Neoantigen-specific T-cell Responses Research Articles

T-cell Responses to Individualized Neoantigen Therapy mRNA-4157 (V940) Alone or in Combination with Pembrolizumab in the Phase 1 KEYNOTE-603 Study.

mRNA-4157 (V940) is an individualized neoantigen therapy targeting up to 34 patient-specific tumor neoantigens to induce T-cell responses and potentiate antitumor activity. We report mechanistic insights into the immunogenicity of mRNA-4157 via characterization of T-cell responses to neoantigens from the first-in-human, phase 1, KEYNOTE-603 study (NCT03313778) in patients with resected non-small cell lung cancer (Part A: 1-mg mRNA-4157, n = 4) or resected cutaneous melanoma (Part D: 1-mg mRNA-4157 + 200-mg pembrolizumab, n = 12). Safety, tolerability, and immunogenicity were assessed. All patients experienced ≥1 treatment-emergent adverse event; there were no grade 4/5 adverse events or dose-limiting toxicities. mRNA-4157 alone induced consistent de novo and strengthened preexisting T-cell responses to targeted neoantigens. Following combination therapy, sustained mRNA-4157-induced neoantigen-specific T-cell responses and expansion of cytotoxic CD8 and CD4 T cells were observed. These findings show the potential of a novel mRNA individualized neoantigen therapy approach in oncology. Significance: The safety and immunogenicity results from this phase 1 study of mRNA-4157 as adjuvant monotherapy or combination therapy with pembrolizumab show generation of de novo and enhancement of existing neoantigen-specific T-cell responses and provide mechanistic proof of concept to support further development of mRNA-4157 for patients with resected solid tumors. See related commentary by Berraondo et al., p. 2021.

Inhibition of DNMTs increases neoantigen-reactive T-cell toxicity against microsatellite-stable colorectal cancer in combination with radiotherapy

The therapeutic efficacy of immunotherapy is limited in the majority of colorectal cancer patients due to the low mutational and neoantigen burdens in this immunogenically “cold” microsatellite stability-colorectal cancer (MSS-CRC) cohort. Here, we showed that DNA methyltransferase (DNMT) inhibition upregulated neoantigen-bearing gene expression in MSS-CRC, resulting in increased neoantigen presentation by MHC class I in tumor cells and leading to increased neoantigen-specific T-cell activation in combination with radiotherapy. The cytotoxicity of neoantigen-reactive T cells (NRTs) to DNMTi-treated cancer cells was highly cytotoxic, and these cells secreted high IFNγ levels targeting MSS-CRC cells after ex vivo expansion of NRTs with DNMTi-treated tumor antigens. Moreover, the therapeutic efficacy of NRTs further increased when NRTs were combined with radiotherapy in vivo. Administration of DNMTi-augmented NRTs and radiotherapy achieved an ∼50 % complete response and extended survival time in an immunocompetent MSS-CRC animal model. Moreover, remarkably, splenocytes from these mice exhibited neoantigen-specific T-cell responses, indicating that radiotherapy in combination with DNMTi-augmented NRTs prolonged and increased neoantigen-specific T-cell toxicity in MSS-CRC patients. In addition, these DNMTi-augmented NRTs markedly increase the therapeutic efficacy of cancer vaccines and immune checkpoint inhibitors (ICIs). These data suggest that a combination of radiotherapy and epi-immunotherapeutic agents improves the function of ex vivo-expanded neoantigen-reactive T cells and increases the tumor-specific cytotoxic effector population to enhance therapeutic efficacy in MSS-CRC.

Phase I Trial of Viral Vector-Based Personalized Vaccination Elicits Robust Neoantigen-Specific Antitumor T-Cell Responses.

