753 InhibigenTM administration promotes aberrant T cell responses in cancer but may be beneficial for amelioration of autoimmune disease

Background

Selecting neoantigens that generate robust anti-tumor T cell responses remains a challenge for cancer immunotherapy design. The ATLASTM platform, a functional recall assay using patient autologous cells, identifies both stimulatory and inhibitory (Inhibigen) neoantigens via up- or downregulation of T cell cytokine secretion.1 We propose that stimulatory neoantigens are ideal targets for cancer vaccines and T cell therapies. In contrast, data suggest that Inhibigens be excluded, due to their association with accelerated tumor growth and dampened immunity in a murine melanoma model.2 While detrimental to cancer immunotherapy, the Inhibigen-associated downregulation of cytokine production may be beneficial in the context of autoimmunity.

Methods

ATLAS screens were performed as previously described.1 2 Peptide vaccines containing tumor-specific neoantigens ± Inhibigens were evaluated in prophylactic and therapeutic B16F10 melanoma tumor models for immunogenicity and efficacy. RNAseq analysis was performed on T cells sorted from draining lymph nodes of vaccinated tumor-bearing mice. For experimental autoimmune encephalomyelitis (EAE) studies, mice were administered a vaccine containing MOG peptide ± the melanoma MMP9FS Inhibigen. Immune responses and phenotypic analyses for both models were measured by flow cytometry, ELISPOT, and immunohistochemistry.

Results

In the melanoma model, inclusion of the Inhibigen MMP9FS accelerated tumor growth in a non-dose dependent manner and abrogated immune responses. RNAseq of T cells from tumor-bearing mice vaccinated with MMP9FS showed a higher level of differentially expressed genes (adjusted P value of <0.05) in TCR-signaling regulation and suppressor GO pathways (>5 distinct pathways/gene) as compared to stimulatory controls, indicating Inhibigen-specific effects on T cells. In the EAE model of autoimmunity, animals treated with MOG peptide + MMP9FS exhibited dampened anti-MOG immune responses, delayed disease onset, reduced disease incidence and scoring (average 1 vs. 3) and decreased spinal cord immune infiltration as compared to control vaccination. These data indicate that Inhibigen administration has the potential to ameliorate autoimmune sequelae, independent of cognate antigen expression.

Conclusions

Functional identification and exclusion of Inhibigens from cancer immunotherapies may be critical to protective immunity since their inclusion can result in quelling of otherwise beneficial immune responses. Conversely, Inhibigen-specific responses can dampen destructive autoimmune sequelae. Mechanistic studies show altered T cell signaling pathways in the context of therapeutic Inhibigen vaccination. These data suggest that Inhibigen-specific responses, while detrimental for the treatment of cancer, may have a therapeutic benefit in other disease contexts.

References

Nogueira C, Kaufmann JK, Lam H, Flechtner JB. Improving cancer immunotherapies through empirical neoantigen selection. Trends in Cancer 2018;4(2):97–100.

Lam H, et al. An empirical antigen selection method identifies neoantigens that either elicit broad anti-tumor response or drive tumor growth. Cancer Discovery 2021;11(3):696–713.

Ethics Approval

All animal studies were undertaken in conformity with the Cambridge, MA Ordinance 1086 of the city's Municipal Code and in accordance with the policies and protocols approved by Genocea's Institutional Animal Care and Use Committee (IACUC).

Abstract 1762: InhibigensTM subvert otherwise-efficacious cancer vaccines and immunotherapies in conjunction with alterations in the tumor microenvironment

The current study explores the mechanism of Inhibigens: a new class of immune-dampening cancer neoantigens. Inhibigens are identified through Genocea's ATLASTM platform, an empirical and unbiased bioassay that utilizes autologous patient cells to characterize tumor mutations that elicit anti-tumor CD4+ and CD8+ immune responses. Unexpectedly, ATLAS also identifies inhibitory neoantigens (Inhibigens) that lead to downregulation of T cell inflammatory cytokine secretion. Previous studies demonstrated that when a single ATLAS-identified Inhibigen was administered to B16F10 tumor-bearing mice, it completely abrogated immunogenicity and efficacy of a protective vaccine. Thus, it is critical that detrimental Inhibigens be excluded from targeted immunotherapies and further studied to understand their global importance in cancer. Here we report progress in uncovering mechanisms of Inhibigen function.

