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Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood

Peng, Songming and Zaretsky, Jesse M. and Ng, Alphonsus H. C. and Chour, William and Bethune, Michael T. and Choi, Jongchan and Hsu, Alice and Holman, Elizabeth and Ding, Xiaozhe and Guo, Katherine and Kim, Jungwoo and Xu, Alexander M. and Heath, John E. and Noh, Won Jun and Zhou, Jing and Su, Yapeng and Lu, Yue and McLaughlin, Jami and Cheng, Donghui and Witte, Owen N. and Baltimore, David and Ribas, Antoni and Heath, James R. (2019) Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood. Cell Reports, 28 (10). pp. 2728-2738. ISSN 2211-1247. PMCID PMC6774618.

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Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
Peng, Songming0000-0002-2742-6584
Ng, Alphonsus H. C.0000-0003-0074-4598
Chour, William0000-0003-1817-0123
Kim, Jungwoo0000-0002-5215-2044
Xu, Alexander M.0000-0003-4877-4358
Lu, Yue0000-0001-9036-2803
Witte, Owen N.0000-0003-4461-4533
Baltimore, David0000-0001-8723-8190
Heath, James R.0000-0001-5356-4385
Additional Information:© 2019 The Author(s). Under a Creative Commons license Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) Received 4 July 2017, Revised 4 May 2019, Accepted 29 July 2019, Available online 3 September 2019. We acknowledge the following agencies and foundations for support: The Stand Up to Cancer Foundation and the Cancer Research Institute (A.R. and J.R.H.), the National Cancer Institute (1U54 CA199090 and R01-CA170689 to J.R.H. and R35 CA197633 to A.R.), the Jean Perkins Foundation (J.R.H., principal investigator [PI]), and Caltech (internal support through a CI2 grant). O.N.W. is supported by the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research. A.H.C.N. is supported by a Banting Postdoctoral Fellowship from the Government of Canada. A.M.X. is supported by a Ruth L. Kirschstein F32 Postdoctoral Fellowship from the National Cancer Institute (1F32CA213966-01). We thank Eugene Barsov and Richard Morgan (NCI) for providing the retroviral MSGV vector. Author Contributions: S.P., J.M.Z., A.H.C.N., W.C., M.T.B., O.N.W., D.B., A.R., and J.R.H. designed the experiments. A.R. ran the trials that provided patient samples in this study. S.P., J.M.Z., A.H.C.N., W.C., M.T.B., A.H., E.H., X.D., K.G., J.K., A.M.X., J.E.H., W.J.N., J.Z., Y.S., Y.L., J.M., and D.C. did the experiments. S.P., J.M.Z., A.H.C.N, M.T.B., A.R., and J.R.H. wrote the paper. Data and Code Availability: Putative neoantigens, mutated gene expression, and predicted binding affinity for patient #1, #2 and #3 are available in Table S2. A limited number of putative neoantigens and predicted binding affinity for patient #4 are available in Table S2. The published article also includes neoantigen-specific T cell counts enumerated during this study for the indicated neoantigen. The whole-exome sequencing data have been deposited to the Sequence Read Archive (SRA, under accession number NCBI SRA: SRP067938 for a separate study (Hugo et al., 2016). The transcriptome data have been deposited (NCBI GEO: GSE78220) for a separate study (Hugo et al., 2016). The patient ID numbering in NCBI SRA: SRP67938 and NCBI GEO: GSE78220 are not the same as in this manuscript; use direct SRR mapping in Table S1 for correctness. Declaration of Interests: D.B., A.R., and J.R.H. are scientific co-founders of PACT Pharma, a company that is seeking to commercialize certain aspects of the NP-barcoded NACS technology. S.P., A.H.C.N., W.C., J.C., and J.R.H. have at least one patent related to this work.
Funding AgencyGrant Number
Stand up to Cancer FoundationUNSPECIFIED
Cancer Research InstituteUNSPECIFIED
NIH1U54 CA199090
NIHR35 CA197633
Jean Perkins FoundationUNSPECIFIED
Caltech Innovation Initiative (CI2)UNSPECIFIED
Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUNSPECIFIED
Natural Sciences and Engineering Research Council of Canada (NSERC)UNSPECIFIED
NIH Postdoctoral Fellowship1F32CA213966-01
National Cancer InstituteUNSPECIFIED
Subject Keywords:neoantigens; cancer immunotherapy; nanotechnology; microfluidics; T cell receptor
Issue or Number:10
PubMed Central ID:PMC6774618
Record Number:CaltechAUTHORS:20190903-130240129
Persistent URL:
Official Citation:Songming Peng, Jesse M. Zaretsky, Alphonsus H.C. Ng, William Chour, Michael T. Bethune, Jongchan Choi, Alice Hsu, Elizabeth Holman, Xiaozhe Ding, Katherine Guo, Jungwoo Kim, Alexander M. Xu, John E. Heath, Won Jun Noh, Jing Zhou, Yapeng Su, Yue Lu, Jami McLaughlin, Donghui Cheng, Owen N. Witte, David Baltimore, Antoni Ribas, James R. Heath, Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood, Cell Reports, Volume 28, Issue 10, 2019, Pages 2728-2738.e7, ISSN 2211-1247, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:98389
Deposited By: George Porter
Deposited On:04 Sep 2019 15:03
Last Modified:04 Oct 2019 14:59

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