CoChat
Sign Up
PreprintCited by 19CAR-T cell therapy researchImmunotherapy and Immune ResponsesCancer Immunotherapy and Biomarkers

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Structural principles of peptide-centric Chimeric Antigen Receptor recognition guide therapeutic expansion

Open access
Sun, Yi, Florio, Tyler J., Gupta, Sagar, Young, Michael C., Marshall, Quinlen F., Garfinkle, Samuel E., Papadaki, Georgia F., Truong, Hau V., Mycek, Emily, Li, Peiyao, Farrel, Alvin, Church, Nicole L., Jabar, Shereen, Beasley, Matthew D., Kiefel, Ben R., Yarmarkovich, Mark, Mallik, Leena, Maris, John M., Sgourakis, Nikolaos G.·2023·Science Immunology
DOI 10.1101/2023.05.24.542108PMC PMC10782944

Preprint — published as 10.1126/sciimmunol.adj5792 · Paper page

Open this paper in CoChat — free account

Abstract

Peptide-Centric Chimeric Antigen Receptors (PC-CARs), which recognize oncoprotein epitopes displayed by human leukocyte antigens (HLAs) on the cell surface, offer a promising strategy for targeted cancer therapy 1 . We have previously developed a PC-CAR targeting a neuroblastoma- associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes 2 . Here, we determine the 2.1 Å structure of the PC-CAR:PHOX2B/HLA-A*24:02/β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). The PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactivity group, covering a combined American population frequency of up to 25.2%. Comprehensive characterization using biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation and CAR-T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.05.24.542108