In ATLAS screening assays, patient-derived antigen-presenting cells (APCs) are fed with E. coli bacteria expressing individual mutations from the patient's mutanome with or without pore-forming listeriolysin O (cLLO), and subsequently exposed to patient-derived CD8+ or CD4+ T cells, respectively; T cell cytokine secretion determines antigen-specific responses. Unlike in silico approaches, ATLAS accounts for the complexity of antigen processing, the diversity of MHC class I and II alleles across races and ethnicities, and the diversity of T cell repertoires across individuals. ATLAS screening of B16F10 mouse melanoma previously identified stimulatory neoantigens and Inhibigens that were either protective or deleterious to tumor progression when included in vaccines, respectively. Current studies explore the tumor microenvironment (TME) and systemic immunity in Inhibigen-administered mice ± checkpoint inhibitors (CPI).

Inhibigens accelerated tumor growth compared to protective vaccines, abrogated vaccine-driven infiltration of T cells and myeloid cells into the TME, and impaired the synergistic effects of vaccination and CPI therapy with corresponding deficiencies in the TME. In vitro studies thus far exclude cell killing and MHC competition as Inhibigen mechanisms of action. Ongoing studies evaluating Inhibigen modulation of APC and T cell function in vitro and in vivo will be presented.

Our data enforce the necessity of identifying Inhibigens empirically and excluding them from cancer vaccines and immunotherapies. Genocea's GEN-009 and GEN-011 phase 1/2 clinical trials utilize ATLAS to identify optimal neoantigens and omit Inhibigens from cancer vaccines and T cell therapies. Ongoing exploration of Inhibigen phenotypes and mechanisms will illuminate new paradigms of cancer immunology and potentially pave the way for novel cancer immunotherapies.

Citation Format: Hanna Starobinets, Victoria L. Devault, Stephanie Rinaldi, Julie Arnold, Osaruese Odeh, Cindy Nguyen, Jessica B. Flechtner, Hubert Lam. InhibigensTM subvert otherwise-efficacious cancer vaccines and immunotherapies in conjunction with alterations in the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1762.

Autophagy in stromal fibroblasts promotes tumor desmoplasia and mammary tumorigenesis

In this study, Rudnick et al. use mouse mammary cancer models and syngeneic transplantation assays to demonstrate that genetic ablation of stromal fibroblast autophagy significantly impedes fundamental elements of the stromal desmoplastic response, including collagen and proinflammatory cytokine secretion, extracellular matrix stiffening, and neoangiogenesis. Their findings suggest the efficacy of autophagy inhibition is shaped by the ability of host stromal fibroblast autophagy to support tumor desmoplasia.

Autophagy inhibitors are currently being evaluated in clinical trials for the treatment of diverse cancers, largely due to their ability to impede tumor cell survival and metabolic adaptation. More recently, there is growing interest in whether and how modulating autophagy in the host stroma influences tumorigenesis. Fibroblasts play prominent roles in cancer initiation and progression, including depositing type 1 collagen and other extracellular matrix (ECM) components, thereby stiffening the surrounding tissue to enhance tumor cell proliferation and survival, as well as secreting cytokines that modulate angiogenesis and the immune microenvironment. This constellation of phenotypes, pathologically termed desmoplasia, heralds poor prognosis and reduces patient survival. Using mouse mammary cancer models and syngeneic transplantation assays, we demonstrate that genetic ablation of stromal fibroblast autophagy significantly impedes fundamental elements of the stromal desmoplastic response, including collagen and proinflammatory cytokine secretion, extracellular matrix stiffening, and neoangiogenesis. As a result, autophagy in stromal fibroblasts is required for mammary tumor growth in vivo, even when the cancer cells themselves remain autophagy-competent . We propose the efficacy of autophagy inhibition is shaped by this ability of host stromal fibroblast autophagy to support tumor desmoplasia.

