Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity

Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic.

SIGNIFICANCE

This work demonstrates that METTL3 inhibition stimulates a cell-intrinsic interferon response through dsRNA formation. This immunomodulatory mechanism is distinct from current immunotherapeutic agents and provides the molecular rationale for combination with anti-PD-1 immune-checkpoint blockade to augment antitumor immunity. This article is featured in Selected Articles from This Issue, p. 2109.

The PARP1 Inhibitor AZD5305 Impairs Ovarian Adenocarcinoma Progression and Visceral Metastases in Patient-derived Xenografts Alone and in Combination with Carboplatin

PARP inhibitors (PARPi) have changed the management of patients with ovarian cancer and their effectiveness has been demonstrated especially in homologous recombination repair–deficient tumors. These first-generation drugs target PARP1, but also PARP2 and other family members potentially responsible for adverse effects that limit their therapeutic potential and restrict their use in combination with chemotherapeutic agents.

We investigated ovarian cancer patient-derived xenografts (OC-PDXs) to assess whether malignant progression could be impaired by a novel inhibitor selective for PARP1 (AZD5305) and to assess the potential of its combination with carboplatin (CPT), the standard-of-care for patients with ovarian cancer.

In BRCA-mutated OC-PDXs, AZD5305 achieved greater tumor regressions and longer duration of response as well as a superior impairment of visceral metastasis and improved survival benefit compared with the first-generation dual PARP1/2 inhibitors.

The combination of AZD5305 plus CPT was more efficacious than single agents. Subcutaneously growing tumors experienced regression that persisted after therapy stopped. Combination efficacy was greater against tumors that did not respond well to platinum, even at a dose at which AZD5305 monotherapy was ineffective. The combination therapy impaired metastatic dissemination and significantly prolonged the lifespan of mice bearing OC-PDXs in their abdomen. This combination benefit was evident even when CPT was used at suboptimal doses, and was superior to full-dose platinum treatment.

These preclinical studies demonstrate that the PARP1-selective inhibitor AZD5305 retains and improves the therapeutic benefit of the first-generation PARPi, providing an opportunity to maximize benefits for this class of anticancer agents.

Design and Preclinical Evaluation of a Novel B7-H4-Directed Antibody-Drug Conjugate, AZD8205, Alone and in Combination with the PARP1-Selective Inhibitor AZD5305

PURPOSE

We evaluated the activity of AZD8205, a B7-H4-directed antibody-drug conjugate (ADC) bearing a novel topoisomerase I inhibitor (TOP1i) payload, alone and in combination with the PARP1-selective inhibitor AZD5305, in preclinical models.

EXPERIMENTAL DESIGN

IHC and deep-learning-based image analysis algorithms were used to assess prevalence and intratumoral heterogeneity of B7-H4 expression in human tumors. Several TOP1i-ADCs, prepared with Val-Ala or Gly-Gly-Phe-Gly peptide linkers, with or without a PEG8 spacer, were compared in biophysical, in vivo efficacy, and rat toxicology studies. AZD8205 mechanism of action and efficacy studies were conducted in human cancer cell line and patient-derived xenograft (PDX) models.

RESULTS

Evaluation of IHC-staining density on a per-cell basis revealed a range of heterogeneous B7-H4 expression across patient tumors. This informed selection of bystander-capable Val-Ala-PEG8-TOP1i payload AZ14170133 and development of AZD8205, which demonstrated improved stability, efficacy, and safety compared with other linker-payload ADCs. In a study of 26 PDX tumors, single administration of 3.5 mg/kg AZD8205 provided a 69% overall response rate, according to modified RECIST criteria, which correlated with homologous recombination repair (HRR) deficiency (HRD) and elevated levels of B7-H4 in HRR-proficient models. Addition of AZD5305 sensitized very low B7-H4-expressing tumors to AZD8205 treatment, independent of HRD status and in models representing clinically relevant mechanisms of PARPi resistance.

CONCLUSIONS

These data provide evidence for the potential utility of AZD8205 for treatment of B7-H4-expressing tumors and support the rationale for an ongoing phase 1 clinical study (NCT05123482). See related commentary by Pommier and Thomas, p. 991.

Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication

N6-methyladenosine (m6A) is an abundant internal RNA modification, influencing transcript fate and function in uninfected and virus-infected cells. Installation of m6A by the nuclear RNA methyltransferase METTL3 occurs cotranscriptionally; however, the genomes of some cytoplasmic RNA viruses are also m6A-modified. How the cellular m6A modification machinery impacts coronavirus replication, which occurs exclusively in the cytoplasm, is unknown. Here we show that replication of SARS-CoV-2, the agent responsible for the COVID-19 pandemic, and a seasonal human β-coronavirus HCoV-OC43, can be suppressed by depletion of METTL3 or cytoplasmic m6A reader proteins YTHDF1 and YTHDF3 and by a highly specific small molecule METTL3 inhibitor. Reduction of infectious titer correlates with decreased synthesis of viral RNAs and the essential nucleocapsid (N) protein. Sites of m6A modification on genomic and subgenomic RNAs of both viruses were mapped by methylated RNA immunoprecipitation sequencing (meRIP-seq). Levels of host factors involved in m6A installation, removal, and recognition were unchanged by HCoV-OC43 infection; however, nuclear localization of METTL3 and cytoplasmic m6A readers YTHDF1 and YTHDF2 increased. This establishes that coronavirus RNAs are m6A-modified and host m6A pathway components control β-coronavirus replication. Moreover, it illustrates the therapeutic potential of targeting the m6A pathway to restrict coronavirus reproduction.

Abstract C056: MIV-818 stimulates an antitumor immune response in vitro and enhances the effects of pembrolizumab

Purpose: Investigation of immune-modulating activity of MIV-818. Background: MIV-818, a phosphoramidate prodrug of troxacitabine was designed to target the active metabolite troxacitabine-triphosphate to the liver while minimizing systemic exposure. MIV-818 is being developed for the treatment of cancer in the liver, and is currently being evaluated in a phase 1/2 study. Preclinical studies have demonstrated that some DNA damaging agents may further enhance antitumor immune responses in addition to direct cytotoxic effects. We therefore investigated whether MIV-818 induces similar immunomodulating effects as single agent or in combination with pembrolizumab. Methods: Immune-mediated tumor cell killing was determined by co-culturing labelled SKOV3 cancer cells with peripheral blood mononuclear cells (PBMC) and quantified over time using the IncuCyte ZOOM system. Effects on inflamed host tumor microenvironments (TMEs) were investigated by cytokine profiling co-cultures of activated PBMCs, primary fibroblasts or endothelial cells and HT29 colon adenocarcinoma cells. Effects on Staphylococcal enterotoxin B (SEB)-stimulated PBMC were determined by quantifying thymidine incorporation, and cytokine expression in supernatants. Results: Co-incubation of SKOV3 and PBM cells with MIV-818 induced a substantially higher level of apoptosis in the cancer cells (74±25%) compared to co-incubation in the absence of MIV-818 (37±23%). MIV-818 inhibited the proliferation of SKOV-3 cells in the absence PBMCs, but with no significant induction of apoptosis (IC50 7.5nM; ≤5% apoptosis). In a more complex model of the immune TME, MIV-818 treatment impacted inflammatory and angiogenesis-related responses in both the stromal and vascular co-culture systems, increasing IFNγ, IL-10, IL-17A, and TNFα in a manner comparable to that of pembrolizumab alone while also inhibiting IL-6. Combining MIV-818 with pembrolizumab further enhanced an immune-stimulatory effect by increasing IL-10, IL-17A and IFNy, while also modulating immune-related (GranB, IL-2, IL-6), and inflammation-related cytokines (VCAM-1, IP-10, TNFα). MIV-818 demonstrated dose-dependent inhibitory effect on proliferation of SEB-stimulated PBMCs. Despite this growth inhibitory effect, it led to a strong, dose-dependent, increase in IL-2 levels as a single agent which was further enhanced in combination with pembrolizumab. Conclusions: MIV-818 exerts favorable immunomodulating effects in vitro by increasing immune cytokine levels and the PBMC-mediated killing of cancer cells. These effects are further enhanced in combination with pembrolizumab and support future combination of MIV-818 with PD-(L)1 inhibitors in patients with HCC and other liver cancers. The effects of MIV-818 on tumor immune activation markers are being assessed the ongoing phase 1/2 clinical trial.

