Journal Articles

Nonsense-mediated mRNA decay inhibition reshapes the cancer immunopeptidome Featured  

Vendramin, Fu, Fernandez Patel, Zhao, et al. investigated nonsense-mediated mRNA decay (NMD) in cancer, and detected high activity of this pathway in tumors, with lower scores associated with better ICB responses in clinical data. Inhibition of SMG1 reduced NMD activity and resulted in significant increases in immunogenic MHC-I-presented neoantigens. This resulted in improved antitumor immune responses and synergized with ICB in vivo.

Vendramin, Fu, Fernandez Patel, Zhao, et al. investigated nonsense-mediated mRNA decay (NMD) in cancer, and detected high activity of this pathway in tumors, with lower scores associated with better ICB responses in clinical data. Inhibition of SMG1 reduced NMD activity and resulted in significant increases in immunogenic MHC-I-presented neoantigens. This resulted in improved antitumor immune responses and synergized with ICB in vivo.

ABSTRACT: DNA mutations are a well-characterized source of neoepitopes in immunotherapy. Here, we examined the contribution of dysregulated RNA processing to neoantigen production. Leveraging multi-omics and checkpoint inhibitor (CPI) response data from >1,000 patients, we identified reduced activity of the nonsense-mediated mRNA decay (NMD) pathway kinase SMG1 as a predictor of improved CPI response. NMD inhibition through SMG1 targeting stabilized transcripts containing premature termination codons, most of which were of non-mutational origin. This reshaped the major histocompatibility complex class I (MHC class I)-bound immunopeptidome and increased neoantigen abundance to levels comparable to high mutation burden tumors. Functionally, NMD inhibition drove antigen-dependent T cell-mediated tumor cell killing in vitro, promoted activation of tissue-resident T cells in patient-derived models ex vivo, and improved CPI efficacy in vivo. Our findings establish NMD inhibition as a strategy to harness a previously inaccessible source of canonical and non-canonical neoantigens, with the potential to increase tumor immunogenicity across cancers.

Author Info: (1) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Lab, The Francis Crick Inst

Author Info: (1) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. Electronic address: r.vendramin@ucl.ac.uk. (2) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Pre-Cancer Immunology Lab, University College London Cancer Institute, London, UK. (3) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Organelle Dynamics Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK; Organelle Dynamics Lab, the Francis Crick Institute, London, UK. (4) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. (5) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (6) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (7) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (8) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (9) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (10) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (11) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (12) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Drug Discovery Technology Laboratories, Ono Pharmaceutical Co. Ltd., Osaka, Japan. (13) Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK. (14) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (15) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (16) CRUK City of London Centre Single Cell Genomics Facility, University College London Cancer Institute, London, UK; Bioinformatics Hub, University College London Cancer Institute, London, UK. (17) Proteomics Research Translational Technology Platform, University College London Cancer Institute, London, UK. (18) CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK. (19) CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Immune Regulation and Tumor Immunotherapy Group, University College London Cancer Institute, London, UK. (20) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Division of Medicine, University College London, London, UK. (21) Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands. (22) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (23) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. (24) Research Department of Haematology, University College London Cancer Institute, London, UK. (25) CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Immune Regulation and Tumor Immunotherapy Group, University College London Cancer Institute, London, UK; Immune Regulation Lab, Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK. (26) Organoid Translational Technology Platform, University College London Cancer Institute, London, UK. (27) Proteomics Research Translational Technology Platform, University College London Cancer Institute, London, UK. (28) Department of Research Pathology, University College London Cancer Institute, London, UK. (29) CRUK City of London Explant and Patient-Derived Xenograft Core, London, UK. (30) CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK. (31) Organelle Dynamics Lab, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK; Organelle Dynamics Lab, the Francis Crick Institute, London, UK. (32) Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK. (33) CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Pre-Cancer Immunology Lab, University College London Cancer Institute, London, UK. (34) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (35) Cancer Evolution and Genome Instability Lab, The Francis Crick Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. Electronic address: charles.swanton@crick.ac.uk. (36) CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Immune Regulation and Tumor Immunotherapy Group, University College London Cancer Institute, London, UK. Electronic address: s.quezada@ucl.ac.uk. (37) The Tumor Immunogenomics and Immunosurveillance Lab, University College London Cancer Institute, London, UK; CRUK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. Electronic address: k.litchfield@ucl.ac.uk.

Nous-209 neoantigen vaccine for cancer prevention in Lynch syndrome carriers: a phase 1b/2 trial Spotlight 

D’Alise and Willis et al. presented results from a phase 1b/2 single-arm trial of 45 Lynch syndrome (LS) carriers treated with Nous-209 – an IM, heterologous, prime/boost, virus-based vaccine encoding 209 frameshift peptides (FSPs) shared across neoplasms with microsatellite instability (MSI). Potent/durable vaccine-induced FSP-specific IFNγ-producing CD4+ and cytotoxic CD8+ T cell responses were observed in all 37 evaluable participants. Peptide–HLA predictions helped identify >100 FSPs, which were immunogenic in vitro and detected in datasets of LS MSI-high colorectal pre-cancers/cancers. The vaccine was safe, and no participants had advanced adenomas or CRC at the end of the study.