Inhibigens™ drive pro-tumor responses and may act through non-classical inhibitory mechanisms

The ATLAS™ platform screens a patient’s tumor mutanome with autologous T cells and antigen presenting cells to identify targets for cancer immunotherapy. Tumor mutations that lead to increased T cell responses are deemed stimulatory (neoantigens), while those rendering decreased responses are defined as Inhibigens. In B16F10 mouse melanoma, therapeutic neoantigen vaccination resulted in durable protection, while Inhibigen co-administration resulted in a remarkable reversal of protection and abrogation of anti-tumor responses. The Inhibigen-related pro-tumor effects were not reduced by αPD-1 therapy, and administration of αCTLA-4 resulted in modest benefit, suggesting that Inhibigen-specific responses can overpower current standard-of-care immunotherapies. The tumor microenvironment of Inhibigen-vaccinated mice was immune cold, with dramatic decreases in infiltrating T cells and myeloid cells relative to controls. Inhibigen effects were not associated with classical inhibitory mechanisms such as an overabundance of CD4+CD25+Foxp3+Tregs, MHC competition or downregulation. In addition, T cell proliferation appeared unaffected by Inhibigen administration. Time course experiments revealed that Inhibigen-specific phenotypes (e.g. defective T cell IFNγ production) occur as early as 4 days post vaccination, suggesting deficiencies related to T cell priming. RNAseq analyses showed distinct changes in T cell transcriptional patterns between neoantigen and Inhibigen-experienced T cells. Taken together, these data reveal a potential non-classical inhibitory mechanism by which responses to naturally occurring cancer mutations may promote tumor growth and reverse beneficial anti-tumor immune responses.

An Empirical Antigen Selection Method Identifies Neoantigens That Either Elicit Broad Antitumor T-cell Responses or Drive Tumor Growth

Neoantigens are critical targets of antitumor T-cell responses. The ATLAS bioassay was developed to identify neoantigens empirically by expressing each unique patient-specific tumor mutation individually in Escherichia coli, pulsing autologous dendritic cells in an ordered array, and testing the patient's T cells for recognition in an overnight assay. Profiling of T cells from patients with lung cancer revealed both stimulatory and inhibitory responses to individual neoantigens. In the murine B16F10 melanoma model, therapeutic immunization with ATLAS-identified stimulatory neoantigens protected animals, whereas immunization with peptides associated with inhibitory ATLAS responses resulted in accelerated tumor growth and abolished efficacy of an otherwise protective vaccine. A planned interim analysis of a clinical study testing a poly-ICLC adjuvanted personalized vaccine containing ATLAS-identified stimulatory neoantigens showed that it is well tolerated. In an adjuvant setting, immunized patients generated both CD4⁺ and CD8⁺ T-cell responses, with immune responses to 99% of the vaccinated peptide antigens. SIGNIFICANCE: Predicting neoantigens in silico has progressed, but empirical testing shows that T-cell responses are more nuanced than straightforward MHC antigen recognition. The ATLAS bioassay screens tumor mutations to uncover preexisting, patient-relevant neoantigen T-cell responses and reveals a new class of putatively deleterious responses that could affect cancer immunotherapy design.This article is highlighted in the In This Issue feature, p. 521.

