Abstract CT153: TiTAN: a phase 1 study of GEN-011, a neoantigen-targeted peripheral blood-derived T cell therapy with broad neoantigen targeting

TiTAN™ is an open-label, multi-center Phase1/2a trial evaluating safety, tolerability, T-cell persistence and proliferation, and clinical activity in patients with some solid tumors. Adoptive T-cell therapies (ACT) have resulted in durable clinical responses in some patients, but many are resistant. Resistance may be due to multiple factors including antigen heterogeneity or loss, immune editing, exhausted immune responses or naturally occurring immune suppressive T-cell responses. Tumors can also express Inhibigens™, antigenic targets of suppressive T cells, which may be inadvertently expanded in the non-specific ACT manufacturing process. In animal models, Inhibigen-specific responses drive tumor hyperprogression. GEN-011, a neoantigen-targeted, autologous peripheral T cell (NPT) therapy, contains tumor-specific T cells with broad neoantigen specificity. Patients undergo sequencing of tumor from fixed tissue and selection of neoantigens by ATLAS™, an ex vivo assay that directly identifies immunogenic neoantigens for use in manufacturing NPTs, and also Inhibigens for exclusion. The patient’s peripheral T cells and monocyte-derived dendritic cells are incorporated into the proprietary PLANET™ manufacturing process where they are specifically stimulated with up to 30 ATLAS-confirmed neoantigens in a scalable, closed system. The TiTAN clinical trial is testing a low dose regimen of GEN-011 without lymphodepletion and a single dose of GEN-011 with lymphodepletion and IL-2. To date, 19 patients with assorted solid tumors have been screened with ATLAS, prioritizing an average of 12 neoantigens (range 0-43) and excluding 14 Inhibigens (range 1-55) per patient. Of the 10 patients entering PLANET, 100% have successfully yielded a released drug product. To date, 5 patients with NSCLC or SCCHN have been dosed with escalating cell numbers and lymphodepletion/IL-2 regimens without DLT. Early data show effector and central memory T-cell proliferation by day 5 post infusion, which peak between days 8 and 15. Neoantigen-specific T cells remain detectable in the peripheral blood for at least 36 days. Early best response from 4 evaluable patients are one PD and one mixed response in the low dose cohort, and in the more intense regimen a SD with reduction in tumor with resolution of pain and neuropathy extending for 2 months, and the fourth had stable disease. Maximum grade 2 CRS and one grade 2 ICANS peaked around day 8 in parallel to cell expansion and no patients required tocilizumab or corticosteroids. Upcoming patients will receive more intensive lymphodepletion and then higher dose IL-2. Taken together, these early data support the biological activity of GEN-011. Using a personalized immune assay to identify neoantigens, and to exclude Inhibigens, to generate tumor specific T cells may offer a more accessible and promising ACT for treating solid tumors.

Citation Format: Maura Gillison, Jiaxin Niu, Daniel Olson, Mark Stein, David Aggen, Utkarsh Acharya, Benjamin Creelan, Richard Hernandez, Jessica Price, Kevin J. Mancini, Louisa Dowal, James Foti, Vijetha Vemulapalli, Mara Shainheit, Masoud Golshadi, Raymond D. Stapleton, Jessica B. Flechtner, Thomas A. Davis. TiTAN: a phase 1 study of GEN-011, a neoantigen-targeted peripheral blood-derived T cell therapy with broad neoantigen targeting [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 CT153.

Abstract 2745: The PLANET manufacturing process reproducibly generates high-quality neoantigen-targeted peripheral T cells (NPTs) for adoptive T cell therapy in the TiTAN clinical trial

Background: Neoantigen (neoAg)-specific T cells can be found in the peripheral blood of patients with solid tumors, and the infiltration of fresh, peripherally derived T cells into tumors has been associated with successful outcomes after checkpoint blockade therapy. We previously described the development of our PLANET™ manufacturing process to create NPTs, based on the empirical identification of neoAgs using the ex vivo ATLAS™ bioassay, for adoptive transfer into patients with cancer. We have initiated the TiTAN™ clinical trial (NCT04596033) to evaluate this candidate immunotherapy, GEN-011, in subjects with checkpoint refractory solid tumors. Here we report the successful manufacturing of NPTs to support the ongoing trial.

