A survey conducted by the Therapeutic Product Immunogenicity (TPI) community within the American Association of Pharmaceutical Scientists (AAPS) posed questions to the participants on their immunogenicity risk assessment strategies prior to clinical development. The survey was conducted in 2 phases spanning 5 years, and queried information about in silico algorithms and in vitro assay formats for immunogenicity risk assessments and how the data were used to inform early developability effort in discovery, chemistry, manufacturing and control (CMC), and non-clinical stages of development. The key findings representing the trends from a majority of the participants included the use of high throughput in silico algorithms, human immune cell-based assays, and proteomics based outputs, as well as specialized assays when therapeutic mechanism of action could impact risk assessment. Additional insights into the CMC-related risks could also be gathered with the same tools to inform future process development and de-risk critical quality attributes with uncertain and unknown risks. The use of the outputs beyond supporting early development activities was also noted with participants utilizing the risk assessments to drive their clinical strategy and streamline bioanalysis.

BackgroundThe emergence of novel SARS-CoV-2 variants that resist neutralizing antibodies drew the attention to cellular immunity and calls for the development of alternative vaccination strategies to combat the pandemic. Here, we have assessed the kinetics of T cell responses and protective efficacy against severe COVID-19 in pre- and post-exposure settings, elicited by PolyPEPI-SCoV-2, a peptide based T cell vaccine.Methods75 Syrian hamsters were immunized subcutaneously with PolyPEPI-SCoV-2 on D0 and D14. On D42, hamsters were intranasally challenged with 102 TCID50 of the virus. To analyze immunogenicity by IFN-γ ELISPOT and antibody secretion, lymphoid tissues were collected both before (D0, D14, D28, D42) and after challenge (D44, D46, D49). To measure vaccine efficacy, lung tissue, throat swabs and nasal turbinate samples were assessed for viral load and histopathological changes. Further, body weight was monitored on D0, D28, D42 and every day after challenge.ResultsThe vaccine induced robust activation of T cells against all SARS-CoV-2 structural proteins that were rapidly boosted after virus challenge compared to control animals (~4-fold, p<0.05). A single dose of PolyPEPI-SCoV-2 administered one day after challenge also resulted in elevated T cell response (p<0.01). The vaccination did not induce virus-specific antibodies and viral load reduction. Still, peptide vaccination significantly reduced body weight loss (p<0.001), relative lung weight (p<0.05) and lung lesions (p<0.05), in both settings.ConclusionOur study provides first proof of concept data on the contribution of T cell immunity on disease course and provide rationale for the use of T cell-based peptide vaccines against both novel SARS-CoV-2 variants and supports post-exposure prophylaxis as alternative vaccination strategy against COVID-19.

Re-activation of tumor-reactive T cells with so-called immune checkpoint inhibitors (ICIs) has translated into significant clinical breakthroughs. Specifically, antibodies directed against CTLA-4 and PD-L1/PD-1 have yielded long-term remission and cure in many solid as well as hematological malignancies. However, as not all cancer types respond to current ICI therapies, the quest for novel strategies to re-enable anti-tumor immunity by blocking immune checkpoints or by activating prominent co-stimulatory receptors is crucial. The field of cancer immunology has developed rapidly over the past decades, with numerous studies adding up to the complexity of immune-related interactions taking place in the tumor microenvironment. Compounds or combinations of compounds designed to target traditional or novel pathways require early evaluation of effectiveness on in vitro assays using primary immune cells or representative mouse models. On top of classical T cell bioassays, expanding on current methods and the development novel strategies to assess the modulation of cancer-related immunological networks is a continuously important process. One classical approach is the functional evaluation of compounds in a mixed lymphocyte reaction (MLR). Here, the potency of drug candidates to promote physiological T cell responses can be evaluated. Antigen-specific immune responses can be further assessed in Cytomegalovirus (CMV) recall- or in Staphylococcal enterotoxin B (SEB) activation assays. Additionally, it might also be beneficial to generate tumor-associated antigen-specific T cell pools or clones to be used in functional assays. The classical MLR assay could be expanded on by e.g., inclusion of specific tumor cell populations or T regulatory (Treg) cells, as evaluating reduced cancer cell viability, or reversing loss of immune effector cell functionality can be of interest. Furthermore, real-time evaluation of cancer cell killing by T cells upon addition of drug candidates could also provide pivotal information on the compound’s functional dynamics. With our deepening understanding of cancer-related immunological networks it becomes clear that different drug candidates may require customized and fine-tuned T cell bioassays to assess their full therapeutic potential. Moreover, quality controlled primary immune cells are an essential factor for the robustness of these assays and to yield reproducible and consistent results. Collectively, taking in mind these aspects will ease decision making and accelerate the drug discovery pipeline. Citation Format: Thibaut J. Janss, Martijn Vlaming, Simon Lefevre, Johan Arnold, Ellen Boelen, Sofie Pattijn. Functional evaluation of immuno-oncology drug candidates in customized and fine-tuned T cell bioassays to assess therapeutic potential [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 619.