Abstract 6680: Inclusion of inhibitory neoantigens can abolish efficacy of otherwise protective therapeutic anti-tumor vaccines

Identification of neoantigens that can elicit strong anti-tumor responses has become critical to vaccine design for cancer immunotherapy. Conventional methods for in silico neoantigen identification have yielded poor predictive value, highlighting the need for methods that identify bona fide neoantigen targets. The Genocea ATLAS™ platform uses autologous antigen presenting cells and T cells to identify pre-existing CD4+ and/or CD8+ T cell responses to patient-specific mutations and therefore selects confirmed neoantigens that can be used for vaccines and cell therapies. Screened neoantigens are characterized as stimulatory or inhibitory based on up- or downregulation of inflammatory cytokine secretion compared to baseline controls. In the mouse B16F10 melanoma model, therapeutic immunization with stimulatory neoantigen peptides arrested tumor growth whereas in contrast, inhibitory antigen immunization (henceforth referred to as inhibigens) resulted in accelerated tumor progression. The presence of an inhibigen in an otherwise protective vaccine formulation completely abolished protection. Global IFNγ responses to neoantigens were abrogated in these mice as measured by ELISpot suggesting that inhibigen pro-tumor responses can be immunodominant. Analysis of tumor-infiltrating lymphocytes (TILs) from mice immunized with ATLAS-identified neoantigen ± inhibigen peptide vaccines revealed significant alterations in the tumor microenvironment. Inclusion of inhibigens resulted in low T cell infiltration into tumors and increased expression of TIL inhibitory surface markers (e.g. PD-1, LAG-3). Immunological mechanisms of the inhibitory phenomenon are currently being explored. These data promote rational methods for neoantigen identification and highlight the potential advantages of excluding deleterious inhibigens from cancer vaccines and immunotherapies. GEN-009, a personalized cancer vaccine filtered for inclusion of only ATLAS-identified neoantigens (excluding inhibigens) is currently being evaluated in a Phase 1/2a clinical trial (NCT03633110).

Citation Format: Victoria L. DeVault, Hanna Starobinets, Sanmit Adhikari, Simran Singh, Stephanie Rinaldi, Brendan Classon, Jessica B. Flechtner, Hubert Lam. Inclusion of inhibitory neoantigens can abolish efficacy of otherwise protective therapeutic anti-tumor vaccines [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6680.

Inhibigens, personal neoantigens that drive suppressive T cell responses, abrogate protection of therapeutic anti-tumor vaccines

Therapeutic cancer vaccine efficacy is reliant on tumor-specific neoantigens. Empirical methods to identify relevant neoantigens may overcome poor predictive values of current in silico approaches. The ATLAS™ platform is a personalized bioassay that uses high-throughput screening of autologous APCs and T cells against a patient’s mutanome to identify neoantigens that are characterized as stimulatory or inhibitory (inhibigens) based on changes in T cell cytokine secretion. In a B16F10 murine model, therapeutic vaccination with ATLAS-identified neoantigens resulted in arrested tumor growth with durable immune responses that protected mice from re-challenge. Mice that were vaccinated with an inhibigen and neoantigen combination had significantly abrogated tumor protection relative to controls. IFNγ ELISpot analysis revealed that inhibigen vaccination suppressed all antigen-specific immune responses, suggesting that inhibigens can be immunodominant. Inhibigen vaccinated mice had multiple tumor microenvironment changes including reduced T cell infiltration, altered CD8+/CD4+ T cell ratios and increased inhibitory marker expression relative to controls. These results indicate that the presence of inhibigens in an otherwise protective vaccine can alter the tumor microenvironment and abolish T cell-mediated protection. Epitope mapping of neoantigens and inhibigens and tetramer design for differential gene signature analysis of inhibigen-specific T cells is being performed. These data suggest that identification and exclusion of inhibigens from cancer vaccines is critical to prevent unintended pro-tumor responses.

