Early Clinical Success of MTA-Cooperative PRMT5 Inhibitors for the Treatment of CDKN2A/MTAP-Deleted Cancers

SUMMARY

CDKN2A encodes the tumor suppressors p16 and p14ARF and is the most common homozygously deleted gene in all human cancers; tumors frequently codelete the nearby gene MTAP, creating a dependency on PRMT5. In this issue of Cancer Discovery, Engstrom and colleagues report an MTA-cooperative PRMT5 methyltransferase inhibitor MRTX1719 that selectively kills CDKN2A/MTAP-codeleted cancers and demonstrates early efficacy in clinical trials for solid tumors harboring the CDKN2A/MTAP codeletion. See related article by Engstrom et al., p. 2412 (1).

Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction

PRMT5 and its substrate adaptor proteins (SAPs), pICln and Riok1, are synthetic lethal dependencies in MTAP-deleted cancer cells. SAPs share a conserved PRMT5 binding motif (PBM) which mediates binding to a surface of PRMT5 distal to the catalytic site. This interaction is required for methylation of several PRMT5 substrates, including histone and spliceosome complexes. We screened for small molecule inhibitors of the PRMT5-PBM interaction and validated a compound series which binds to the PRMT5-PBM interface and directly inhibits binding of SAPs. Mode of action studies revealed the formation of a covalent bond between a halogenated pyridazinone group and cysteine 278 of PRMT5. Optimization of the starting hit produced a lead compound, BRD0639, which engages the target in cells, disrupts PRMT5-RIOK1 complexes, and reduces substrate methylation. BRD0639 is a first-in-class PBM-competitive inhibitor that can support studies of PBM-dependent PRMT5 activities and the development of novel PRMT5 inhibitors that selectively target these functions.

Molecular basis for substrate recruitment to the PRMT5 methylosome

PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.

A conditional mouse expressing an activating mutation in NRF2 displays hyperplasia of the upper gastrointestinal tract and decreased white adipose tissue

Activation of the nuclear factor (erythroid-derived 2)-like 2 (NFE2L2 or NRF2) transcription factor is a critical and evolutionarily conserved cellular response to oxidative stress, metabolic stress, and xenobiotic insult. Deficiency of NRF2 results in hypersensitivity to a variety of stressors, whereas its aberrant activation contributes to several cancer types, most commonly squamous cell carcinomas of the esophagus, oral cavity, bladder, and lung. Between 10% and 35% of patients with squamous cell carcinomas display hyperactive NRF2 signaling, harboring activating mutations and copy number amplifications of the NFE2L2 oncogene or inactivating mutations or deletions of KEAP1 or CUL3, the proteins of which co-complex to ubiquitylate and degrade NRF2 protein. To better understand the role of NRF2 in tumorigenesis and more broadly in development, we engineered the endogenous Nfe2l2 genomic locus to create a conditional mutant LSL-Nrf2^E79Q mouse model. The E79Q mutation, one of the most commonly observed NRF2-activating mutations in human squamous cancers, codes for a mutant protein that does not undergo KEAP1/CUL3-dependent degradation, resulting in its constitutive activity. Expression of NRF2 E79Q protein in keratin 14 (KRT14)-positive murine tissues resulted in hyperplasia of squamous cell tissues of the tongue, forestomach, and esophagus, a stunted body axis, decreased weight, and decreased visceral adipose depots. RNA-seq profiling and follow-up validation studies of cultured NRF2^E79Q murine esophageal epithelial cells revealed known and novel NRF2-regulated transcriptional programs, including genes associated with squamous cell carcinoma (e.g. Myc), lipid and cellular metabolism (Hk2, Ppard), and growth factors (Areg, Bmp6, Vegfa). These data suggest that in addition to decreasing adipogenesis, KRT14-restricted NRF2 activation drives hyperplasia of the esophagus, forestomach, and tongue, but not formation of squamous cell carcinoma. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Health co-benefits and mitigation costs as per the Paris Agreement under different technological pathways for energy supply

