Driver Mutations Dictate the Immunologic Landscape and Response to Checkpoint Immunotherapy of Glioblastoma

The composition of the tumor immune microenvironment (TIME) is considered a key determinant of patients' response to immunotherapy. The mechanisms underlying TIME formation and development over time are poorly understood. Glioblastoma (GBM) is a lethal primary brain cancer for which there are no curative treatments. GBMs are immunologically heterogeneous and impervious to checkpoint blockade immunotherapies. Utilizing clinically relevant genetic mouse models of GBM, we identified distinct immune landscapes associated with expression of EGFR wild-type and mutant EGFRvIII cancer driver mutations. Over time, accumulation of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) was more pronounced in EGFRvIII-driven GBMs and was correlated with resistance to PD-1 and CTLA-4 combination checkpoint blockade immunotherapy. We determined that GBM-secreted CXCL1/2/3 and PMN-MDSC-expressed CXCR2 formed an axis regulating output of PMN-MDSCs from the bone marrow leading to systemic increase in these cells in the spleen and GBM tumor-draining lymph nodes. Pharmacologic targeting of this axis induced a systemic decrease in the numbers of PMN-MDSC, facilitated responses to PD-1 and CTLA-4 combination checkpoint blocking immunotherapy, and prolonged survival in mice bearing EGFRvIII-driven GBM. Our results uncover a relationship between cancer driver mutations, TIME composition, and sensitivity to checkpoint blockade in GBM and support the stratification of patients with GBM for checkpoint blockade therapy based on integrated genotypic and immunologic profiles.

Abstract B15: Tumor genotype dependency of checkpoint blockade therapy in EGFR-driven glioblastoma

Background and Rationale: The tumor microenvironment plays a significant role in tumor progression and how patients respond to therapy. Recent work suggests that tumor genotypes significantly influence the immune landscapes of tumors and guide the degree of immune suppression; however, detailed mechanistic insights remain scant. Glioblastoma multiforme (GBM) is an aggressive primary brain cancer with a poor median survival of approximately 15 months. Approximately 60% of GBMs harbor overexpression of EGFR, of which 50% contain a specific mutant of EGFR (EGFRvIII). Downstream signaling of EGFRvIII differs from EGFR. Utilizing genetically engineered mouse models of EGFR- and EGFRvIII-driven GBM, we determined 1) the two GBMs comprise distinct immune landscapes, 2) EGFR GBMs respond to checkpoint blockade immunotherapy whereas EGFRvIII GBMs do not, and 3) how the unique cellular composition of EGFRvIII GBM immune landscapes actively suppresses the effects of checkpoint blockade.

Methods: Conditional transgenic EGFR or EGFRvIII, CDKN2A null, PTEN floxed mice with a floxed luciferase reporter were stereotactically injected intracranially with iCre lentivirus to initiate GBMs. Cohorts of mice were imaged using bioluminescence (BLI) to detect and stage GBMs for treatment studies. Mice were randomly enrolled in treatments with antibodies against murine PD-1, CTLA-4 or combination, or matching IgG controls every 3 days for 3 doses. Treated mice were monitored for overall survival and tumor response by BLI. Mice were also sacrificed at predetermined time points before and after therapy to determine the immune landscape by flow cytometry.

Results: We identified that, strikingly, only combination blockade of PD-1/CTLA-4 was effective in prolonging survival in EGFR GBMs but not in EGFRvIII GBMs. Flow cytometric studies demonstrate that response to combination blockade is dependent on the balance of CD8 T-cells to immunosuppressive PMN-MDSC infiltrates. Interestingly, EGFRvIII GBMs have higher PMN-MDSC infiltrates, which are associated with insensitivity to checkpoint blockade. Depletion of PMN-MDSCs in EGFR tumors restores sensitivity to monotherapy checkpoint blockade whereas depletion of PMN-MDSCs in EGFRvIII tumors restores sensitivity to combination treatment. Furthermore, EGFRvIII GBMs have higher mRNA expression of ligands for the neutrophil chemokine CXCR2 receptor compared to EGFR GBMs, suggesting a mechanism for the observed higher infiltration of PMN-MDSCs and resistance to checkpoint blockade in EGFRvIII GBMs.

Conclusions: We present that combination blockade of PD-1/CTLA-4 provides survival benefit in EGFR GBMs whereas monotherapies are ineffective. All treatment conditions are ineffective in EGFRvIII GBMs. Flow cytometry analysis and depletion studies demonstrate that PMN-MDSCs play a role by limiting the efficacy of PD-1/CTLA-4 response. Our data point to the use of CXCR2 inhibitors in combination with checkpoint blockade as a potential approach for treatment of GBM.

Citation Format: Alan T. Yeo, Alain Charest. Tumor genotype dependency of checkpoint blockade therapy in EGFR-driven glioblastoma [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B15.

