Neoantigen-specific T-cell Research Articles

Neoantigen-Specific T-Cell Immune Responses: The Paradigm of NPM1-Mutated Acute Myeloid Leukemia

The C-terminal aminoacidic sequence from NPM1-mutated protein, absent in normal human tissues, may serve as a leukemia-specific antigen and can be considered an ideal target for NPM1-mutated acute myeloid leukemia (AML) immunotherapy. Different in silico instruments and in vitro/ex vivo immunological platforms have identified the most immunogenic epitopes from NPM1-mutated protein. Spontaneous development of endogenous NPM1-mutated-specific cytotoxic T cells has been observed in patients, potentially contributing to remission maintenance and prolonged survival. Genetically engineered T cells, namely CAR-T or TCR-transduced T cells, directed against NPM1-mutated peptides bound to HLA could prospectively represent a promising therapeutic approach. Although either adoptive or vaccine-based immunotherapies are unlikely to be highly effective in patients with full-blown leukemia, these strategies, potentially in combination with immune-checkpoint inhibitors, could be promising in maintaining remission or preemptively eradicating persistent measurable residual disease, mainly in patients ineligible for allogeneic hematopoietic stem cell transplant (HSCT). Alternatively, neoantigen-specific donor lymphocyte infusion derived from healthy donors and targeting NPM1-mutated protein to selectively elicit graft-versus-leukemia effect may represent an attractive option in subjects experiencing post-HSCT relapse. Future studies are warranted to further investigate dynamics of NPM1-mutated-specific immunity and explore whether novel individualized immunotherapies may have potential clinical utility in NPM1-mutated AML patients.

Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing

BackgroundRecognition of neoantigens by T cells plays a major role in cancer immunotherapy. Identification of neoantigen-specific T-cell receptors (TCRs) has become a critical research tool for studying T cell-mediated responses...

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.

Adoptive transfer of neoantigen-specific T-cell therapy is feasible in older patients with higher-risk myelodysplastic syndrome

BackgroundMyelodysplastic syndromes (MDS) represent the most common type of acquired bone marrow failure in adults and is characterized by ineffective maturation of myeloid precursor cells and peripheral cytopenias associated with higher rates of infection, bleeding and transfusion dependence. In higher-risk patients with MDS who relapse or do not respond after standard hypomethylating agent (HMA) therapy, the 2-year survival rate is 15%. MethodsHere the authors report the feasibility and safety of a novel experimental T-cell therapy called personalized adoptive cell therapy, which selects, immunizes and expands T cells against MDS-specific mutations and is targeted to patient-specific tumor cell neoantigens. Somatic mutations serve as the pathogenic drivers of cancer, including MDS, as these transformative genetic mutations may generate novel immunogenic proteins (i.e., neopeptides and possible neoantigens) that may be targeted therapeutically. ResultsThe authors demonstrate that the adaptive immune system can be trained ex vivo to recognize neopeptides as neoantigens and that the infusion of culture-expanded, neoantigen-immunized autologous T cells has been feasible and safe in the three patients treated to date. DiscussionThe authors report on early results from their first-in-human phase 1 clinical trial that aims to assess the safety and tolerability of this novel form of adoptive T-cell immunotherapy for HMA-refractory patients with higher-risk MDS.

In vitro induction of neoantigen-specific T cells in myelodysplastic syndrome, a disease with low mutational burden

Therapies that utilize immune checkpoint inhibition work by leveraging mutation-derived neoantigens and have shown greater clinical efficacy in tumors with higher mutational burden. Whether tumors with a low mutational burden are susceptible to neoantigen-targeted therapy has not been fully addressed. To examine the feasibility of neoantigen-specific adoptive T-cell therapy, the authors studied the T-cell response against somatic variants in five patients with myelodysplastic syndrome (MDS), a malignancy with a very low tumor mutational burden. DNA and RNA from tumor (CD34+) and normal (CD3+) cells isolated from the patients’ blood were sequenced to predict patient-specific MDS neopeptides. Neopeptides representing the somatic variants were used to induce and expand autologous T cells ex vivo, and these were systematically tested in killing assays to determine the proportion of neopeptides yielding neoantigen-specific T cells. The authors identified a total of 32 somatic variants (four to eight per patient) and found that 21 (66%) induced a peptide-specific T-cell response and 19 (59%) induced a T-cell response capable of killing autologous tumor cells. Of the 32 somatic variants, 11 (34%) induced a CD4+ response and 11 (34%) induced a CD8+ response that killed the tumor. These results indicate that in vitro induction of neoantigen-specific T cells is feasible for tumors with very low mutational burden and that this approach warrants investigation as a therapeutic option for such patients.