Citation Format: Fredrik G Oberg, Karin Tunblad, Ana Slipicevic, Richard Bethell, Mark R Albertella. MIV-818 stimulates an antitumor immune response in vitro and enhances the effects of pembrolizumab [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C056. doi:10.1158/1535-7163.TARG-19-C056

Abstract 5137: Parallel approaches to the discovery of novel BRD4 inhibitors

Epigenetic signalling is essential for the regulation of gene expression and cellular development, and disruption of these pathways has been identified in a wide range of tumours. The ϵ-N-acetylation of lysine residues (Kac) within histone tails is one of the most abundant epigenetic modifications and bromodomain containing proteins (BRD) represent an important class of reader protein that recognize and bind such residues. BRD4 is a critical mediator of transcription, functioning to recruit the positive transcription elongation factor complex (P-TEFb) and resulting in increased expression of growth-promoting genes. Inhibition of BRD4 has been shown to result in tumour growth inhibition both in vitro and in vivo. In addition, BRD4 has been shown to be a proto-oncogene which is mutated by chromosomal translocations in the rare form of NUT midline carcinoma.

Although the interaction between bromodomains and acetylated histone represents a protein-protein interaction, co-crystal structures have demonstrated that Kac is recognized by a central deep hydrophobic cavity, which represents “an attractive druggable pocket”. We performed a virtual screen based on modelling known BRD4 inhibitors in crystal structures of both BRD4 domain 1 and domain 2. The virtual screen used a combination of substructure, shape, electrostatic and docking methods combining the strengths of each of these approaches to select compounds from commercially available sources. In addition, we screened BRD4 binding domain 1 against an Argenta fragment library using surface plasmon resonance. A number of novel hits were identified from these screening approaches (up to 18µM in potency) and crystal structures obtained for key hits.

We developed a comprehensive screening cascade validated with tool compounds for profiling hits, starting with an in vitro Brd4 AlphaScreen binding assay and comprising a number of cellular pharmacodynamic assays evaluating effects on established biomarkers of BRD4 inhibition. These screening assays included mRNA analyses for c-myc, p21 and bcl2, a c-myc promoter reporter assay and were confirmed by Western analyses. Phenotypic assays based on growth inhibition of multiple myeloma and acute myeloid leukemia cell lines were also established.

Citation Format: David H. Jones, Marcel J. de Groot, Robert Heald, Ebenezer Arhin, Ria Goodwin, Brenda Burton, Jan Kulagowski, David Brown, Steven Irving, Richard Bazin, Deborah Bruce, Rene Devos, Steven Price, Nick Ray, Peter Lockey, John Montana, Mark R. Albertella, Simon R. Green. Parallel approaches to the discovery of novel BRD4 inhibitors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5137. doi:10.1158/1538-7445.AM2014-5137

In vivo activation of the hypoxia-targeted cytotoxin AQ4N in human tumor xenografts

AQ4N (banoxantrone) is a prodrug that, under hypoxic conditions, is enzymatically converted to a cytotoxic DNA-binding agent, AQ4. Incorporation of AQ4N into conventional chemoradiation protocols therefore targets both oxygenated and hypoxic regions of tumors, and potentially will increase the effectiveness of therapy. This current pharmacodynamic and efficacy study was designed to quantify tumor exposure to AQ4 following treatment with AQ4N, and to relate exposure to outcome of treatment. A single dose of 60 mg/kg AQ4N enhanced the response of RT112 (bladder) and Calu-6 (lung) xenografts to treatment with cisplatin and radiation therapy. AQ4N was also given to separate cohorts of tumor-bearing mice 24 hours before tumor excision for subsequent analysis of metabolite levels. AQ4 was detected by high performance liquid chromatography/mass spectrometry in all treated samples of RT112 and Calu-6 tumors at mean concentrations of 0.23 and 1.07 microg/g, respectively. These concentrations are comparable with those shown to be cytotoxic in vitro. AQ4-related nuclear fluorescence was observed in all treated tumors by confocal microscopy, which correlated with the high performance liquid chromatography/mass spectrometry data. The presence of the hypoxic marker Glut-1 was shown by immunohistochemistry in both Calu-6 tumors and RT112 tumors, and colocalization of AQ4 fluorescence and Glut-1 staining strongly suggested that AQ4N was activated in these putatively hypoxic areas. This is the first demonstration that AQ4N will increase the efficacy of chemoradiotherapy in preclinical models; the intratumoral levels of AQ4 found in this study are comparable with tumor AQ4 levels found in a recent phase I clinical study, which suggests that these levels could be potentially therapeutic.

