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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Retraction Note: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:872. [PMID: 37938785 PMCID: PMC10665177 DOI: 10.1038/s41586-023-06731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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2
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:820-827. [PMID: 37938771 PMCID: PMC10665195 DOI: 10.1038/s41586-023-06706-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023]
Abstract
The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.
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Affiliation(s)
- Mark Yarmarkovich
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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3
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Heard A, Landmann JH, Hansen AR, Papadopolou A, Hsu YS, Selli ME, Warrington JM, Lattin J, Chang J, Ha H, Haug-Kroeper M, Doray B, Gill S, Ruella M, Hayer KE, Weitzman MD, Green AM, Fluhrer R, Singh N. Antigen glycosylation regulates efficacy of CAR T cells targeting CD19. Nat Commun 2022; 13:3367. [PMID: 35690611 PMCID: PMC9188573 DOI: 10.1038/s41467-022-31035-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/31/2022] [Indexed: 01/16/2023] Open
Abstract
While chimeric antigen receptor (CAR) T cells targeting CD19 can cure a subset of patients with B cell malignancies, most patients treated will not achieve durable remission. Identification of the mechanisms leading to failure is essential to broadening the efficacy of this promising platform. Several studies have demonstrated that disruption of CD19 genes and transcripts can lead to disease relapse after initial response; however, few other tumor-intrinsic drivers of CAR T cell failure have been reported. Here we identify expression of the Golgi-resident intramembrane protease Signal peptide peptidase-like 3 (SPPL3) in malignant B cells as a potent regulator of resistance to CAR therapy. Loss of SPPL3 results in hyperglycosylation of CD19, an alteration that directly inhibits CAR T cell effector function and suppresses anti-tumor cytotoxicity. Alternatively, over-expression of SPPL3 drives loss of CD19 protein, also enabling resistance. In this pre-clinical model these findings identify post-translational modification of CD19 as a mechanism of antigen escape from CAR T cell therapy.
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Affiliation(s)
- Amanda Heard
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jack H Landmann
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alkmini Papadopolou
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Yu-Sung Hsu
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mehmet Emrah Selli
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John M Warrington
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John Lattin
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jufang Chang
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Helen Ha
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Martina Haug-Kroeper
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Balraj Doray
- Division of Hematology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Saar Gill
- Division of Hematology and Oncology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO, USA
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Nathan Singh
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA.
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4
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2021; 599:477-484. [PMID: 34732890 PMCID: PMC8599005 DOI: 10.1038/s41586-021-04061-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022]
Abstract
The majority of oncogenic drivers are intracellular proteins, thus constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient to generate responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins that are essential for tumourigenesis and focus on targeting the unmutated peptide QYNPIRTTF, discovered on HLA-A*24:02, which is derived from the neuroblastoma dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (CARs) using a counter-panning strategy with predicted potentially cross-reactive peptides. We further hypothesized that peptide-centric CARs could recognize peptides on additional HLA allotypes when presented in a similar manner. Informed by computational modelling, we showed that PHOX2B peptide-centric CARs also recognize QYNPIRTTF presented by HLA-A*23:01 and the highly divergent HLA-B*14:02. Finally, we demonstrated potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that peptide-centric CARs have the potential to vastly expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and widen the population of patients who would benefit from such therapy by breaking conventional HLA restriction.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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Abstract
Chimeric antigen receptor (CAR) T cells have revolutionized the management of B cell malignancies. These synthetic molecules are composed of peptide fragments from several distinct immune cell proteins and link highly-specific antigen recognition with potent T cell activation. Despite impressive results in many, less than half of patients treated will achieve durable remission after CAR therapy. Recent studies have identified the central role that each structural component of the CAR molecule plays in regulating T cell function. Significant effort has been dedicated to exploring strategies to improve the design of CARs themselves or integrate their activity with other regulatory circuits to enable more precise function. In this review, we will summarize recent pre-clinical and clinical studies that have evaluated novel CAR design formats.
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Affiliation(s)
- Amanda Heard
- Division of Oncology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Jufang Chang
- Division of Oncology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - John M Warrington
- Medical Scientist Training Program, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Nathan Singh
- Division of Oncology, Washington University School of Medicine, St Louis, MO, 63110, USA.
