Abstract

We report a patient relapsing 9 months after CD19-targeted CAR T cell (CTL019) infusion with CD19 leukemia that aberrantly expressed the anti-CD19 CAR. The CAR gene was unintentionally introduced into a single leukemic B cell during T cell manufacturing, and its product bound in cis to the CD19 epitope on the surface of leukemic cells, masking it from recognition by and conferring resistance to CTL019.

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Data availability

All requests for raw and analyzed data and materials are promptly reviewed by the University of Pennsylvania Center for Innovation to see whether the request is subject to any intellectual property or confidentiality obligations. Patient-related data not included in the paper were generated as part of clinical trials and may be subject to patient confidentiality. Any data and materials that can be shared will be released via a Material Transfer Agreement. All raw and analyzed sequencing data can be found at the NCBI Sequence Read Archive (accession number: SRP155722; analyses of lentiviral integration sites, RNA sequencing and DNA sequencing of genes potentially associated with CD19  relapse) and Adaptive Biotechnologies’ immuneACCESS database (http://clients.adaptivebiotech.com/pub/Ruella-2018-naturemedicine).

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Acknowledgements

The authors would like to thank the staff in the Product Development and Correlative Sciences laboratory for helpful discussions and analytical support, staff in Clinical Cell and Vaccine Production Facility for manufacturing and analytical support, and staff in the Stem Cell and Xenograft Facility for animal support (University of Pennsylvania, Philadelphia, PA). The authors would like to thank E. Sotillo and A. Thomas-Tikhonenko (Children’s Hospital of Philadelphia, PA) for providing the CD19 CRISPR–Cas9 knock-out NALM-6 cells and B. Jena and L. Cooper (MD Anderson Cancer Center, Houston, TX) for providing the Alexa-Fluor-647-conjugated anti-idiotype antibody. The chimeric antigen receptor used in this study was obtained under a Material transfer agreement (MTA) from Campana and Imai at St. Jude Children’s Research Hospital and was subsequently modified by cloning into a lentiviral vector and expressed with a eukaryotic promoter. This work was supported by grants from the University of Pennsylvania–Novartis Alliance (principal investigator (PI), C.H.J), National Institutes of Health (NIH) 5R01CA120409 (PI, C.H.J), the EMD–Serono Cancer Immunotherapy Clinical Fellowship by the Society for Immunotherapy of Cancer (SITC) (PI, M.R.), the Bristol–Myers Squibb Oncology Fellowship in Clinical Cancer Research by the American Association for Cancer Research (AACR) (PI, M.R.), the Gabrielle’s Angel Foundation (PI, M.R.; PI, D.M.B.; and PI, J.A.F.), the SIES–AIL fellowship by the Italian Society for Experimental Hematology and the Italian Leukemia Association (PI, M.R.), the ASH-Scholar Award (P.I., M.R.), NIH NCI 1K99CA212302-01A1 (PI, M.R.), NIH NCI P01CA214278-01 (PI, C.H.J.) the St. Baldrick’s Foundation Scholar Award (PI, D.M.B.) and NCI T32CA009140 (J.A.F).

Author information

Author notes

  1. These authors contributed equally to this work: Marco Ruella, Jun Xu, David M. Barrett.

  2. These authors jointly directed this work: Simon F. Lacey, J. Joseph Melenhorst.

Affiliations

  1. Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    • Marco Ruella
    • , Jun Xu
    • , Joseph A. Fraietta
    • , Tyler J. Reich
    • , David E. Ambrose
    • , Michael Klichinsky
    • , Olga Shestova
    • , Prachi R. Patel
    • , Irina Kulikovskaya
    • , Farzana Nazimuddin
    • , Vijay G. Bhoj
    • , Bruce L. Levine
    • , Regina M. Young
    • , John Scholler
    • , Saar I. Gill
    • , Carl H. June
    • , Simon F. Lacey
    •  & J. Joseph Melenhorst
  2. Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    • Marco Ruella
    • , Jun Xu
    • , Joseph A. Fraietta
    • , Vijay G. Bhoj
    • , Bruce L. Levine
    • , Carl H. June
    • , Simon F. Lacey
    •  & J. Joseph Melenhorst
  3. Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA

    • Marco Ruella
    • , Jun Xu
    • , Joseph A. Fraietta
    • , Vijay G. Bhoj
    • , Bruce L. Levine
    • , Saar I. Gill
    • , Carl H. June
    • , Simon F. Lacey
    •  & J. Joseph Melenhorst
  4. Parker Institute for Cellular Immunotherapy at the University of Pennsylvania, Philadelphia, PA, USA

    • Marco Ruella
    • , Joseph A. Fraietta
    •  & Carl H. June
  5. Division of Hematology–Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    • Marco Ruella
    •  & Saar I. Gill
  6. Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    • David M. Barrett
    • , Shannon L. Maude
    •  & Stephan A. Grupp
  7. Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    • Michael Klichinsky
  8. Novartis Institutes for Biomedical Research, Cambridge, MA, USA

    • Elena J. Orlando
    •  & Hans Bitter
  9. University of Colorado, Children’s Hospital Colorado, Denver, CO, USA

    • Terry J. Fry
  10. Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    • Christopher L. Nobles
    •  & Frederic D. Bushman

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Contributions

M.R., J.X., D.M.B., T.J.R., S.I.G., S.A.G., C.H.J., S.F.L., and J.J.M formulated the ideas and planned the experiments. M.R., J.X., D.M.B., T.J.R., M.K., O.S., F.N., D.E.A., I.K., J.A.F., J.S., P.R.P, V.G.B., C.L.N., F.D.B. E.J.O., and H.B. performed the experiments, analyzed the data, and contributed to the manuscript. J.X, M.K., and T.J.R. performed the confocal imaging. C.L.N. and F.D.B. performed the lentivirus integration site analysis. S.L.M., D.M.B., and S.A.G. managed Patient #107 in the clinic. M.R., J.J.M, and S.F.L. wrote the manuscript; S.A.G., B.L.L., R.M.Y., J.S., and C.H.J. edited the manuscript. D.M.B., M.R., and O.S. performed the animal experiments. T.J.F provided clinical care and identified CARB recurrence. All the authors reviewed and accepted the contents of the article. M.R., J.X, and D.M.B equally contributed to this manuscript. S.F.L and J.J.M. share senior authorship.

Competing interests

C.H.J., J.J.M., M.R., J.S., J.A.F., R.M.Y., and S.I.G. work under a research collaboration involving the University of Pennsylvania and the Novartis Institutes of Biomedical Research, Inc. and are inventors of intellectual property (IP) licensed by the University of Pennsylvania to Novartis. C.L.N. has IP in a CART-related patent. B.L.L. is a consultant for CRC Oncology, Cure Genetics, Novartis and a member of the Scientific Advisory Board for Brammer Bio, Incysus, Avectas. B.L.L. is the founder of and has equity in Tmunity Therapeutics and receives Research Funding from Novartis and Tmunity. S.F.L. receives Novartis, Tmunity and Parker Institute for Cancer immunotherapy research funding and has CART-related IP. S.A.G. discloses Novartis research funding and consultancy. E.O. and H.B. are employed by Novartis. All the other authors have no competing interests.

Corresponding authors

Correspondence to Carl H. June or J. Joseph Melenhorst.

Supplementary information

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DOI

https://doi.org/10.1038/s41591-018-0201-9

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