Reader TTS

ABSTRACT Several current immunotherapy approaches target private neoantigens derived from mutations that are unique to individual patients’ tumors. However, immunotherapeutic agents can also

be developed against public neoantigens derived from recurrent mutations in cancer driver genes. The latter approaches target proteins that are indispensable for tumor growth, and each

therapeutic agent can be applied to numerous patients. Here we review the opportunities and challenges involved in the identification of suitable public neoantigen targets and the

development of therapeutic agents targeting them. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS

Access through your institution Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription $29.99 / 30 days cancel any time Learn more

Subscribe to this journal Receive 12 digital issues and online access to articles $119.00 per year only $9.92 per issue Learn more Buy this article * Purchase on SpringerLink * Instant

access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions *

Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS IDENTIFICATION OF NEOANTIGENS FOR INDIVIDUALIZED THERAPEUTIC CANCER VACCINES Article 01 February 2022

NEOANTIGENS: PROMISING TARGETS FOR CANCER THERAPY Article Open access 06 January 2023 NEOANTIGEN IMMUNOGENICITY LANDSCAPES AND EVOLUTION OF TUMOR ECOSYSTEMS DURING IMMUNOTHERAPY WITH

NIVOLUMAB Article 30 September 2024 DATA AVAILABILITY Data for The Cancer Genome Atlas mutation frequencies used in the analyses presented in Fig. 3 and Table 2 are available from the

National Cancer Institute Genomics Data Commons (https://gdc.cancer.gov/). Data for the HLA frequencies used in the analyses presented in Tables 1 and 2 and Supplementary Table 1 are

available from the Allele Frequency Net Database (http://www.allelefrequencies.net/) and National Marrow Donor Program

(https://bioinformatics.bethematchclinical.org/hla-resources/haplotype-frequencies/high-resolution-hla-alleles-and-haplotypes-in-the-us-population/). Data for cancer incidence used in the

analyses presented in Fig. 3 and Table 2 are available from the National Cancer Institute Surveillance, Epidemiology, and End Results Program

(https://seer.cancer.gov/statfacts/html/common.html). Data for ethnicity representation in the United States used in the analyses presented in Tables 1 and 2 and Supplementary Table 1 are

available from the United States Census Bureau (https://www.census.gov/quickfacts/fact/table/US/PST045219). CHANGE HISTORY * _ 29 JULY 2021 A Correction to this paper has been published:

https://doi.org/10.1038/s43018-021-00246-0 _ REFERENCES * Schumacher, T. N., Scheper, W. & Kvistborg, P. Cancer neoantigens. _Annu. Rev. Immunol._ 37, 173–200 (2019). Article  CAS 

PubMed  Google Scholar  * Vogelstein, B. et al. Cancer genome landscapes. _Science_ 339, 1546–1558 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  * Leko, V. & Rosenberg,

S. A. Identifying and targeting human tumor antigens for T cell-based immunotherapy of solid tumors. _Cancer Cell_ 38, 454–472 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Deniger, D. C. et al. T-cell responses to TP53 ‘hotspot’ mutations and unique neoantigens expressed by human ovarian cancers. _Clin. Cancer Res._ 24, 5562–5573 (2018). Article  CAS  PubMed

  PubMed Central  Google Scholar  * Parkhurst, M. R. et al. Unique neoantigens arise from somatic mutations in patients with gastrointestinal cancers. _Cancer Discov._ 9, 1022–1035 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Guedan, S., Ruella, M. & June, C. H. Emerging cellular therapies for cancer. _Annu. Rev. Immunol._ 37, 145–171 (2019). Article 

CAS  PubMed  Google Scholar  * Reiter, J. G. et al. An analysis of genetic heterogeneity in untreated cancers. _Nat. Rev. Cancer_ 19, 639–650 (2019). Article  CAS  PubMed  PubMed Central 

Google Scholar  * McGranahan, N. & Swanton, C. Neoantigen quality, not quantity. _Sci. Transl. Med._ 11, eaax7918 (2019). Article  PubMed  Google Scholar  * Rosenthal, R. et al.

Neoantigen-directed immune escape in lung cancer evolution. _Nature_ 567, 479–485 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Hsiue, E. H.-C. et al. Targeting a

neoantigen derived from a common _TP53_ mutation. _Science_ 371, eabc8697 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Heinrich, M. C. et al. Avapritinib in advanced

PDGFRA D842V-mutant gastrointestinal stromal tumour (NAVIGATOR): a multicentre, open-label, phase 1 trial. _Lancet Oncol._ 21, 935–946 (2020). Article  CAS  PubMed  Google Scholar  * Hong,

D. S. et al. Larotrectinib in patients with TRK fusion-positive solid tumours: a pooled analysis of three phase 1/2 clinical trials. _Lancet Oncol._ 21, 531–540 (2020). Article  CAS  PubMed

  PubMed Central  Google Scholar  * Marty, R. et al. MHC-I genotype restricts the oncogenic mutational landscape. _Cell_ 171, 1272–1283.e15 (2017). Article  CAS  PubMed  PubMed Central 

Google Scholar  * Marty Pyke, R. et al. Evolutionary pressure against MHC class II binding cancer mutations. _Cell_ 175, 416–428.e13 (2018). Article  PubMed  Google Scholar  * Van den

Eynden, J., Jiménez-Sánchez, A., Miller, M. L. & Larsson, E. Lack of detectable neoantigen depletion signals in the untreated cancer genome. _Nat. Genet._ 51, 1741–1748 (2019). Article 

