Journal Articles

First-in-human testing of a mutant KRAS vaccine for pancreatic cancer interception in high-risk cohorts Spotlight 

In a phase 1 trial, Haldar, Huff, et al. treated 20 volunteers with high-risk of PDAC development (based on family history or genetics, plus radiographic indication of a precursor lesion/cyst) with a prophylactic SLP vaccine against 6 common KRAS mutations. The vaccine was well tolerated, and 90% of recipients developed mutant KRAS-specific T cell responses, although response rates varied against individual KRAS mutations. Polyfunctional, memory mKRAS-specific CD4+ and CD8+ T cells and novel clonotypes were detected and persisted 1-2 years after vaccination. No patients developed PDAC over a 16.5-month follow-up, and many had evidence of cyst regression or resolution.

Contributed by Alex Najibi

In a phase 1 trial, Haldar, Huff, et al. treated 20 volunteers with high-risk of PDAC development (based on family history or genetics, plus radiographic indication of a precursor lesion/cyst) with a prophylactic SLP vaccine against 6 common KRAS mutations. The vaccine was well tolerated, and 90% of recipients developed mutant KRAS-specific T cell responses, although response rates varied against individual KRAS mutations. Polyfunctional, memory mKRAS-specific CD4+ and CD8+ T cells and novel clonotypes were detected and persisted 1-2 years after vaccination. No patients developed PDAC over a 16.5-month follow-up, and many had evidence of cyst regression or resolution.

Contributed by Alex Najibi

ABSTRACT: Pancreatic ductal adenocarcinoma (PDAC) arises from precursor lesions over a decade-plus, offering a window for interception in high-risk individuals, but current surveillance detects a minority of precursors. Mutant KRAS (mKRAS) is present in most PDACs and their precursors, making it an appealing target for immune-based interception. We conducted a phase I, first-in-human study of a peptide vaccine targeting six common KRAS mutations (mKRAS-VAX) in 20 individuals with hereditary PDAC predisposition and a radiographic pancreatic abnormality (NCT05013216) to assess safety, immunogenicity, and T cell persistence. Adverse events were grade 1-2. Vaccination elicited a significant mKRAS-specific T cell response in 18/20 participants (90%). Longitudinal TCR sequencing demonstrated persistence of vaccine-induced mKRAS-specific clonotypes for up to 2 years. Over a median follow-up of 16.5 months, no participants developed PDAC. These findings demonstrate that mKRAS-VAX is safe and generates durable T cell responses, which support the advancement of mKRAS-targeted vaccination for PDAC interception.

Author Info: (1) The University of Texas MD Anderson Cancer Center Houston, TX United States. ROR: https://ror.org/04twxam07 (2) Johns Hopkins Medicine Baltimore United States. ROR: https://ror

Author Info: (1) The University of Texas MD Anderson Cancer Center Houston, TX United States. ROR: https://ror.org/04twxam07 (2) Johns Hopkins Medicine Baltimore United States. ROR: https://ror.org/037zgn354 (3) Johns Hopkins Medicine Baltimore, Maryland United States. ROR: https://ror.org/037zgn354 (4) Johns Hopkins Medicine Baltimore, Maryland United States. ROR: https://ror.org/037zgn354 (5) Johns Hopkins Medicine Baltimore, MD United States. ROR: https://ror.org/037zgn354 (6) Johns Hopkins University United States. ROR: https://ror.org/00za53h95 (7) Johns Hopkins Medicine Baltimore, MD United States. ROR: https://ror.org/037zgn354 (8) Johns Hopkins School of Medicine Baltimore, MD United States. (9) Icahn School of Medicine at Mount Sinai New York United States. ROR: https://ror.org/04a9tmd77 (10) Johns Hopkins Medicine Baltimore, MD United States. ROR: https://ror.org/037zgn354 (11) Johns Hopkins Medicine Baltimore United States. ROR: https://ror.org/037zgn354 (12) The Johns Hopkins Medical Institutions Baltimore, MD United States. (13) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (14) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (15) Johns Hopkins Medicine Baltimore United States. ROR: https://ror.org/037zgn354 (16) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (17) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (18) Sidney Kimmel Comprehensive Cancer Center Baltimore, Maryland United States. ROR: https://ror.org/05m5b8x20 (19) Johns Hopkins Medicine Baltimore, MD United States. ROR: https://ror.org/037zgn354 (20) Johns Hopkins Medicine Baltimore, MD United States. ROR: https://ror.org/037zgn354 (21) Sidney Kimmel Comprehensive Cancer Center Baltimore, MD United States. ROR: https://ror.org/05m5b8x20 (22) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (23) Johns Hopkins Medicine Baltimore, MD United States. ROR: https://ror.org/037zgn354 (24) Johns Hopkins Medicine Baltimore United States. ROR: https://ror.org/037zgn354 (25) Johns Hopkins University Baltimore, Maryland United States. ROR: https://ror.org/00za53h95 (26) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (27) Johns Hopkins University Baltimore, MD United States. ROR: https://ror.org/00za53h95 (28) Johns Hopkins Medicine Baltimore, Maryland United States. ROR: https://ror.org/037zgn354