CRISPR/Cas9-based editing of a sensitive transcriptional regulatory element to achieve cell type-specific knockdown of the NEMO scaffold protein

The use of alternative promoters for the cell type-specific expression of a given mRNA/protein is a common cell strategy. NEMO is a scaffold protein required for canonical NF-κB signaling. Transcription of the NEMO gene is primarily controlled by two promoters: one (promoter B) drives NEMO transcription in most cell types and the second (promoter D) is largely responsible for NEMO transcription in liver cells. Herein, we have used a CRISPR/Cas9-based approach to disrupt a core sequence element of promoter B, and this genetic editing essentially eliminates expression of NEMO mRNA and protein in 293T human kidney cells. By cell subcloning, we have isolated targeted 293T cell lines that express no detectable NEMO protein, have defined genomic alterations at promoter B, and do not support activation of canonical NF-κB signaling in response to treatment with tumor necrosis factor. Nevertheless, non-canonical NF-κB signaling is intact in these NEMO-deficient cells. Expression of ectopic wild-type NEMO, but not certain human NEMO disease mutants, in the edited cells restores downstream NF-κB signaling in response to tumor necrosis factor. Targeting of the promoter B element does not substantially reduce NEMO expression (from promoter D) in the human SNU-423 liver cancer cell line. Thus, we have created a strategy for selectively eliminating cell type-specific expression from an alternative promoter and have generated 293T cell lines with a functional knockout of NEMO. The implications of these findings for further studies and for therapeutic approaches to target canonical NF-κB signaling are discussed.

Abstract A34: Understanding mechanisms of checkpoint blockade in EGFR-driven glioblastoma

Background and Rationale: Glioblastoma multiforme (GBM) is the most common type of malignant glioma and has a poor prognosis, which calls for the exploration of alternative therapeutic approaches. Checkpoint blockade immunotherapies have produced significant clinical responses among a spectrum of malignancies. There are ongoing clinical trials for treatment of GBM with checkpoints inhibitors; however, it is anticipated that responses will be varied. With a preclinical GBM mouse model, we systematically evaluated the antitumor efficacy of antibodies targeting PD-1 and CTLA-4 administered as single agent monotherapy or combination in an EGFR genetically driven immunocompetent mouse model of GBM. In addition, we performed comprehensive immunophenotyping in EGFR-driven GBM.

Methods: Transgenic EGFR, CDKN2A null, PTEN floxed mice with a floxed luciferase reporter were stereotactically injected intracranially with a TGFa- iCre lentivirus. Cohorts of mice were imaged with bioluminescence to detect growing tumors and were treated with murine monoclonal antibodies against PD-1, CTLA-4 and combination every 3 days for 3 doses beginning post tumor detection. Treated mice and controls were followed for overall survival and analysis of tumor infiltrating immune cells. Another cohort of mice was sacrificed 3 days post completion of treatment and immunophenotyping was performed by flow cytometry.

Results: We observe that only mice treated with combination blockade of PD-1 and CTLA-4 had improved survival compared to untreated controls. Single agent monotherapies were ineffective as measured in no improvement in survival compared to controls. A small subset of mice treated with combination blockade of PD-1 and CTLA-4 displayed long term survival up to 100 days post tumor detection. Bioluminescence imaging revealed cytostatic effects in mice treated with combination blockade of PD-1 and CTLA-4 and in a smaller subset, sustained regression. Monotherapy treatment displayed continuing tumor growth similar to untreated controls. Characterization of tumor infiltrating immune cells displayed evidence that only combination treatment of PD-1 and CTLA-4 correlates with an increase in the number of CD8 T cell infiltrate and a decrease in the number of granulocytic MDSC (G-MDSC) infiltrate while monotherapy does not affect the ratio of CD8 to G-MDSC.

Conclusions: Immune checkpoint blockade of both PD-1 and CTLA-4 provides survival benefit whereas monotherapies are ineffective in our genetically engineered mouse model of GBM. Studies aimed at revealing the mechanisms of immune-mediated anti-tumor activity from combination blockade are ongoing. Analyses of tumor infiltrating immune cells suggest that the ratio of CD8 to G-MDSCs correlate with efficacy of combination blockade of PD-1 and CTLA-4. Depletion experiments are ongoing to address the role of CD8 and MDSCs in mediating anti-tumor immunity upon single and combination blockade of PD-1 and CTLA-4 in EGFR-driven GBM.

Citation Format: Alan T. Yeo, Alain Charest. Understanding mechanisms of checkpoint blockade in EGFR-driven glioblastoma [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A34.