Personalized vaccines targeting multiple neoantigens (nAgs) are a promising strategy for eliciting a diversified antitumor T-cell response to overcome tumor heterogeneity. NOUS-PEV is a vector-based personalized vaccine, expressing 60 nAgs and consists of priming with a nonhuman Great Ape Adenoviral vector (GAd20) followed by boosts with Modified Vaccinia Ankara. Here, we report data of a phase Ib trial of NOUS-PEV in combination with pembrolizumab in treatment-naïve patients with metastatic melanoma (NCT04990479). The feasibility of this approach was demonstrated by producing, releasing, and administering to 6 patients 11 of 12 vaccines within 8 weeks from biopsy collection to GAd20 administration. The regimen was safe, with no treatment-related serious adverse events observed and mild vaccine-related reactions. Vaccine immunogenicity was demonstrated in all evaluable patients receiving the prime/boost regimen, with detection of robust neoantigen-specific immune responses to multiple neoantigens comprising both CD4 and CD8 T cells. Expansion and diversification of vaccine-induced T-cell receptor (TCR) clonotypes was observed in the posttreatment biopsies of patients with clinical response, providing evidence of tumor infiltration by vaccine-induced neoantigen-specific T cells. These findings indicate the ability of NOUS-PEV to amplify and broaden the repertoire of tumor-reactive T cells to empower a diverse, potent, and durable antitumor immune response. Finally, a gene signature indicative of the reduced presence of activated T cells together with very poor expression of the antigen-processing machinery genes has been identified in pretreatment biopsies as a potential biomarker of resistance to the treatment.

Abstract B017: NINJA PDAC: A robust murine pancreatic cancer organoid transplant model with inducible neoantigens for studying tumor microenvironment interactions with anti-tumor T-cell immunity

Abstract Pancreatic ductal adenocarcinoma (PDAC) is highly lethal due to early metastasis and poor therapeutic response including to anti-PD1/CTLA4-based immunotherapy, characteristics attributed to a desmoplastic tumor microenvironment (TME) and low immunogenicity. However, long-term human PDAC survivors exhibit higher neoantigen expression with active T-cell immunogenicity, and most human PDAC express predicted neoepitopes, arguing that T-cell mediated anti-tumor immunity shapes PDAC progression. By contrast, tumors in classical pre-clinical (KRASLSL-G12D; TRP53F/F; pancreas-specific Cre, or KPC) murine models exhibit low neoantigen burden, are non-immunogenic, with growth kinetics independent of T cells, making them poorly suited to study T-cell immunity. Combined chemoimmunotherapy regimens for human PDAC might be developed more efficiently via preclinical studies in murine models with physiologic stroma, defined neoantigens that can be induced in established tumors, and measurable neoantigen-specific T-cell responses. We developed NINJA PDAC, a novel, robust transplantable murine pancreatic cancer organoid model, to study neoantigen-specific anti-tumor T-cell responses and how they are influenced by the TME. The NINJA (Damo et al., 2021) system allows for spatially (Cre) and temporally (doxycycline+tamoxifen) controlled inducible expression of LCMV-derived neoantigens with low-to-moderate MHCI/II-binding affinity (GP33 and GP66, respectively) comparable to human PDAC, in Kras-mutated, p53-deficient PDAC organoids. Transplanted NINJA PDAC organoids engraft robustly both subcutaneously and orthotopically in syngeneic mice, with reproducible kinetics. Unlike 2D cell line transplants, these organoid-derived tumors have a complex ductal architecture, immune islands, and fibrotic stroma more representative of human PDAC. T-cell depletion studies demonstrated that full rejection of tumors with constitutive neoantigen expression (NINJA ‘ON’) requires both CD4+ and CD8+ neoantigen-specific T-cells, allowing the study of the roles of both helper and cytotoxic T-cells in anti-PDAC immunity. ‘Poised’ NINJA PDAC organoids do not express neoantigen until induction, and we confirmed high tumor neoantigen expression can be induced with doxycycline/tamoxifen in vivo (38%±18% neoantigen-expressing tumor cells). Early induction in vivo leads to intratumoral CD3+ T-cell infiltration, with increased neoantigen-specific (H2Db/gp33-41-tetramer positive) T-cells in tumors and tumor-draining lymph nodes. Late induction in vivo leads to neoantigen induction, but more muted T-cell infiltration and minimally attenuated tumor growth, suggesting a role of an established TME in suppressing T-cell responses. NINJA PDAC is a promising model that affords a high-fidelity toolset to study how murine neoantigen-specific anti-tumor T-cell responses are perturbed by the TME and further altered by host variables (such as obesity) that modulate the TME with the potential to expedite the development of new combination immunotherapies. Citation Format: Jeremy B. Jacox, Gena G. Foster, Dhruvi Shah, Nikhil S. Joshi, Mandar D. Muzumdar. NINJA PDAC: A robust murine pancreatic cancer organoid transplant model with inducible neoantigens for studying tumor microenvironment interactions with anti-tumor T-cell immunity [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B017.