Mutant KRAS peptide vaccine with dual checkpoint blockade in metastatic colorectal cancer: a phase I trial Spotlight 

Wang et al. evaluated a combination of nivolumab, ipilimumab, and mKRAS-VAX (six 21-mer synthetic long peptides targeting common KRAS mutations) in 13 heavily pretreated patients with MMRp/MSS metastatic colorectal cancer. Treatment was well tolerated, with a 15% overall response rate and a median progression-free and overall survival of 2 and 24.9 months, respectively. Direct ex vivo peptide stimulation revealed reactive T cell responses in 75% of patients, which reached 100% following in vitro expansion (mainly CD4+ and polyfunctional). Tumor infiltration by peripheral mKRAS-reactive T cells was associated with tumor regression.

Contributed by Ute Burkhardt

Wang et al. evaluated a combination of nivolumab, ipilimumab, and mKRAS-VAX (six 21-mer synthetic long peptides targeting common KRAS mutations) in 13 heavily pretreated patients with MMRp/MSS metastatic colorectal cancer. Treatment was well tolerated, with a 15% overall response rate and a median progression-free and overall survival of 2 and 24.9 months, respectively. Direct ex vivo peptide stimulation revealed reactive T cell responses in 75% of patients, which reached 100% following in vitro expansion (mainly CD4+ and polyfunctional). Tumor infiltration by peripheral mKRAS-reactive T cells was associated with tumor regression.

Contributed by Ute Burkhardt

ABSTRACT: Immune checkpoint inhibitors (ICIs) have limited activity in mismatch repair proficient or microsatellite stable (MMRp/MSS) colorectal cancer (CRC). KRAS mutations, present in approximately 40% of these cancers, can generate neoantigens that are targets for therapeutic vaccines. In this single-arm, phase I study (NCT04117087), we evaluated mKRAS-VAX, a pooled mutant KRAS (mKRAS) peptide vaccine targeting six KRAS mutations with nivolumab and ipilimumab in 13 patients with pretreated metastatic MMRp/MSS CRC. Both primary endpoints of safety and immunogenicity (within 17 weeks post-vaccination) were met. Secondary endpoints included treatment efficacy defined by RECIST v1.1 criteria. All adverse events attributed to mKRAS-VAX were grade 1 or 2, and the addition of mKRAS-VAX did not increase the frequency of severe immune-related adverse events beyond the expected profile of dual ICIs alone. mKRAS-VAX elicited an increase in tumor-specific mKRAS-reactive T-cells in 8/12 biomarker-evaluable patients (75%) by direct ex vivo IFN_ ELISpot and in 12 patients (100%) following in vitro expansion. Our findings support further development of mKRAS vaccines with ICIs for advanced MMRp/MSS CRC.

Author Info: (1) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University S

Author Info: (1) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (2) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (3) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (4) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (5) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (6) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. Department of Hematology/Oncology, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. (7) Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. (8) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (9) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (10) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (11) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (12) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (13) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (14) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (15) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (16) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (17) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (18) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (19) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (20) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (21) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. (22) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. (23) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. nilo.azad@jhu.edu. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. nilo.azad@jhu.edu. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. nilo.azad@jhu.edu. (24) Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. nzaidi1@jhmi.edu. Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. nzaidi1@jhmi.edu. The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University of Medicine, Baltimore, MD, USA. nzaidi1@jhmi.edu.

A distinct antigen presentation pathway drives potent T cell immunity in lipid nanoparticle-based mRNA vaccines Spotlight 

Muro and Wang et al. studied mechanisms by which lipid nanoparticle-encapsulated mRNA (mRNA-LNP) vaccines induce significantly higher levels of antigen-specific cytotoxic T cells and T cell-dependent antibodies compared to conventional adjuvant-based immunization. Using model antigens, mRNA-LNP induced Th1-skewed murine CD4+ T cell differentiation, followed by production of class-switched IgGs (IgG2b and IgG2c) and long-term cytotoxic CD8+ T cells. Unlike traditional cDC1-mediated cross-presentation, mRNA-LNPs were primarily found in migratory cDC2 cells in draining lymph nodes, resulting in strong, persistent antigen presentation.

Contributed by Katherine Turner

Muro and Wang et al. studied mechanisms by which lipid nanoparticle-encapsulated mRNA (mRNA-LNP) vaccines induce significantly higher levels of antigen-specific cytotoxic T cells and T cell-dependent antibodies compared to conventional adjuvant-based immunization. Using model antigens, mRNA-LNP induced Th1-skewed murine CD4+ T cell differentiation, followed by production of class-switched IgGs (IgG2b and IgG2c) and long-term cytotoxic CD8+ T cells. Unlike traditional cDC1-mediated cross-presentation, mRNA-LNPs were primarily found in migratory cDC2 cells in draining lymph nodes, resulting in strong, persistent antigen presentation.

