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Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms

Kimiko Kuroki, Haruki Matsubara, Ryo Kanda, Naoyuki Miyashita, Mitsunori Shiroishi, Yuko Fukunaga, Jun Kamishikiryo, Atsushi Fukunaga, Hideo Fukuhara, Kaoru Hirose, Joan S. Hunt, Yuji Sugita, Shunsuke Kita, Toyoyuki Ose and Katsumi Maenaka
J Immunol November 6, 2019, ji1900562; DOI: https://doi.org/10.4049/jimmunol.1900562
Kimiko Kuroki
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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  • ORCID record for Kimiko Kuroki
Haruki Matsubara
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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Ryo Kanda
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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Naoyuki Miyashita
†RIKEN, Kobe 650-0047, Japan;
‡Department of Computational Systems Biology, Kindai University, Kinokawa 649-6493, Japan;
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Mitsunori Shiroishi
§Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
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Yuko Fukunaga
¶Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
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Jun Kamishikiryo
‖Faculty of Pharmaceutical Sciences, Fukuyama University, Fukuyama 729-0292, Japan; and
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Atsushi Fukunaga
¶Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
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Hideo Fukuhara
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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Kaoru Hirose
¶Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
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Joan S. Hunt
#Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
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Yuji Sugita
†RIKEN, Kobe 650-0047, Japan;
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Shunsuke Kita
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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Toyoyuki Ose
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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Katsumi Maenaka
*Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
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Key Points

  • The β2m-free HLA-G1 isoform tends to dimerize and further multimerize.

  • The β2m-free HLA-G1 isoform specifically binds to LILRB2 with avidity effects.

  • The crystal structure of LILRB1/HLA-G1 complex showed a flexible binding manner.

Abstract

Human leukocyte Ig-like receptors (LILR) LILRB1 and LILRB2 are immune checkpoint receptors that regulate a wide range of physiological responses by binding to diverse ligands, including HLA-G. HLA-G is exclusively expressed in the placenta, some immunoregulatory cells, and tumors and has several unique isoforms. However, the recognition of HLA-G isoforms by LILRs is poorly understood. In this study, we characterized LILR binding to the β2-microglobulin (β2m)-free HLA-G1 isoform, which is synthesized by placental trophoblast cells and tends to dimerize and multimerize. The multimerized β2m-free HLA-G1 dimer lacked detectable affinity for LILRB1, but bound strongly to LILRB2. We also determined the crystal structure of the LILRB1 and HLA-G1 complex, which adopted the typical structure of a classical HLA class I complex. LILRB1 exhibits flexible binding modes with the α3 domain, but maintains tight contacts with β2m, thus accounting for β2m-dependent binding. Notably, both LILRB1 and B2 are oriented at suitable angles to permit efficient signaling upon complex formation with HLA-G1 dimers. These structural and functional features of ligand recognition by LILRs provide novel insights into their important roles in the biological regulations.

Footnotes

  • This work was partly supported by the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from Agency for Medical Research and Development Grant JP19am0101001, Hokkaido University, Global Facility Center, Pharma Science Open Unit, funded by Ministry of Education, Culture, Sports, Science and Technology Grant “Support Program for Implementation of New Equipment Sharing System,” Hokkaido University Biosurface Project, Takeda Science Foundation, and Japan Society for the Promotion of Science KAKENHI Grants 23770102 and 25870019. K.K. is supported by the Naito Foundation Subsidy for Female Researchers after Maternity Leave, and the Support Office for Female Researchers at Hokkaido University.

  • The atomic coordinates and structure factors presented in this article have been submitted to the Protein Data Bank under accession number 6K60.

  • The online version of this article contains supplemental material.

  • Received May 31, 2019.
  • Accepted October 5, 2019.
  • Copyright © 2019 by The American Association of Immunologists, Inc.
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The Journal of Immunology: 208 (9)
The Journal of Immunology
Vol. 208, Issue 9
1 May 2022
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Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms
Kimiko Kuroki, Haruki Matsubara, Ryo Kanda, Naoyuki Miyashita, Mitsunori Shiroishi, Yuko Fukunaga, Jun Kamishikiryo, Atsushi Fukunaga, Hideo Fukuhara, Kaoru Hirose, Joan S. Hunt, Yuji Sugita, Shunsuke Kita, Toyoyuki Ose, Katsumi Maenaka
The Journal of Immunology November 6, 2019, ji1900562; DOI: 10.4049/jimmunol.1900562

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Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms
Kimiko Kuroki, Haruki Matsubara, Ryo Kanda, Naoyuki Miyashita, Mitsunori Shiroishi, Yuko Fukunaga, Jun Kamishikiryo, Atsushi Fukunaga, Hideo Fukuhara, Kaoru Hirose, Joan S. Hunt, Yuji Sugita, Shunsuke Kita, Toyoyuki Ose, Katsumi Maenaka
The Journal of Immunology November 6, 2019, ji1900562; DOI: 10.4049/jimmunol.1900562
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