Programming peptide-oligonucleotide nano-assembly for engineering of neoantigen vaccine with potent immunogenicity.

Background: Neoantigen nanovaccine has been recognized as a promising treatment modality for personalized cancer immunotherapy. However, most current nanovaccines are carrier-dependent and the manufacturing process is complicated, resulting in potential safety concerns and suboptimal codelivery of neoantigens and adjuvants to antigen-presenting cells (APCs). Methods: Here we report a facile and general methodology for nanoassembly of peptide and oligonucleotide by programming neoantigen peptide with a short cationic module at N-terminus to prepare nanovaccine. The programmed peptide can co-assemble with CpG oligonucleotide (TLR9 agonist) into monodispersed nanostructures without the introduction of artificial carrier. Results: We demonstrate that the engineered nanovaccine promoted the codelivery of neoantigen peptides and adjuvants to lymph node-residing APCs and instigated potent neoantigen-specific T-cell responses, eliciting neoantigen-specific antitumor immune responses with negligible systemic toxicity. Furthermore, the antitumor T-cell immunity is profoundly potentiated when combined with anti-PD-1 therapy, leading to significant inhibition or even complete regression of established melanoma and MC-38 colon tumors. Conclusions: Collectively, this work demonstrates the feasibility and effectiveness of personalized cancer nanovaccine preparation with high immunogenicity and good biosafety by programming neoantigen peptide for nanoassembly with oligonucleotides without the aid of artificial carrier.

A Sampling of Highlights from the Literature.

What We're Reading| May 03 2023 A Sampling of Highlights from the Literature: Article Recommendations from Our Deputy and Senior Editors Author & Article Information Online ISSN: 2326-6074 Print ISSN: 2326-6066 ©2023 American Association for Cancer Research2023American Association for Cancer Research Cancer Immunol Res (2023) 11 (5): 557. https://doi.org/10.1158/2326-6066.CIR-11-5-WWR Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record May 3 2023 Citation A Sampling of Highlights from the Literature: Article Recommendations from Our Deputy and Senior Editors. Cancer Immunol Res 1 May 2023; 11 (5): 557. https://doi.org/10.1158/2326-6066.CIR-11-5-WWR Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search Polyclonal neoantigen-specific T-cell responses associate with anti–PD-1 benefit (from Alex Ritter, Jennifer Lippincott Schwartz and Gillian Griffiths via NIH Flickr) To better understand differences in the immune response in patients with metastatic melanoma who do and do not have a clinical response to anti–PD-1 therapy, Puig-Saus et al. generated neoantigen-specific T cells from 11 patients using personalized neoantigen peptide–HLA libraries. Responding and nonresponding patients had neoantigen-specific CD8+ T cells in peripheral blood and tumor that recognized a limited number of mutations, but the CD8+ T cells from those who responded to therapy were more polyclonal, with multiple neoantigen-specific T-cell receptor clonotypes for the mutations, and were detected longitudinally, highlighting important immune characteristics of a successful clinical response to anti–PD-1 therapy. Puig-Saus C, …, Ribas A. Nature 2023 March 8;615:697–704. Neutrophils have a key role in tumor control following immunotherapy (from SVG) Neutrophils can have both pro- and... You do not currently have access to this content.