Contributed by Katherine Turner

ABSTRACT: Lipid nanoparticle-encapsulated mRNA (mRNA-LNP) vaccines trigger the potent differentiation of antigen-specific cytotoxic CD8 T cells in addition to antibody production. Despite its high immunogenicity, the cellular mechanisms by which mRNA-LNP induces such unusual immune responses remain largely unclear. Here, we show that mRNA-LNP induces potent and long-lasting CD8 T cell expansion through an antigen presentation mechanism that differs from that of conventional adjuvants. In mice immunized with mRNA-LNP, the number of antigen-specific CD8 T cells was one order of magnitude higher than that induced by combining antigen proteins with immunostimulants such as lipopolysaccharide or polyinosinic:polycytidinic acid. Intramuscularly administered mRNA-LNPs were mainly taken up by migratory type 2 conventional dendritic cells in draining lymph nodes, resulting in notably strong and persistent antigen presentation through major histocompatibility complex class I. Furthermore, CD8 T cell induction by mRNA-LNP required migratory dendritic cells but not the traditional cross-presentation pathway that is otherwise essential for antiviral and antitumor immunity. Thus, the mRNA-LNP formulation exerts unconventional immune responses through a different antigen-presentation pathway from conventional component vaccines.

Author Info: (1) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. Division of Molecular Pathology, Research Institute for Bi

Author Info: (1) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan. (2) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. (3) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. (4) Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan. (5) Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. Division of Rheumatology, Department of Medicine, University of California San Diego, La Jolla, CA, United States. (6) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. (7) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. Division of Immune Environment Dynamics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan. Immune Network Research Unit, Institute for Frontier Science Initiative InFiniti, Kanazawa University, Kanazawa, Japan. (8) Department of Laboratory Animal Medicine, National Institute of Global Health and Medicine, Japan Institute for Health and Security (JIHS), Tokyo, Japan. (9) Department of Laboratory Animal Medicine, National Institute of Global Health and Medicine, Japan Institute for Health and Security (JIHS), Tokyo, Japan. (10) Kyoto University Immunomonitoring Center, Liaison Office, Kyoto University, Kyoto, Japan. Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan. (11) Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. (12) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan. (13) Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.

Enhancement of ferroptosis in escape variant tumor cells by IFN-γ derived from antigen-specific T cells controls tumor with heterogeneity

Spotlight 

To enhance immunotherapy efficacy against escape variant clones, Ehara et al. combined MART-1 TCR-T cells with the ferroptosis inducer RSL3. IFNγ secreted by the TCR-T cells enhanced the susceptibility of melanoma cells to ferroptosis. In mice injected with an equal mix of 526MEL and β2mKO cells, the combination treatment inhibited tumor growth, including reduction of the HLA-negative tumor mass, and significantly increased T cell infiltration compared to controls. In patients with melanoma, high expression of IFNγ signature genes STAT1 and IRF1 and low expression of SLC2A2 (counteracting ferroptosis) predicted better outcomes.

Contributed by Ute Burkhardt

To enhance immunotherapy efficacy against escape variant clones, Ehara et al. combined MART-1 TCR-T cells with the ferroptosis inducer RSL3. IFNγ secreted by the TCR-T cells enhanced the susceptibility of melanoma cells to ferroptosis. In mice injected with an equal mix of 526MEL and β2mKO cells, the combination treatment inhibited tumor growth, including reduction of the HLA-negative tumor mass, and significantly increased T cell infiltration compared to controls. In patients with melanoma, high expression of IFNγ signature genes STAT1 and IRF1 and low expression of SLC2A2 (counteracting ferroptosis) predicted better outcomes.

Contributed by Ute Burkhardt

ABSTRACT: Tumor masses often exhibit heterogeneity, including escape variant clones that lack antigen-presenting machinery and/or tumor antigens, which poses a major challenge to immunotherapy. Ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, has been shown to effectively induce cell death in various tumor cells. Recent studies have reported that IFN-γ suppresses the expression of System Xc-, thereby enhancing the induction of ferroptosis. Based on this, we hypothesized that combining immunotherapy with ferroptosis inducers could enhance antitumor effects against both antigen-positive and antigen-negative tumor cells. We found that combining RSL3, a ferroptosis inducer, with MART-1-specific TCR-T cells eradicates a heterogeneous tumor model consisting of human melanoma cells and their β2 microglobulin knockout counterparts. In NOG mice, this combination therapy demonstrates a significant antitumor effect against tumors with heterogeneity. These findings suggest that integrating ferroptosis inducers with immunotherapy could overcome the limitations imposed by escape variant tumor clones, offering a promising strategy for cancer treatment.