CAS  PubMed  PubMed Central  Google Scholar  * Pardoll, D. Cancer and the immune system: basic concepts and targets for intervention. _Semin. Oncol._ 42, 523–538 (2015). Article  CAS  PubMed

  PubMed Central  Google Scholar  * Castle, J. C., Uduman, M., Pabla, S., Stein, R. B. & Buell, J. S. Mutation-derived neoantigens for cancer immunotherapy. _Front. Immunol._ 10, 1856

(2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Segal, N. H. et al. Epitope landscape in breast and colorectal cancer. _Cancer Res._ 68, 889–892 (2008). Article  CAS  PubMed

  Google Scholar  * Thorsson, V. et al. The immune landscape of cancer. _Immunity_ 48, 812–830.e14 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Garcia-Garijo, A., Fajardo,

C. A. & Gros, A. Determinants for neoantigen identification. _Front. Immunol._ 10, 1392 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bassani-Sternberg, M. et al.

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. _Nat. Commun._ 7, 13404 (2016). Article  CAS  PubMed  PubMed Central

  Google Scholar  * Chheda, Z. S. et al. Novel and shared neoantigen derived from histone 3 variant H3.3K27M mutation for glioma T cell therapy. _J. Exp. Med._ 215, 141–157 (2018). Article 

CAS  PubMed  PubMed Central  Google Scholar  * Narayan, R. et al. Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin. _PLoS ONE_ 14, e0219547 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Wang, Q. et al. Direct detection and quantification of neoantigens. _Cancer Immunol. Res._ 7, 1748–1754 (2019). Article  CAS  PubMed 

PubMed Central  Google Scholar  * Kalaora, S. et al. Combined analysis of antigen presentation and T-cell recognition reveals restricted immune responses in melanoma. _Cancer Discov._ 8,

1366–1375 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Arnaud, M. et al. Biotechnologies to tackle the challenge of neoantigen identification. _Curr. Opin. Biotechnol._

65, 52–59 (2020). Article  CAS  PubMed  Google Scholar  * Gerber, H.-P., Sibener, L. V., Lee, L. J. & Gee, M. H. Identification of antigenic targets. _Trends Cancer_ 6, 299–318 (2020).

Article  CAS  PubMed  Google Scholar  * Sharkey, M. S., Lizée, G., Gonzales, M. I., Patel, S. & Topalian, S. L. CD4+ T-cell recognition of mutated B-RAF in melanoma patients harboring

the V599E mutation. _Cancer Res._ 64, 1595–1599 (2004). Article  CAS  PubMed  Google Scholar  * Yamamoto, T. N., Kishton, R. J. & Restifo, N. P. Developing neoantigen-targeted T

cell-based treatments for solid tumors. _Nat. Med._ 25, 1488–1499 (2019). Article  CAS  PubMed  Google Scholar  * Jaigirdar, A., Rosenberg, S. A. & Parkhurst, M. A high-avidity

WT1-reactive T-cell receptor mediates recognition of peptide and processed antigen but not naturally occurring WT1-positive tumor cells. _J. Immunother._ 39, 105–116 (2016). Article  CAS 

PubMed  PubMed Central  Google Scholar  * Tran, E. et al. Immunogenicity of somatic mutations in human gastrointestinal cancers. _Science_ 350, 1387–1390 (2015). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Smith, K. N. et al. Persistent mutant oncogene specific T cells in two patients benefitting from anti-PD-1. _J. Immunother. Cancer_ 7, 40 (2019). Article  PubMed

  PubMed Central  Google Scholar  * Tran, E. et al. T-cell transfer therapy targeting mutant KRAS in cancer. _N. Engl. J. Med._ 375, 2255–2262 (2016). Article  CAS  PubMed  PubMed Central 

Google Scholar  * Chen, F. et al. Neoantigen identification strategies enable personalized immunotherapy in refractory solid tumors. _J. Clin. Invest._ 129, 2056–2070 (2019). Article  PubMed

  PubMed Central  Google Scholar  * Veatch, J. R. et al. Tumor-infiltrating BRAFV600E-specific CD4+ T cells correlated with complete clinical response in melanoma. _J. Clin. Invest._ 128,

1563–1568 (2018). Article  PubMed  PubMed Central  Google Scholar  * Clark, R. E. et al. Direct evidence that leukemic cells present HLA-associated immunogenic peptides derived from the

BCR–ABL b3a2 fusion protein. _Blood_ 98, 2887–2893 (2001). Article  CAS  PubMed  Google Scholar  * Van der Lee, D. I. et al. Mutated nucleophosmin 1 as immunotherapy target in acute myeloid

leukemia. _J. Clin. Invest._ 129, 774–785 (2019). Article  PubMed  PubMed Central  Google Scholar  * Biernacki, M. A. et al. CBFB–MYH11 fusion neoantigen enables T cell recognition and

killing of acute myeloid leukemia. _J. Clin. Invest._ 130, 5127–5141 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Xie, G. et al. CAR-T cells targeting a nucleophosmin

neoepitope exhibit potent specific activity in mouse models of acute myeloid leukaemia. _Nat. Biomed. Eng_. https://doi.org/10.1038/s41551-020-00625-5 (2020). * Douglass, J. et al.