A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine

Glioblastoma multiforme (GBM) is an aggressive primary brain cancer that includes focal amplification of PDGFRα and for which there are no effective therapies. Herein, we report the development of a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of overexpressed PDGFRα, and the analysis of GBM signaling pathways using proteomics. We discover the tubulin-binding protein Stathmin1 (STMN1) as a PDGFRα phospho-regulated target, and that this mis-regulation confers sensitivity to vinblastine (VB) cytotoxicity. Treatment of PDGFRα-positive mouse and a patient-derived xenograft (PDX) GBMs with VB in mice prolongs survival and is dependent on STMN1. Our work reveals a previously unconsidered link between PDGFRα activity and STMN1, and highlight an STMN1-dependent cytotoxic effect of VB in GBM.

Immune Checkpoint Blockade Biology in Mouse Models of Glioblastoma

Glioblastoma Multiforme (GBM) is a highly malignant primary brain cancer that is associated with abysmal prognosis. The median survival of GBM patients is ∼15 months and there have not been any significant advance in therapies in over a decade, leaving treatment options limited. There is clearly an unmet need for GBM treatment. Immunotherapies are treatments based on usurping the power of the host's immune system to recognize and eliminate cancer cells. They have recently proven to be a successful strategy for combating a variety of cancers. Of the various types of immunotherapies, checkpoint blockade approaches have thus far produced significant clinical responses in several cancers including melanoma, non small-cell lung cancer, renal cancer, and prostate cancer. This review focuses on the biological rationale for using checkpoint blockade immunotherapeutic approaches in primary brain cancer and an up-to-date summary of current and ongoing checkpoint inhibitors-based clinical trials for malignant glioma. In addition, we expand on new concepts for further improving checkpoint blockade treatments, with a particular focus on the advantages of using genetically engineered mouse models for studies of immunotherapies in GBM. J. Cell. Biochem. 118: 2516-2527, 2017. © 2017 Wiley Periodicals, Inc.

Adaptive Significance of ERα Splice Variants in Killifish (Fundulus heteroclitus) Resident in an Estrogenic Environment

The possibility that chronic, multigenerational exposure to environmental estrogens selects for adaptive hormone-response phenotypes is a critical unanswered question. Embryos/larvae of killifish from an estrogenic-polluted environment (New Bedford Harbor, MA [NBH]) compared with those from a reference site overexpress estrogen receptor alpha (ERα) mRNA but are hyporesponsive to estradiol. Analysis of ERα mRNAs in the two populations revealed differences in splicing of the gene encoding ERα (esr1). Here we tested the transactivation functions of four differentially expressed ERα mRNAs and tracked their association with the hyporesponsive phenotype for three generations after transfer of NBH parents to a clean environment. Deletion variants ERαΔ6 and ERαΔ6-8 were specific to NBH killifish, had dominant negative functions in an in vitro reporter assay, and were heritable. Morpholino-mediated induction of ERαΔ6 mRNA in zebrafish embryos verified its role as a dominant negative ER on natural estrogen-responsive promoters. Alternate long (ERαL) and short (ERαS) 5'-variants were similar transcriptionally but differed in estrogen responsiveness (ERαS ≫ ERαL). ERαS accounted for high total ERα expression in first generation (F1) NBH embryos/larvae but this trait was abolished by transfer to clean water. By contrast, the hyporesponsive phenotype of F1 NBH embryos/larvae persisted after long-term laboratory holding but reverted to a normal or hyper-responsive phenotype after two or three generations, suggesting the acquisition of physiological or biochemical traits that compensate for ongoing expression of negative-acting ERαΔ6 and ERαΔ6-8 isoforms. We conclude that a heritable change in the pattern of alternative splicing of ERα pre-mRNA is part of a genetic adaptive response to estrogens in a polluted environment.

Disulfide-mediated stabilization of the IκB kinase binding domain of NF-κB essential modulator (NEMO)

Human NEMO (NF-κB essential modulator) is a 419 residue scaffolding protein that, together with catalytic subunits IKKα and IKKβ, forms the IκB kinase (IKK) complex, a key regulator of NF-κB pathway signaling. NEMO is an elongated homodimer comprising mostly α-helix. It has been shown that a NEMO fragment spanning residues 44–111, which contains the IKKα/β binding site, is structurally disordered in the absence of bound IKKβ. Herein we show that enforcing dimerization of NEMO_1–120 or NEMO_44–111 constructs through introduction of one or two interchain disulfide bonds, through oxidation of the native Cys54 residue and/or at position 107 through a Leu107Cys mutation, induces a stable α-helical coiled-coil structure that is preorganized to bind IKKβ with high affinity. Chemical and thermal denaturation studies showed that, in the context of a covalent dimer, the ordered structure was stabilized relative to the denatured state by up to 3 kcal/mol. A full-length NEMO-L107C protein formed covalent dimers upon treatment of mammalian cells with H₂O₂. Furthermore, NEMO-L107C bound endogenous IKKβ in A293T cells, reconstituted TNF-induced NF-κB signaling in NEMO-deficient cells, and interacted with TRAF6. Our results indicate that the IKKβ binding domain of NEMO possesses an ordered structure in the unbound state, provided that it is constrained within a dimer as is the case in the constitutively dimeric full-length NEMO protein. The stability of the NEMO coiled coil is maintained by strong interhelix interactions in the region centered on residue 54. The disulfide-linked constructs we describe herein may be useful for crystallization of NEMO’s IKKβ binding domain in the absence of bound IKKβ, thereby facilitating the structural characterization of small-molecule inhibitors.