Author Info: (1) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (2) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (3) Nagasaki University Nagasaki Japan

Author Info: (1) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (2) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (3) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (4) Aichi Cancer Center Research Institute Chikusa-ku, Nagoya, Aichi Japan. (5) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (6) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (7) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (8) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (9) Takara Bio Inc. Kusatsu, Shiga Japan. (10) Takara Bio Inc. Otsu, Shiga Japan. (11) Nagasaki University Nagasaki Japan. ROR: https://ror.org/058h74p94 (12) Nagasaki University Nagasaki, Nagasaki Japan. ROR: https://ror.org/058h74p94

Targeting non-canonical antigens unlocks functional T-cell responses in renal cell carcinoma Spotlight 

Using immunopeptidomics and exome and transcriptome sequencing, Wang et al. analyzed 22 RCC samples and identified HLA-I-presented non-canonical tumor-specific antigens (TSA) derived from human endogenous retroviruses and long non-­coding RNAs, with some shared across patients. TSA-reactive T cells in the TIME primarily expressed an exhausted phenotype. T cells expressing TSA-reactive TCRs isolated using scRNA seq mediated tumor cell killing/ regression in vitro in RCC patient-derived tumor-­like cell clusters cocultured with autologous peripheral lymphocytes and in mouse xenograft models, particularly combined with anti-PD-1.

Contributed by Paula Hochman

Using immunopeptidomics and exome and transcriptome sequencing, Wang et al. analyzed 22 RCC samples and identified HLA-I-presented non-canonical tumor-specific antigens (TSA) derived from human endogenous retroviruses and long non-­coding RNAs, with some shared across patients. TSA-reactive T cells in the TIME primarily expressed an exhausted phenotype. T cells expressing TSA-reactive TCRs isolated using scRNA seq mediated tumor cell killing/ regression in vitro in RCC patient-derived tumor-­like cell clusters cocultured with autologous peripheral lymphocytes and in mouse xenograft models, particularly combined with anti-PD-1.

Contributed by Paula Hochman

BACKGROUND: Renal cell carcinoma (RCC) frequently exhibits favorable responses to immunotherapy, despite a low tumor mutational burden, suggesting a critical role for non-mutational antigens presented by human leukocyte antigen class I in activating CD8(+) T cells. METHODS: To systematically identify non-canonical tumor-specific antigens, we developed an integrated proteogenomic approach to RCC samples by combining immunopeptidomics with exome and transcriptome sequencing. We subsequently primed and expanded antigen-reactive T cells in vitro, isolated a panel of antigen-specific T-cell receptors, and characterized their functionality. Finally, we investigated the tumor-killing and regression of non-canonical antigen-reactive T cells using patient-derived tumor-like cell clusters and mouse models. RESULTS: We discovered a diverse repertoire of non-canonical tumor-specific antigens derived from human endogenous retroviruses (hERVs) and long non-coding RNAs (lncRNAs), many of which were shared across patients. Single-cell RNA sequencing further revealed that T cells reactive to these antigens were enriched within exhausted subsets in the tumor microenvironment, indicative of persistent antigen-specific stimulation. Functionally, T cells engineered to recognize these non-canonical antigens mediated potent tumor cell killing both in vitro and in vivo. Our findings establish hERV-derived and lncRNA-derived antigens as key drivers of RCC immunogenicity and highlight their strong potential as targets for T-cell-based immunotherapy. CONCLUSIONS: Our work is the first to demonstrate that non-canonical antigens drive immunogenicity in low-mutation RCC, thereby resolving a key question in cancer immunology-how tumors with low mutational burden can provoke robust T-cell responses.

Author Info: (1) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future T

Author Info: (1) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (2) Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. (3) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (4) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (5) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (6) Innovative Vaccine and Immunotherapy Research Center, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. (7) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (8) Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. (9) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (10) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (11) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (12) Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China jzxi@pku.edu.cn bqye@pku.edu.cn yexiongjun@cicams.ac.cn. (13) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China jzxi@pku.edu.cn bqye@pku.edu.cn yexiongjun@cicams.ac.cn. (14) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China jzxi@pku.edu.cn bqye@pku.edu.cn yexiongjun@cicams.ac.cn.

Immune microenvironment and noncoding RNA shape early colorectal carcinogenesis in patients with premalignant lesions Spotlight 

Morgand et al. performed a retrospective, longitudinal study characterizing 258 pre-malignant colorectal lesions across discovery and validation cohorts. Patients were stratified based on polyps per year. Sequenced lesions shared few mutations, suggesting their sporadic and independent origin. Patients with the lowest polyp development rates exhibited lesions characterized by high immune cell infiltration and mature TLSs persisting from initial polyp onset to recurrent lesions. Such lesions showed increased expression of non-coding RNAs, which were associated with higher predicted immunogenicity and increased T cell density in tumor centers.

Contributed by Paula Hochman

Morgand et al. performed a retrospective, longitudinal study characterizing 258 pre-malignant colorectal lesions across discovery and validation cohorts. Patients were stratified based on polyps per year. Sequenced lesions shared few mutations, suggesting their sporadic and independent origin. Patients with the lowest polyp development rates exhibited lesions characterized by high immune cell infiltration and mature TLSs persisting from initial polyp onset to recurrent lesions. Such lesions showed increased expression of non-coding RNAs, which were associated with higher predicted immunogenicity and increased T cell density in tumor centers.