Methods: Apheresis, FFPE tumor and saliva samples were procured from subjects who consented to participate in the trial. Monocytes and T cells were isolated and cryopreserved. Patient-specific neoAgs against which their T cells were responsive were identified with ATLAS, and up to 30 neoAgs were prioritized for manufacture; pro-tumor Inhibigens™ were excluded. Cryopreserved peripheral blood monocytes and T cells were thawed, monocytes derived into dendritic cells, and then neoAg-specific T cells expanded in the fully closed PLANET manufacturing process. The NPTs were formulated and cryopreserved for administration to patients after release testing.

Results: Subjects with five different solid tumor types contributed to these data: CSC, NSCLC, SCLC, SCCHN, and melanoma. A median of 2.1bn monocytes and 6bn T cells were cryopreserved from apheresis products (N=17). The median TMB was 1.8mut/Mb (range 0.01-36.6) with 473 somatic mutations (range 32-8893); the number of non-synonymous mutations ranged from 9 to 767. ATLAS screens identified a mean of 13±4 neoAgs and 11±3 Inhibigens, resulting in an average of 13 (range 2-30) unique neoAgs in each PLANET manufacturing process. Upon conclusion of manufacturing, the mean yield per patient was 1.6±0.3bn NPTs across runs (N=9) completed by the time of data cutoff. Characterization tests revealed the NPTs were consistently 80-90% CD8+ and 10-20% CD4+ T cells, of which 97% (range 64.9-99.8%) were effector memory and 1% (range 0.1-32.3%) central memory. The median purity at release was 98% with 82% viability. By functional assessments, the NPTs retained specificity for 91% (range 82-100%) of their intended neoAg targets (N=4). Administratable doses were successfully manufactured for 100% of patients to date.

Conclusions: NPTs can routinely be manufactured in a GMP setting to treat patients with solid tumors. By expanding fresh, non-exhausted NeoAg-specific T cells with known tumor specificity from the periphery, GEN-011 has the potential to provide clinical benefits of TIL with greater accessibility and minimal irrelevant T cells. The TiTAN trial is ongoing.

Citation Format: Harshal Zope, Rounak Nande, Manish Jain, Charley Hubbard, Louisa Dowal, James Foti, James Loizeaux, Crystal Cabral, Daniel B. DeOliveira, Guohan Yang, Mercay Reuter, Jessica Baker Flechtner, Raymond Stapleton. The PLANET manufacturing process reproducibly generates high-quality neoantigen-targeted peripheral T cells (NPTs) for adoptive T cell therapy in the TiTAN clinical trial [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 2745.

Abstract LB-223: ATLASTMreveals a dominant inhibitory antigen in melanoma patients, and a reduced breadth of tumor-associated antigen-specific T cells in non-responders to checkpoint blockade

Broadly reinvigorating the T cell response by blocking immune-inhibitory receptors can produce durable clinical benefit in 20-40% of melanoma patients. Due to low response rates and potential toxicity of checkpoint therapy, identification of biomarkers to predict response to immune checkpoint inhibitors (ICIs) has the potential to stratify patients and increase the efficacy of ICI therapy in treated patients. However, to date, the significant effort to identify biomarkers has yielded unreliable predictors. To better understand ICI response and resistance, we profiled T cell responses to a panel of known tumor-associated antigens (TAAs).

The ex vivo ATLAS™ technology enables comprehensive profiling of a patient’s antigen-specific T cells, with putative antigens expressed as individual clones, processed by the subject’s own antigen presenting cells and presented to autologous CD4+ or CD8+ T cells for measurement of recall responses. A unique feature of ATLAS is the ability to identify stimulatory and inhibitory T cell responses based on cytokine secretion that statistically exceeds or is reduced, respectively, relative to baseline controls.