The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARSCoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8(+) T cell immunosurveillance during the first year of the pandemic.

Introducing the gene therapy product into human cells requires a vector that will deliver the gene into the cells and incorporate those genes into the gene expression mechanism in those cells. One of the issues is the induction of an unwanted immune response that can have an influence on the efficacy and potency of the treatment. Additionally, pre-existing immunity towards AAV and CRISPR can also neutralize the therapeutic effect. Comprehensive assessment of human immune responses to gene therapy candidates includes characterization of humoral and cellular immunogenicity specific for both the viral vector and the expressed transgene (protein) product before and after dose administration. In vitro assays such as dendritic cell activation and T cell proliferation assays can be used to assess this unwanted immunogenicity in an early phase. Additionally, innate assays such as dendritic cell activation assays can be used for the evaluation of potential impurities and innate response inducing contaminants. Sensitive Fluorospot assays can be used to monitor patient’ specific immunogenicity both at the T and B cell level. The advantage of the Fluorospot technology is the sensitivity to detect responses on a single cell level and measure up to 4 analytes simultaneously. For all in vitro assays, the quality and functionality of the primary cells is important to assure reproducibility and solid assay performance. Citation Format: Jana Schockaert, Thibaut J. Janss, Juliette Lamy, Aurélie Mazy, Ellen Boelen, Simon Lefevre, Sofie Pattijn. The use of in vitro assays to assess and measure gene therapy immunogenicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3288.

Targeted activation of tumor infiltrating lymphocytes in the tumor microenvironment (TME) with so-called immune checkpoint inhibitors (ICIs) has resulted in the development of revolutionizing therapeutic anti-tumor strategies. A deepening understanding of the TME has followed in the ability to see beyond current immune checkpoint strategies. It becomes clear that players like Tumor Associated Macrophages (TAM) and Myeloid Derived Suppressor Cells (MDSC) play a significant role by downregulating anti-tumor responses. Their presence and roles in the TME open novel possibilities for modulation of the TME. To study these mechanisms, bioassays mimicking the suppressive activity of these cells on lymphocytes were developed. With regulatory functions in both innate and adaptive immune responses and different phenotypic profiles that classically are divided into M1-like and M2-like, macrophages undeniably represent important players in the TME. Where classically activated M1-like macrophages comprise immune effector cells with an inflammatory phenotype, alternatively activated M2-like macrophages display suppressive activities. Correspondingly, a variety of solid tumors are found to be enriched with these M2-like macrophages, suppressing anti-tumor immunity. The diverse roles of macrophage subtypes are still being explored and their phenotypic classification is likely more complex than the classical M1-like and M2-like. However, in vitro assays based on these 2 subtypes can be a first step to screen for the impact of test molecules on the phenotype and function of macrophages and their subsequent effect on lymphocytes. Using in vitro polarization and functional assays, the impact of test molecules on M1-like and M2-like macrophage generation and polarization can be assessed. The impact of test molecules on macrophage functionality can be further evaluated using a macrophage suppressive assay. Here the ability of test molecules to enhance the stimulating effect of M1-like macrophages or to reverse the suppressive effect of M2-like macrophages on lymphocytes can be evaluated by assessing their proliferation and cytokine production. Moreover, the potential stimulatory effect of test compounds on macrophages to perform Antibody-dependent cellular phagocytosis (ADCP) of tumor cells in co-culture assays could be another strategy to review therapeutic potential. Collectively, the development of novel bioassays contributes to a better understanding of the TME and thereby illuminates the steps required to elicit anti-tumor immune responses. It further aids the functional assessment of potential of new drugs, the design of clinical trials and the discovery of relevant biomarkers. Citation Format: Thibaut J. Janss, Simon Lefevre, Martijn Vlaming, Johan Arnold, Ellen Boelen, Sofie Pattijn. In vitro suppressive bioassays using macrophages for the evaluation of immuno-oncology drug [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2120.

