Recent observations on cancer cell metabolism indicate increased serine synthesis from glucose as a marker of poor prognosis. We have predicted that a fraction of the synthesized serine is routed to a pathway for ATP production. The pathway is composed by reactions from serine synthesis, one-carbon (folate) metabolism and the glycine cleavage system (SOG pathway). Here we show that the SOG pathway is upregulated at the level of gene expression in a subset of human tumors and that its level of expression correlates with gene signatures of cell proliferation and Myc target activation. We have also estimated the SOG pathway metabolic flux in the NCI60 tumor-derived cell lines, using previously reported exchange fluxes and a personalized model of cell metabolism. We find that the estimated rates of reactions in the SOG pathway are highly correlated with the proliferation rates of these cell lines. We also observe that the SOG pathway contributes significantly to the energy requirements of biosynthesis, to the NADPH requirement for fatty acid synthesis and to the synthesis of purines. Finally, when the PC-3 prostate cancer cell line is treated with the antifolate methotrexate, we observe a decrease in the ATP levels, AMP kinase activation and a decrease in ribonucleotides and fatty acids synthesized from [1,2-13C2]-D-glucose as the single tracer. Taken together our results indicate that the SOG pathway activity increases with the rate of cell proliferation and it contributes to the biosynthetic requirements of purines, ATP and NADPH of cancer cells.

BackgroundAlthough cells require nutrients to proliferate, most nutrient exchange rates of the NCI60 panel of cancer cell lines correlate poorly with their proliferation rate. Here, we provide evidence indicating that this inconsistency is rooted in the variability of cell size.ResultsWe integrate previously reported data characterizing genome copy number variations, gene expression, protein expression and exchange fluxes with our own measurements of cell size and protein content in the NCI60 panel of cell lines. We show that protein content, DNA content, and protein synthesis per cell are proportional to the cell volume, and that larger cells proliferate slower than smaller cells. We estimate the metabolic fluxes of these cell lines and show that their magnitudes are proportional to their protein synthesis rate and, after correcting for cell volume, to their proliferation rate. At the level of gene expression, we observe that genes expressed at higher levels in smaller cells are enriched for genes involved in cell cycle, while genes expressed at higher levels in large cells are enriched for genes expressed in mesenchymal cells. The latter finding is further corroborated by the induction of those same genes following treatment with TGFβ, and the high vimentin but low E-cadherin protein levels in the larger cells. We also find that aromatase inhibitors, statins and mTOR inhibitors preferentially inhibit the in vitro growth of cancer cells with high protein synthesis rates per cell.ConclusionsThe NCI60 cell lines display various metabolic activities, and the type of metabolic activity that they possess correlates with their cell volume and protein content. In addition to cell proliferation, cell volume and/or biomarkers of protein synthesis may predict response to drugs targeting cancer metabolism.

Fusions involving the oncogenic gene RET have been observed in thyroid and lung cancers. Here we report RET gene alterations, including amplification, missense mutations, known fusions, novel fusions, and rearrangements in breast cancer. Their frequency, oncogenic potential, and actionability in breast cancer are described. Two out of eight RET fusions (NCOA4-RET and a novel RASGEF1A-RET fusion) and RET amplification were functionally characterized and shown to activate RET kinase and drive signaling through MAPK and PI3K pathways. These fusions and RET amplification can induce transformation of non-tumorigenic cells, support xenograft tumor formation, and render sensitivity to RET inhibition. An index case of metastatic breast cancer progressing on HER2-targeted therapy was found to have the NCOA4-RET fusion. Subsequent treatment with the RET inhibitor cabozantinib led to a rapid clinical and radiographic response. RET alterations, identified by genomic profiling, are promising therapeutic targets and are present in a subset of breast cancers.