Pre- and post-treatment CD4+ and CD8+ T cell responses to a library of 56 known TAAs were profiled from 16 patients with metastatic melanoma undergoing ICI therapy. Consistent with previous studies, a low frequency of responses was observed from both T cell subsets. Overall, there were fewer responses detected in non-responders than in responders both pre- and post-treatment; in fact, no stimulatory CD8+ T cell responses were identified in non-responders prior to ICI therapy. Surprisingly, one TAA elicited only inhibitory responses across most subjects, independently of clinical outcome and predominantly from the CD8+ T cell subset. Hierarchical clustering showed that patient responses are similar to themselves across visits, but the antigen profiles across patients did not cluster by visit or treatment response.

ATLAS provides a powerful, non-invasive, blood-based platform for the interrogation of peripheral T cell responses. Our data show that melanoma patients who are non-responsive to ICI therapy have a limited T cell response to TAAs. In addition, one TAA elicited a dominant inhibitory response across patients. Upon further refinement, patient-specific responses may allow for prediction of advanced melanoma patients for whom checkpoint therapy would prove successful.

Citation Format: Louisa Dowal, Anna Lyubetskaya, Crystal Cabral, Mariya Croll, Christopher Warren, James Perry, Melissa Hayes, James Loizeaux, James Foti, Jessica B. Flechtner, Jason R. Dobson, F. Stephen Hodi, Wendy Broom. ATLASTMreveals a dominant inhibitory antigen in melanoma patients, and a reduced breadth of tumor-associated antigen-specific T cells in non-responders to checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-223.

A phase 1/2a study of GEN-009, a neoantigen vaccine based on autologous peptide immune responses

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Background: Tumor-specific neoantigens provide individualized targets for immunotherapy. In silico selection methods are sub-optimal at predicting immunogenic targets, missing up to 70% of true neoantigens. ATLAS is a powerful tool that screens all candidate neoantigens for pre-existing patient-specific CD4 or CD8 responses in an HLA agnostic assessment. ATLAS also identifies inhibitory peptides that may suppress tumor immunity and accelerate tumor progression. The GEN-009 vaccine contains stimulatory but no inhibitory peptide antigens. Methods: GEN-009-101 is a first-in-human phase 1/2a study testing platform feasibility, safety, immunogenicity and clinical activity in selected solid tumors. After next-generation tumor sequencing and cytokine-based ATLAS assessment using autologous T cells and APCs, up to 20 stimulatory synthetic long peptides are used in each personalized vaccine. GEN-009 is administered with poly-ICLC on weeks 0, 3, 6, 12 and 24. Part A, a safety and immunogenicity pilot, has completed target enrollment of patients without evidence of disease to receive GEN-009; Part B has 5 tumor-specific cohorts of up to 15 pts naïve to PD-1 blockade who will receive GEN-009 with a SOC immunotherapy; Part C: up to 15 pts refractory to PD-1 inhibitors will receive GEN-009 monotherapy. Results: GEN-009 has been successfully generated for patients. Repeated dosing has been well tolerated with mild local discomfort and no DLT. ATLAS screening results below show notable interpatient variability; one subject had only CD4 neoantigens, one had only CD8, another had a strong CD8 bias, and one patient had prominent inhibitory peptides. Conclusions: GEN-009 is a neoantigen vaccine that personalizes tumor specific targets and the individual patient’s capacity to respond. Immunogenicity data will assess CD4 and CD8 T cell responses to each vaccine neoantigen. Clinical trial information: NCT03633110. [Table: see text]

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 >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.