Bispecific antibodies targeting mutant _RAS_ neoantigens. _Sci. Immunol._ 6, eabd5515 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Gjertsen, M. K., Bjorheim, J.,

Saeterdal, I., Myklebust, J. & Gaudernack, G. Cytotoxic CD4+ and CD8+ T lymphocytes, generated by mutant p21-_ras_ (12VAL) peptide vaccination of a patient, recognize 12VAL-dependent

nested epitopes present within the vaccine peptide and kill autologous tumour cells carrying this mutation. _Int. J. Cancer_ 72, 784–790 (1997). Article  CAS  PubMed  Google Scholar  *

Malekzadeh, P. et al. Antigen experienced T cells from peripheral blood recognize p53 neoantigens. _Clin. Cancer Res._ 26, 1267–1276 (2020). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Tubb, V. M. et al. Isolation of T cell receptors targeting recurrent neoantigens in hematological malignancies. _J. Immunother. Cancer_ 6, 70 (2018). Article  PubMed  PubMed

Central  Google Scholar  * Gros, A. et al. Recognition of human gastrointestinal cancer neoantigens by circulating PD-1+ lymphocytes. _J. Clin. Invest._ 129, 4992–5004 (2019). Article  CAS 

PubMed  PubMed Central  Google Scholar  * Wang, Q. J. et al. Identification of T-cell receptors targeting KRAS-mutated human tumors. _Cancer Immunol. Res._ 4, 204–214 (2016). Article  CAS 

PubMed  Google Scholar  * Lo, W. et al. Immunologic recognition of a shared p53 mutated neoantigen in a patient with metastatic colorectal cancer. _Cancer Immunol. Res._ 7, 534–543 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Strønen, E. et al. Targeting of cancer neoantigens with donor-derived T cell receptor repertoires. _Science_ 352, 1337–1341 (2016).

Article  PubMed  Google Scholar  * Calis, J. J. A., de Boer, R. J. & Keşmir, C. Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire.

_PLoS Comput. Biol._ 8, e1002412 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Shao, X. M. et al. High-throughput prediction of MHC class I and II neoantigens with

MHCnuggets. _Cancer Immunol. Res._ 8, 396–408 (2020). Article  CAS  PubMed  Google Scholar  * Bulik-Sullivan, B. et al. Deep learning using tumor HLA peptide mass spectrometry datasets

improves neoantigen identification. _Nat. Biotechnol._ 37, 55–63 (2019). Article  CAS  Google Scholar  * Sarkizova, S. et al. A large peptidome dataset improves HLA class I epitope

prediction across most of the human population. _Nat. Biotechnol._ 38, 199–209 (2020). Article  CAS  PubMed  Google Scholar  * Abelin, J. G. et al. Defining HLA-II ligand processing and

binding rules with mass spectrometry enhances cancer epitope prediction. _Immunity_ 51, 766–779.e17 (2019). Article  CAS  PubMed  Google Scholar  * Vita, R. et al. The immune epitope

database (IEDB) 3.0. _Nucleic Acids Res._ 43, D405–D412 (2015). Article  CAS  PubMed  Google Scholar  * Vizcaíno, J. A. et al. 2016 update of the PRIDE database and its related tools.

_Nucleic Acids Res._ 44, D447–D456 (2016). Article  PubMed  Google Scholar  * Shao, W. et al. The SysteMHC Atlas project. _Nucleic Acids Res._ 46, D1237–D1247 (2018). Article  CAS  PubMed 

Google Scholar  * Hundal, J. et al. pVACtools: a computational toolkit to identify and visualize cancer neoantigens. _Cancer Immunol. Res._ 8, 409–420 (2020). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Wells, D. K. et al. Key parameters of tumor epitope immunogenicity revealed through a consortium approach improve neoantigen prediction. _Cell_ 183, 818–834.e13

(2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Jappe, E. C. et al. Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for

immunotherapy design. _Nat. Commun._ 11, 6305 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bentzen, A. K. et al. T cell receptor fingerprinting enables in-depth

characterization of the interactions governing recognition of peptide–MHC complexes. _Nat. Biotechnol._ 36, 1191–1196 (2018). Article  CAS  Google Scholar  * Zhang, S.-Q. et al.

High-throughput determination of the antigen specificities of T cell receptors in single cells. _Nat. Biotechnol._ 36, 1156–1159 (2018). Article  CAS  Google Scholar  * Peng, S. et al.

Sensitive detection and analysis of neoantigen-specific T cell populations from tumors and blood. _Cell Rep._ 28, 2728–2738.e7 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Moritz, A. et al. High-throughput peptide–MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules. _Sci. Immunol._ 4, eaav0860 (2019). Article 

CAS  PubMed  Google Scholar  * Saini, S. K. et al. Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells. _Sci. Immunol._ 4, eaau9039 (2019).

Article  CAS  PubMed  Google Scholar  * Overall, S. A. et al. High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange. _Nat. Commun._ 11, 1909 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Zaretsky, J. M. et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. _N. Engl. J. Med._ 375, 819–829

(2016). Article  CAS  PubMed  PubMed Central  Google Scholar  * Sánchez-Paulete, A. R. et al. Antigen cross-presentation and T-cell cross-priming in cancer immunology and immunotherapy.