Cancer and the web

The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time. Much of this information is available publicly on the Internet and ranges from general information about different cancers from a patient or clinical viewpoint, through to databases suitable for cancer researchers of all backgrounds, to very specific sites dedicated to individual genes or molecules. A simple search for 'cancer' from a typical Web browser search engine yields more than half a million hits; an even more specific search for 'leukaemia' (>40 000 hits) or 'p53' (>5700 hits) yields far too many hits to allow one to identify particular sites of interest. This review aims to provide a brief guide to some of the resources and databases that can be used as springboards to home in rapidly on information relevant to many fields of cancer research. As such, this article will not focus on a single website but hopes to illustrate some of the ways that postgenomic biology is revolutionizing cancer research. It will cover genomics and proteomics approaches that have been applied to studying global expression patterns in cancers, in addition to providing links ranging from general information about cancer to specific cancer gene mutation databases.

Selective Tumor Targeting by the Hypoxia-Activated Prodrug AQ4N Blocks Tumor Growth and Metastasis in Preclinical Models of Pancreatic Cancer

PURPOSE

The antitumor activities and pharmacokinetics of the hypoxia-activated cytotoxin AQ4N and its metabolites were assessed in several preclinical models of pancreatic cancers.

EXPERIMENTAL DESIGN

The cytotoxic effects of AQ4N prodrug and its bioreduced form, AQ4, were tested against multiple human tumor cell lines using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays. Nude mice bearing s.c. or orthotopically implanted human BxPC-3 or Panc-1 tumor cells were treated with AQ4N. Tumor growth inhibition, time to progression/end point, and liver metastasis were evaluated in treatment versus control groups. Plasma and tumor levels of AQ4N and its metabolites were quantitated by liquid chromatography-tandem mass spectrometry.

RESULTS

In contrast to AQ4N, the bioreduced AQ4 metabolite displayed potent cytotoxicity in many human tumor lines, including those derived from human pancreatic adenocarcinomas. Single-agent administration of AQ4N significantly delayed tumor growth, progression, and survival in a manner comparable with gemcitabine in multiple pancreatic tumor models in vivo. Survival increases were accompanied by a reduction in incidence and spread of liver metastasis. Quantitation of AQ4N and its metabolites in tumor-bearing mice showed that the prodrug is rapidly cleared from the circulation by 24 h and neither of the bioreduced metabolites was detected in plasma. In contrast, AQ4N readily penetrated BxPC-3 tumors and the cytotoxic AQ4 metabolite rapidly accumulated in tumor tissues at high levels in a dose-dependent fashion.

CONCLUSION

AQ4N undergoes rapid and selective conversion into the potent antineoplastic metabolite AQ4 in tumors in vivo and provides proof of principle for the use of hypoxia-activated prodrugs in the treatment against pancreatic cancers.

A role for polymerase eta in the cellular tolerance to cisplatin-induced damage

Mutation of the POLH gene encoding DNA polymerase eta (pol eta) causes the UV-sensitivity syndrome xeroderma pigmentosum-variant (XP-V) which is linked to the ability of pol eta to accurately bypass UV-induced cyclobutane pyrimidine dimers during a process termed translesion synthesis. Pol eta can also bypass other DNA damage adducts in vitro, including cisplatin-induced intrastrand adducts, although the physiological relevance of this is unknown. Here, we show that independent XP-V cell lines are dramatically more sensitive to cisplatin than the same cells complemented with functional pol eta. Similar results were obtained with the chemotherapeutic agents, carboplatin and oxaliplatin, thus revealing a general requirement for pol eta expression in providing tolerance to these platinum-based drugs. The level of sensitization observed was comparable to that of XP-A cells deficient in nucleotide excision repair, a recognized and important mechanism for repair of cisplatin adducts. However, unlike in XP-A cells, the absence of pol eta expression resulted in a reduced ability to overcome cisplatin-induced S phase arrest, suggesting that pol eta is involved in translesion synthesis past these replication-blocking adducts. Subcellular localization studies also highlighted an accumulation of nuclei with pol eta foci that correlated with the formation of monoubiquitinated proliferating cell nuclear antigen following treatment with cisplatin, reminiscent of the response to UV irradiation and further indicating a role for pol eta in dealing with cisplatin-induced damage. Together, these data show that pol eta represents an important determinant of cellular responses to cisplatin, which could have implications for acquired or intrinsic resistance to this key chemotherapeutic agent.