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 72

  1. 2021, TCR-like CARss and TCR-CARs targeting neoepitopes: an emerging potential, Cancer Gene Ther, 28, 581, 10.1038/s41417-021-00307-7 · DOI
  2. 2021, Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs, Nature, 599, 477, 10.1038/s41586-021-04061-6 · DOI
  3. 2023, CAR immune cells: design principles, resistance and the next generation, Nature, 614, 635, 10.1038/s41586-023-05707-3 · DOI
  4. 10.1056/nejmra1706169 · DOI
  5. 10.1056/NEJMoa1709866 · DOI · Paper page
  6. 10.1182/bloodadvances.2020003092 · DOI
  7. 2022, PSMA-targeting TGFβ-insensitive armored CAR T cells in metastatic castration-resistant prostate cancer: a phase 1 trial, Nat. Med, 28, 724, 10.1038/s41591-022-01726-1 · DOI
  8. 2023, GD2-CART01 for Relapsed or Refractory High-Risk Neuroblastoma, N. Engl. J. Med, 388, 1284, 10.1056/NEJMoa2210859 · DOI
  9. 10.1038/s41586-022-04489-4 · DOI
  10. 2021, Targeting public neoantigens for cancer immunotherapy. Nat, Cancer, 2, 487
  11. 10.1016/j.chembiol.2010.05.011 · DOI · Paper page
  12. de Souza, J. E. S. et al. SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins. Cancer Immun. 12, 15 (2012).
  13. 10.1016/j.it.2016.08.010 · DOI · Paper page
  14. 2016, Neuroblastoma, Nat. Rev. Dis. Primer, 2, 1
  15. 2022, Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants, Protein Sci. Publ. Protein Soc, 31, e4379, 10.1002/pro.4379 · DOI · Paper page
  16. 10.1146/annurev.immunol.23.021704.115658 · DOI
  17. 10.1146/annurev-immunol-032414-112334 · DOI
  18. 10.1111/j.1399-0039.1997.tb02891.x · DOI
  19. 2017, NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data, J. Immunol. Baltim. Md, 199, 3360
  20. 1998, Strong alloantigenicity of the alpha-helices residues of the MHC class I molecule, J. Immunol. Baltim. Md 1950, 161, 148
  21. 10.1073/pnas.89.22.10915 · DOI · Paper page
  22. 10.1016/j.jmb.2007.05.022 · DOI
  23. Sun, Y. et al. Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes. Sci. Adv. 9, eade7151 (2023). · DOI
  24. 10.1073/pnas.1608820113 · DOI
  25. 10.1073/pnas.92.11.5042 · DOI
  26. 2022, Discrete LAT condensates encode antigen information from single pMHC:TCR binding events, Nat. Commun, 13, 7446, 10.1038/s41467-022-35093-9 · DOI
  27. 2021, The discriminatory power of the T cell receptor, eLife, 10, e67092, 10.7554/eLife.67092 · DOI
  28. Burton, J. et al. Inefficient exploitation of accessory receptors reduces the sensitivity of chimeric antigen receptors. Proc. Natl. Acad. Sci. 120, e2216352120 (2023). · DOI
  29. 2018, Affinity-enhanced T-cell receptors for adoptive T-cell therapy targeting MAGE-A10: strategy for selection of an optimal candidate, Oncoimmunology, 8, e1532759
  30. 2003, Purification of correctly oxidized MHC class I heavy-chain molecules under denaturing conditions: A novel strategy exploiting disulfide assisted protein folding, Protein Sci. Publ. Protein Soc, 12, 551, 10.1110/ps.0233003 · DOI
  31. 10.1007/978-1-59745-398-1_25 · DOI
  32. Gupta, S. , Nerli, S. , Kandy, S. K. , Mersky, G. L. & Sgourakis, N. G. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. 2023.03.20.533510 Preprint at https://doi.org/10.1101/2023.03.20.533510 (2023). · DOI · Paper page
  33. Kozakov, D. et al. Encounter complexes and dimensionality reduction in protein–protein association. eLife 3, e01370 (2014). · DOI
  34. 1998, A very high level of crossreactivity is an essential feature of the T-cell receptor, Immunol, 19, 395
  35. 10.1038/nri3279 · DOI
  36. 10.1016/j.immuni.2009.12.002 · DOI
  37. 10.1016/j.cell.2007.01.048 · DOI
  38. 10.1038/sj.emboj.7601605 · DOI
  39. 2022, Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen, Nat. Commun, 13, 5333, 10.1038/s41467-022-32811-1 · DOI
  40. 10.1126/science.abc8697 · DOI · Paper page
  41. 2023, Advances in antibody-based therapy in oncology. Nat, Cancer, 4, 165
  42. 10.1038/s41587-022-01567-w · DOI
  43. 10.1107/s0907444909047337 · DOI · Paper page
  44. 10.1107/S0907444912001308 · DOI · Paper page
  45. 10.1016/S0076-6879(03)74014-2 · DOI
  46. 10.1107/S0907444910045749 · DOI · Paper page
  47. 10.1107/S0907444904019158 · DOI · Paper page
  48. 10.1107/S2052252514009324 · DOI
  49. 10.1016/0022-2836(87)90412-8 · DOI · Paper page
  50. 10.1016/j.jmb.2016.08.019 · DOI · Paper page
  51. 10.1107/S0021889807021206 · DOI · Paper page
  52. Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. 2021.10.04.463034 Preprint at https://doi.org/10.1101/2021.10.04.463034 (2022). · DOI · Paper page
  53. 10.1002/prot.21123 · DOI
  54. 10.1093/nar/28.1.235 · DOI · Paper page
  55. 2020, RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences, Nucleic Acids Res, 49, D437
  56. 2019, TCR3d: The T cell receptor structural repertoire database, Bioinforma. Oxf. Engl, 35, 5323
  57. Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015). · DOI · Paper page
  58. 10.1038/s41589-018-0096-2 · DOI
  59. 10.1063/1.2408420 · DOI
  60. 10.1016/0263-7855(96)00018-5 · DOI · Paper page
  61. 10.1006/jmbi.1998.2091 · DOI
  62. 10.4049/jimmunol.1900915 · DOI
  63. 10.1093/nar/gkg563 · DOI
  64. 2020, High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange, Nat. Commun, 11, 1909, 10.1038/s41467-020-15710-1 · DOI
  65. 10.1093/nar/gkz1029 · DOI · Paper page
  66. 10.1093/nar/gkz950 · DOI
  67. 10.1016/j.humimm.2013.06.025 · DOI
  68. 10.1371/journal.pone.0024109 · DOI
  69. 10.1016/B978-0-12-381270-4.00019-6 · DOI
  70. Pei, R. , Lee, J. , Shih, N.-J. , Chen, M. & Terasaki, P. I . Single human leukocyte antigen flow cytometry beads for accurate identification of human leukocyte antigen antibody specificities. Transplantation 75, 43 (2003). · DOI
  71. Wittenbrink, N. et al. A novel approach reveals that HLA class 1 single antigen bead-signatures provide a means of high-accuracy pre-transplant risk assessment of acute cellular rejection in renal transplantation. BMC Immunol. 20, 11 (2019). · DOI
  72. 10.1126/science.274.5284.94 · DOI · Paper page