_Ann. Oncol._ 28, xii44–xii55 (2017). Article  PubMed  Google Scholar  * Marino, F. et al. Biogenesis of HLA ligand presentation in immune cells upon activation reveals changes in peptide

length preference. _Front. Immunol._ 11, 1981 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Purcell, A. W., Ramarathinam, S. H. & Ternette, N. Mass spectrometry-based

identification of MHC-bound peptides for immunopeptidomics. _Nat. Protoc._ 14, 1687–1707 (2019). Article  CAS  PubMed  Google Scholar  * Klatt, M. G. et al. Solving an MHC allele-specific

bias in the reported immunopeptidome. _JCI Insight_ 5, e141264 (2020). Article  PubMed Central  Google Scholar  * Cafri, G. et al. mRNA vaccine-induced neoantigen-specific T cell immunity in

patients with gastrointestinal cancer. _J. Clin. Invest._ 130, 5976–5988 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bocchia, M. et al. Complete molecular response in

CML after p210 BCR–ABL1-derived peptide vaccination. _Nat. Rev. Clin. Oncol._ 7, 600–603 (2010). Article  PubMed  Google Scholar  * Chatani, P. D. & Yang, J. C. Mutated RAS: targeting

the ‘untargetable’ with T cells. _Clin. Cancer Res._ 26, 537–544 (2020). Article  CAS  PubMed  Google Scholar  * Comoli, P. et al. BCR–ABL-specific T-cell therapy in Ph+ ALL patients on

tyrosine-kinase inhibitors. _Blood_ 129, 582–586 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  * Veatch, J. R. et al. Endogenous CD4+ T cells recognize neoantigens in lung

cancer patients, including recurrent oncogenic _KRAS_ and _ERBB2_ (_Her2_) driver mutations. _Cancer Immunol. Res._ 7, 910–922 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Roth, T. L. et al. Reprogramming human T cell function and specificity with non-viral genome targeting. _Nature_ 559, 405–409 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Querques, I. et al. A highly soluble Sleeping Beauty transposase improves control of gene insertion. _Nat. Biotechnol._ 37, 1502–1512 (2019). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Liddy, N. et al. Monoclonal TCR-redirected tumor cell killing. _Nat. Med._ 18, 980–987 (2012). Article  CAS  PubMed  Google Scholar  * Lowe, K. L. et al. Novel TCR-based

biologics: mobilising T cells to warm ‘cold’ tumours. _Cancer Treat. Rev._ 77, 35–43 (2019). Article  CAS  PubMed  Google Scholar  * Lu, Y.-C. et al. An efficient single-cell RNA-seq

approach to identify neoantigen-specific T cell receptors. _Mol. Ther._ 26, 379–389 (2018). Article  CAS  PubMed  Google Scholar  * Dijkstra, K. K. et al. Generation of tumor-reactive T

cells by co-culture of peripheral blood lymphocytes and tumor organoids. _Cell_ 174, 1586–1598.e12 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Paria, B. C. et al. Rapid

identification and evaluation of neoantigen-reactive T-cell receptors from single cells. _J. Immunother_. https://doi.org/10.1097/CJI.0000000000000342 (2020). * Spindler, M. J. et al.

Massively parallel interrogation and mining of natively paired human TCRαβ repertoires. _Nat. Biotechnol._ 38, 609–619 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Goebeler, M.-E. & Bargou, R. C. T cell-engaging therapies—BiTEs and beyond. _Nat. Rev. Clin. Oncol._ 17, 418–434 (2020). Article  PubMed  Google Scholar  * MacKay, M. et al. The

therapeutic landscape for cells engineered with chimeric antigen receptors. _Nat. Biotechnol._ 38, 233–244 (2020). Article  CAS  PubMed  Google Scholar  * Skora, A. D. et al. Generation of

MANAbodies specific to HLA-restricted epitopes encoded by somatically mutated genes. _Proc. Natl Acad. Sci. USA_ 112, 9967–9972 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar 

* Miller, M. S. et al. An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation. _J. Biol. Chem._ 294, 19322–19334 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Dao, T. et al. Therapeutic bispecific T-cell engager antibody targeting the intracellular oncoprotein WT1. _Nat. Biotechnol._ 33,

1079–1086 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  * Chang, A. Y. et al. A therapeutic T cell receptor mimic antibody targets tumor-associated PRAME peptide/HLA-I

antigens. _J. Clin. Invest._ 127, 2705–2718 (2017). Article  PubMed  PubMed Central  Google Scholar  * Ahmed, M. et al. TCR-mimic bispecific antibodies targeting LMP2A show potent activity

against EBV malignancies. _JCI Insight_ 3, e97805 (2018). Article  PubMed Central  Google Scholar  * Low, L., Goh, A., Koh, J., Lim, S. & Wang, C.-I. Targeting mutant p53-expressing

tumours with a T cell receptor-like antibody specific for a wild-type antigen. _Nat. Commun._ 10, 5382 (2019). Article  PubMed  PubMed Central  Google Scholar  * Sharma, P., Harris, D. T.,

Stone, J. D. & Kranz, D. M. T-cell receptors engineered de novo for peptide specificity can mediate optimal T-cell activity without self cross-reactivity. _Cancer Immunol. Res._ 7,

2025–2035 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Riley, T. P. et al. T cell receptor cross-reactivity expanded by dramatic peptide–MHC adaptability. _Nat. Chem.