Contributed by Paula Hochman

D’Alise and Willis et al. presented results from a phase 1b/2 single-arm trial of 45 Lynch syndrome (LS) carriers treated with Nous-209 – an IM, heterologous, prime/boost, virus-based vaccine encoding 209 frameshift peptides (FSPs) shared across neoplasms with microsatellite instability (MSI). Potent/durable vaccine-induced FSP-specific IFNγ-producing CD4+ and cytotoxic CD8+ T cell responses were observed in all 37 evaluable participants. Peptide–HLA predictions helped identify >100 FSPs, which were immunogenic in vitro and detected in datasets of LS MSI-high colorectal pre-cancers/cancers. The vaccine was safe, and no participants had advanced adenomas or CRC at the end of the study.

Contributed by Paula Hochman

ABSTRACT: Cancer interception is a preventative approach aiming to reduce cancer incidence by targeting precancers and early-stage cancers. Lynch syndrome (LS) is a prevalent hereditary cancer syndrome affecting ~1 in 300 individuals, with an overall lifetime cancer risk as high as 80%. LS is caused by germline mutations in the DNA mismatch repair genes, leading to microsatellite instability (MSI) and accumulation of shared mutations. When these occur in coding regions, they generate frameshift peptides (FSPs). Nous-209 is a neoantigen-directed immunotherapy based on a heterologous prime boost using great ape adenovirus and modified vaccinia virus Ankara encoding 209 FSPs shared across MSI neoplasms. We present the results from cohort 1 of a phase 1b/2 single-arm trial of Nous-209 for cancer interception in LS carriers (n = 45). Safety and immunogenicity were coprimary endpoints. Safety was assessed in 45 participants. Vaccination was safe with no intervention-related serious adverse events (AEs). The most common AEs were injection-site reactions (any grade in 91% of participants after prime and 76% after boost with no grade 3) and fatigue (any grade in 80% after prime and 53% after boost with 4% grade 3 after prime or after boost). Neoantigen-specific immune responses were observed after vaccination in 100% of evaluable participants (n = 37), with induction of potent T cell immunity (mean response at peak of ~1,100 interferon-γ spot-forming cells per million peripheral blood mononuclear cells). The immune response was durable and detectable at 1 year in 85% of participants. Both CD8+ and CD4+ T cells were induced, recognizing multiple FSPs. Peptide-human leukocyte antigen predictions allowed the identification of >100 immunogenic FSPs with demonstration of cytotoxic activity in vitro. Immunogenic FSPs were found in independent datasets of LS MSI colorectal precancers and cancers. These results highlight Nous-209 ability to efficiently stimulate immunity against neoantigens in LS, supporting its development for cancer interception (ClinicalTrials.gov identifier: NCT05078866 ).

Author Info: (1) Nouscom SRL, Rome, Italy. (2) Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (3) Department of Clinical C

Author Info: (1) Nouscom SRL, Rome, Italy. (2) Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (3) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (4) Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA. (5) University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA. (6) City of Hope Comprehensive Cancer Center, Duarte, CA, USA. (7) Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (8) University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA. (9) Nouscom SRL, Rome, Italy. (10) Nouscom SRL, Rome, Italy. (11) Nouscom SRL, Rome, Italy. (12) Nouscom SRL, Rome, Italy. (13) Nouscom SRL, Rome, Italy. (14) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (15) Nouscom SRL, Rome, Italy. (16) Nouscom AG, Basel, Switzerland. (17) Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (18) Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (19) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (20) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (21) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (22) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (23) Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA. (24) Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA. (25) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (26) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (27) Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA. Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA. (28) Nouscom SRL, Rome, Italy. e.scarselli@nouscom.com. (29) Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. EVilar@mdanderson.org.

Individualized mRNA vaccines evoke durable T cell immunity in adjuvant TNBC Featured  

Sahin, Schmidt, et al. conducted a clinical study of patients with early-stage TNBC who were treated with a personalized neoantigen mRNA vaccine strategy following standard therapy. Durable neoantigen-specific CD8+ and CD4+ T cell responses were detected, with 10/14 patients remaining relapse-free during long-term follow-up. Several resistance mechanisms were uncovered in three patients with recurrences; a weak vaccine-induced response, recurrence related to the primary tumor not used for vaccine creation, and downregulation of antigen presentation in tumor cells.

Sahin, Schmidt, et al. conducted a clinical study of patients with early-stage TNBC who were treated with a personalized neoantigen mRNA vaccine strategy following standard therapy. Durable neoantigen-specific CD8+ and CD4+ T cell responses were detected, with 10/14 patients remaining relapse-free during long-term follow-up. Several resistance mechanisms were uncovered in three patients with recurrences; a weak vaccine-induced response, recurrence related to the primary tumor not used for vaccine creation, and downregulation of antigen presentation in tumor cells.