The need to better understand the tumor microenvironment (TME) dictates the characterization of the cell types involved, the roles they play and how they respond to treatment. To develop novel cancer immunotherapies, in vitro primary immune cell bioassays offer an early assessment of their effects on the various players of the TME. Cytotoxic cells are key players in the anti-tumor immune response. CD8+ T cells, also known as cytotoxic T lymphocytes, recognize and kill cells presenting antigens bound to MHC class I molecules, such as neoantigens present on the tumor cell surface. Activation of CD8+ T cells requires at least two signals from antigen presenting cells: binding of their T cell receptor (TCR) to the appropriate peptide presented on MHC I and co-stimulation by B7 binding to CD28. However, the TME possesses several mechanisms to reduce immune cell activity, such as the expression of checkpoint inhibitors dampening the immune system. Natural killer (NK) cells represent another type of cytotoxic cells, with their innate immune activity dictating an important role in anti-tumor immunity. NK cells induce apoptosis via the release of perforin and granzymes from granules, eliminating cells lacking expression MHC I, including cancer cells that have lost expression of MHC I. However, also the activity of NK cells can be hampered in the TME, notably by the PD1/PDL1 interaction.Increasing the activity of CD8+ T and NK cells as a therapeutic anti-tumor strategy has become an important point of attention. Such strategies can have several shapes, with Antibody-dependent cell-mediated cytotoxicity (ADCC) activity of IgG1 isotypes being one of the mechanisms that can be exploited by immunoglobulin-based therapeutics. Another way to increase the killing of tumor cells is to re-direct T cells to tumor cells by employing bi-specific antibodies targeting specific tumor associated antigens. Using this strategy, T cell activation can be concentrated in the TME, thereby also avoiding off-tumor activity. Real-time in vitro assessment of the potential enhanced killing capacity of CD8+ T and NK cells elicited by test molecules could further provide pivotal information on the functional dynamics of test molecules. Using high quality primary human immune cells, in vitro bioassays were developed with improved robustness and reproducibility to screen for the potential to enhance tumor cell killing by novel therapeutics. The ability to evaluate the compounds capacity to increase or induce a cytotoxic activity profile and thereby facilitate the anti-tumor immune response is essential in the early drug development process. Citation Format: Johan Arnold, Thibaut J. Janss, Simon Lefevre, Martijn Vlaming, Ellen Boelen, Sofie Pattijn. In vitro killing assays for evaluation of immuno-oncology drug candidates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1389.

SUMMARY The rapid, global dispersion of SARS-CoV-2 since its initial identification in December 2019 has led to the emergence of a diverse range of variants. The initial concerns regarding the virus were quickly compounded with concerns relating to the impact of its mutated forms on viral infectivity, pathogenicity and immunogenicity. To address the latter, we seek to understand how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic, before mass vaccination. We analyzed a total of 330,246 high quality SARS-CoV-2 genome assemblies sampled across 143 countries and all major continents. Strikingly, we found that specific mutational patterns in SARS-CoV-2 diversify T cell epitopes in an HLA supertype-dependent manner. In fact, we observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family. In addition, we show that this predicted global loss of epitopes is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7 supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic. Together, our study lays the foundation to help understand how SARS-CoV-2 mutants shape the repertoire of T cell targets and T cell immunity across human populations. The proposed theoretical framework has implications in viral evolution, disease severity, vaccine resistance and herd immunity.