Biol._ 14, 934–942 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Gejman, R. S. et al. Identification of the targets of T-cell receptor therapeutic agents and cells by use

of a high-throughput genetic platform. _Cancer Immunol. Res._ 8, 672–684 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ataie, N. et al. Structure of a TCR mimic antibody

with target predicts pharmacogenetics. _J. Mol. Biol._ 428, 194–205 (2016). Article  CAS  PubMed  Google Scholar  * Hellman, L. M. et al. Improving T cell receptor on-target specificity via

structure-guided design. _Mol. Ther._ 27, 300–313 (2019). Article  CAS  PubMed  Google Scholar  * Holland, C. J. et al. Specificity of bispecific T cell receptors and antibodies targeting

peptide–HLA. _J. Clin. Invest._ 130, 2673–2688 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Sim, M. J. W. et al. High-affinity oligoclonal TCRs define effective adoptive T

cell therapy targeting mutant KRAS-G12D. _Proc. Natl Acad. Sci. USA_ 117, 12826–12835 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Wu, D., Gallagher, D. T., Gowthaman,

R., Pierce, B. G. & Mariuzza, R. A. Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen. _Nat. Commun._ 11, 2908 (2020). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Hu, Z. et al. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. _Nat. Med._ 27, 515–525

(2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Blass, E. & Ott, P. A. Advances in the development of personalized neoantigen-based therapeutic cancer vaccines. _Nat.

Rev. Clin. Oncol._ 18, 215–229 (2021). Article  PubMed  PubMed Central  Google Scholar  * Rosenberg, S. A., Yang, J. C. & Restifo, N. P. Cancer immunotherapy: moving beyond current

vaccines. _Nat. Med._ 10, 909–915 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  * Klebanoff, C. A., Acquavella, N., Yu, Z. & Restifo, N. P. Therapeutic cancer vaccines:

are we there yet? _Immunol. Rev._ 239, 27–44 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Vormehr, M., Türeci, Ö. & Sahin, U. Harnessing tumor mutations for truly

individualized cancer vaccines. _Annu. Rev. Med._ 70, 395–407 (2019). Article  CAS  PubMed  Google Scholar  * Mehta, N. K. et al. Pharmacokinetic tuning of protein–antigen fusions enhances

the immunogenicity of T-cell vaccines. _Nat. Biomed. Eng._ 4, 636–648 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ott, P. A. et al. A phase Ib trial of personalized

neoantigen therapy plus anti-PD-1 in patients with advanced melanoma, non-small cell lung cancer, or bladder cancer. _Cell_ 183, 347–362.e24 (2020). Article  CAS  PubMed  Google Scholar  *

Sahin, U. et al. An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma. _Nature_ 585, 107–112 (2020). Article  CAS  PubMed  Google Scholar  * Romero, P. et al. The Human

Vaccines Project: a roadmap for cancer vaccine development. _Sci. Transl. Med._ 8, 334ps9 (2016). Article  PubMed  Google Scholar  * Türeci, Ö. et al. Challenges towards the realization of

individualized cancer vaccines. _Nat. Biomed. Eng._ 2, 566–569 (2018). Article  PubMed  Google Scholar  * Van Poelgeest, M. I. E. et al. Vaccination against oncoproteins of HPV16 for

noninvasive vulvar/vaginal lesions: lesion clearance is related to the strength of the T-cell response. _Clin. Cancer Res._ 22, 2342–2350 (2016). Article  CAS  PubMed  Google Scholar  *

Schumacher, T. et al. A vaccine targeting mutant IDH1 induces antitumour immunity. _Nature_ 512, 324–327 (2014). Article  CAS  PubMed  Google Scholar  * Pan, J. et al. Immunoprevention of

KRAS-driven lung adenocarcinoma by a multipeptide vaccine. _Oncotarget_ 8, 82689–82699 (2017). Article  PubMed  PubMed Central  Google Scholar  * Morrison, A. H., Byrne, K. T. &

Vonderheide, R. H. Immunotherapy and prevention of pancreatic cancer. _Trends Cancer_ 4, 418–428 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Weber, E. W., Maus, M. V.

& Mackall, C. L. The emerging landscape of immune cell therapies. _Cell_ 181, 46–62 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Rafiq, S., Hackett, C. S. &

Brentjens, R. J. Engineering strategies to overcome the current roadblocks in CAR T cell therapy. _Nat. Rev. Clin. Oncol._ 17, 147–167 (2020). Article  PubMed  Google Scholar  * Depil, S.,

Duchateau, P., Grupp, S. A., Mufti, G. & Poirot, L. ‘Off-the-shelf’ allogeneic CAR T cells: development and challenges. _Nat. Rev. Drug Discov._ 19, 185–199 (2020). Article  CAS  PubMed

  Google Scholar  * Liu, E. et al. Use of CAR-transduced natural killer cells in CD19-positive lymphoid tumors. _N. Engl. J. Med._ 382, 545–553 (2020). Article  CAS  PubMed  PubMed Central 

Google Scholar  * Mo, F. et al. Engineered off-the-shelf therapeutic T cells resist host immune rejection. _Nat. Biotechnol._ 39, 56–63 (2021). Article  CAS  PubMed  Google Scholar  * Smith,

T. T. et al. In situ programming of leukaemia-specific T cells using synthetic DNA nanocarriers. _Nat. Nanotechnol._ 12, 813–820 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar

  * Agarwal, S. et al. In vivo generation of CAR T cells selectively in human CD4+ lymphocytes. _Mol. Ther._ 28, 1783–1794 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Roybal, K. T. & Lim, W. A. Synthetic immunology: hacking immune cells to expand their therapeutic capabilities. _Annu. Rev. Immunol._ 35, 229–253 (2017). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Lynn, R. C. et al. c-Jun overexpression in CAR T cells induces exhaustion resistance. _Nature_ 576, 293–300 (2019). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Yamamoto, T. N. et al. T cells genetically engineered to overcome death signaling enhance adoptive cancer immunotherapy. _J. Clin. Invest._ 129, 1551–1565 (2019). Article  PubMed