OncoVEXmGM-CSFexpands tumor antigen-specific CD8+ T-cell response in preclinical models

BackgroundCheckpoint inhibitors targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) have demonstrated clinical efficacy in advanced melanoma, but only a...

Towards next‐generation TIL therapy: TILs enriched in neoepitope‐specific T cells

Towards next‐generation TIL therapy: TILs enriched in neoepitope‐specific T cells

Combination Neoantigen-Based Dendritic Cell Vaccination and Adoptive T-Cell Transfer Induces Antitumor Responses Against Recurrence of Hepatocellular Carcinoma.

A high rate of recurrence after curative therapy is a major challenge for the management of hepatocellular carcinoma (HCC). Currently, no effective adjuvant therapy is available to prevent HCC recurrence. We designed a personalized neoantigen-loaded dendritic cell vaccine and neoantigen-activated T-cell therapy, and used it as adjuvant therapy to treat 10 patients with HCC who had undergone curative resection or radiofrequency ablation in the first stage of a phase II trial (NCT03067493). The primary outcomes were safety and neoantigen-specific immune response. Disease-free survival (DFS) was also evaluated. The immunotherapy was successfully administered to all the patients without unexpected delay and demonstrated a reasonable safety profile with no grade ≥3 treatment-related side effects reported. Seventy percent of patients generated de novo circulating multiclonal neoantigen-specific T-cell responses. Induced neoantigen-specific immunity was maintained over time, and epitope spreading was observed. Patients who generated immune responses to treatment exhibited prolonged DFS compared with nonresponders (P = 0.012), with 71.4% experiencing no relapse for 2 years after curative treatment. High expression of an immune stimulatory signature, enhanced immune-cell infiltration (i.e., CD8+ T cells), and upregulated expression of T-cell inflammatory gene profiles were found in the primary tumors of the responders. In addition, neoantigen depletion (immunoediting) was present in the recurrent tumors compared with the primary tumors (7/9 vs. 1/17, P = 0.014), suggesting that immune evasion occurred under the pressure of immunotherapy. Our study indicates that neoantigen-based combination immunotherapy is feasible, safe, and has the potential to reduce HCC recurrence after curative treatment.

Functional analysis of peripheral and intratumoral neoantigen-specific TCRs identified in a patient with melanoma

BackgroundNeoantigens derived from somatic mutations correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of therapeutic approaches in personalized...

High-throughput identification of conditional MHCI ligands and scaled-up production of conditional MHCI complexes.

Despite the need to monitor the impact of Cancer Immunotherapy (CI)/Immuno-Oncology (IO) therapeutics on neoantigen-specific T-cell responses, very few clinical programs incorporate this aspect of immune monitoring due to the challenges in high-throughput (HTP) generation of Major Histocompatibility Complex Class I (MHCI) tetramers across a wide range of HLA alleles. This limitation was recently addressed through the development of MHCI complexes with peptides containing a nonnatural UV cleavable amino acid (conditional MHCI ligands) that enabled HTP peptide exchange upon UV exposure. Despite this advancement, the number of alleles with known conditional MHCI ligands is limited. We developed a novel workflow to enable identification and validation of conditional MHCI ligands across a range of HLA alleles. First, known peptide binders were screened via an enzyme-linked immunosorbent assay (ELISA) assay. Conditional MHCI ligands were designed using the highest-performing peptides and evaluated in the same ELISA assay. The top performers were then selected for scale-up production. Next-generation analytical techniques (LC/MS, SEC-MALS, and 2D LC/MS) were used to characterize the complex after refolding with the conditional MHCI ligands. Finally, we used 2D LC/MS to evaluate peptide exchange with these scaled-up conditional MHCI complexes after UV exposure with validated peptide binders. Successful peptide exchange was observed for all conditional MHCI ligands upon UV exposure, validating our screening approach. This approach has the potential to be broadly applied and enable HTP generation of MHCI monomers and tetramers across a wider range of HLA alleles, which could be critical to enabling the use of MHCI tetramers to monitor neoantigen-specific T-cells in the clinic.