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.

Trial in progress: Neoadjuvant immune checkpoint blockade in resectable malignant pleural mesothelioma.

TPS9078 Background: While the role of surgery in limited-stage (stage I-III) malignant pleural mesothelioma (MPM) is controversial, many centers have adopted an aggressive tri-modality approach incorporating (neo)adjuvant chemotherapy, surgical resection and radiotherapy. Despite this, most patients relapse and die from their disease. Immune checkpoint blockade (ICB) has shown promise in advanced MPM, but the mechanisms of response and resistance remain elusive. Improving the mechanistic understanding of ICB in MPM while concurrently optimizing the treatment strategy for limited-stage MPM are two urgent unmet needs. This multicenter multi-arm phase I/II study seeks to evaluate the safety and feasibility of neoadjuvant ICB in resectable MPM, incorporating novel genomic and immunologic analyses to deliver mechanistic insight into the biology of ICB in MPM. Methods: Patients with surgically resectable stage I-III treatment-naïve epithelioid or biphasic MPM receive neoadjuvant treatment with nivolumab every 2 weeks for 3 doses with or without 1 dose of ipilimumab (arm A: nivolumab monotherapy; arm B: nivolumab + ipilimumab). After macroscopic complete resection, patients receive optional investigator-choice adjuvant chemotherapy +/- radiation. Following this, patients will receive up to 1 year of adjuvant nivolumab. Feasibility and safety are co-primary endpoints of this study with feasibility defined by a delay in surgery of ≤24 days from the preplanned surgical date and safety defined by adverse events according to CTCAE v5.0. Bayesian-designed stopping rules have been implemented for feasibility and safety. Secondary endpoints include assessment of pathologic response and radiographic response using RECIST 1.1 for MPM. Correlative analyses will be performed on tissue specimens obtained pre- and post-ICB, as well as blood obtained pre, during, and post-ICB. Key correlates include multiplex immunofluorescence and longitudinal ctDNA assessment. Whole exome sequencing, T-cell receptor sequencing, and the MANAFEST functional neoantigen assay will be utilized to identify neoantigen-specific T-cell clonotypes and track these clonotypes temporally (during/post ICB) and spatially (across immune compartments). Single-cell RNA sequencing will be used to characterize the functionality of expanded T-cell clonotypes. Accrual to arm B will commence following complete accrual to arm A with a planned total enrollment of 30 patients. This study is open with 1 patient enrolled at the time of submission. Clinical trial information: NCT03918252.

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.

Abstract 2230: Diversity of peripheral CD8+PD-1+ T cells is a novel predictive biomarker for response to anti-PD-1 antibody treatment in lung cancer patients