Abstract The need to better understand the tumor microenvironment (TME) dictates the characterization of the cell types involved, the roles they play and how they respond to treatment. To develop better cancer immunotherapies, in vitro primary immune cell bioassays offer an early assessment of their effects on the various players of the TME. Cytotoxic cells are key players in the anti-tumor immune response. CD8+ T cells, also known as cytotoxic T lymphocytes, recognize and kill cells presenting antigens bound to MHC class I molecules, such as neoantigen present on the tumor cells. Activation of CD8+ T cells requires at least two signals from antigen presenting cells: binding of their T cell receptor (TCR) to the appropriate peptide presented on MHC I and co-stimulation by B7 binding to CD28. However, tumor environment developed different mechanisms to reduce this immune cell killing such as checkpoint inhibitors expression. In that case, the immune system will be dampened. A second type of cytotoxic cells, named Natural killer cells, are an innate immune cell type that plays an important role in anti-cancer immunity. NK cells target cells lacking MHC I expression, including cancer cells that have lost expression of MHC I. NK cells induce apoptosis in cancer cells via release of perforin and granzymes from granules, like CD8+ T cells. But here too, NK cells can be broken down by the tumor cells, notably by the PD1/PDL1 interaction. Increasing their efficacy as a therapeutic strategy has made the development of new therapeutics enhancing their anti-tumor response a priority. Those new therapeutics can have several shapes. The Antibody-dependent cell-mediated cytotoxicity (ADCC) activity of the IgG1 isotypes is one of the mechanisms that can be applied by immunoglobulin-based therapeutics. Another way to increase the killing of cancer cells is to target tumor antigens expressed by those cells using for example bispecific molecules that will enhance on the other side the T cell activation. Using primary immune cells, in vitro bioassays were developed to better screen the potential effect of new therapeutics on immune cell killing activity. Their ability to increase or induce a cytotoxic activity and facilitate the anti-tumor immune response can as a result be assessed early in the drug development process. Citation Format: Thibaut J. Janss, Juliette Lamy, Johan Arnold, Ellen Boelen, Sofie Pattijn. In vitro killing assays for immuno oncology candidates [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 3199.

Abstract The need to better understand the tumor microenvironment (TME) dictates the characterization of the cell types involved, the roles they play and how they respond to treatment. To develop better cancer immunotherapies, in vitro primary immune cell bioassays offer an early assessment of their effects on the various players of the TME. Exhausted T cells were first discovered in LCMV virus infections where chronic stimulation due to remaining virus antigens leads to T cells that stop responding to stimulation and lose their functionality (cytokine secretion and cytotoxic activity). The same phenotype was afterwards found in the tumor microenvironment where a lot of T cells were found to be “anergic”. Reversing their loss of functionality as a therapeutic strategy has made the characterization of these exhausted T cells a priority. Their phenotype is currently defined by an increase in the expression of a specific set of cell surface markers such as PD-1, TIM-3 and LAG-3. As exhaustion builds, the expression of these markers increases while T cell functionality decreases. The loss of functionality is defined by a reduction in cytokine secretion, proliferation, and cytotoxic activity in the presence of an antigen. To evaluate this phenotype in more depth, transcription factors can also be monitored. For example, BLIMP-1 and BATF, which play a role in PD-1 expression, are shown to increase following exhaustion. New therapeutics that can reverse exhausted phenotype lead to a new population of T cells called reinvigorated T cells which possesses high effector activity such as cytotoxicity towards cancer cells. Using primary immune cells, in vitro bioassays were developed to better screen the potential effect of new therapeutics on exhausted T cells. Their ability to reverse the exhausted phenotype and facilitate the anti-tumour immune response can as a result be assessed early in the drug development process. Citation Format: Thibaut J. Janss, Juliette Lamy, Johan Arnold, Sofie Pattijn. In vitro exhausted T cell assays [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 3198.

Long-term immunity to coronaviruses likely stems from T cell activity. We present here a novel approach for the selection of immunoprevalent SARS-CoV-2-derived T cell epitopes using an in silico cohort of HLA-genotyped individuals with different ethnicities. Nine 30-mer peptides derived from the four major structural proteins of SARS-CoV-2 were selected and included in a peptide vaccine candidate to recapitulate the broad virus-specific T cell responses observed in natural infection. PolyPEPI-SCoV-2-specific, polyfunctional CD8(+) and CD4(+) T cells were detected in each of the 17 asymptomatic/mild COVID-19 convalescents' blood against on average seven different vaccine peptides. Furthermore, convalescents' complete HLA-genotype predicted their T cell responses to SARS-CoV-2-derived peptides with 84% accuracy. Computational extrapolation of this relationship to a cohort of 16,000 HLA-genotyped individuals with 16 different ethnicities suggest that PolyPEPI-SCoV-2 vaccination will likely elicit multi-antigenic T cell responses in 98% of individuals, independent of ethnicity. PolyPEPI-SCoV-2 administered with Montanide ISA 51 VG generated robust, Th1-biased CD8(+), and CD4(+) T cell responses against all represented proteins, as well as binding antibodies upon subcutaneous injection into BALB/c and hCD34(+) transgenic mice modeling human immune system. These results have implications for the development of global, highly immunogenic, T cell-focused vaccines against various pathogens and diseases.