A Local and Low-Dose Chemotherapy/Autophagy-Enhancing Regimen Treatment Markedly Inhibited the Growth of Established Solid Tumors Through a Systemic Antitumor Immune Response.

Chemotherapy is one of the main options for the treatment of a variety of malignant tumors. However, the severe side effects resulting from the killing of normal proliferating cells limit the application of cancer-targeting chemotherapeutic drugs. To improve the efficacy of classic systemic chemotherapy, the local delivery of high-dose chemotherapeutic drugs was developed as a method to enhance local drug concentrations and minimize systemic toxicity. Studies have demonstrated that chemotherapy is often accompanied by cancer-associated immunogenic cell death (ICD) and that autophagy is involved in the induction of ICD. To improve the efficacy of local cancer chemotherapy, we hypothesized that the local delivery of chemotherapeutic plus autophagy-enhancing agents would enhance the promotive effects of ICD on the antitumor immune response. Here, we report that a low-dose chemotherapy/autophagy enhancing regimen (CAER) not only resulted in the increased death of B16F10 and 4T1 tumor cells, but also induced higher levels of autophagy in vitro. Importantly, the local delivery of the CARE drugs significantly inhibited tumor growth in B16F10 and 4T1 tumor-bearing mice. Systemic antitumor T-cell immunity was observed in vivo, including neoantigen-specific T-cell responses. Furthermore, bioinformatic analysis of human breast cancer and melanoma tissues showed that autophagy-associated gene expression was upregulated in tumor samples. Increased autophagy and immune cell infiltration in tumor tissues were positively correlated with good prognosis of tumor patients. This work highlights a new approach to improve the effects of local chemotherapy and enhance systemic antitumor immunity.

Synthetic High-density Lipoprotein Nanodiscs for Personalized Immunotherapy Against Gliomas.

Gliomas are brain tumors with dismal prognoses. The standard-of-care treatments for gliomas include surgical resection, radiation, and temozolomide administration; however, they have been ineffective in providing significant increases in median survival. Antigen-specific cancer vaccines and immune checkpoint blockade may provide promising immunotherapeutic approaches for gliomas. We have developed immunotherapy delivery vehicles based on synthetic high-density lipoprotein (sHDL) loaded with CpG, a Toll-like receptor-9 agonist, and tumor-specific neoantigens to target gliomas and elicit immune-mediated tumor regression. We demonstrate that vaccination with neoantigen peptide-sHDL/CpG cocktail in combination with anti-PD-L1 immune checkpoint blocker elicits robust neoantigen-specific T-cell responses against GL261 cells and eliminated established orthotopic GL261 glioma in 33% of mice. Mice remained tumor free upon tumor cell rechallenge in the contralateral hemisphere, indicating the development of immunologic memory. Moreover, in a genetically engineered murine model of orthotopic mutant IDH1 (mIDH1) glioma, sHDL vaccination with mIDH1 neoantigen eliminated glioma in 30% of animals and significantly extended the animal survival, demonstrating the versatility of our approach in multiple glioma models. Overall, our strategy provides a general roadmap for combination immunotherapy against gliomas and other cancer types.

Abstract CT173: PGV-001: A phase I trial of a multipeptide personalized neoantigen vaccine in the adjuvant setting