A coding region polymorphism exists in the TP53 gene (Pro47Ser; rs1800371) in individuals of African descent, which reduces p53 tumor suppressor function in a mouse model. It has been unclear whether this functionally significant polymorphism alters cancer risk in humans. This analysis included 6907 women with breast cancer and 7644 controls from the AMBER, ROOT, and AABC consortia. We used multivariable logistic regression to estimate associations between the TP53 Pro47Ser allele and overall breast cancer risk. Because polymorphisms in TP53 tend to be associated with cancer risk in pre-menopausal women, we also limited our analyses to this population in the AMBER and ROOT consortia, where menopausal status was known, and conducted a fixed effects meta-analysis. In an analysis of all women in the AMBER, ROOT, and AABC consortia, we found no evidence for association of the Pro47Ser variant with breast cancer risk. However, when we restricted our analysis to only pre-menopausal women from the AMBER and ROOT consortia, there was a per allele odds ratio of 1.72 (95% confidence interval 1.08–2.76; p-value = 0.023). Although the Pro47Ser variant was not associated with overall breast cancer risk, it may increase risk among pre-menopausal women of African ancestry. Following up on more studies in human populations may better elucidate the role of this variant in breast cancer etiology. However, because of the low frequency of the polymorphism in women of African ancestry, its impact at a population level may be minimal.

360385 Background: RELATIVITY-047, a global, randomized, double-blind, phase II/III study, met its primary endpoint of progression-free survival (PFS). Relatlimab and nivolumab (RELA + NIVO) as a fixed-dose combination (FDC) demonstrated a significant PFS benefit (median PFS was 10.1 months [mo]; 95% CI, 6.4–15.7) with RELA + NIVO vs. 4.6 mo (95% CI, 3.4–5.6) with NIVO; hazard ratio (HR) 0.75 (95% CI, 0.6–0.9; p = .0055), with a manageable safety profile, compared to NIVO alone in patients with previously untreated metastatic or unresectable melanoma (Lipson EJ et al. J Clin Oncol 2021;39[15_suppl]:9503P). Here we report updated PFS and the first disclosure of secondary endpoints, overall survival (OS), and overall response rate (ORR). Methods: Patients were randomized 1:1 to receive RELA 160 mg + NIVO 480 mg FDC or NIVO 480 mg alone, given intravenously every 4 weeks, as previously described (Lipson EJ et al. J Clin Oncol 2021;39[15_suppl]:9503P). The primary endpoint of PFS per RECIST v1.1 was assessed by blinded independent central review (BICR). Secondary endpoints were OS and ORR by BICR, to be tested hierarchically. The OS boundary for statistical significance was p < .04302 (2-sided) based on 69% power for a target HR of 0.75. Results: Patients (714 patients) were randomly selected to receive RELA + NIVO (355 patients) or NIVO (359 patients). Median follow-up was 19.3 mo. Updated median PFS was 10.2 mo (95% CI, 6.5–14.8) with RELA + NIVO vs. 4.6 mo (95% CI, 3.5–6.4) with NIVO (HR 0.78; 95% CI, 0.6–0.9). Median OS was not reached (NR; 95% CI, 34.2–NR) with RELA + NIVO vs. 34.1 mo (95% CI. 25.2–NR) with NIVO (HR 0.80; 95% CI, 0.6–1.0; p = .0593). OS rates at 12 mo were 77.0% (95% CI, 72.2–81.1) vs. 71.6% (95% CI, 66.6–76.0) and at 24 mo were 63.7% (95% CI, 58.1–68.7) vs. 58.3% (95% CI, 52.7–63.4) with RELA + NIVO vs. NIVO, respectively. Subsequent systemic therapy rates and types were generally similar between treatment groups. Confirmed ORR per BICR was 43.1% (95% CI, 37.9–48.4) with RELA + NIVO vs. 32.6% (95% CI, 27.8–37.7) with NIVO. Complete responses were observed in 16.3% of patients on RELA + NIVO vs. 14.2% on NIVO. Grade 3/4 treatment-related adverse events (TRAEs) were observed in 75 (21.1%) patients on RELA + NIVO and 40 (11.1%) on NIVO. There were four treatment-related deaths in the RELA + NIVO group and two in the NIVO group. TRAEs (any grade) leading to treatment discontinuation were observed in 54 (15.2%) patients on RELA + NIVO and 26 (7.2%) on NIVO. Conclusions: RELA + NIVO continued to demonstrate a PFS benefit vs. NIVO alone in patients with previously untreated metastatic or unresectable melanoma, consistent with the primary analysis. RELA + NIVO demonstrated a 20% reduction in risk of death and numerically improved OS rates vs. NIVO, although statistical significance was not reached for this secondary endpoint. ORR was higher with RELA + NIVO vs. NIVO. The safety profile of RELA + NIVO remained manageable with no new or unexpected safety signals. Clinical trial information: NCT03470922.