Contributed by Paula Hochman

ABSTRACT: Early cancer detection and prophylactic intervention remain the primary strategies for reducing colorectal carcinoma incidence and mortality. Although the immune microenvironment and tumor-associated antigens have been shown to play a pivotal role in carcinogenesis, the factors shaping immune dynamics during the premalignant phase remain poorly understood. In this study, we performed a comprehensive multimodal characterization of the immune microenvironment in 258 longitudinal premalignant colorectal lesions. Using a discovery cohort of 135 lesions from 26 patients stratified by low versus high polyp development rate, we identified distinct immune states associated with polyp burden. These findings were validated in an independent cohort of 123 lesions from 43 patients. Lesions from patients with low polyp development rates exhibited signatures of robust immune surveillance characterized by enhanced adaptive immune infiltration, including defined T cell subsets, and a higher prevalence of mature tertiary lymphoid structures compared with lesions from patients with high polyp frequency. These immune features were accompanied by increased expression of noncoding RNAs. These transcripts were predicted to encode noncanonical antigens with high MHC-I (major histocompatibility complex class I) binding affinity, potentially increasing lesion immunogenicity. We propose that early carcinogenesis is shaped by the immune microenvironment in association with noncoding RNAs, revealing potential early biomarkers in individuals at high risk of developing colorectal cancer.

Author Info: (1) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers,

Author Info: (1) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (2) Institut Roi Albert II, Department of Medical Oncology Cliniques Universitaires St-Luc and Institut de Recherche Clinique et Experimentale (Pole MIRO), UniversitŽ Catholique de Louvain, 1200 Brussels, Belgium. (3) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (4) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (5) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (6) Department of Pathology, Cliniques Universitaires St-Luc and Institut de Recherche Clinique et Experimentale (Pole GAEN) UniversitŽ Catholique de Louvain, 1200 Brussels, Belgium. (7) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (8) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (9) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (10) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (11) UniversitŽ Paris CitŽ, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, 75015 Paris, France. (12) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (13) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (14) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (15) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (16) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (17) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (18) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. (19) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. Assistance Publique-H™pitaux de Paris (AP-HP), Immunomonitoring Platform, Laboratory of Immunology, Georges Pompidou European Hospital, 75015 Paris, France. (20) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. Assistance Publique-H™pitaux de Paris (AP-HP), Immunomonitoring Platform, Laboratory of Immunology, Georges Pompidou European Hospital, 75015 Paris, France. (21) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. Assistance Publique-H™pitaux de Paris (AP-HP), Immunomonitoring Platform, Laboratory of Immunology, Georges Pompidou European Hospital, 75015 Paris, France. (22) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France. Assistance Publique-H™pitaux de Paris (AP-HP), Immunomonitoring Platform, Laboratory of Immunology, Georges Pompidou European Hospital, 75015 Paris, France. (23) Sidra Medicine, P.O. Box 26999, Doha, Qatar. (24) Sidra Medicine, P.O. Box 26999, Doha, Qatar. (25) Sidra Medicine, P.O. Box 26999, Doha, Qatar. (26) Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami, Miami, FL 33136, USA. (27) Sidra Medicine, P.O. Box 26999, Doha, Qatar. Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy. (28) INSERM, Laboratory of Integrative Cancer Immunology, F-75006 Paris, France. Equipe LabellisŽe Ligue Contre le Cancer, F-75006 Paris, France. Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, UniversitŽ Paris CitŽ, F-75006 Paris, France.

The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM Spotlight 

Freeburg and Chafamo et al. performed longitudinal single-cell profiling of CSF and tumors from 18 patients with recurrent GBM treated with a single intracerebroventricular dose of bivalent EGFR-IL13Rα2 CAR T cells. CAR T cells peaked at 7 days and showed increased cytotoxicity and exhaustion in CSF. Endogenous cytotoxic NK cells, Tregs, and “scavenger” myeloid cells also increased dose-dependently. Responses correlated with increased CD56dimCD16+ NK cells, while Treg expansion and a high baseline number of immunosuppressive myeloid cells correlated with non-response, emphasizing the endogenous immune system’s role in CAR T cell efficacy.

Contributed by Katherine Turner

Freeburg and Chafamo et al. performed longitudinal single-cell profiling of CSF and tumors from 18 patients with recurrent GBM treated with a single intracerebroventricular dose of bivalent EGFR-IL13Rα2 CAR T cells. CAR T cells peaked at 7 days and showed increased cytotoxicity and exhaustion in CSF. Endogenous cytotoxic NK cells, Tregs, and “scavenger” myeloid cells also increased dose-dependently. Responses correlated with increased CD56dimCD16+ NK cells, while Treg expansion and a high baseline number of immunosuppressive myeloid cells correlated with non-response, emphasizing the endogenous immune system’s role in CAR T cell efficacy.