ABSTRACT: Triple-negative breast cancer (TNBC) is frequently associated with metastatic relapse, even at an early stage(1). Here we assessed an individualized neoantigen mRNA vaccine in 14 patients with TNBC following surgery and after neoadjuvant or adjuvant therapy. In peripheral blood of nearly all patients, high-magnitude, vaccine-induced, mostly de novo T cell responses to multiple neoantigens were detected that remained functional for several years. Characterization of individual patients revealed that a large proportion of these T cells developed into two subsets: a late-differentiated phenotype with markers indicative of 'ready-to-act' cytotoxic effector T cells, and T cells with a stem cell-like memory phenotype. Eleven patients remained relapse-free for up to six years post-vaccination. Recurrence occurred in three patients: the individual with the weakest vaccine-induced T cell response relapsed, but achieved complete remission on subsequent anti-PD-1 therapy; another patient had a tumour with low major histocompatibility complex (MHC) class I expression with MHC class I-deficient cells growing out under vaccination; and the third patient was BRCA-positive and had a recurrence from a genetically distinct primary tumour. These findings demonstrate the feasibility of individualized RNA vaccines in TNBC, document persistence of vaccine-induced, functional neoantigen-specific T cells and provide insights into possible immune escape mechanisms that will guide future approaches.

Author Info: (1) BioNTech Group, Mainz, Germany. ugur.sahin@biontech.de. TRON, Mainz, Germany. ugur.sahin@biontech.de. HI-TRON Mainz, Mainz, Germany. ugur.sahin@biontech.de. (2) Department of O

Author Info: (1) BioNTech Group, Mainz, Germany. ugur.sahin@biontech.de. TRON, Mainz, Germany. ugur.sahin@biontech.de. HI-TRON Mainz, Mainz, Germany. ugur.sahin@biontech.de. (2) Department of Obstetrics and Gynecology, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany. (3) BioNTech Group, Mainz, Germany. (4) BioNTech Group, Mainz, Germany. (5) BioNTech Group, Mainz, Germany. (6) BioNTech Group, Mainz, Germany. (7) BioNTech Group, Mainz, Germany. (8) TRON, Mainz, Germany. (9) BioNTech Group, Mainz, Germany. (10) BioNTech Group, Mainz, Germany. (11) BioNTech Group, Mainz, Germany. (12) BioNTech Group, Mainz, Germany. (13) BioNTech Group, Mainz, Germany. (14) BioNTech Group, Mainz, Germany. (15) BioNTech Group, Mainz, Germany. (16) BioNTech Group, Mainz, Germany. (17) BioNTech Group, Mainz, Germany. (18) BioNTech Group, Mainz, Germany. (19) Department of Immunology, Genetics and Pathology, Uppsala University Hospital, Uppsala, Sweden. (20) Division Gynecologic Oncology, National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany. (21) Klinik fŸr Frauenheilkunde und Geburtshilfe, Helios Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany. (22) BioNTech Group, Mainz, Germany. HI-TRON Mainz, Mainz, Germany.

Sensitive detection of cancer antigens enabled by user-defined peptide libraries Spotlight 

To support more sensitive immunopeptidomics analyses, Manakongtreecheep and Ctortecka et al. developed Pepyrus to rapidly and scalably generate user-defined peptide libraries in E. coli that could provide chromatographic and spectral references. Papyrus-enabled data-independent acquisition (DIA) allowed sensitive and high-confidence detection of lower-affinity and less abundant clinically relevant HLA-bound peptides, including neoantigens in complex patient samples. Further, a spectral library encompassing HIF-inducible ERVs for a renal cell carcinoma sample was reused “off-the-shelf” to analyze a melanoma sample, and identified ERV-derived peptides.

Contributed by Ute Burkhardt

To support more sensitive immunopeptidomics analyses, Manakongtreecheep and Ctortecka et al. developed Pepyrus to rapidly and scalably generate user-defined peptide libraries in E. coli that could provide chromatographic and spectral references. Papyrus-enabled data-independent acquisition (DIA) allowed sensitive and high-confidence detection of lower-affinity and less abundant clinically relevant HLA-bound peptides, including neoantigens in complex patient samples. Further, a spectral library encompassing HIF-inducible ERVs for a renal cell carcinoma sample was reused “off-the-shelf” to analyze a melanoma sample, and identified ERV-derived peptides.