Abstract Background: Mutation-derived tumor antigens (MTAs) arise as a result of somatic mutations, such as nucleotide substitutions and small insertions/deletions. MTAs can serve as specific targets for antitumor therapy, including neoantigen vaccines. The goal of neoantigen vaccination is to help prime T cells to recognize such tumor-specific mutations. Here we describe a phase I trial testing a personalized genomic vaccine (PGV-001) in multiple histologies in the adjuvant setting (NCT02721043). Methods: This trial included patients with histologic diagnosis of solid malignancies or multiple myeloma with a >30% risk of recurrence but no measurable disease at the time of first vaccination. For each patient, HLA typing was performed, and the patient's tumor and germline DNA and tumor RNA were sequenced. Mutated peptides containing predicted neoantigens were selected using the OpenVax computational pipeline, which prioritizes somatic mutations by expression of the mutant allele in the tumor RNA and predicted MHC class I epitope binding for the patient's HLA type. A maximum of 10 peptides was included in each patient's personalized vaccine. The vaccine was administered over the course of 6 months, given in combination with poly-ICLC as the adjuvant. The primary objectives were to determine safety and tolerability, feasibility, and immunogenicity of the PGV-001 neoantigen vaccine. Results: The neoantigen vaccine was successfully administered to 13 patients, spanning 5 different tumor types. For each patient, an average of 1730 somatic mutations were identified (range 521-5106), of which 349 were coding variants (range 68-1493), 88 were coding and expressed in the tumor RNA (range 9-233), and 71 were coding, expressed and resulted in predicted MHC class I ligands (range 8-193). The urothelial, head & neck, and lung tumors resulted in larger numbers of predicted neoantigens than in the cases of multiple myeloma or breast tumors. Despite this difference, each of the 13 patient tumor samples showed enough of a neoantigen load to enable vaccination. We have also initiated analysis of immunogenicity, and early reports demonstrate neoantigen-specific CD4 and CD8 T-cell responses. Conclusions: The PGV-001 personalized neoantigen vaccine was successfully administered to 13 patients, where each patient's neoantigen load was adequate for vaccine synthesis. While we have demonstrated the computational feasibility of identification of neoantigens for inclusion in the PGV-001 genomic vaccine, clinical outcomes will be reported separately. Citation Format: Julia Kodysh, Thomas Marron, Alex Rubinsteyn, Tim O'Donnell, John Finnigan, Ana Blazquez, Mansi Saxena, Marcia Meseck, Philip Friedlander, Nina Bhardwaj. PGV-001: A phase I trial of a multipeptide personalized neoantigen vaccine in the adjuvant setting [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 CT173.

Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma.

Somatic mutations in cancer cells can give rise to novel protein sequences that can be presented by antigen-presenting cells as neoantigens to the host immune system. Tumor neoantigens represent excellent targets for immunotherapy, due to their specific expression in cancer tissue. Despite the widespread use of immunomodulatory drugs and immunotherapies that recharge T and NK cells, there has been no direct evidence that neoantigen-specific T-cell responses are elicited in multiple myeloma. Using next-generation sequencing data we describe the landscape of neo-antigens in 184 patients with multiple myeloma and successfully validate neoantigen-specific T cells in patients with multiple myeloma and support the feasibility of neoantigen-based therapeutic vaccines for use in cancers with intermediate mutational loads such as multiple myeloma. In this study, we demonstrate an increase in neoantigen load in relapsed patients with multiple myeloma as compared with newly diagnosed patients with multiple myeloma. Moreover, we identify shared neoantigens across multiple patients in three multiple myeloma oncogenic driver genes (KRAS, NRAS, and IRF4). Next, we validate neoantigen T-cell response and clonal expansion in correlation with clinical response in relapsed patients with multiple myeloma. This is the first study to experimentally validate the immunogenicity of predicted neoantigens from next-generation sequencing in relapsed patients with multiple myeloma. Our findings demonstrate that somatic mutations in multiple myeloma can be immunogenic and induce neoantigen-specific T-cell activation that is associated with antitumor activity in vitro and clinical response in vivo. Our results provide the foundation for using neoantigen targeting strategies such as peptide vaccines in future trials for patients with multiple myeloma.

Neoantigens in Hematological Malignancies-Ultimate Targets for Immunotherapy?