Abstract Background: Anti-PD-1 antibodies (nivolumab) are effective in the treatment of many cancers, including malignant melanoma, non-small cell lung cancer (NSCLC), renal cell cancer, and head and neck squamous cell carcinoma. Immune checkpoint inhibitors (ICIs) are only effective in around 20% of patients, which saw a demand for the development of biomarkers that predict a therapeutic response before administering treatment. As the biomarkers intratumoral PD-L1 expression and tumor mutation burden (TMB) both require tumor tissue biopsy, there is now a demand for safer and less invasive biomarkers. Peripheral and tumor CD8+PD-1+ T cells share neoantigen-specific T-cell receptors (TCRs), and are presumed to act as effector T cells with an antitumor effect at the tumor site. We analyzed the diversity in terms of TCR α and β repertoires on peripheral CD8+PD-1+ T cells and examined the relationship between this diversity and therapeutic effect of nivolumab. Methods: This study used patients administered nivolumab after exhibiting no response to chemotherapy for recurrence following surgery. Peripheral blood mononuclear cells were collected from patients before administration of nivolumab. CD8+PD-1+ T cells were subjected to FACS sorting, NGS-based TCR repertoire analysis was performed by Repertoire Genesis Inc., and TCR diversity was evaluated statistically. CT scan was performed during week 12 of treatment and used to determine response to nivolumab. This study was approved by the Ethical Committee of Hyogo College of Medicine. Results: Six of 12 patients responded to treatment. Upon comparing these responders (CR, PR) with non-responders (SD, PD), there were no differences in the proportion of PD-1+ in CD8+ T cells and the proportion of CD8+PD-1+ T cells in gated lymphocytes. TCR α diversity was significantly higher among responders than non-responders based on Shannon index, Simpson index and DE50 (P < 0.05, P < 0.05, P < 0.01, respectively). TCR β diversity was also significantly higher among responders than non-responders based on Shannon index, Simpson index and DE50 (all P < 0.01). Progression-free survival (PFS) was 371 days for responders and 148 days for non-responders. Overall survival (OS) was 633 days for responders and 308 days for non-responders, showing a significant difference between the groups. Conclusion: TCR repertoire analysis was performed on CD8+PD-1+ T cells in easily-obtainable peripheral blood before nivolumab treatment in patients with NSCLC, and nivolumab was observed to be effective in patients with high TCR diversity. This result indicates the TCR diversity of peripheral CD8+PD-1+ T cells is effective as a predictive biomarker for response to ICI therapy. In the future, we intend to analyze TMB and neoepitopes using surgical specimens of these patients and determine the efficacy of this biomarker for cancers other than NSCLC. Citation Format: Seiji Matsumoto, Takaji Matsutani, Yoshiko Fujita, Kazutaka Kitaura, Tohoru Nakamichi, Akifumi Nakamura, Ayumi Kuroda, Masaki Hashimoto, Nobuyuki Kondo, Ryuji Suzuki, Seiki Hasegawa. Diversity of peripheral CD8+PD-1+ T cells is a novel predictive biomarker for response to anti-PD-1 antibody treatment in lung cancer patients [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 2230.

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.

Correlation between peripheral CD8+PD-1+ T cells diversity, tumor mutation burden (TMB) and T cell clones with anti-PD-1 antibody treatment of lung cancer patients: TCR repertoire as a novel predictive biomarker.

e14041 Background: Anti-PD-1 antibodies (nivolumab) are effective in the treatment of many cancers. There is a demand for less invasive biomarkers. Peripheral and tumor CD8+PD-1+ T cells share neoantigen-specific T-cell receptors (TCRs), and are presumed to act as effector T cells with an antitumor effect at the tumor site. We analyzed the diversity in terms of TCR α and β repertoires on peripheral CD8+PD-1+ T cells, tumor mutation burden and examined the relationship between this diversity and therapeutic effect of nivolumab. Methods: This study used patients administered nivolumab after exhibiting no response to chemotherapy for recurrence following surgery. Peripheral blood mononuclear cells were collected from patients before administration of nivolumab. CD8+PD-1+ T cells were subjected to FACS sorting, NGS-based TCR repertoire analysis was performed by Repertoire Genesis Inc., and TCR diversity was evaluated statistically. This study was approved by the Ethical Committee of Hyogo College of Medicine. Results: Six of 12 patients responded to treatment. Upon comparing these responders (CR, PR) with non-responders (SD, PD), there were no differences in the proportion of PD-1+ in CD8+ T cells and the proportion of CD8+PD-1+ T cells in gated lymphocytes. TCR α diversity was significantly higher among responders than non-responders based on Shannon index, Simpson index and DE50 (P < 0.05, P < 0.05, P < 0.01, respectively). TCR β diversity was also significantly higher among responders than non-responders based on Shannon index, Simpson index and DE50 (all P < 0.01). Progression-free survival (PFS) was 371 days for responders and 148 days for non-responders. Overall survival (OS) was 633 days for responders and 308 days for non-responders, showing a significant difference between the groups. TCR repertoire was proportional to TMB. Clones found in multiple patients were more frequent in indel than in SNP. Conclusions: TCR repertoire analysis was performed on CD8+PD-1+ T cells in easily-obtainable peripheral blood before nivolumab treatment in patients with NSCLC, and nivolumab was observed to be effective in patients with high TCR diversity. This result indicates the TCR diversity of peripheral CD8+PD-1+ T cells is effective as a predictive biomarker for response to ICI therapy.

5th Annual Immuno-Oncology 360° Conference: Spanning Science and Business to Bring New Therapies to Patients

5th Annual Immuno-Oncology 360° Conference: Spanning Science and Business to Bring New Therapies to Patients

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.