Abstract 730: Neoantigen identification using the ATLAS T cell profiling platform highlights the need to empirically define neoantigens

Neoantigens arise from tumor-specific, somatic mutations and have the potential to be recognized by T cells that are associated with anti-tumor immune responses. Since they are non-self, they are hypothesized to provide an attractive therapeutic modality because T cells that can respond to those sequences have not undergone thymic selection. The ATLASTM platform enables identification of biologically relevant CD4+ and CD8+ T cell neoantigens in any subject in an unbiased manner, overcoming the limitations of conventional in silico predictive approaches. The ATLAS platform utilizes matched patient tumor biopsy and blood samples to identify recall T cell responses to tumor specific mutations. From patient peripheral blood, CD14+ monocytes were isolated and differentiated into dendritic cells (MDDCs), and T cells were sorted into CD4+ and CD8+ populations and non-specifically expanded. Tumor-specific changes (single nucleotide variants and insertion/deletions) were identified through whole exome sequencing and cloned into E. coli expression vectors with and without co-expressed listeriolysin O to enable presentation via MHC class I or class II, respectively. For each patient, their unique clones were co-cultured with autologous MDDCs in an ordered array, then their CD4+ or CD8+ T cells were added and incubated overnight. T cell activation was determined by measurement of TNF-α and IFN-γ levels in the supernatants by a Meso-Scale Discovery assay. Neoantigens were defined as clones that elicited cytokine responses >2 median absolute deviations from the median of negative control clones. Historically, ATLAS has identified CD4+ and CD8+ T cells responses to up to 15% of mutant polypeptide sequences. Here we will present ATLAS profiling of T cell responses to >2,500 potential neoantigens, across a broad cohort of patients with different tumor types, including tumors with a wide range of mutational burden. T cell responses detected by ATLAS challenge assumptions in the field, with the majority of empirically identified neoantigens not predicted by algorithms, and many predicted neoantigens demonstrating “inhibitory” activity. When exploring neoantigens selected by ATLAS by tumor type, no patterns in overall mutational burden, RNA expression level, or DNA mutant allele frequency have yet been identified. We will also present broader functional analysis, including pathway analysis of proteins containing neoantigens, review of the immunogenicity of known oncogenes and features of immunogenic peptide sequences. The ATLAS platform empirically defines which potential neoantigens created by somatic mutations elicit immune responses in individual patients independently of a patient's HLA type and T cell receptor repertoire. This approach provides the opportunity to identify better targets to include in a personalized vaccine formulation.

Citation Format: Jason Dobson, Huilei Xu, Johanna Kaufmann, James Foti, Jin Yuan, Michael O''Keeffe, Crystal Cabral, James Loizeaux, Christopher Warren, Ning Wu, Erick Donis, Kyle Ferber, Pamela Carroll, Jessica B. Flechtner, Wendy Broom. Neoantigen identification using the ATLAS T cell profiling platform highlights the need to empirically define neoantigens [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 730.

Report on the Development of the Advanced Encryption Standard (AES)

In 1997, the National Institute of Standards and Technology (NIST) initiated a process to select a symmetric-key encryption algorithm to be used to protect sensitive (unclassified) Federal information in furtherance of NIST's statutory responsibilities. In 1998, NIST announced the acceptance of 15 candidate algorithms and requested the assistance of the cryptographic research community in analyzing the candidates. This analysis included an initial examination of the security and efficiency characteristics for each algorithm. NIST reviewed the results of this preliminary research and selected MARS, RC™, Rijndael, Serpent and Twofish as finalists. Having reviewed further public analysis of the finalists, NIST has decided to propose Rijndael as the Advanced Encryption Standard (AES). The research results and rationale for this selection are documented in this report.

[Characteristics of the Gypsy population]

"The study sums up the number and socio-economic characteristics of [the] gipsy population in Hungary. The history of gipsy surveys, dating back more than one hundred years, is reviewed.... The present situation is described drawing on the 1990 population census and the data of a special gipsy survey carried out in 1993. In the course of their analysis the authors discuss in detail the demographic characteristics, regional structure, labour market position, household budget situation, and housing conditions of gipsies." (SUMMARY IN ENG)