  PubMed Central  Google Scholar  * Stadtmauer, E. A. et al. CRISPR-engineered T cells in patients with refractory cancer. _Science_ 367, eaba7365 (2020). Article  CAS  PubMed  Google

Scholar  * Davenport, A. J. et al. Chimeric antigen receptor T cells form nonclassical and potent immune synapses driving rapid cytotoxicity. _Proc. Natl. Acad. Sci. USA_ 115, E2068–E2076

(2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Roda-Navarro, P. & Álvarez-Vallina, L. Understanding the spatial topology of artificial immunological synapses assembled

in T cell-redirecting strategies: a major issue in cancer immunotherapy. _Front. Cell Dev. Biol._ 7, 370 (2019). Article  PubMed  Google Scholar  * Skokos, D. et al. A class of costimulatory

CD28-bispecific antibodies that enhance the antitumor activity of CD3-bispecific antibodies. _Sci. Transl. Med._ 12, eaaw7888 (2020). Article  CAS  PubMed  Google Scholar  * Salter, A. I.

et al. Phosphoproteomic analysis of chimeric antigen receptor signaling reveals kinetic and quantitative differences that affect cell function. _Sci. Signal._ 11, eaat6753 (2018). Article 

PubMed  PubMed Central  Google Scholar  * Ramello, M. C. et al. An immunoproteomic approach to characterize the CAR interactome and signalosome. _Sci. Signal._ 12, eaap9777 (2019). Article 

CAS  PubMed  PubMed Central  Google Scholar  * Liu, Y. et al. Chimeric STAR receptors using TCR machinery mediate robust responses against solid tumors. _Sci. Transl. Med._ 13, eabb5191

(2021). Article  CAS  PubMed  Google Scholar  * Harris, D. T. et al. Comparison of T cell activities mediated by human TCRs and CARs that use the same recognition domains. _J. Immunol._ 200,

1088–1100 (2018). Article  CAS  PubMed  Google Scholar  * Gudipati, V. et al. Inefficient CAR-proximal signaling blunts antigen sensitivity. _Nat. Immunol._ 21, 848–856 (2020). Article  CAS

  PubMed  Google Scholar  * Wu, L., Wei, Q., Brzostek, J. & Gascoigne, N. R. J.Signaling from T cell receptors (TCRs) and chimeric antigen receptors (CARs) on T cells. _Cell. Mol.

Immunol._ 17, 600–612 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Fry, T. J. et al. CD22-targeted CAR T cells induce remission in B-ALL that is naive or resistant to

CD19-targeted CAR immunotherapy. _Nat. Med._ 24, 20–28 (2018). Article  CAS  PubMed  Google Scholar  * Bossi, G., Buisson, S., Oates, J., Jakobsen, B. K. & Hassan, N. J.

ImmTAC-redirected tumour cell killing induces and potentiates antigen cross-presentation by dendritic cells. _Cancer Immunol. Immunother._ 63, 437–448 (2014). Article  CAS  PubMed  Google

Scholar  * Wu, T. et al. Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses. _Nat. Commun._ 10, 2846 (2019). Article  PubMed 

PubMed Central  Google Scholar  * Huang, J. et al. A single peptide–major histocompatibility complex ligand triggers digital cytokine secretion in CD4+ T cells. _Immunity_ 39, 846–857

(2013). Article  CAS  PubMed  Google Scholar  * Nerreter, T. et al. Super-resolution microscopy reveals ultra-low CD19 expression on myeloma cells that triggers elimination by CD19 CAR-T.

_Nat. Commun._ 10, 3137 (2019). Article  PubMed  PubMed Central  Google Scholar  * Pillai, V. et al. CAR T-cell therapy is effective for CD19-dim B-lymphoblastic leukemia but is impacted by

prior blinatumomab therapy. _Blood Adv._ 3, 3539–3549 (2019). Article  PubMed  PubMed Central  Google Scholar  * Majzner, R. G. et al. Tuning the antigen density requirement for CAR T-cell

activity. _Cancer Discov._ 10, 702–723 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Stone, J. D., Aggen, D. H., Schietinger, A., Schreiber, H. & Kranz, D. M. A

sensitivity scale for targeting T cells with chimeric antigen receptors (CARs) and bispecific T-cell engagers (BiTEs). _Oncoimmunology_ 1, 863–873 (2012). Article  PubMed  PubMed Central 

Google Scholar  * Deng, Q. et al. Characteristics of anti-CD19 CAR T cell infusion products associated with efficacy and toxicity in patients with large B cell lymphomas. _Nat. Med._ 26,

1878–1887 (2020). Article  PubMed  PubMed Central  Google Scholar  * Nobles, C. L. et al. CD19-targeting CAR T cell immunotherapy outcomes correlate with genomic modification by vector

integration. _J. Clin. Invest._ 130, 673–685 (2020). Article  CAS  PubMed  Google Scholar  * Sheih, A. et al. Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in

patients undergoing CD19 CAR-T immunotherapy. _Nat. Commun._ 11, 219 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Tran, E. et al. Cancer immunotherapy based on

mutation-specific CD4+ T cells in a patient with epithelial cancer. _Science_ 344, 641–645 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  * Zacharakis, N. et al. Immune

recognition of somatic mutations leading to complete durable regression in metastatic breast cancer. _Nat. Med._ 24, 724–730 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Keskin, D. B. et al. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. _Nature_ 565, 234–239 (2019). Article  CAS  PubMed  Google Scholar  * Hilf, N.

