Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood
Authors: Alexander M Xu
Owen N Witte
Antoni Ribas
Jongchan Choi
Elizabeth Holman
Won Jun Noh
Songming Peng
David Baltimore
Jesse M Zaretsky
Xiaozhe Ding
James R Heath
Jami McLaughlin
Alphonsus H C Ng
Michael T Bethune
Alice Hsu
Donghui Cheng
Katherine Guo
Jing Zhou
Jungwoo Kim
Yapeng Su
John E Heath
Yue Lu
William Chour
Journal: Cell Reports (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: T cell receptor; cancer immunotherapy; microfluidics; nanotechnology; neoantigens.
Affiliations: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA., Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA., Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA., Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA., Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA., Institute for Systems Biology, Seattle, WA 98109, USA., Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA., Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA., Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA., Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA. Electronic address: .

Abstract:  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. 

Retracted: No

PubPeer comments:
 Hi, can the authors please explain, how they arrived at the 94% recovery shown in figure 1 c? According to the methods: *Varying numbers (0, 8, 16, 32, 64, and 128) of F5 engineered T cells were spiked into 10,000 CD8+ donor PBMCs. * From the results part: *However, the NP-bar-coded NACS method captured 94% of the expected MART-1 specific T cells, whereas the flow method detected only 52%.* The figure clearly shows that less cells were recovered compared to the spike in. When spiking in 128 cells in a 10 k background, the authors were able to find around 40 cells. The slope of their straight line fit is 0.32 and I would expect a slope close to 1 for a recovery rate so close to 100%. Please clarify how you arrived at the number! Many thanks ,