Contributed by Ute Burkhardt

ABSTRACT: Human leukocyte antigen (HLA)-bound tumor peptides can be routinely isolated from cancer samples and identified using mass spectrometry (MS). However, MS approaches can be stochastic or rely on spectral libraries, which are not customarily available for individual-specific peptides, thus limiting the ability to discover novel peptides. Here, we introduce Pepyrus, which generates user-defined, individual-specific or disease-specific peptide libraries in Escherichia coli to improve the sensitivity and confidence of MS peptide identification, including lowly abundant neoantigens. Using Pepyrus-generated peptide libraries paired with an HLA-specific data-independent acquisition strategy, we recover >75% of the expected sequences per single injection for libraries of >10,000 peptides and identify 0.1_fmol of spiked-in peptides in a complex background. We apply Pepyrus to create personalized libraries, facilitating identification of clinically relevant HLA peptides, including several novel peptides from cell lines derived from persons with melanoma and renal cell carcinoma. Pepyrus enables identification of rare HLA-bound peptides and provides the ability to generate large training datasets to improve spectra, retention time and ion mobility prediction tools.

Author Info: (1) Broad Institute of MIT and Harvard, Cambridge, MA, USA. Harvard Medical School, Boston, MA, USA. Dana Farber Cancer Institute, Boston, MA, USA. (2) Broad Institute of MIT and H

Author Info: (1) Broad Institute of MIT and Harvard, Cambridge, MA, USA. Harvard Medical School, Boston, MA, USA. Dana Farber Cancer Institute, Boston, MA, USA. (2) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (3) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (4) Broad Institute of MIT and Harvard, Cambridge, MA, USA. Dana Farber Cancer Institute, Boston, MA, USA. (5) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (6) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (7) Dana Farber Cancer Institute, Boston, MA, USA. (8) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (9) Dana Farber Cancer Institute, Boston, MA, USA. (10) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (11) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (12) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (13) Harvard Medical School, Boston, MA, USA. Dana Farber Cancer Institute, Boston, MA, USA. (14) Dana Farber Cancer Institute, Boston, MA, USA. (15) Department of Pathology, University of Michigan, Ann Arbor, MI, USA. (16) Dana Farber Cancer Institute, Boston, MA, USA. (17) Broad Institute of MIT and Harvard, Cambridge, MA, USA. Harvard Medical School, Boston, MA, USA. Dana Farber Cancer Institute, Boston, MA, USA. Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA. Technical University of Denmark, Lyngby, Denmark. (18) Broad Institute of MIT and Harvard, Cambridge, MA, USA. Harvard Medical School, Boston, MA, USA. Dana Farber Cancer Institute, Boston, MA, USA. (19) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (20) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (21) Broad Institute of MIT and Harvard, Cambridge, MA, USA. (22) Broad Institute of MIT and Harvard, Cambridge, MA, USA. nhacohen@broadinstitute.org. Harvard Medical School, Boston, MA, USA. nhacohen@broadinstitute.org. Massachusetts General Hospital, Krantz Family Center for Cancer Research, Boston, MA, USA. nhacohen@broadinstitute.org. (23) Broad Institute of MIT and Harvard, Cambridge, MA, USA. scarr@broad.mit.edu. (24) Broad Institute of MIT and Harvard, Cambridge, MA, USA. jabelin@broadinstitute.org. Dana Farber Cancer Institute, Boston, MA, USA. jabelin@broadinstitute.org. (25) Broad Institute of MIT and Harvard, Cambridge, MA, USA. catherine_wu@dfci.harvard.edu. Harvard Medical School, Boston, MA, USA. catherine_wu@dfci.harvard.edu. Dana Farber Cancer Institute, Boston, MA, USA. catherine_wu@dfci.harvard.edu.

Mutant KRAS vaccine with dual checkpoint blockade in resected pancreatic cancer: a phase I trial Spotlight 

Huff et al. investigated a pooled peptide vaccine covering six KRAS mutations, plus ipilimumab and nivolumab in resected PDAC. mKRAS-specific T cell responses emerged in 11/12 patients, and 4/12 remained disease-free at ~36 months. Of the six KRAS mutations, G12D was the least immunogenic, and disease recurred in all patients with this mutation. Restimulated T cells were primarily CD4+, particularly Th1-like Tcm, and expressed mKRAS-reactive TCRs, including monoreactive, polyreactive, and public clonotypes. TCR-transduced T cell lines were activated by tumor cell lines pulsed with their cognate peptide, but not by controls, indicating TCR specificity.

Contributed by Morgan Janes

Huff et al. investigated a pooled peptide vaccine covering six KRAS mutations, plus ipilimumab and nivolumab in resected PDAC. mKRAS-specific T cell responses emerged in 11/12 patients, and 4/12 remained disease-free at ~36 months. Of the six KRAS mutations, G12D was the least immunogenic, and disease recurred in all patients with this mutation. Restimulated T cells were primarily CD4+, particularly Th1-like Tcm, and expressed mKRAS-reactive TCRs, including monoreactive, polyreactive, and public clonotypes. TCR-transduced T cell lines were activated by tumor cell lines pulsed with their cognate peptide, but not by controls, indicating TCR specificity.