This study assesses the reductions in air pollution emissions and subsequent beneficial health effects from different global mitigation pathways consistent with the 2 °C stabilization objective of the Paris Agreement. We use an integrated modelling framework, demonstrating the need for models with an appropriate level of technology detail for an accurate co-benefit assessment. The framework combines an integrated assessment model (GCAM) with an air quality model (TM5-FASST) to obtain estimates of premature mortality and then assesses their economic cost. The results show that significant co-benefits can be found for a range of technological options, such as introducing a limitation on bioenergy, carbon capture and storage (CCS) or nuclear power. Cumulative premature mortality may be reduced by 17-23% by 2020-2050 compared to the baseline, depending on the scenarios. However, the ratio of health co-benefits to mitigation costs varies substantially, ranging from 1.45 when a bioenergy limitation is set to 2.19 when all technologies are available. As for regional disaggregation, some regions, such as India and China, obtain far greater co-benefits than others.

Mercury Benefits of Climate Policy in China: Addressing the Paris Agreement and the Minamata Convention Simultaneously

National commitments under the Paris Agreement on climate change interact with other global environmental objectives, such as those of the Minamata Convention on Mercury. We assess how mercury emissions and deposition reductions from national climate policy in China under the Paris Agreement could contribute to the country's commitments under the Minamata Convention. We examine emissions under climate policy scenarios developed using a computable general equilibrium model of China's economy, end-of-pipe control scenarios that meet China's commitments under the Minamata Convention, and these policies in combination, and evaluate deposition using a global atmospheric transport model. We find climate policy in China can provide mercury benefits when implemented with Minamata policy, achieving in the year 2030 approximately 5% additional reduction in mercury emissions and deposition in China when climate policy achieves a 5% reduction per year in carbon intensity (CO₂ emissions 9.7 Gt in 2030). This corresponds to 63 Mg additional mercury emissions reductions in 2030 when implemented with Minamata Convention policy, compared to Minamata policy implemented alone. Climate policy provides emissions reductions in sectors not considered under the Minamata Convention, such as residential combustion. This changes the combination of sectors that contribute to emissions reductions.

Identification and Characterization of MCM3 as a Kelch-like ECH-associated Protein 1 (KEAP1) Substrate

KEAP1 is a substrate adaptor protein for a CUL3-based E3 ubiquitin ligase. Ubiquitylation and degradation of the antioxidant transcription factor NRF2 is considered the primary function of KEAP1; however, few other KEAP1 substrates have been identified. Because KEAP1 is altered in a number of human pathologies and has been proposed as a potential therapeutic target therein, we sought to better understand KEAP1 through systematic identification of its substrates. Toward this goal, we combined parallel affinity capture proteomics and candidate-based approaches. Substrate-trapping proteomics yielded NRF2 and the related transcription factor NRF1 as KEAP1 substrates. Our targeted investigation of KEAP1-interacting proteins revealed MCM3, an essential subunit of the replicative DNA helicase, as a new substrate. We show that MCM3 is ubiquitylated by the KEAP1-CUL3-RBX1 complex in cells and in vitro Using ubiquitin remnant profiling, we identify the sites of KEAP1-dependent ubiquitylation in MCM3, and these sites are on predicted exposed surfaces of the MCM2-7 complex. Unexpectedly, we determined that KEAP1 does not regulate total MCM3 protein stability or subcellular localization. Our analysis of a KEAP1 targeting motif in MCM3 suggests that MCM3 is a point of direct contact between KEAP1 and the MCM hexamer. Moreover, KEAP1 associates with chromatin in a cell cycle-dependent fashion with kinetics similar to the MCM2-7 complex. KEAP1 is thus poised to affect MCM2-7 dynamics or function rather than MCM3 abundance. Together, these data establish new functions for KEAP1 within the nucleus and identify MCM3 as a novel substrate of the KEAP1-CUL3-RBX1 E3 ligase.

Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display

In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1-NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1-NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions.

Abstract LB-081: Elucidating the function of MCM3 ubiquitination by KEAP1: crosstalk between redox-sensing and cell cycle progression

While the KEAP1-NRF2 axis is essential for maintaining redox homeostasis, whether KEAP1 has alternative functions and how this pathway crosstalks with other important cellular processes remains unknown. KEAP1 targets the NRF2 transcription factor for proteasomal degradation in a redox-sensitive manner. Thus, this pathway serves as the cell's primary response to elevated reactive oxygen species. Importantly, KEAP1-NRF2 are frequently mutated in cancer, most strikingly in non-small cell lung cancer, where KEAP1 or NRF2 are mutated in 20-30% of patient tumors.

