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Supplementary Table 7 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table 1 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table 3 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table 5 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table 6 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figures 8-12 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 5 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table 4 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 1 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table 2 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 2 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 4 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary References from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 6 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 7 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Figure 3 from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Supplementary Table and Figure Legends from Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244)

Selumetinib (AZD6244, ARRY-142886) is a selective, non–ATP-competitive inhibitor of mitogen-activated protein/extracellular signal–regulated kinase kinase (MEK)-1/2. The range of antitumor activity seen preclinically and in patients highlights the importance of identifying determinants of response to this drug. In large tumor cell panels of diverse lineage, we show that MEK inhibitor response does not have an absolute correlation with mutational or phospho-protein markers of BRAF/MEK, RAS, or phosphoinositide 3-kinase (PI3K) activity. We aimed to enhance predictivity by measuring pathway output through coregulated gene networks displaying differential mRNA expression exclusive to resistant cell subsets and correlated to mutational or dynamic pathway activity. We discovered an 18-gene signature enabling measurement of MEK functional output independent of tumor genotype. Where the MEK pathway is activated but the cells remain resistant to selumetinib, we identified a 13-gene signature that implicates the existence of compensatory signaling from RAS effectors other than PI3K. The ability of these signatures to stratify samples according to functional activation of MEK and/or selumetinib sensitivity was shown in multiple independent melanoma, colon, breast, and lung tumor cell lines and in xenograft models. Furthermore, we were able to measure these signatures in fixed archival melanoma tumor samples using a single RT-qPCR–based test and found intergene correlations and associations with genetic markers of pathway activity to be preserved. These signatures offer useful tools for the study of MEK biology and clinical application of MEK inhibitors, and the novel approaches taken may benefit other targeted therapies. Cancer Res; 70(6); 2264–73

The ‘membrane pacemaker’ hypothesis provides a putative mechanistic linkage between variations in energy metabolism, rates of ageing and lifespan across different species. Within species we have found positive associations between longevity and metabolism, which contrast the inter-specific trends. It is of interest to know therefore how levels of lipid desaturation in membranes are linked to variation in metabolism between individuals within species. We explored this problem by extracting membrane fatty acids from the livers of mice that varied in their metabolic rate, in a strain (MF1) where we have previously demonstrated a positive association between metabolism and lifespan. We measured resting metabolic rate (RMR) in 60 mice, each measured on three occasions, and measured their body compositions using dual energy X-ray absorptiometry (DXA). We selected 28 individuals that exhibited a wide variation in their mean resting metabolic rates (RMR) and extracted membrane lipids from the livers of these mice post mortem and analysed them for the patterns of contribution of different fatty acids. We then sought associations between the levels of membrane desaturation and the individual variability in RMR, using the proportional contributions of each fatty acid as predictors in a stepwise regression or by re-describing the variation in fatty acyl lipids using a PCA analysis and then seeking associations between scores on the derived components and RMR. We used whole animal RMRs and also RMR with the effects of body composition (fat free mass) removed. The level of individual variation in RMR was consistent with our previous observations. There was a significant positive association (p = 0.019) between the proportion of palmitic acid (16:0) in the membranes and RMR, which was strengthened (p = 0.014) when we adjusted RMR for differences in fat free mass. The proportion of palmitic acid (16:0) explained 20.9% of the individual variation in residual RMR. There was no association between RMR or mass adjusted RMR and the proportional representation of any other fatty acid, including 22:6 (DHA) predicted by the membrane pacemaker hypothesis to be of particular significance. High levels of saturated fatty acids in the membranes of mice with high rates of metabolism may contribute to their greater longevity, but the mechanism tying together increased membrane saturation with elevated RMR remains unclear.

Endothelin-1 is overexpressed in several tumor types. Activation of the endothelin-A (ETA) receptor may promote cell growth, angiogenesis and invasion, and inhibits the apoptotic process, while activation of the endothelin-B (ETB) receptor may induce cell death by apoptosis and inhibit tumor progression. Hypermethylation and subsequent silencing of the ETB receptor gene promoter has been reported in some cancer types. As the endothelin pathway is subject to research for pharmacological cancer treatment, we investigated the extent of epigenetic deregulation of the ETB receptor gene in non-small cell lung cancer (NSCLC). We scanned 64 NSCLC paired tumor/normal surgical specimens for the ETB receptor promoter for methylation by developing four pyrosequencing assays that covered 24 CpGs. The ETB receptor promoter was significantly hypermethylated in 31 (48%) of tumor samples, presenting considerably higher methylation in 22/24 CpG sites compared with the normal counterpart tissues. ETB receptor mRNA levels were reduced in all lung tumors compared with normal adjacent lung tissue, indicating the potentially important involvement of this gene in lung cancer development. Furthermore, tumor samples with ETB receptor gene methylation tended to have lower receptor mRNA levels compared with unmethylated tumor specimens, suggesting a primary epigenetic role in ETB receptor silencing. Our results point to a significant involvement of ETB receptor epigenetic deregulation in the pathogenesis of lung cancer making the gene a promising candidate biomarker for response to regimens modulating the endothelin axis.

Endothelin-1 is overexpressed in several tumor types. Activation of the endothelin-A (ETA) receptor may promote cell growth, angiogenesis and invasion, and inhibits the apoptotic process, while activation of the endothelin-B (ETB) receptor may induce cell death by apoptosis and inhibit tumor progression. Hypermethylation and subsequent silencing of the ETB receptor gene promoter has been reported in some cancer types. As the endothelin pathway is subject to research for pharmacological cancer treatment, we investigated the extent of epigenetic deregulation of the ETB receptor gene in non-small cell lung cancer (NSCLC). We scanned 64 NSCLC paired tumor/normal surgical specimens for the ETB receptor promoter for methylation by developing four pyrosequencing assays that covered 24 CpGs. The ETB receptor promoter was significantly hypermethylated in 31 (48%) of tumor samples, presenting considerably higher methylation in 22/24 CpG sites compared with the normal counterpart tissues. ETB receptor mRNA levels were reduced in all lung tumors compared with normal adjacent lung tissue, indicating the potentially important involvement of this gene in lung cancer development. Furthermore, tumor samples with ETB receptor gene methylation tended to have lower receptor mRNA levels compared with unmethylated tumor specimens, suggesting a primary epigenetic role in ETB receptor silencing. Our results point to a significant involvement of ETB receptor epigenetic deregulation in the pathogenesis of lung cancer making the gene a promising candidate biomarker for response to regimens modulating the endothelin axis.