Contributed by Morgan Janes

ABSTRACT: In this phase I study, we test a pooled synthetic long peptide vaccine targeting the six KRAS mutations (G12V, G12A, G12R, G12C, G12D, G13D) with ipilimumab and nivolumab in resected pancreatic adenocarcinoma. Co-primary endpoints include safety and maximal percent change of IFNγ-producing mutant KRAS T cell responses in the blood within 17 weeks. Secondary endpoints include disease-free survival, overall survival, and maximal percent change of IFNγ-producing mutant KRAS T cell responses at any time after vaccination. Vaccine-related adverse events are grade 1-2. 11/12 and 10/12 patients generate a significant increase in average T cell response to 6 mutant KRAS antigens and tumor-specific response, respectively. Immunophenotyping demonstrate Th1 CD4 central memory and effector memory T cells, and CD8 effector memory T cells at a lower frequency. The vaccine also generates cross-reactive T cells that recognize more than one mutant KRAS antigen. These findings support the safety and diverse anti-tumor immunity of mutant KRAS vaccines (NCT04117087).

Author Info: (1) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins

Author Info: (1) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (2) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (3) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (4) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (5) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (6) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (7) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (8) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (9) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (10) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (11) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (12) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (13) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (14) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. (15) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (16) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (17) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (18) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. (19) Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA. (20) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Howard Hughes Medical Institute, Chevy Chase, MD, USA. Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. (21) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Howard Hughes Medical Institute, Chevy Chase, MD, USA. Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. (22) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (23) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (24) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (25) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (26) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (27) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (28) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (29) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (30) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (31) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (32) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (33) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (34) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (35) Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA. (36) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (37) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (38) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. ejaffee@jhmi.edu. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. ejaffee@jhmi.edu. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. ejaffee@jhmi.edu. (39) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. nzaidi1@jhmi.edu. Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. nzaidi1@jhmi.edu. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. nzaidi1@jhmi.edu.

Cross-presentation of dead cell-associated antigens shapes the neoantigenic landscape of tumor immunity Featured  

Lim, Schulz, et al. studied the functioning of the F-actin receptor DNGR-1 on cDC1s, and the impact of cross-presentation on immunoediting of tumors using chemical carcinogenesis models. Dead cell-associated antigens anchored to F-actin were found to be cross-presented by cDC1s to CD8+ T cells, in a process dependent on DNGR-1 signaling. Loss of this DNGR-1-mediated cross-presentation resulted in faster tumor growth and limited priming of T cells specific for F-actin-binding proteins (FABP). This FABP neoantigen cross-presentation by cDC1s impacted immune visibility and immunoediting of tumors.

Lim, Schulz, et al. studied the functioning of the F-actin receptor DNGR-1 on cDC1s, and the impact of cross-presentation on immunoediting of tumors using chemical carcinogenesis models. Dead cell-associated antigens anchored to F-actin were found to be cross-presented by cDC1s to CD8+ T cells, in a process dependent on DNGR-1 signaling. Loss of this DNGR-1-mediated cross-presentation resulted in faster tumor growth and limited priming of T cells specific for F-actin-binding proteins (FABP). This FABP neoantigen cross-presentation by cDC1s impacted immune visibility and immunoediting of tumors.

ABSTRACT: Type 1 conventional dendritic cells (cDC1s) acquire and cross-present tumor antigens to prime CD8⁺ T cells. Whether this selects for specific neoantigens is unclear. DNGR-1 (CLEC9A), a cDC1 receptor for F-actin exposed on dead cells, promotes cross-presentation of cell-associated antigens. Here we show that DNGR-1-deficient mice develop chemically induced tumors more rapidly and at higher incidence, and these are more frequently rejected on transplantation into wild-type recipients. Whole-exome sequencing reveals enrichment of predicted neoantigens derived from mutated F-actin-binding proteins. Consistent with this observation, tethering model antigens to F-actin enhances DNGR-1-dependent cross-presentation. These results suggest that DNGR-1-mediated recognition of F-actin exposed by dead cancer cells favors priming of CD8⁺ T cells specific for cytoskeletal neoantigens, which can then drive immune escape of cancer cells lacking or reverting those mutations. Thus, neoantigen cross-presentation by cDC1 can determine the immune visibility of the tumor mutational landscape and sculpt cancer evolution by immunoediting.