The overexpression of specialized DNA polymerases in cancer

Specialized DNA polymerases are required to bypass DNA damage lesions that would otherwise cause replication arrest and cell death. When operating on non-canonical templates, such as undamaged DNA or on non-cognate lesions, these polymerases exhibit considerably reduced fidelity, resulting in the generation of mutations. Ectopic overexpression of these polymerases can also lead to an increased mutation rate and an enhanced capability of DNA repair, suggesting that they could potentially act as oncogenes if they were overexpressed in cancers. Here, we examine expression patterns of DNA polymerases in matched normal and tumor samples from a diverse range of tissues. As well as investigating the specialized polymerases beta, lambda, iota and kappa, we also investigate the expression of the replicative polymerases alpha, delta and epsilon. The data presented provide evidence for the overexpression of specialized polymerases in tumors, with more than 45% of the 68 tumor samples studied demonstrating greater than two-fold enhanced expression of at least one specialized polymerase. Of particular note, DNA polymerase beta (pol beta) was found to be overexpressed at both the mRNA and protein level in approximately one third of all tumor types studied, with overexpression being particularly frequent in uterus, ovary, prostate and stomach samples. Pols lambda, and iota were also found to be overexpressed to a significant extent in a range of tumor types, albeit less frequently than pol beta. In contrast, pol kappa was rarely found to be overexpressed in tumors but was found to be commonly underexpressed in many samples. Downregulation of pol beta expression by siRNA resulted in an increased sensitivity to the chemotherapeutic agent cisplatin, suggesting a role for this polymerase in providing tolerance to cisplatin-induced damage. These observations suggest that specialised DNA polymerases, and particularly pol beta, could be considered both as caretaker genes altered during tumorigenesis, and as potential drug targets to sensitise tumors to chemotherapy.

Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit (CSNK2B)

A wide range of autoimmune and other diseases are known to be associated with the major histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility antigens in the class I and class II regions, but some appear to be more strongly associated with genes in the central 1100-kb class III region, making it important to characterize this region fully for the presence of novel genes. An approximately 220-kb segment of DNA in the class III region separating the Hsp70 (HSPA1L) and BAT1 (D6S8IE) genes, which was previously known to contain 14 genes, has been analyzed for the presence of additional genes. Genomic DNA fragments spanning the gaps between the known genes were used as probes to isolate cDNAs corresponding to five new genes within this region. Evidence from Northern blot analysis and exon trapping experiments that suggested the presence of at least two more new genes was also obtained. Partial cDNA and complete exonic genomic sequencing of one of the new genes has identified it as the casein kinase II beta subunit (CSNK2B). Two of the other novel genes lie within a region syntenic to that implicated in susceptibility to experimental allergic orchitis in the mouse, an autoimmune disease of the testis, and represent additional candidates for the Orch-1 locus associated with this disease. In addition, characterization of the 13-kb intergenic gap separating the RD (D6545) and G11 (D6S60E) genes has revealed the presence of a gene encoding a 1246-amino-acid polypeptide that shows significant sequence similarity to the yeast anti-viral Ski2p gene product.

Characterization of a novel gene in the human major histocompatibility complex that encodes a potential new member of the I kappa B family of proteins

At least 110 genes are now known to be located in the 4000 kb of DNA encompassing the human major histocompatibility complex (MHC) in the chromosome band 6p21.3. Recent genomic sequence analysis of a 90 kb segment of DNA containing the tumour necrosis factor genes in the class III region of the MHC has predicted the presence of three potential exons mapping between the BAT1 and TNFB genes (12). A near full-length cDNA clone corresponding to a novel gene located between BAT1 and TNFB that contains sequence corresponding to one of these putative exons, has been isolated from a premonocytic leukaemic cell line cDNA library. Characterization of this gene reveals that it spans 13.5 kb of DNA, with the 3' end of the gene lying approximately 12 kb from the 5' end of the TNFB gene. The cDNA hybridizes to a approximately 1.6 kb mRNA in a number of different cell types, including monocytes, T cells, B cells and hepatocytes. The putative polypeptide encoded by this cDNA is 381 amino acids in length, with a non-glycosylated M(r) of 43214. It contains one partial and two full ANK repeats, which bear a marked similarity to those in the I kappa B family of proteins, suggesting that the protein encoded by the novel gene could represent a divergent member of this family.