Metadata

Authors
Sun, Y., Florio, T. J., Gupta, S., Young, M. C., Marshall, Q. F., Garfinkle, S. E., Papadaki, G. F., Truong, H. V., Mycek, E., Li, P., Farrel, A., Church, N. L., Jabar, S., Beasley, M. D., Kiefel, B. R., Yarmarkovich, M., Mallik, L., Maris, J. M., & Sgourakis, N. G.
Affiliations
Children's Hospital of Philadelphia (US)
Corresponding author
Sgourakis, Nikolaos G.
ORCID
Venue
Science Immunology
Publisher
openRxiv
Published
2023-05-24
Volume
8
Issue
90
Pages
eadj5792-eadj5792
ISSN
2470-9468 (ISSN-L)
DOI
10.1101/2023.05.24.542108
PMC
PMC10782944
OpenAlex
W4389233063
Cited by
19
References
1
Citations by year
2026: 6 · 2025: 8 · 2024: 4 · 2023: 1
FWCI
2.31
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Science Immunology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, other-oa)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion, other-oa)
  • PubMed Central (submittedVersion)
Funders
  • U.S. Department of Energy (76SF00515, DE‐SC0012704, DE–AC02–76SF00515, KP1607011, Contract No: DESC0012704, AC02‐76SF00515, No. DE-SC0012704, SC0012704., No. DE-AC02–76SF00515, P30GM133893, Contract No. DE-AC02-76SF00515, P30-GM133894, DE-AC02-)
  • American Association for Cancer Research (SU2C-AACR-DT-27-17)
  • St. Baldrick's Foundation (SU2C-AACR-DT-27–17)
  • Children's Hospital of Philadelphia
  • Entertainment Industry Foundation
  • Cancer Research UK (CGCATF2021/100014)
  • National Institutes of Health (17-ID-1, DE-AC02-76SF00515)
  • Office of Science (AC02-76SF00515, DE-SC-0012704, No. DE-SC0012704, DE-AC02-76SF0051 5, DE-AC02, Contract No. DE-SC0012704, SC0012704, 76SF00515, KP1607011)
  • Stand Up To Cancer (SU2C-AACR-DT-27-17)
  • National Cancer Institute (OT2CA278687, U54CA232568, R35CA220500)
  • National Institute of General Medical Sciences (DE-AC02-76SF00515, 17-ID-1, P30GM133893, P30GM133894, R35GM125034)
  • National Institute of Allergy and Infectious Diseases (R01AI143997)
  • Biological and Environmental Research (DE-SC0012704, DE- AC0276SF00515, P30GM133894, KP1607011)
  • Moonshot Research and Development Program
  • Brookhaven National Laboratory (SC0012704, No. DE-SC0012704, DE- SC0012704, Contract No. DE-SC0012704)
  • SLAC National Accelerator Laboratory (DEAC02−76SF00515, AC02‐76SF00515, Contract No. DE-AC02-76SF00515)
  • Cancer Moonshot
Topics
  • Health Sciences › Medicine › Oncology › CAR-T cell therapy research
  • Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
  • Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
Keywords
PHOX2B, HLA-A*24:02, CAR T-cell therapy, neuroblastoma, hypervariable region, peptide backbone conformation, antigen recognition, crystal structure, HLA-A9

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review