Abstract The increasing interest in the tumour microenvironment leads to focus on new bioassays to represent all the players of the cancer immune response. Some of these players like Tumour Associated Macrophages (TAM) and Myeloid Derived Suppressor Cells (MDSC) play an important role by downregulating the anti-tumour response. Their regulation mechanisms constitute an important target for new therapeutics. In order to study these mechanisms in a human model, suppressive bioassays, mimicking the suppressive action of these cells on T cells activations, were developed. One of the important players in the tumor microenvironment are the macrophages which possess important active and regulatory functions in both innate and adaptive immune responses. Classical activated macrophages, also classified as M1-like macrophages, comprise immune effector cells with an acute inflammatory phenotype while the alternatively activated M2-like macrophages have suppressive and healing capacities. Tumor associated macrophages (TAMs) are present at high densities in solid tumors and share many characteristics with so called M2 macrophages. Although distinguished classification and in vitro generation and polarization of M1- and M2-like macrophages is challenging, in vitro assays can be a first step to screen the effect of the test molecules on the phenotype and function of the macrophages. For example, macrophage precursors display extraordinary plasticity in response to exogenous and endogenous stimuli which can lead them to M2-polarized macrophages or towards the M1-activated status. Using in vitro polarization and functional macrophage assays, one can screen molecules with the potential to influence M1 and M2 like macrophage generation and polarization. Next to that, the effect of the test molecules on the function of the macrophages can be evaluated using a macrophage suppressive assay. Here the ability of the molecules to reverse the stimulating effect of the M1-macropahges or suppressive effect of the M2-macrophages on T cells can be determined by measuring their proliferation and cytokine production. Myeloid-derived suppressor cells (MDSC) can also be found in the tumour microenvironment and present a highly suppressive phenotype. Their role in relation to cancer development and progression has shown to be of great importance. Therefore, the ability of molecules to reverse the suppressive function of the MDSC can be evaluated in vitro using these cell-type specific suppressive bioassays. The use of the bioassays contributes to a better understanding of the tumour microenvironment and the steps needed to generate an anti-tumour response by the immune system will help to assess the functional potential of new drugs, design clinical trials and ultimately discover relevant biomarkers. Citation Format: Amin Osmani, Thibaut Janss, Thibault Jonckheere, Séverine Giltaire, Sofie Pattijn, Jana Schockaert. Suppressive bioassays using macrophages and MDSCs [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 414.

Abstract New immuno-oncology mAbs or agents with other structures have revolutionized treatment options for several malignancies in the past few years, and more are currently being evaluated in the clinic. The development of new therapeutics comes with a series of challenges and questions, of which one is the risk for unwanted immunogenicity which can lead to decreased efficacy and safety concerns. Today, both in silico and in vitro preclinical tools are available to identify early on therapeutic candidates with a high immunogenicity risk potential. Additionally, certain tools can be used to mitigate the immunogenicity potential, and thus improve and accelerate therapeutic drug development and reduce the number of clinical failures. Often used as a first step is an in silico T cell epitope prediction algorithm such as NetMHCIIpan which can be used to assess and compare the immunogenic potential of the lead candidates and guide de-immunization strategies. Further monitoring of the immunogenic risk can be performed using different in vitro assays: a peptide screen assay, to enable the exclusion of immunogenic peptides and the inclusion of low risk sequences; a dendritic cell activation assay to assess immunogenicity signals for the whole product; the MAPPs or MHC Associated Peptide Proteomics, assay to follow uptake, processing and presenting of biotherapeutics by dendritic cells and identify specific regions of concern, and; in vitro T cell proliferation and activation assays to determine and rank the immunogenic risk of the test proteins. The compilation of the different datasets and translation of the results into a comprehensive risk management plan, allows selection of the best candidates to move forward into humans, deimmunization of test candidates and identification and discontinuation of the high-risk candidates as early as possible. Citation Format: Amin Osmani, Sofie Pattijn, Jana Schockaert, Aurélie Mazy, Chloé Ackaert. Immunogenicity risk assessment and mitigation tools [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 701.