Contributed by Katherine Turner

ABSTRACT: Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, with a median survival of under 15 months and no effective treatment after recurrence. A recent phase 1 trial of intracerebroventricular bivalent chimeric antigen receptor (CAR) T cells in recurrent GBM, registered at ClinicalTrials.gov (NCT05168423), showed promising responses, including tumor reduction and prolonged survival. However, relapse remains common. We performed in-depth profiling of longitudinal cerebrospinal fluid (CSF) and tumor samples from responders and non-responders to characterize immune dynamics following infusion. Our study reveals that, although CAR T cells activate post infusion across all patients, outcomes were defined by divergent remodeling of the endogenous immune landscape. Cytotoxic natural killer cell expansion characterized responders, whereas regulatory T cell expansion and abundant baseline immunosuppressive scavenger myeloid cells characterized non-responders. These findings indicate that host immune cells play a critical role in CAR T cell therapy for GBM, suggesting that combinatorial strategies modulating the endogenous immune compartment could improve next-generation treatments.

Author Info: (1) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (2) Cancer Biology Department, Perelman School of Medicin

Author Info: (1) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (2) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (3) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (4) Department of Pathology, Case Western Reserve University School of Medicine and Case Comprehensive Cancer Center, Cleveland, OH, USA. (5) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (6) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (7) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (8) Department of Pathology, Case Western Reserve University School of Medicine and Case Comprehensive Cancer Center, Cleveland, OH, USA. (9) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (10) Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (11) Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (12) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (13) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (14) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (15) Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (16) Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA. (17) UniversitŽ Paris CitŽ, INSERM, PARCC, Paris, France; Department of Immunology, APHP, H™pital EuropŽen Georges Pompidou (HEGP)-H™pital Necker, Paris, France. (18) Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, INSERM, UniversitŽ Paris CitŽ, 75006 Paris, France. (19) CellAction, Center for Cancer Immunotherapy, INSERM U932, Institut Curie, Saint-Cloud, France. (20) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (21) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (22) Clinical Immunology Laboratory, Institut Curie, Paris, France. (23) Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France. (24) Department of Translational Research, PSL University, Institut Curie, Paris, France; INSERM U1330, PSL University, Institut Curie Research Center, Paris, France. (25) CellAction, Center for Cancer Immunotherapy, INSERM U932, Institut Curie, Saint-Cloud, France. (26) CellAction, Center for Cancer Immunotherapy, INSERM U932, Institut Curie, Saint-Cloud, France; Clinical Hematology Unit, Institut Curie, Saint-Cloud, France. (27) Departments of Dermatology and Pathology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (28) Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. (29) Kite, a Gilead Company, Santa Monica, CA, USA. (30) Comparative Pathology Core, Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA. (31) Comparative Pathology Core, Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA. (32) Comparative Pathology Core, Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA. (33) Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (34) Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (35) Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (36) Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA. (37) Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, INSERM, UniversitŽ Paris CitŽ, 75006 Paris, France; ƒquipe labellisŽe Ligue Contre le Cancer, Centre de Recherche des Cordeliers, 15 rue de l'Žcole de mŽdecine, 75006 Paris, France. (38) Centre de Recherche des Cordeliers, Sorbonne UniversitŽ, INSERM, UniversitŽ Paris CitŽ, 75006 Paris, France; ƒquipe labellisŽe Ligue Contre le Cancer, Centre de Recherche des Cordeliers, 15 rue de l'Žcole de mŽdecine, 75006 Paris, France. (39) UniversitŽ Paris CitŽ, INSERM, PARCC, Paris, France; Department of Immunology, APHP, H™pital EuropŽen Georges Pompidou (HEGP)-H™pital Necker, Paris, France. (40) Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (41) Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France. (42) Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA. (43) GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (44) Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (45) Department of Pathology, Case Western Reserve University School of Medicine and Case Comprehensive Cancer Center, Cleveland, OH, USA; Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA. (46) GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. (47) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA. (48) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; GBM Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: binderz@pennmedicine.upenn.edu. (49) Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; UniversitŽ Paris CitŽ, INSERM, PARCC, Paris, France; Clinical Laboratory, H™pital Foch, Suresnes, France. Electronic address: c.alanio@hopital-foch.com. (50) Cancer Biology Department, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: dana.silverbush@pennmedicine.upenn.edu.

Immunoediting restricts clonal neoantigens in primary, treatment-naive human tumors Spotlight 

To investigate immunoediting in human tumors, Borden et al. analyzed primary, treatment-naive cSCC tumors, which frequently arise in immunosuppressed patients following solid organ transplant, suggesting immune involvement. Compared to tumors from immunodeficient patients or just poorly infiltrated tumors, tumors from immunocompetent patients with high infiltration showed lower overall and clonal mutation burdens, and a lower frequency of variant alleles with high predicted neoantigen:MHC-I binding affinity. Further, neoantigens that shared features with validated immunogenic neoantigens were decreased in clonal versus subclonal cancer cells.