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Yarmarkovich M, Warrington JM, Marshall QF, Shen H, Li W, Beasley M, Marco MD, Stevanovic S, Sgourakis NG, Dimitrov D, Smith P, Maris JM. Abstract 1493: Discovery and CAR T targeting of lineage-restricted neuroblastoma oncoproteins. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The MHC presents a snapshot of the intracellular proteome for surveillance by T cells, including peptides from mutated proteins (neoantigens) and nonmutated but aberrantly expressed proteins. Though peptides derived from nonmutated oncoproteins may be presented on MHC, self-antigens are not normally immunogenic to native T cells. Neuroblastoma presents a unique combination of challenges in identifying and targeting tumor-specific antigens: low mutational burden and low MHC expression.
Methods and Results: Using an immunogenomic and immunopeptidomics approach in 16 human neuroblastoma samples, we identified 265 novel antigens presented on MHC and prioritized 6 (including the PHOX2B master regulator) as lead preclinical candidates based on: 1) binding affinity to common HLA alleles, 2) extent of differential gene expression, 3) lack of MHC presentation in healthy tissue, 4) biological relevance to neuroblastoma, and 5) recurrence across multiple tumors. We validated PHOX2B binding to the predicted HLA allele A24 using crystallography of the refolded peptide-MHC (pMHC) complex, and confirmed the peptide sequence using LC/MS/MS of the synthetic peptide. Upon antigen validation, we engineered CAR receptors to induce immunogenicity to self-antigens. Phage display libraries were used to pan for tumor-specific scFv's, using predicted cross-reactive pMHCs as decoys, generating candidate scFv's that were cloned into CAR constructs. We developed an algorithm to predict cross-reactivity against normal tissue pMHCs and screened CARs for cross-reactivity, prioritizing constructs with high tumor antigen affinity and low cross-reactivity. Lead CARs demonstrate complete elimination of tumor cells in less than 24 hours using 1:1 E:T ratios in neuroblastoma cells, and not in other cancer lines expressing HLA-A24 but not PHOX2B, demonstrating highly specific and potent killing. Robust CAR killing was induced by pulsing HLA-A24+/PHOX2B- melanoma cells with PHOX2B peptide but not with potential cross-reactive peptides. Finally, two lead CAR constructs induced complete regression of established neuroblastoma HLA-A24+ SKNAS xenografts, with additional murine trials ongoing.
Conclusion: Neuroblastomas present a unique ligandome, including a significant number of antigens derived from lineage-restricted oncoproteins. We demonstrate proof-of-concept using scFv-based CARs to target the previously undruggable PHOX2B transcription factor in in vitro and in vivo studies. These data provide a basis for targeting non-immunogenic lineage-restricted oncoproteins using CAR T cells in neuroblastoma and other human cancers.
Citation Format: Mark Yarmarkovich, John M. Warrington, Quinlen F. Marshall, Helena Shen, Wei Li, Matt Beasley, Moreno Di Marco, Stefan Stevanovic, Nikolaos G. Sgourakis, Dimiter Dimitrov, Peter Smith, John M. Maris. Discovery and CAR T targeting of lineage-restricted neuroblastoma oncoproteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1493.
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Affiliation(s)
| | | | | | - Helena Shen
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Wei Li
- 2University of Pittsburgh, Pittsburgh, PA
| | | | | | | | | | | | | | - John M. Maris
- 1Children's Hospital of Philadelphia, Philadelphia, PA
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Yarmarkovich M, Warrington JM, Farrel A, Maris JM. Abstract PO-049: SARS-CoV-2 multiepitope vaccine constructs designed to drive long-term immunity in the majority of the population. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.covid-19-po-049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The current SARS-CoV-2 pandemic has precipitated an urgent need for a safe and effective vaccine to be developed and deployed in a highly accelerated timeframe as compared to standard vaccine development processes. Upfront selection of epitopes most likely to induce a safe and effective immune response can accelerate these efforts. Optimally designed vaccines maximize immunogenicity towards regions of proteins that contribute most to protective immunity, while minimizing the antigenic load contributed by unnecessary protein domains that may result in autoimmunity, reactogenicity, or enhanced infectivity. Adopting tools developed for population-scale characterization of HLA presentation of tumor antigens and cross-reactivity of TCRs with tumor self-antigens, we have generated an immunogenicity map of SARS-CoV-2 to inform vaccine design based on analyses across five parameters: 1) stimulation of CD4 and CD8 T cells; 2) immunogenicity across the majority of human HLA alleles; 3) targeting both evolutionarily conserved regions, as well as newly divergent regions of the virus that increase infectivity; 4) targeting linear and conformational B-cell epitopes; and 5) targeting viral regions with the highest degree of dissimilarity to the self-immunopeptidome such as to maximize safety and immunogenicity. Using these analyses, we have generated 11 SARS-CoV-2 vaccine constructs optimized for long-term immunity across the majority of the population. These constructs contain combinations of epitopes selected from our analysis such as to drive affinity-enhanced memory response in combination with current spike protein vaccine strategies, for use as T-cell vaccines, and a stand-alone vaccine designed to drive memory B- and T-cell responses in the majority of the population. Epitopes were optimized using our immunogenicity algorithm to minimize immunogenicity across the junctions between epitopes and cloned into pVAX vectors, using signal peptides targeting the lysosome, ER, and cytoplasmic secretion, such as to promote presentation to CD4, CD8, and B cells, respectively. Finally, we describe methods for identifying immunodominant epitopes arising from vaccination using barcoded, multiplexed tetramers. Vaccine constructs are currently undergoing testing in transgenic mice expressing human HLA-A2. We expect that these constructs will help drive long-term immunity across the population, targeting conserved regions across multiple coronaviruses.
