth and survival of cancer cells [20,118]. Further investigation may be needed of how the interplay between the action of individual drugs and OCM