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Systematic mining and quantification reveal the dominant contribution of non-HLA variations to acute graft-versus-host disease

Cellular & Molecular Immunology volume 22, pages 501–511 (2025)Cite this article

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Abstract

Human leukocyte antigen (HLA) disparity between donors and recipients is a key determinant triggering intense alloreactivity, leading to a lethal complication, namely, acute graft-versus-host disease (aGVHD), after allogeneic transplantation. Moreover, aGVHD remains a cause of mortality after HLA-matched allogeneic transplantation. Protocols for HLA-haploidentical hematopoietic cell transplantation (haploHCT) have been established successfully and widely applied, further highlighting the urgency of performing panoramic screening of non-HLA variations correlated with aGVHD. On the basis of our time-consecutive large haploHCT cohort (with a homogenous discovery set and an extended confirmatory set), we first delineated the genetic landscape of 1366 samples to quantitatively model aGVHD risk by assessing the contributions of HLA and non-HLA genes together with clinical factors. In addition to identifying multiple loss-of-function (LoF) risk variations in non-HLA coding genes, our data-driven study revealed that non-HLA genetic variations, independent of HLA disparity, contributed the most to the occurrence of aGVHD. This unexpected major effect was verified in an independent cohort that received HLA-identical sibling HCT. Subsequent functional experiments further revealed the roles of a representative non-HLA LoF gene and LoF gene pair in regulating the alloreactivity of primary human T cells. Our findings highlight the importance of non-HLA genetic risk in the new era of transplantation and propose a new direction to explore the immunogenetic mechanism of alloreactivity and to optimize donor selection strategies for allogeneic transplantation.

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Data availability

The raw data have been deposited at GSA (https://ngdc.cncb.ac.cn/gsa/) under the accession number PRJCA009965. All custom scripts used for analyses are available online (http://agvhd.gao-lab.org/). Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Prof. Xiao-Jun Huang.

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Acknowledgements

This work was supported by the Major Program of the National Natural Science Foundation of China (No. 82293630), the Peking University Medicine Fund for the world’s leading discipline or discipline cluster development (No. 71003Y3035), the National Key Research and Development Program of China (Nos. 2022YFA0103300, 2017YFA0104500, and 2016YFC0901603), and the State Key Laboratory of Gene Function and Modulation Research and the Beijing Advanced Innovation Center for Genomics (ICG) at Peking University.

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  1. These authors contributed equally: Shuang Liang, Yu-Jian Kang.

Authors and Affiliations

  1. Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Cell and Gene Therapy for Hematologic Malignancies, Peking University, Beijing, China

    Shuang Liang, Mingrui Huo, Min Ling, Keli Yue, Yu Wang, Lan-Ping Xu, Xiao-Hui Zhang, Ning Wu, Ruoyang Liu, Xinyu Dong, Jiangying Liu & Xiao-Jun Huang

  2. Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China

    Shuang Liang, Min Ling, Keli Yue & Xiao-Jun Huang

  3. State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing, China

    Yu-Jian Kang, De-Chang Yang, Chen-Rui Xia, Jing-Yi Li & Ge Gao

  4. School of Medicine, Chongqing University, Chongqing, China

    Yu-Jian Kang

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Contributions

SL, Y-JK, JL, GG, and X-JH: study design and project coordination. SL, MH, ML, and KY: cohort and sample collection and experimental design. YW, L-PX, X-HZ, NW, RL, and XD: cohort and sample collection. Y-JK, SL, MH, D-CY, C-RX, J-YL, JL, GG, and X-JH: data analyses. D-CY and Y-JK: web server development. SL, Y-JK, and JL: writing–original draft. JL, GG, and X-JH: writing–review & editing. JL, GG, and X-JH: project administration.

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Correspondence to Jiangying Liu, Ge Gao or Xiao-Jun Huang.

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Liang, S., Kang, YJ., Huo, M. et al. Systematic mining and quantification reveal the dominant contribution of non-HLA variations to acute graft-versus-host disease. Cell Mol Immunol 22, 501–511 (2025). https://doi.org/10.1038/s41423-025-01273-y

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