Citation Format: Mark Yarmarkovich, John M. Warrington, Alvin Farrel, John M. Maris. SARS-CoV-2 multiepitope vaccine constructs designed to drive long-term immunity in the majority of the population [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr PO-049.
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Affiliation(s)
| | | | - Alvin Farrel
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - John M. Maris
- Children's Hospital of Philadelphia, Philadelphia, PA
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8
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Yarmarkovich M, Warrington JM, Farrel A, Maris JM. Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-Term Population-Scale Immunity. Cell Rep Med 2020; 1:100036. [PMID: 32835302 PMCID: PMC7276303 DOI: 10.1016/j.xcrm.2020.100036] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/29/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on major histocompatibility complex (MHC) class I and II across the vast majority of the population. We further prioritize genomic regions that generate highly dissimilar peptides from the human proteome and are also predicted to produce B cell epitopes. We propose sixty-five 33-mer peptide sequences, a subset of which can be tested using DNA or mRNA delivery strategies. These include peptides that are contained within evolutionarily divergent regions of the spike protein reported to increase infectivity through increased binding to the ACE2 receptor and within a newly evolved furin cleavage site thought to increase membrane fusion. Validation and implementation of this vaccine concept could specifically target specific vulnerabilities of SARS-CoV-2 and should engage a robust adaptive immune response in the vast majority of the population.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John M. Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Yarmarkovich M, Warrington JM, Farrel A, Maris JM. A SARS-CoV-2 Vaccination Strategy Focused on Population-Scale Immunity. SSRN 2020:3575161. [PMID: 32714112 PMCID: PMC7366814 DOI: 10.2139/ssrn.3575161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/05/2020] [Indexed: 11/15/2022]
Abstract
Here we propose a vaccination strategy for SARS-CoV-2 based on identification of both highly conserved regions of the virus and newly acquired adaptations that are presented by MHC class I and II across the vast majority of the population, are highly dissimilar from the human proteome, and are predicted B cell epitopes. We present 65 peptide sequences that we expect to result in a safe and effective vaccine which can be rapidly tested in DNA, mRNA, or synthetic peptide constructs. These include epitopes that are contained within evolutionarily divergent regions of the spike protein reported to increase infectivity through increased binding to the ACE2 receptor, and within a novel furin cleavage site thought to increase membrane fusion. This vaccination strategy specifically targets unique vulnerabilities of SARS-CoV-2 and should engage a robust adaptive immune response in the vast majority of the human population.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research; Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - John M. Warrington
- Division of Oncology and Center for Childhood Cancer Research; Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alvin Farrel
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research; Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104
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Yarmarkovich M, Warrington JM, Farrel A, Maris JM. A SARS-CoV-2 Vaccination Strategy Focused on Population-Scale Immunity. bioRxiv 2020:2020.03.31.018978. [PMID: 32511347 PMCID: PMC7255782 DOI: 10.1101/2020.03.31.018978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here we propose a vaccination strategy for SARS-CoV-2 based on identification of both highly conserved regions of the virus and newly acquired adaptations that are presented by MHC class I and II across the vast majority of the population, are highly dissimilar from the human proteome, and are predicted B cell epitopes. We present 65 peptide sequences that we expect to result in a safe and effective vaccine which can be rapidly tested in DNA, mRNA, or synthetic peptide constructs. These include epitopes that are contained within evolutionarily divergent regions of the spike protein reported to increase infectivity through increased binding to the ACE2 receptor, and within a novel furin cleavage site thought to increase membrane fusion. This vaccination strategy specifically targets unique vulnerabilities of SARS-CoV-2 and should engage a robust adaptive immune response in the vast majority of the human population.
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