Recombinant DNA technology has, in the last decades, contributed to a vast expansion of the use of protein drugs as pharmaceutical agents. However, such biological drugs can lead to the formation of anti-drug antibodies (ADAs) that may result in adverse effects, including allergic reactions and compromised therapeutic efficacy. Production of ADAs is most often associated with activation of CD4 T cell responses resulting from proteolysis of the biotherapeutic and loading of drug-specific peptides into major histocompatibility complex (MHC) class II on professional antigen-presenting cells. Recently, readouts from MHC-associated peptide proteomics (MAPPs) assays have been shown to correlate with the presence of CD4 T cell epitopes. However, the limited sensitivity of MAPPs challenges its use as an immunogenicity biomarker. In this work, MAPPs data was used to construct an artificial neural network (ANN) model for MHC class II antigen presentation. Using Infliximab and Rituximab as showcase stories, the model demonstrated an unprecedented performance for predicting MAPPs and CD4 T cell epitopes in the context of protein-drug immunogenicity, complementing results from MAPPs assays and outperforming conventional prediction models trained on binding affinity data.

Abstract The need to better understand the tumour microenvironment (TME) dictates the characterization of the cell types involved, the roles they play and how they respond to treatment. To develop better cancer immunotherapies, in vitro primary immune cell bioassays offer an early assessment of their effects on the various players of the TME. Here we describe the development of an exhausted T cell assay and demonstrate its potential in identifying candidates that can reverse exhaustion. Exhausted T cells were first discovered in LCMV virus infections where chronic stimulation due to remaining virus antigens leads to T cells that stop responding to stimulation and lose their functionality (cytokine secretion and cytotoxic activity). The same phenotype was afterwards found in the tumor microenvironment where a lot of T cells were found to be “anergic”. Reversing their loss of functionality as a therapeutic strategy has made the characterization of these exhausted T cells a priority. Their phenotype is currently defined by an increase in the expression of a specific set of cell surface markers such as PD-1, TIM-3 and LAG-3. As exhaustion builds, the expression of these marker increases while T cell functionality decreases. The loss of functionality is defined by a reduction in cytokine secretion, proliferation and cytotoxic activity in the presence of an antigen. To evaluate this phenotype in more depth, transcription factors can also be monitored. For example, BLIMP-1 and BATF, which play a role in PD-1 expression, are shown to increase following exhaustion. Using primary immune cells, in vitro bioassays were developed to better screen the potential effect of new therapeutics on exhausted T cells. Their ability to reverse the exhausted phenotype and facilitate the anti-tumour immune response can as a result be assessed early in the drug development process. These experiments help advance our understanding of the tumour microenvironment and optimize the therapeutic effects of new drugs, design better clinical trials and ultimately discover relevant biomarkers. Citation Format: Amin Osmani, Juliette Lamy, Thibaut Janss, Séverine Giltaire, Sofie Pattijn, Jana Schockaert. In vitro exhausted T cell assay for immuno-oncology candidates [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 4992.

We developed a global peptide vaccine against SARS-CoV-2 that addresses the dual challenges of heterogeneity in the immune responses of different individuals and potential heterogeneity of the infecting virus. PolyPEPI-SCoV-2 is a polypeptide vaccine containing nine 30-mer peptides derived from all four major structural proteins of the SARS-CoV-2. Vaccine peptides were selected based on their frequency as HLA class I and class II personal epitopes (PEPIs) restricted to multiple autologous HLA alleles of individuals in an in silico cohort of 433 subjects of different ethnicities. PolyPEPI-SCoV-2 vaccine administered with Montanide ISA 51VG adjuvant generated robust, Th1-biased CD8 + and CD4 + T cell responses against all four structural proteins of the virus, as well as binding antibodies upon subcutaneous injection into BALB/c and CD34 + transgenic mice. In addition, PolyPEPI-SCoV-2-specific, polyfunctional CD8 + and CD4 + T cells were detected ex vivo in each of the 17 asymptomatic/mild COVID-19 convalescents’ blood investigated, 1–5 months after symptom onset. The PolyPEPI-SCoV-2-specific T cell repertoire used for recovery from COVID-19 was extremely diverse: donors had an average of seven different peptide-specific T cells, against the SARS-CoV-2 proteins; 87% of donors had multiple targets against at least three SARS-CoV-2 proteins and 53% against all four. In addition, PEPIs determined based on the complete HLA class I genotype of the convalescent donors were validated, with 84% accuracy, to predict PEPI-specific CD8 + T cell responses measured for the individuals. Extrapolation of the above findings to a US bone marrow donor cohort of 16,000 HLA-genotyped individuals with 16 different ethnicities (n=1,000 each ethnic group) suggest that PolyPEPI-SCoV-2 vaccination in a general population will likely elicit broad, multi-antigenic CD8 + and CD4 + T cell responses in 98% of individuals, independent of ethnicity, including Black, Asian, and Minority Ethnic (BAME) cohorts.