Abstract P2-09-04: Identification of a neoantigen targeted by tumor-infiltrating lymphocytes in a patient with Her2+ breast cancer

Abstract Background: Recent studies have demonstrated that the number of tumor infiltrating lymphocytes (TILs) positively correlates with outcome and response to chemotherapy in patients with HER2+ and Triple-Negative Breast Cancer (TNBC). Furthermore, first studies of immune-checkpoint inhibitors showed promising results in those patients. However, the targets of those TILs remain unknown. Neoantigens, which arise in the process of tumorigenesis, appear as potential targets. They can elicit high avidity, tumor-specific T-cell responses. Thus, it is the aim of our study to ascertainif these TILs are directed against tumor-specific mutations. Methods: TILs from breast cancer biopsies taken at the time point of diagnosis were expanded by unspecific stimulation. Additionally, we used the Gentle Macs Dissociator in combination with flow cytometry to investigate the number of TILs in the tumor tissue. Furthermore, we performed whole-genome sequencing of tumor tissue and as reference autologous blood cells to determine tumor-specific mutations. Mutations leading to a non-synonymous amino acid change were analyzed for RNA expression of the encoding gene as well as to determine potential neoantigens. Neoantigens were evaluated for their potential binding to the patient's specific HLA molecules. Peptides for potential neoantigens were synthesized, loaded onto autologous antigen presenting cells (APCs) and cocultured with TILs. All IFNγ producing T-cells were clonally expanded and retested for peptide specificity to identify neoantigen specific T-cell clones. Results: Our flow cytometric analysis of the tumor biopsy for more than 300 patients showed higher frequencies of TILs in TNBC as compared to other types of breast cancer or patients without malignancy. Screening for neoantigen specific T-cells in one patient led to identification of three peptide-specific CD4+ T-cell clones isolated from HER2+ breast cancer tissue taken at the time point of diagnosis. All T-cell clones specifically recognized the same tumor-specific mutation and not the wildtype counterpart. Furthermore, we demonstrated that these T-cell clones also recognized the endogenously expressed mutated antigen. This verified the ability of processing and presentation of the respective protein. Interestingly, we could also isolate a T-cell clone recognizing the same neoantigen in the resected tumor tissue after neoadjuvant therapy. Based on CDR3 sequencing we could prove that the four T-cell clones represented individual clones. This confirms the polyclonal nature of the immune response. Moreover, we showed that the same neoepitope was presented in two different HLA restriction molecules of the patient with three of the clones recognizing it in HLA-DPB1*0401 and one in HLA-DPB1*0201. These results further underline the immunogenicity of this neoantigen. Conclusion: In conclusion, our data demonstrate tumor-specificity of TILs in a patient with HER2+ breast cancer. Furthermore, we show the feasibility to identify individual cancer specific T-cell targets in breast cancer patients. These results may contribute to the development of targeted patient-specific immunotherapies in the future. Citation Format: Reimann H, Nguyen A, Hübner H, Erber R, Bausenwein J, Van der Meijden ED, Lux MP, Jud S, Griffioen M, Rauh C, Sanborn JZ, Benz SC, Rabizadeh S, Beckmann MW, Mackensen A, Rübner M, Fasching PA, Kremer AN. Identification of a neoantigen targeted by tumor-infiltrating lymphocytes in a patient with Her2+ breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-09-04.

Peptide vaccines in early breast cancer

The immune system plays a dual role of host-protecting and tumor-promoting, as elegantly expressed by the ‘cancer immunoediting’ hypothesis. Although breast cancer has not been traditionally considered to be immunogenic, recently there is accumulating and solid evidence on the association between immune system and breast cancer. To mount an effective anti-tumor response, host immunosurveillance must recognize tumor-specific epitopes, thus defining the antigenicity of a tumor. Neoantigens are mutant cancer peptides that arise as terminal products of the expression of somatic cancer mutations. Neoantigens and major histocompatibility complex (MHC) proteins present together to effector cells of the immune system. Neoantigen vaccines have shown promising results in inducing neoantigen-specific T-cell responses. Currently, cancer vaccines are under evaluation in breast cancer to avoid recurrences in patients at high risk despite optimal standard therapy. Given the promise of a very specific long-term antitumor immune response, the development of cancer vaccines continues is of great interest. Combinations of neoantigen vaccines and other immunotherapies are also studied to evade cancer immune escape.