Abstract 5718: Ex vivo ATLAS-identification of neoantigens for personalized cancer immunotherapy in mouse melanoma

Neoantigens are emerging as attractive vaccine targets for personalized cancer immunotherapy. As opposed to tumor-associated antigens, neoantigens contain non-synonymous mutations that enable their identification as foreign targets not subject to central tolerance in the thymus. Personalized cancer vaccines leverage neoantigens to specifically direct the immune system to recognize cancer cells for the coordinated attack and destruction of tumors. While in silico methods are commonly used to predict immunogenic neoantigens primarily via putative binding to major histocompatibility complexes (MHC), the positive predictive value of these approaches is low as they cannot account for the complexity of antigen processing, the diversity of MHC class I and class II alleles, and the additional steps of T cell activation. Ex vivo technologies have the potential to overcome the limitations of neoantigen identification by utilizing biologically-relevant testing. ATLAS™ is an unbiased immune response profiling platform that enables comprehensive screening of a tumor mutanome by using a patient's own autologous immune cells, specifically monocyte-derived dendritic cells (MDDC) as antigen presenting cells (APCs) and sorted CD8+ and CD4+ T cells. By utilizing autologous APCs and T cells, ATLAS is agnostic to MHC diversity and assesses preexisting T cell responses to any given mutation. Patient MDDC are pulsed with an ordered array of Escherichia coli expressing patient-specific mutations as short polypeptides. CD8+ and CD4+ T cell response screening is performed using APCs and E. coli with and without pore-forming lysteriolysin O (cLLO) facilitating MHC class I or class II presentation, respectively. Thus, preexisting patient T cell responses to cancer antigens can be characterized by inflammatory cytokine secretion. We utilized a mouse melanoma model to demonstrate the capability of the ATLAS platform for identification of vaccine neoantigens. Whole exome sequencing was performed on B16F10 melanomas resected from C57BL/6 mice, identifying &gt;1600 non-somatic, non-silent mutations. E. coli libraries individually expressing all mutations were constructed and used to screen APCs and T cells from the spleens of B16F10 tumor-bearing mice. Biologically relevant neoantigens were identified by their ability to modulate the secretion of inflammatory cytokines by CD4+ and CD8+ T cells. The significance of the identified neoantigens in comparison to predicted and previously reported B16F10 antigens is described. Top neoantigen candidates were selected and manufactured as synthetic long peptides. Therapeutic vaccination with ATLAS-identified neoantigens in tumor challenge studies is planned and progress will be reported. These studies demonstrate a biologically-relevant approach to improve neoantigen selection for personalized cancer vaccine design enabling improved therapeutic efficacy.

Citation Format: Hanna Starobinets, Catarina Nogueira, Kyle Ferber, Huilei Xu, Abha Dhaneshwar, Jason R. Dobson, James Loizeaux, James Foti, Michael O'Keefe, Erick Donis, Wendy Broom, Pamela Carroll, Paul Kirschmeier, Jessica B. Flechtner, Hubert Lam. Ex vivo ATLAS-identification of neoantigens for personalized cancer immunotherapy in mouse melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5718.

Antitumor adaptive immunity remains intact following inhibition of autophagy and antimalarial treatment

The rising success of cancer immunotherapy has produced immense interest in defining the clinical contexts that may benefit from this therapeutic approach. To this end, there is a need to ascertain how the therapeutic modulation of intrinsic cancer cell programs influences the anticancer immune response. For example, the role of autophagy as a tumor cell survival and metabolic fitness pathway is being therapeutically targeted in ongoing clinical trials that combine cancer therapies with antimalarial drugs for the treatment of a broad spectrum of cancers, many of which will likely benefit from immunotherapy. However, our current understanding of the interplay between autophagy and the immune response remains incomplete. Here, we have evaluated how autophagy inhibition impacts the antitumor immune response in immune-competent mouse models of melanoma and mammary cancer. We observed equivalent levels of T cell infiltration and function within autophagy-competent and -deficient tumors, even upon treatment with the anthracycline chemotherapeutic doxorubicin. Similarly, we found equivalent T cell responses upon systemic treatment of tumor-bearing mice with antimalarial drugs. Our findings demonstrate that antitumor adaptive immunity is not adversely impaired by autophagy inhibition in these models, allowing for the future possibility of combining autophagy inhibitors with immunotherapy in certain clinical contexts.