et al. Actively personalized vaccination trial for newly diagnosed glioblastoma. _Nature_ 565, 240–245 (2019). Article  CAS  PubMed  Google Scholar  * Platten, M. et al. A vaccine targeting

mutant IDH1 in newly diagnosed glioma. _Nature_ https://doi.org/10.1038/s41586-021-03363-z (2021). * Linnemann, C. et al. High-throughput epitope discovery reveals frequent recognition of

neo-antigens by CD4+ T cells in human melanoma. _Nat. Med._ 21, 81–85 (2015). Article  CAS  PubMed  Google Scholar  * Germano, G. et al. CD4 T cell dependent rejection of beta 2

microglobulin null mismatch repair deficient tumors. _Cancer Discov_. https://doi.org/10.1158/2159-8290.CD-20-0987 (2021). * Oh, D. Y. et al. Intratumoral CD4+ T cells mediate anti-tumor

cytotoxicity in human bladder cancer. _Cell_ 181, 1612–1625.e13 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Hwang, M. S. et al. Targeting loss of heterozygosity for

cancer-specific immunotherapy. _Proc. Natl Acad. Sci. USA_ 118, e2022410118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Gonzalez-Galarza, F. F. et al. Allele Frequency

Net Database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. _Nucleic Acids Res._ 48, D783–D788 (2020). CAS  PubMed  Google Scholar  *

Maiers, M., Gragert, L. & Klitz, W. High-resolution HLA alleles and haplotypes in the United States population. _Hum. Immunol._ 68, 779–788 (2007). Article  CAS  PubMed  Google Scholar 

* Somasundaram, R. et al. Human leukocyte antigen-A2-restricted CTL responses to mutated BRAF peptides in melanoma patients. _Cancer Res._ 66, 3287–3293 (2006). Article  CAS  PubMed  Google

Scholar  * Malekzadeh, P. et al. Neoantigen screening identifies broad TP53 mutant immunogenicity in patients with epithelial cancers. _J. Clin. Invest._ 129, 1109–1114 (2019). Article 

PubMed  Google Scholar  * Linard, B. et al. A _ras_-mutated peptide targeted by CTL infiltrating a human melanoma lesion. _J. Immunol._ 168, 4802–4808 (2002). Article  CAS  PubMed  Google

Scholar  * Andersen, M. H. et al. Immunogenicity of constitutively active V599EBRaf. _Cancer Res._ 64, 5456–5460 (2004). Article  CAS  PubMed  Google Scholar  * Cancer Genome Atlas Research

Network et al. The Cancer Genome Atlas Pan-Cancer analysis project. _Nat. Genet._ 45, 1113–1120 (2013). Download references ACKNOWLEDGEMENTS We thank J. Cohen, M. Miller, S. Paul and K.

Wright for insightful discussions, and E. Cook for assistance with Figs. 1 and 2. This work was supported by the Virginia and D. K. Ludwig Fund for Cancer Research, Lustgarten Foundation for

Pancreatic Cancer Research, Commonwealth Fund, Burroughs Wellcome Career Award for Medical Scientists, Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Bloomberg Philanthropies, Mark

Foundation for Cancer Research, NIH Cancer Center Support Grant P30 CA006973 and National Cancer Institute grant R37 CA230400. A.H.P., B.J.M., J.D. and S.R.D. were supported by NIH T32 grant

GM136577. M.F.K. was supported by NIH T32 grant AR048522. AUTHOR INFORMATION Author notes * Michael S. Hwang Present address: Genentech, Inc., South San Francisco, CA, USA AUTHORS AND

AFFILIATIONS * Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA Alexander H. Pearlman, Michael S. Hwang, 

Maximilian F. Konig, Emily Han-Chung Hsiue, Jacqueline Douglass, Sarah R. DiNapoli, Brian J. Mog, Chetan Bettegowda, Nicholas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein & Shibin

Zhou * Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA Alexander H. Pearlman,

 Michael S. Hwang, Maximilian F. Konig, Emily Han-Chung Hsiue, Jacqueline Douglass, Sarah R. DiNapoli, Brian J. Mog, Chetan Bettegowda, Nicholas Papadopoulos, Kenneth W. Kinzler, Bert

Vogelstein & Shibin Zhou * Howard Hughes Medical Institute, Chevy Chase, MD, USA Alexander H. Pearlman, Michael S. Hwang, Maximilian F. Konig, Emily Han-Chung Hsiue, Jacqueline Douglass,

 Sarah R. DiNapoli, Brian J. Mog & Bert Vogelstein * Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA Maximilian F.

Konig * Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA Brian J. Mog * Department of Neurosurgery, The Johns Hopkins University School of Medicine,

Baltimore, MD, USA Chetan Bettegowda * Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA Chetan Bettegowda, Drew M. Pardoll, Sandra B. Gabelli, 

Kenneth W. Kinzler, Bert Vogelstein & Shibin Zhou * Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA Drew M. Pardoll, 

Nicholas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein & Shibin Zhou * Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore,

MD, USA Sandra B. Gabelli * Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA Sandra B. Gabelli * Department of Pathology, The Johns Hopkins

University School of Medicine, Baltimore, MD, USA Nicholas Papadopoulos & Bert Vogelstein * Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of

Medicine, Baltimore, MD, USA Nicholas Papadopoulos, Kenneth W. Kinzler & Bert Vogelstein Authors * Alexander H. Pearlman View author publications You can also search for this author

inPubMed Google Scholar * Michael S. Hwang View author publications You can also search for this author inPubMed Google Scholar * Maximilian F. Konig View author publications You can also

search for this author inPubMed Google Scholar * Emily Han-Chung Hsiue View author publications You can also search for this author inPubMed Google Scholar * Jacqueline Douglass View author

publications You can also search for this author inPubMed Google Scholar * Sarah R. DiNapoli View author publications You can also search for this author inPubMed Google Scholar * Brian J.