Contributed by Lauren Hitchings

To investigate immunoediting in human tumors, Borden et al. analyzed primary, treatment-naive cSCC tumors, which frequently arise in immunosuppressed patients following solid organ transplant, suggesting immune involvement. Compared to tumors from immunodeficient patients or just poorly infiltrated tumors, tumors from immunocompetent patients with high infiltration showed lower overall and clonal mutation burdens, and a lower frequency of variant alleles with high predicted neoantigen:MHC-I binding affinity. Further, neoantigens that shared features with validated immunogenic neoantigens were decreased in clonal versus subclonal cancer cells.

Contributed by Lauren Hitchings

ABSTRACT: T cell targeting of cancer cells alters the tumor antigen landscape in preclinical models. Here, we examined the impact of immunoediting on the antigenic landscape of primary, treatment-naive human tumors. Cutaneous squamous cell carcinoma tumors from immunocompetent and immunosuppressed patients revealed consistent tumor mutational signatures; however, high-immune-infiltrate tumors from immunocompetent patients had lower overall mutational burdens and lower clonal mutational burdens compared with low-infiltrate tumors from immunocompetent patients and tumors from immunosuppressed patients. The lower clonal mutational burden in high-immune-infiltrate tumors from immunocompetent patients persisted after accounting for tumor purity and growth rate. Predicted neoantigen: major histocompatibility complex (MHC) class I binding affinity decreased with increasing variant allele frequency, demonstrating restriction of mutations encoding MHC-binding neoantigens. Neoantigens with features shared with validated immunogenic neoantigens were decreased in clonal relative to subclonal cancer cell populations in high-immune-infiltrate tumors from immunocompetent patients. Thus, the immune system restricts cancer cells expressing immunogenic antigens from clonal populations in primary, treatment-naive human tumors.

Author Info: (1) Department of Dermatology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; Phoenix Veterans Affairs Health Care System, Phoenix, AZ 85012, USA. (2)

Author Info: (1) Department of Dermatology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; Phoenix Veterans Affairs Health Care System, Phoenix, AZ 85012, USA. (2) Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA. (3) Department of Dermatology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA. (4) Department of Dermatology, Mayo Clinic Health System, Scottsdale, AZ 85259, USA. (5) Department of Dermatology, Mayo Clinic Health System, Scottsdale, AZ 85259, USA. (6) Department of Dermatology, Mayo Clinic Health System, Scottsdale, AZ 85259, USA. (7) Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Champaign, IL 61801, USA. (8) Department of Dermatology, Mayo Clinic Health System, Scottsdale, AZ 85259, USA. (9) Department of Dermatology, Mayo Clinic Health System, Scottsdale, AZ 85259, USA. (10) Department of Dermatology, Mayo Clinic Health System, Scottsdale, AZ 85259, USA. (11) Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA. (12) BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA; R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85724, USA. (13) School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA. (14) School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA. (15) Department of Dermatology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; Phoenix Veterans Affairs Health Care System, Phoenix, AZ 85012, USA; University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA. Electronic address: khasting@arizona.edu.

Adjuvant personalized multivalent neoantigen DNA vaccination for MGMT unmethylated glioblastoma: a phase 1 trial Spotlight 

In a phase 1 study, Garfinkle et al. vaccinated 9 patients with MGMT unmethylated glioblastoma with a personalized DNA-based vaccine following surgical resection and radiation. GNOS-PVO1 encoded up to 40 neoantigens identified from 3–4 distinct tumor regions per patient, and was well tolerated. The median 24-month survival rate was 33%, including a patient who remained disease-free over 4 years after diagnosis. Survival correlated with increases in peripheral CD8+CD69+ and CD8+IFNγ+ T cells. Increased tumor-infiltrating CD8+ T cells, with expanded de novo and pre-existing TCR clonotypes in the tumor and blood, were observed upon vaccination.

Contributed by Ute Burkhardt

In a phase 1 study, Garfinkle et al. vaccinated 9 patients with MGMT unmethylated glioblastoma with a personalized DNA-based vaccine following surgical resection and radiation. GNOS-PVO1 encoded up to 40 neoantigens identified from 3–4 distinct tumor regions per patient, and was well tolerated. The median 24-month survival rate was 33%, including a patient who remained disease-free over 4 years after diagnosis. Survival correlated with increases in peripheral CD8+CD69+ and CD8+IFNγ+ T cells. Increased tumor-infiltrating CD8+ T cells, with expanded de novo and pre-existing TCR clonotypes in the tumor and blood, were observed upon vaccination.