Abstract C263: mTOR inhibition specifically sensitizes colorectal cancers with KRAS or BRAF mutations to BCL-2/BCL-XL inhibition by suppressing MCL-1

Colorectal cancers (CRCs) harboring KRAS or BRAF mutations are refractory to current targeted therapies. Using data from a high-throughput drug screen, we have developed a novel therapeutic strategy that combines targeting of the apoptotic machinery using the BCL-2 family inhibitor ABT-263 (navitoclax) in combination with a TORC1/2 inhibitor, AZD8055. This combination leads to efficient apoptosis specifically in KRAS mutant (MT) and BRAF MT but not wild-type (WT) CRC cells. This specific susceptibility results from TORC1/2 inhibition leading to suppression of MCL-1 expression in mutant, but not wild-type CRCs, leading to abrogation of BIM/MCL-1 complexes. This combination strategy leads to tumor regressions in both KRAS MT colorectal cancer xenograft and genetically-engineered mouse models of CRC, but not in the corresponding KRAS WT CRC models. These data suggest that the combination of BCL-2/XL inhibitors with TORC1/2 inhibitors constitutes a promising targeted therapy strategy to treat these recalcitrant cancers.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C263.

Citation Format: Erin M. Coffee, Anthony C. Faber, Carlotta Costa, Anahita Dastur, Hiromichi Ebi, Aaron N. Hata, Alan T. Yeo, Elena J, Youngchul Song, Ah Ting Tam, Jessica L. Boisvert, Randy J. Milano, Jatin Roper, David P. Kodack, Rakesh K. Jain, Ryan B. Corcoran, Miguel N. Rivera, Sridhar Ramaswamy, Kenneth E. Hung, Cyril H. Benes, Jeffrey A. Engelman. mTOR inhibition specifically sensitizes colorectal cancers with KRAS or BRAF mutations to BCL-2/BCL-XL inhibition by suppressing MCL-1. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C263.

mTOR inhibition specifically sensitizes colorectal cancers with KRAS or BRAF mutations to BCL-2/BCL-XL inhibition by suppressing MCL-1

Colorectal cancers harboring KRAS or BRAF mutations are refractory to current targeted therapies. Using data from a high-throughput drug screen, we have developed a novel therapeutic strategy that targets the apoptotic machinery using the BCL-2 family inhibitor ABT-263 (navitoclax) in combination with a TORC1/2 inhibitor, AZD8055. This combination leads to efficient apoptosis specifically in KRAS- and BRAF-mutant but not wild-type (WT) colorectal cancer cells. This specific susceptibility results from TORC1/2 inhibition leading to suppression of MCL-1 expression in mutant, but not WT, colorectal cancers, leading to abrogation of BIM/MCL-1 complexes. This combination strategy leads to tumor regressions in both KRAS-mutant colorectal cancer xenograft and genetically engineered mouse models of colorectal cancer, but not in the corresponding KRAS-WT colorectal cancer models. These data suggest that the combination of BCL-2/BCL-XL inhibitors with TORC1/2 inhibitors constitutes a promising targeted therapy strategy to treat these recalcitrant cancers.

Bcl-XL, but not Bcl-2, can protect human B-lymphoma cell lines from parthenolide-induced apoptosis

In this report, we investigated the effects of the natural product parthenolide on human B-lymphoma cell lines. We show that parthenolide inhibited NF-κB transcription factor c-Rel (REL). In addition, the sensitivity of several human B-lymphoma cell lines to parthenolide-induced apoptosis inversely correlated with their levels of anti-apoptosis protein Bcl-X(L). Furthermore, ectopic expression of Bcl-X(L) (but not Bcl-2) in two B-lymphoma cell lines decreased their sensitivity to parthenolide-induced apoptosis. Finally, over-expression of a transforming mutant of REL, which increased expression of endogenous Bcl-X(L), decreased the sensitivity of BJAB B-lymphoma cells to parthenolide-induced apoptosis. These results demonstrate that the NF-κB target gene products Bcl-X(L) and Bcl-2 can play different roles in protecting B-lymphoma cells from chemical-induced apoptosis.