Author Info: (1) Immunobiology Laboratory, The Francis Crick Institute, London, UK. Department of Immunology and Inflammation, Imperial College London, London, UK. Cancer Dynamics Laboratory, T

Author Info: (1) Immunobiology Laboratory, The Francis Crick Institute, London, UK. Department of Immunology and Inflammation, Imperial College London, London, UK. Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK. Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK. Advanced Immunotherapy and Cell Therapy Team, The Christie NHS Foundation Trust, Manchester, UK. (2) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (3) Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK. (4) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (5) Centre for Evolution and Cancer, Institute of Cancer Research, London, UK. Center for Mathematical Modelling, Universidad de Chile, Santiago, Chile. (6) Immunobiology Laboratory, The Francis Crick Institute, London, UK. Cancer Immunosurveillance Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK. (7) Immunobiology Laboratory, The Francis Crick Institute, London, UK. Early Oncology Research and Development, AstraZeneca, Cambridge, UK. (8) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (9) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (10) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (11) Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK. (12) Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK. (13) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (14) Immunobiology Laboratory, The Francis Crick Institute, London, UK. Medical Department, ADM Health and Wellness, London, UK. (15) Immunobiology Laboratory, The Francis Crick Institute, London, UK. (16) Apple Tree Partners, Cambridge, USA. (17) Apple Tree Partners, Cambridge, USA. (18) Adendra Therapeutics Ltd., London, UK. (19) Department of Immunology and Inflammation, Imperial College London, London, UK. (20) Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK. Skin and Renal Unit, The Royal Marsden NHS Foundation Trust, London, UK. Cancer Dynamics Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK. The Christie NHS Foundation Trust, Manchester, UK. (21) Immunobiology Laboratory, The Francis Crick Institute, London, UK. caetano@crick.ac.uk.

Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation Spotlight 

Sagie and Babu et al. showed that antigen-specific killing of tumors by T cells expressing T104 – a novel, potent TCR specific for the HLA-A*03:01-restricted KRAS.G12V neoantigen – and by other neoantigen-specific T cells, TILs, and T cell-engager Abs, was boosted by lymphodepleting Cy-Flu chemotherapy-treated cultures at concentrations that minimized direct tumor cytotoxicity. Sublethal chemotherapy elevated immunoproteasome activity and HLA-I surface expression to increase the number, diversity, and hydrophobicity of therapeutically relevant neoantigen peptides for presentation in vitro and in tumors implanted s.c. into immunodeficient mice.

Contributed by Paula Hochman

Sagie and Babu et al. showed that antigen-specific killing of tumors by T cells expressing T104 – a novel, potent TCR specific for the HLA-A*03:01-restricted KRAS.G12V neoantigen – and by other neoantigen-specific T cells, TILs, and T cell-engager Abs, was boosted by lymphodepleting Cy-Flu chemotherapy-treated cultures at concentrations that minimized direct tumor cytotoxicity. Sublethal chemotherapy elevated immunoproteasome activity and HLA-I surface expression to increase the number, diversity, and hydrophobicity of therapeutically relevant neoantigen peptides for presentation in vitro and in tumors implanted s.c. into immunodeficient mice.

Contributed by Paula Hochman

ABSTRACT: Adoptive cell therapy (ACT) targeting tumor-specific antigens holds promise for solid tumors, but limited neoantigen presentation remains a key barrier to efficacy. Here, we identify and characterize a T cell receptor (TCR), T104, for the KRAS.G12V mutation, a prevalent neoantigen in colorectal, lung, and pancreatic cancers. TCR-T104 selectively recognizes and kills KRAS.G12V-expressing tumor cells. Combining T cell therapy with lymphodepleting chemotherapy significantly enhances tumor cell killing, particularly by TCR-T cells, tumor-infiltrating lymphocytes (TILs), and T cell engager antibodies across multiple cancer types and target antigens. Mechanistically, chemotherapy upregulates immunoproteasome activity and human leukocyte antigen (HLA)-I surface expression. HLA-immunopeptidome analyses reveal that chemotherapy remodels the antigenic landscape across tumor cell lines and in vivo models, increasing peptide abundance and hydrophobicity while altering proteasomal cleavage preferences. These findings establish a synergistic role for chemotherapy in enhancing neoantigen presentation and T cell-mediated tumor recognition and suggest that fine-tuning these regimens could improve ACT efficacy, particularly in tumors with low-abundance neoantigens.

Author Info: (1) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; Jusidman Cancer Center, Sheba Medical Center, Ramat Gan 52621, Israel. (2) Departm

Author Info: (1) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; Jusidman Cancer Center, Sheba Medical Center, Ramat Gan 52621, Israel. (2) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (3) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (4) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (5) Rappaport Technion Cancer Research center, The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel; Institute of Pathology, Rambam Health Care Campus, Haifa 3109601, Israel. (6) Department of Statistics, University of Oxford, OX1 3LB Oxford, UK. (7) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (8) Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, UK. (9) Department of Statistics, University of Oxford, OX1 3LB Oxford, UK. (10) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (11) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (12) Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel. (13) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (14) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (15) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (16) Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, UK. (17) Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel. (18) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (19) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (20) Faculty of Medicine, Hadassah Hebrew-University Medical Center, Jerusalem 91120, Israel. (21) INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel. (22) Jusidman Cancer Center, Sheba Medical Center, Ramat Gan 52621, Israel; Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel. (23) Jusidman Cancer Center, Sheba Medical Center, Ramat Gan 52621, Israel; Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel. (24) Jusidman Cancer Center, Sheba Medical Center, Ramat Gan 52621, Israel; Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel. (25) Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel. (26) Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel. (27) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. (28) Jusidman Cancer Center, Sheba Medical Center, Ramat Gan 52621, Israel; Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel. (29) Sharett Institute of Oncology, Hadassah Cancer Research Institute and The Wohl Institute for Translational Medicine, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel. (30) Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, UK. (31) Department of Statistics, University of Oxford, OX1 3LB Oxford, UK. (32) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel. Electronic address: yardena.samuels@weizmann.ac.il.