Contributed by Ute Burkhardt

ABSTRACT: Glioblastoma is a fatal disease with a median prognosis of 12-18_months. Recent studies have shown encouraging results using neoantigen-based vaccines to stimulate glioblastoma-directed immune responses, but overall immunogenicity has been low. Here, we report the results of an open-label, single-arm, phase 1 clinical trial (GT-20) to evaluate the safety and feasibility (primary endpoints) as well as immunogenicity and preliminary clinical activity (secondary endpoints) of GNOS-PV01 monotherapy, a DNA-based personalized therapeutic cancer vaccine administered following surgical resection and radiation for patients with MGMT unmethylated glioblastoma. The GT-20 study vaccinated nine patients, using up to 40 neoantigens per patient (range, 17-40) without causing any serious adverse events, unexpected toxicities or dose-limiting toxicities. The vaccine induced activation and expansion of circulating peripheral T_cells in all evaluated patients, except one who was being treated with dexamethasone. The secondary endpoint was to evaluate 6_month progression-free survival and 12_month overall survival; each observed in 66.7% of patients. Median progression-free survival was 8.5_months, median overall survival was 16.3_months and survival at 24_months was 33%, including one long-term survivor still alive 4_years from the time of initial surgery. This study met the pre-specified endpoints and supports the use of GNOS-PV01 as a potentially impactful component of glioblastoma immunotherapy. ClinicalTrials.gov: NCT04015700 .

Author Info: (1) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. (2) Geneos Therapeutics, Philadelphia, PA, USA. (3) Department

Author Info: (1) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. (2) Geneos Therapeutics, Philadelphia, PA, USA. (3) Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. (4) Division of Medical Oncology, Washington University School of Medicine, St. Louis, MO, USA. (5) Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA. (6) Division of Medical Oncology, Washington University School of Medicine, St. Louis, MO, USA. The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. (7) The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA. (8) McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. (9) McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. (10) McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. (11) Geneos Therapeutics, Philadelphia, PA, USA. (12) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. (13) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. Biomedical Sciences Graduate Program, The Ohio State University College of Medicine, Columbus, OH, USA. (14) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. The Ohio State University, Columbus, OH, USA. (15) Geneos Therapeutics, Philadelphia, PA, USA. (16) Geneos Therapeutics, Philadelphia, PA, USA. (17) Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA. (18) Geneos Therapeutics, Philadelphia, PA, USA. (19) Geneos Therapeutics, Philadelphia, PA, USA. (20) BioProcess Advantage LLC, Westfield, NJ, USA. (21) Department of Neurology, Mayo Clinic, Rochester, MN, USA. (22) Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. (23) Department of Neurosurgery, University of Missouri, Columbia, MO, USA. (24) The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, USA. (25) Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, USA. (26) The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, USA. (27) The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, USA. (28) Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. (29) Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. (30) Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. (31) Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA. (32) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA. (33) The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA. (34) Geneos Therapeutics, Philadelphia, PA, USA. (35) Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. (36) Division of Medical Oncology, Washington University School of Medicine, St. Louis, MO, USA. tannerjohanns@wustl.edu. The Brain Tumor Center at Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. tannerjohanns@wustl.edu. Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Program, Washington University School of Medicine, St. Louis, MO, USA. tannerjohanns@wustl.edu.

Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery Featured  

Using high-throughput yeast display and protein language models (pLMs), Wang, Yeh, et al. developed a new approach to determine TCR recognition that goes beyond the TCR sequence. This method generates deep peptide recognition profiles (PRPs), with PRP functional distance predicting the specificity of a new TCR, thereby enabling the discovery of novel candidate autoantigens in autoimmune disease.

Using high-throughput yeast display and protein language models (pLMs), Wang, Yeh, et al. developed a new approach to determine TCR recognition that goes beyond the TCR sequence. This method generates deep peptide recognition profiles (PRPs), with PRP functional distance predicting the specificity of a new TCR, thereby enabling the discovery of novel candidate autoantigens in autoimmune disease.

ABSTRACT: Predicting T cell receptor (TCR) specificity on the basis of sequence is challenging because TCRs of similar sequence can recognize entirely different antigens, whereas TCRs of different sequence can recognize the same antigens. Here we present a system that integrates high-throughput yeast display with fine-tuned protein language models (pLMs) to generate deep peptide recognition profiles (PRPs) for individual TCRs, each detailing binding against millions of peptides. We provide detailed PRPs for a panel of HLA-B*27:05-restricted TCRs from persons with ankylosing spondylitis and acute anterior uveitis that almost exclusively recognize peptides through CDR3β. pLMs trained on these PRPs outperform AlphaFold3 and tFold-TCR in predicting T cell activation. We discover and validate novel candidate autoantigens, demonstrate that model generalization to new TCRs correlates with functional distance (PRP divergence) rather than sequence similarity and introduce a model-intrinsic uncertainty metric to quantify prediction confidence. This system and its associated PRP datasets offer a scalable approach to mapping TCR recognition, accelerating antigen discovery and guiding TCR engineering.

Author Info: (1) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University School of Medic

Author Info: (1) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. (2) Biohub, Chicago, IL, USA. Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA. Medical Scientist Training Program, University of Chicago, Chicago, IL, USA. (3) Biohub, Chicago, IL, USA. (4) Biohub, Chicago, IL, USA. (5) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. (6) Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA. (7) Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA. (8) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. (9) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. (10) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. (11) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. (12) Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (13) Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA. (14) Biohub, Chicago, IL, USA. aakhan@uchicago.edu. Departments of Pathology, and Family Medicine, University of Chicago, Chicago, IL, USA. aakhan@uchicago.edu. (15) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu.

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