Neoantigens derive from non-synonymous somatic mutations in malignant cells. Recognition of neoantigens presented via human leukocyte antigen (HLA) molecules on the tumor cell surface by T cells holds promise to enable highly specific and effective anti-cancer immune responses and thus neoantigens provide an exceptionally attractive target for immunotherapy. While genome sequencing approaches already enable the reliable identification of somatic mutations in tumor samples, the identification of mutation-derived, naturally HLA-presented neoepitopes as targets for immunotherapy remains challenging, particularly in low mutational burden cancer entities, including hematological malignancies. Several approaches have been utilized to identify neoepitopes from primary tumor samples. Besides whole genome sequencing with subsequent in silico prediction of potential mutation-derived HLA ligands, mass spectrometry (MS) allows for the only unbiased identification of naturally presented mutation-derived HLA ligands. The feasibility of characterizing and targeting these novel antigens has recently been demonstrated in acute myeloid leukemia (AML). Several immunogenic, HLA-presented peptides derived from mutated Nucleophosmin 1 (NPM1) were identified, allowing for the generation of T-cell receptor-transduced NPM1mut-specific T cells with anti-leukemic activity in a xenograft mouse model. Neoantigen-specific T-cell responses have also been identified for peptides derived from mutated isocitrate dehydrogenase (IDHmut), and specific T-cell responses could be induced by IDHmut peptide vaccination. In this review, we give a comprehensive overview on known neoantigens in hematological malignancies, present possible prediction and discovery tools and discuss their role as targets for immunotherapy approaches.

First Results of Phase I/II Studies Evaluating Viral Vector-Based Heterologous Prime/Boost Immunotherapy Against Predicted HLA Class I Neoantigens Demonstrate CD8 T Cell Responses In Patients with Advanced Cancers

First Results of Phase I/II Studies Evaluating Viral Vector-Based Heterologous Prime/Boost Immunotherapy Against Predicted HLA Class I Neoantigens Demonstrate CD8 T Cell Responses In Patients with Advanced Cancers

Abstract CT096: Phase I study of in situ autologous vaccination for prostate cancer in a neo-adjuvant setting

Abstract Background: Certain solid malignancies like prostate cancer pose two major challenges for effective immunotherapy. The inherently low mutation load and spatial and temporal intra-tumor heterogeneity yields an immune exclusion and development of an “immune desert” within the tumor micro-environment (TME). Additionally, there is a response failure to immunomodulation, due to tumor/patient immunosuppressive mechanisms. In an effort to transform the prostate tumor environment into an immunogenic ecosystem, we are using PolyIC:LC as an immunemodulator. The novelty of this approach is a “host targeted”, in-situ “autovaccination” strategy, which uses the patient’s own tumor as the antigen source leading to activation of both an innate and adaptive immune response. As all patients will have their cancer removed after investigational therapy we can study baseline versus treatment induced changes in bio-specimens collected before, during, and after patients are exposed to PolyIC:LC. Correlative studies include characterization of tissue and systemic biomarkers of response using multiple platforms like cytometry by time of flight (CyTOF), RNA-seq, whole exome sequencing, seromics, TCR-sequencing, neoantigen specific T-cell responses, as well as assessing circulating tumor DNA (ctDNA) at multiple time points to determine the potential in detecting tumor response to immunemodulation. Methods: This is a Phase I dose escalation study (NCT03262103) seeking to determine a safe dose and schedule of intratumoral (IT) plus intramuscular (IM) PolyIC:LC injections prior to radical prostatectomy in patients with prostate cancer. The dose and frequency of IT PolyIC:LC will be increased in successive cohorts using a 3+3 design and traditional dose escalation rules. The dose and schedule of IM PolyIC:LC will remain fixed in successive cohorts. The study will consist of 24 enrolled subjects, recruited into cohorts consisting of a minimum of 3 and maximum of 6 patients per cohort. The first cohort, consisting of three patients, has been completed. Recruitment for the second cohort has begun with two patients already enrolled. The inclusion criteria extend to patients diagnosed with high risk (Gleason 7-10, cT2a-cT3b) clinically localized prostate cancer with no prior hormonal or radiation therapy and with plans to undergo radical prostatectomy. Week 1 serves as the priming course with the patient coming in for a pre-treatment biopsy followed by an IT injection. Weeks 3-6 consist of a booster treatment course with IM injections two times a week. Weeks 7-9 are a rest period with no injections followed by radical prostatectomy at week 10. Blood is drawn at weeks 1, 3, 6, and 9. At the time of surgery, blood, tissue, and lymph node are collected for research purposes. Following each IT and IM injection, the subject remains in clinic for monitoring for at least 1 hour or 30 minutes respectively. Patients are seen 6 weeks post-prostatectomy as per standard of care. The next follow-up visit is approximately 3 months following surgery where the first post-operative PSA check is performed. Assuming PSA levels are undetectable, the patient is followed up at routine intervals for PSA testing. Citation Format: Sujit S. Nair, Rachel Weil, Elena Gonzalez-Gugel, Marcia Meseck, Alex Rubinsteyn, Yulia Kodysh, Akriti Gupta, Keerthi Sadanala, Kacie Schlussel, Kamala Bhatt, Avinash Reddy, Rajan Patel, Tin Thawte, Adam Farkas, Siarhei Dzedzik, Kenneth Haines, Julia Wagner, Macy Robison, Cynthia Knauer, Andres Salazar, Matthew Galsky, Nina Bhardwaj, Ashutosh Tewari. Phase I study of in situ autologous vaccination for prostate cancer in a neo-adjuvant setting [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 CT096.

Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer

BackgroundEfficient identification of neoantigen-specific T-cell responses in epithelial ovarian cancer (EOC) remains a challenge. Existing investigations of spontaneous T-cell response to tumor neoepitope in EOC have taken the approach of comprehensive screening all neoantigen candidates, with a validation rate of 0.5–2%.MethodsWhole-exome and transcriptome sequencing analysis of treatment-naive EOC patients were performed to identify neoantigen candidates, and the immunogenicity of prioritized neoantigens was evaluated by analyzing spontaneous neoantigen-specfic CD4+ and CD8+ T-cell responses in the tumor and/or peripheral blood. The biological relevance of neoantigen-specific T-cell lines and clones were analyzed by evaluating the capacity of autologous ovarian tumor recognition. Genetic transfer of T-cell receptor (TCR) from these neoantigen-specific T-cell clones into peripheral blood T-cells was conducted to generate neoepitope-specific T-cells. The molecular signature associated with positive neoantigen T-cell responses was investigated, and the impacts of expression level and lymphocyte source on neoantigen identification were explored.ResultsUsing a small subset of prioritized neoantigen candidates, we were able to detect spontaneous CD4+ and/or CD8+ T-cell responses against neoepitopes from autologous lymphocytes in half of treatment-naïve EOC patients, with a significantly improved validation rate of 19%. Tumors from patients exhibiting neoantigen-specific T-cell responses exhibited a signature of upregulated antigen processing and presentation machinery, which was also associated with favorable patient survival in the TCGA ovarian cohort. T-cells specific against two mutated cancer-associated genes, NUP214 and JAK1, recognized autologous tumors. Gene-engineering with TCR from these neoantigen-specific T-cell clones conferred neoantigen-reactivity to peripheral T-cells.ConclusionsOur study demonstrated the feasibility of efficiently identifying both CD4+ and CD8+ neoantigen-specific T-cells in EOC. Autologous lymphocytes genetically engineered with tumor antigen-specific TCR can be used to generate cells for use in the personalized adoptive T-cell transfer immunotherapy.

Neo-antigen specific memory T-cell responses in healthy individuals

ABSTRACTThe driver mutations in exon 9 of the calreticulin protein have only been identified in patients with myeloid cancers. We recently demonstrated that healthy individuals display strong and frequent T-cell responses towards this mutation. This memory T-cell response is likely evidence of the elimination of mutated cells in healthy individuals.