Though regulation of NRF2 has long been considered the only physiologically important role for the E3 ligase KEAP1, we have determined that KEAP1 binds the master cell cycle regulator, MCM3, a subunit of the hexameric DNA replication licensing complex, MCM2-7. Excitingly, our ubiquitination assay data establish MCM3 as a new substrate for KEAP1; however, KEAP1 intriguingly does not regulate total cellular levels of MCM3. Consistent with this, we determined that only a small pool of cellular MCM3 is bound to KEAP1, suggesting that KEAP1 may bind and ubiquitinate a highly specified pool of MCM3. To determine the function of KEAP1-dependent ubiquitination of MCM3, we recently applied a new proteomics technique to map the ubiquitinated residues within MCM3 and identify these lysines within the larger MCM2-7 helicase. This mapping and protein modeling has provided new insight into the structure-function relationship of ubiquitinated MCM3.

As MCM2-7 chromatin loading is a highly coordinated, cell cycle-dependent process, we tested whether KEAP1 loaded concurrently onto chromatin. Strikingly, we found that KEAP1 indeed loads onto chromatin during G1 and unloads in late S phase in a similar fashion as the MCM complex, further suggesting KEAP1 regulates the function of this essential cell cycle regulator on chromatin. Given the role of MCM3 in cell cycle progression, we tested whether KEAP1 was required for normal G1 to S phase progression and saw that loss of KEAP1 retards S phase DNA synthesis, which is an MCM-dependent process. Intriguingly, primary, untransformed KEAP1 knockout fibroblasts show decreased growth and aberrant cell cycle patterns consistent with a defect in the G1 to S transition. Overall, these data suggest a novel function for KEAP1 in regulating the MCM complex and cell cycle progression. We postulate that KEAP1 promotes cell cycle progression in a redox-sensitive manner through its association with MCM3 and that this presents a novel mechanism by which cells may halt cell cycle to protect DNA from damage by reactive oxygen species.

Citation Format: Kathleen M. Mulvaney, Jacob Matson, Feng Yan, Dennis Goldfarb, Jeannette Cook, Michael Benjamin Major. Elucidating the function of MCM3 ubiquitination by KEAP1: crosstalk between redox-sensing and cell cycle progression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-081. doi:10.1158/1538-7445.AM2015-LB-081

Proteomic analysis of ubiquitin ligase KEAP1 reveals associated proteins that inhibit NRF2 ubiquitination

Somatic mutations in the KEAP1 ubiquitin ligase or its substrate NRF2 (NFE2L2) commonly occur in human cancer, resulting in constitutive NRF2-mediated transcription of cytoprotective genes. However, many tumors display high NRF2 activity in the absence of mutation, supporting the hypothesis that alternative mechanisms of pathway activation exist. Previously, we and others discovered that via a competitive binding mechanism, the proteins WTX (AMER1), PALB2, and SQSTM1 bind KEAP1 to activate NRF2. Proteomic analysis of the KEAP1 protein interaction network revealed a significant enrichment of associated proteins containing an ETGE amino acid motif, which matches the KEAP1 interaction motif found in NRF2. Like WTX, PALB2, and SQSTM1, we found that the dipeptidyl peptidase 3 (DPP3) protein binds KEAP1 via an "ETGE" motif to displace NRF2, thus inhibiting NRF2 ubiquitination and driving NRF2-dependent transcription. Comparing the spectrum of KEAP1-interacting proteins with the genomic profile of 178 squamous cell lung carcinomas characterized by The Cancer Genome Atlas revealed amplification and mRNA overexpression of the DPP3 gene in tumors with high NRF2 activity but lacking NRF2 stabilizing mutations. We further show that tumor-derived mutations in KEAP1 are hypomorphic with respect to NRF2 inhibition and that DPP3 overexpression in the presence of these mutants further promotes NRF2 activation. Collectively, our findings further support the competition model of NRF2 activation and suggest that "ETGE"-containing proteins such as DPP3 contribute to NRF2 activity in cancer.