Structure guided analysis of KRAS G12 mutants in HLA-A*11:01 reveals a length encoded immunogenic advantage in G12D

KRAS G12 mutations are frequent oncogenic drivers, yet their differential immunogenicity complicates T cell-based therapies. Here, we integrate structural, biophysical, and functional analyses to examine how KRAS G12 variants remodel peptide-MHC-I (pMHC) architecture and T cell receptor (TCR) recognition. Using HLA-A*11:01, we show that single residue substitutions at position 12 induce distinct conformational changes in the MHC groove, with G12D uniquely destabilizing the complex through a buried aspartate side chain. Notably, G12D peptides adopt two registers, a 9-mer and a 10-mer, that diverge sharply in structure and immunogenicity. The 10-mer forms a compact, stable pMHC with a TCR-accessible surface, while the 9-mer adopts a bent conformation incompatible with recognition. Molecular dynamics and NMR titration confirm the superior stability and binding affinity of the 10-mer. These results highlight how peptide length and conformation critically shape immune visibility, offering mechanistic insight for optimizing TCR-T therapies against elusive neoantigens like KRAS G12D.

Author Info: (1) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (2) Department of Anesthesiology, Putuo People's Hospital, School

Author Info: (1) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (2) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (3) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (4) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (5) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (6) Hangzhou Weizhi Biotechnology Co., Ltd, Hangzhou, China. (7) Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China. (8) Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China. (9) State key laboratory of natural and biomimetic drugs, Peking University Health Science Center, Beijing, China. (10) National Facility for Protein Science in Shanghai, ZhangJiang lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China. (11) Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China. (12) Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China. kx2129@tongji.edu.cn. (13) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. lzhao@tongji.edu.cn.

A microenvironment-driven HLA-II-associated insulin neoantigen elicits persistent memory T cell activation in diabetes Spotlight 

Using immunopeptidome analysis in T1D patients, Srivastava et al. discovered a cys-to-ser mutation at position 19 (C19S) of insulin, within an MHC-II binding region. C19S could be contextually elicited via oxidative stress in islets, representing a dominant transformation among single AA variants (SAVs) and post-translational modifications. The conversion was also potentiated in APCs by cytokine exposure. In NOD mice and humans, InsB12-20(C19S) elicited a unique corresponding T cell population that was present in the non-diabetic state, yet expanded with diabetes progression to a greater extent than native InsB12-20-specific T cells, and was enriched in activated, Th1-like memory cells.

Contributed by Morgan Janes

Using immunopeptidome analysis in T1D patients, Srivastava et al. discovered a cys-to-ser mutation at position 19 (C19S) of insulin, within an MHC-II binding region. C19S could be contextually elicited via oxidative stress in islets, representing a dominant transformation among single AA variants (SAVs) and post-translational modifications. The conversion was also potentiated in APCs by cytokine exposure. In NOD mice and humans, InsB12-20(C19S) elicited a unique corresponding T cell population that was present in the non-diabetic state, yet expanded with diabetes progression to a greater extent than native InsB12-20-specific T cells, and was enriched in activated, Th1-like memory cells.

Contributed by Morgan Janes

ABSTRACT: The antigenic landscape of autoimmune diabetes reflects a failure to preserve self-tolerance, yet how novel neoantigens emerge in humans remains incompletely understood. Here we designed an immunopeptidomics-based approach to probe HLA-II-bound, islet-derived neoepitopes in patients with type 1 diabetes. We uncovered a Cys_Ser transformation, conserved between mice and humans, that reshapes autoreactivity to insulin at the single-residue level. This transformation, which we call C19S, arises from oxidative remodeling of insulin in stressed pancreatic islets and also occurs in cytokine-activated antigen-presenting cells, contributing to a feed-forward loop of neoepitope formation and presentation. Despite involving just one amino acid, C19S is recognized by HLA-DQ8-restricted, register-specific CD4(+) T cells that expand at diabetes onset. These neoepitope-specific CD4(+) T cells lack regulatory potential but acquire a poised central memory phenotype that persists throughout disease progression. These findings reveal a distinct, microenvironment-driven route of neoantigen formation that fuels sustained autoreactivity in diabetes.

Author Info: (1) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Hum

Author Info: (1) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (2) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (3) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (4) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (5) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (6) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (7) Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA. (8) Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA. (9) Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA. (10) Department of Pediatrics, Division of Endocrinology, Diabetes, and Metabolism, Washington University School of Medicine, St. Louis, MO, USA. (11) Department of Pediatrics, Division of Endocrinology, Diabetes, and Metabolism, Washington University School of Medicine, St. Louis, MO, USA. (12) Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA. (13) Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA. (14) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. (15) Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA. (16) Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA. (17) Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA. (18) Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA. (19) Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA. (20) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. (21) Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA. Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA. Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. (22) Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA. (23) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. (24) Department of Pediatrics, Division of Endocrinology, Diabetes, and Metabolism, Washington University School of Medicine, St. Louis, MO, USA. (25) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. clichti@wustl.edu. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. clichti@wustl.edu. (26) Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA. wanx@wustl.edu. The Andrew M. and Jane M. Bursky Center for Human Immunology, Washington University School of Medicine, St. Louis, MO, USA. wanx@wustl.edu.

MHC-II-restricted neoantigen vaccine reverses immune microenvironment and overcomes resistance to immune-checkpoint inhibitors in cold tumors Spotlight 

Song, Lu, and Shi et al. demonstrated that an MHC-II restricted neoantigen vaccine (M44) increased inflammatory signaling within the TME, enhanced CD4+ and CD8+ T cell infiltration, and reduced tumor growth in B16 tumors, while showing signs of T cell exhaustion. Vaccination increased the inferred interaction between TIGIT on T cells and its ligand PVR on myeloid cells, impairing the function and proliferation of Th1 and effector and memory CD8+ T cells. M44 vaccine plus TIGIT antibody inhibited tumor growth, enhanced the helper and cytotoxic functions of antigen-specific CD4+ T cells, and increased effector and memory CD8+ T cells.

Contributed by Shishir Pant

Song, Lu, and Shi et al. demonstrated that an MHC-II restricted neoantigen vaccine (M44) increased inflammatory signaling within the TME, enhanced CD4+ and CD8+ T cell infiltration, and reduced tumor growth in B16 tumors, while showing signs of T cell exhaustion. Vaccination increased the inferred interaction between TIGIT on T cells and its ligand PVR on myeloid cells, impairing the function and proliferation of Th1 and effector and memory CD8+ T cells. M44 vaccine plus TIGIT antibody inhibited tumor growth, enhanced the helper and cytotoxic functions of antigen-specific CD4+ T cells, and increased effector and memory CD8+ T cells.

Contributed by Shishir Pant

Background: Cold tumors, characterized by poor T cell infiltration and an immunosuppressive tumor microenvironment (TME), are generally resistant to immune-checkpoint inhibitors (ICIs). Although CD4+ T cells play a critical role in anti-tumor immunity, it remains unclear whether major histocompatibility complex (MHC)-II-restricted neoantigen vaccines can reprogram the immunosuppressive TME and overcome ICI resistance.

Methods: Using the B16F10 model, we evaluated the MHC-II-restricted vaccine efficacy, profiled immune responses via flow cytometry and single-cell RNA sequencing, and identified the potential combination therapy targets poliovirus receptor (PVR) via NicheNet analysis. The combined efficacy was then validated in vitro and in vivo.

Findings: MHC-II-restricted neoantigen vaccine promoted inflammatory signaling within the TME and enhanced infiltration of CD4+ and CD8+ T cells, along with increased interferon (IFN)-γ production and signs of T cell exhaustion, which provided a prerequisite for ICI response. NicheNet analysis revealed enrichment of the inhibitory immune-checkpoint axis PVR-T cell immunoglobulin and ITIM domain (TIGIT) following vaccination. The combination of the vaccines and TIGIT blockade exhibited synergistic anti-tumor efficacy. This combination enhanced cytokine production by antigen-specific T cells, promoted effector memory differentiation, and delayed exhaustion of CD8+ T cells.

Conclusions: MHC-II-restricted neoantigen vaccine remodels the immune inhibitory TME with insufficient T cell infiltration and synergizes with TIGIT blockade to suppress tumor growth, providing a promising combinatorial strategy for cold tumors.

Funding: Supported by the National Key Research and Development Program of China (2023YFC2506400), the National Natural Science Foundation (82373263), and the Fundamental Research Funds for the Central Universities (0214-14380506).

Author Info: (1) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (2) MOE Key Laboratory of Model Animal fo

Author Info: (1) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (2) MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University Medical School, Nanjing 210061, China. (3) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (4) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (5) MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University Medical School, Nanjing 210061, China. (6) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (7) Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210008, China. (8) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (9) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (10) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (11) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China. (12) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University Medical School, Nanjing 210061, China; Wuxi Xishan NJU Institute of Applied Biotechnology, Wuxi 214101, China; ChemBioMed Interdisciplinary Research Center at Nanjing University, Nanjing 210061, China. Electronic address: yanli@nju.edu.cn. (13) Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; ChemBioMed Interdisciplinary Research Center at Nanjing University, Nanjing 210061, China; Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing 211166, China. Electronic address: jiawei99@nju.edu.cn.

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