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Selective HLA knockdown and PD-L1 expression prevent allogeneic CAR-NK cell rejection and enhance safety and anti-tumor responses in xenograft mice

Author

Listed:
  • Fuguo Liu

    (Massachusetts Institute of Technology
    Harvard Medical School)

  • Mubin Tarannum

    (Harvard Medical School)

  • Yingjie Zhao

    (Massachusetts Institute of Technology)

  • Yiming J. Zhang

    (Massachusetts Institute of Technology)

  • James Dongjoo Ham

    (Massachusetts Institute of Technology)

  • Kewen Lei

    (Massachusetts Institute of Technology)

  • Yuhao Qiang

    (Massachusetts Institute of Technology)

  • Xingyu Deng

    (Harvard Medical School)

  • Maily Nguyen

    (Harvard Medical School)

  • Khanhlinh Dinh

    (Harvard Medical School)

  • Shaobo Yang

    (Harvard Medical School)

  • Alaa Kassim Ali

    (Harvard Medical School)

  • Toni K. Choueiri

    (Harvard Medical School)

  • Jerome Ritz

    (Harvard Medical School)

  • Rizwan Romee

    (Harvard Medical School)

  • Jianzhu Chen

    (Massachusetts Institute of Technology)

Abstract

Allogeneic cellular immunotherapy exhibits promising efficacy for cancer treatment, but donor cell rejection remains a major barrier. Here, we systematically evaluate human leukocyte antigens (HLA) and immune checkpoints PD-L1, HLA-E, and CD47 in the rejection of allogeneic NK cells and identify CD8+ T cells as the dominant cell type mediating allorejection. We demonstrate that a single gene construct that combines an shRNA that selectively interferes with HLA class I but not HLA-E expression, a chimeric antigen receptor (CAR), and PD-L1 or single-chain HLA-E (SCE) enables the one-step construction of allogeneic CAR-NK cells that evade host-mediated rejection both in vitro and in a xenograft mouse model. Furthermore, CAR-NK cells overexpressing PD-L1 or SCE effectively kill tumor cells through the upregulation of cytotoxic genes and reduced exhaustion and exhibit a favorable safety profile due to the decreased production of inflammatory cytokines involved in cytokine release syndrome. Thus, our approach represents a promising strategy in enabling “off-the-shelf” allogeneic cellular immunotherapies.

Suggested Citation

  • Fuguo Liu & Mubin Tarannum & Yingjie Zhao & Yiming J. Zhang & James Dongjoo Ham & Kewen Lei & Yuhao Qiang & Xingyu Deng & Maily Nguyen & Khanhlinh Dinh & Shaobo Yang & Alaa Kassim Ali & Toni K. Chouei, 2025. "Selective HLA knockdown and PD-L1 expression prevent allogeneic CAR-NK cell rejection and enhance safety and anti-tumor responses in xenograft mice," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63863-8
    DOI: 10.1038/s41467-025-63863-8
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    References listed on IDEAS

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    1. Eric Vivier & Lucas Rebuffet & Emilie Narni-Mancinelli & Stéphanie Cornen & Rob Y. Igarashi & Valeria R. Fantin, 2024. "Natural killer cell therapies," Nature, Nature, vol. 626(8000), pages 727-736, February.
    2. Eiji Yoshihara & Carolyn O’Connor & Emanuel Gasser & Zong Wei & Tae Gyu Oh & Tiffany W. Tseng & Dan Wang & Fritz Cayabyab & Yang Dai & Ruth T. Yu & Christopher Liddle & Annette R. Atkins & Michael Dow, 2020. "Immune-evasive human islet-like organoids ameliorate diabetes," Nature, Nature, vol. 586(7830), pages 606-611, October.
    3. Veronique M. Braud & David S. J. Allan & Christopher A. O'Callaghan & Kalle Söderström & Annalisa D'Andrea & Graham S. Ogg & Sasha Lazetic & Neil T. Young & John I. Bell & Joseph H. Phillips & Lewis L, 1998. "HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C," Nature, Nature, vol. 391(6669), pages 795-799, February.
    4. Sumin Jo & Shipra Das & Alan Williams & Anne-Sophie Chretien & Thomas Pagliardini & Aude Roy & Jorge Postigo Fernandez & Diane Clerre & Billal Jahangiri & Isabelle Chion-Sotinel & Sandra Rozlan & Emil, 2022. "Endowing universal CAR T-cell with immune-evasive properties using TALEN-gene editing," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
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