Mog View author publications You can also search for this author inPubMed Google Scholar * Chetan Bettegowda View author publications You can also search for this author inPubMed Google

Scholar * Drew M. Pardoll View author publications You can also search for this author inPubMed Google Scholar * Sandra B. Gabelli View author publications You can also search for this

author inPubMed Google Scholar * Nicholas Papadopoulos View author publications You can also search for this author inPubMed Google Scholar * Kenneth W. Kinzler View author publications You

can also search for this author inPubMed Google Scholar * Bert Vogelstein View author publications You can also search for this author inPubMed Google Scholar * Shibin Zhou View author

publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS A.H.P. wrote the original draft of the manuscript. A.H.P., M.S.H., M.F.K., E.H.-C.H., J.D., S.R.D.,

B.J.M., C.B., D.M.P., S.B.G., N.P., K.W.K., B.V. and S.Z. reviewed and edited the manuscript. CORRESPONDING AUTHOR Correspondence to Shibin Zhou. ETHICS DECLARATIONS COMPETING INTERESTS The

Johns Hopkins University has filed patent applications related to technologies described in this paper, on which A.H.P., M.S.H., E.H.-C.H., J.D., B.J.M., N.P., K.W.K., B.V., D.M.P. and S.Z.

are listed as inventors: HLA-restricted epitopes encoded by somatically mutated genes (15/560,241, USPTO; 2016235251, European Patent Office); MANAbodies and Methods of Using (16/614,005,

USPTO; 18802867.4, European Patent Office); MANAbodies Targeting Tumor Antigens and Methods of Using (63/059,638, USPTO; PCT/US2020/065617, World IP Organization). These applications include

methods for identifying public neoantigens and the development of therapeutic agents that target these neoantigens. B.V., K.W.K. and N.P. are founders of Thrive Earlier Detection. K.W.K.

and N.P. are consultants to Thrive Earlier Detection and were on its Board of Directors. B.V., K.W.K., N.P. and S.Z. own equity in Exact Sciences. B.V., K.W.K., N.P., S.Z. and D.M.P. are

founders of, and serve or may serve as consultants to, ManaT Bio, and hold or may hold equity in ManaT Holdings, LLC. B.V., K.W.K., N.P. and S.Z. are founders of, hold equity in and serve as

consultants to Personal Genome Diagnostics. S.Z. has a research agreement with BioMed Valley Discoveries. S.B.G. is a founder of and holds equity in AMS. K.W.K. and B.V. are consultants to

Sysmex, Eisai and Cage Pharma and hold equity in Cage Pharma. B.V. is also a consultant to Catalio. K.W.K., B.V., S.Z. and N.P. are consultants to and hold equity in NeoPhore. N.P. is an

advisor to and holds equity in Cage Pharma. C.B. is a consultant to DePuy Synthes and Bionaut Labs. The companies named above, as well as other companies, have licensed previously described

technologies related to the work described in this paper from Johns Hopkins University. B.V., K.W.K., S.Z., N.P. and C.B. are inventors on some of these technologies. Licenses to these

technologies are or will be associated with equity or royalty payments to the inventors, as well as to Johns Hopkins University. The terms of all of these arrangements are being managed by

Johns Hopkins University in accordance with its conflict of interest policies. M.F.K. received personal fees from Bristol Myers Squibb and Celltrion. D.M.P. reports grant and patent

royalties through his institution from Bristol Myers Squibb, a grant from Compugen, stock from Trieza Therapeutics and Dracen Pharmaceuticals and founder equity from Potenza; is a consultant

for Aduro Biotech, Amgen, AstraZeneca (MedImmune/Amplimmune), Bayer, DNAtrix, Dynavax Technologies Corporation, Ervaxx, FLX Bio, Rock Springs Capital, Janssen, Merck, Tizona and Immunomic

Therapeutics; is on the scientific advisory board of Five Prime Therapeutics, Catalio and WindMIL; and is on the board of directors for Dracen Pharmaceuticals. ADDITIONAL INFORMATION PEER

REVIEW INFORMATION _Nature Cancer_ thanks Michal Bassani-Sternberg and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. PUBLISHER’S NOTE Springer

Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. SUPPLEMENTARY INFORMATION REPORTING SUMMARY SUPPLEMENTARY TABLE Supplementary

Table 1. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Pearlman, A.H., Hwang, M.S., Konig, M.F. _et al._ Targeting public neoantigens for cancer

immunotherapy. _Nat Cancer_ 2, 487–497 (2021). https://doi.org/10.1038/s43018-021-00210-y Download citation * Received: 22 August 2020 * Accepted: 13 April 2021 * Published: 17 May 2021 *

Issue Date: May 2021 * DOI: https://doi.org/10.1038/s43018-021-00210-y SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link

Sorry, a shareable link is not currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative