人类肝移植图谱揭示了一种与早期移植物功能不全发生相关的致病免疫生态位

Xin Shao, Zheng Wang, Kai Wang, Xiaoyan Lu, Ping Zhang, Rongfang Guo, Jie Liao, Penghui Yang, Shusen Zheng, Xiao Xu, Xiaohui Fan

工程(英文) ›› 2024, Vol. 36 ›› Issue (5) : 193-208.

PDF(8677 KB)
PDF(8677 KB)
工程(英文) ›› 2024, Vol. 36 ›› Issue (5) : 193-208. DOI: 10.1016/j.eng.2023.12.004
研究论文
Article

人类肝移植图谱揭示了一种与早期移植物功能不全发生相关的致病免疫生态位

作者信息 +

A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with Early Allograft Dysfunction

Author information +
History +

摘要

肝移植是终末期肝病患者的标准治疗方法。尽管肝移植技术取得了显着进步,但术后早期移植物功能不全(early allograft dysfunction, EAD)的发生会对受者的预后产生不利影响,加剧了当前器官短缺的现状,仍然是一个严重的临床问题。然而,肝脏组织的细胞异质性阻碍了人们对EAD发生的细胞特征和分子事件进行准确表征。为此,本研究从7个患者中收集了来自冷缺血和缺血再灌注两个阶段的12个肝脏样本,构建了包含EAD发生和EAD未发生的人移植肝单细胞转录组图谱。通过分析EAD发生和EAD未发生患者的75 231个单细胞,发现了一种与 EAD发生显著相关的由黏膜相关不变 T 细胞((mucosal associated invariant T cell, MAIT)、颗粒酶B+(GZMB+)和颗粒酶K+(GZMK+)自然杀伤细胞以及S100钙结合蛋白A12+ (S100A12)中性粒细胞组成的免疫生态位。此外,在两个独立队列中也进一步验证了这种免疫生态位的存在及其与EAD 发生的相关性。综上,本文研究结果在单细胞水平上揭示了移植肝的细胞特征以及一种与EAD发生相关的致病免疫生态位,为理解EAD发生发展机制提供了新的见解。

Abstract

Liver transplantation (LT) is the standard therapy for individuals afflicted with end-stage liver disease. Despite notable advancements in LT technology, the incidence of early allograft dysfunction (EAD) remains a critical concern, exacerbating the current organ shortage and detrimentally affecting the prognosis of recipients. Unfortunately, the perplexing hepatic heterogeneity has impeded characterization of the cellular traits and molecular events that contribute to EAD. Herein, we constructed a pioneering single-cell transcriptomic landscape of human transplanted livers derived from non-EAD and EAD patients, with 12 liver samples collected from 7 donors during the cold perfusion and portal reperfusion stages. Comparison of the 75 231 cells of non-EAD and EAD patients revealed an EAD-associated immune niche comprising mucosal-associated invariant T cells, granzyme B+ (GZMB +) granzyme K+ (GZMK +) natural killer cells, and S100 calcium binding protein A12+ (S100A12 +) neutrophils. Moreover, we verified this immune niche and its association with EAD occurrence in two independent cohorts. Our findings elucidate the cellular characteristics of transplanted livers and the EAD-associated pathogenic immune niche at the single-cell level, thus, offering valuable insights into EAD onset.

关键词

人类肝移植 / 早期移植物功能不全 / 致病免疫生态位 / 单细胞分析 / 细胞间通讯

Keywords

Human liver transplantation / Early allograft dysfunction / Pathogenic immune niche / Single-cell analysis / Cell-cell communication

引用本文

导出引用
Xin Shao, Zheng Wang, Kai Wang. 人类肝移植图谱揭示了一种与早期移植物功能不全发生相关的致病免疫生态位. Engineering. 2024, 36(5): 193-208 https://doi.org/10.1016/j.eng.2023.12.004

参考文献

[1]
L.S. Yang, L.L. Shan, A. Saxena, D.L. Morris. Liver transplantation: a systematic review of long-term quality of life. Liver Int, 34 (9) ( 2014), pp. 1298-1313
[2]
C.C. Jadlowiec, T. Taner. Liver transplantation: current status and challenges. World J Gastroenterol, 22 (18) ( 2016), pp. 4438-4445
[3]
M. Deschenes. Early allograft dysfunction: causes, recognition, and management. Liver Transplant, 19 (S2) ( 2013), pp. S6-S8
[4]
J. Zhou, J. Chen, Q. Wei, K. Saeb-Parsy, X. Xu. The role of ischemia/reperfusion injury in early hepatic allograft dysfunction. Liver Transplant, 26 (8) ( 2020), pp. 1034-1048
[5]
V.G. Agopian, M.P. Harlander-Locke, D. Markovic, W. Dumronggittigule, V. Xia, F.M. Kaldas, et al.. Evaluation of early allograft function using the liver graft assessment following transplantation risk score model. JAMA Surg, 153 (5) ( 2018), pp. 436-444
[6]
S. Feng, N.P. Goodrich, J.L. Bragg-Gresham, D.M. Dykstra, J.D. Punch, M.A. DebRoy, et al.. Characteristics associated with liver graft failure: the concept of a donor risk index. Am J Transplant, 6 (4) ( 2006), pp. 783-790
[7]
M. Malinchoc, P.S. Kamath, F.D. Gordon, C.J. Peine, J. Rank, P.C.J. ter Borg. A model to predict poor survival in patients undergoing transjugular intrahepatic portosystemic shunts. Hepatology, 31 (4) ( 2000), pp. 864-871
[8]
T. Ito, B.V. Naini, D. Markovic, A. Aziz, S. Younan, M. Lu, et al.. Ischemia-reperfusion injury and its relationship with early allograft dysfunction in liver transplant patients. Am J Transplant, 21 (2) ( 2021), pp. 614-625
[9]
S. Kageyama, K. Nakamura, B. Ke, R.W. Busuttil, J.W. Kupiec-Weglinski. Serelaxin induces Notch1 signaling and alleviates hepatocellular damage in orthotopic liver transplantation. Am J Transplant, 18 (7) ( 2018), pp. 1755-1763
[10]
J. Zhao, S. Zhang, Y. Liu, X. He, M. Qu, G. Xu, et al.. Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discovery, 6 (1) ( 2020), p. 22
[11]
H. Huang, R. Chen, Y. Lin, J. Jiang, S. Feng, X. Zhang, et al.. Decoding single-cell landscape and intercellular crosstalk in the transplanted liver. Transplantation, 107 (4) ( 2023), pp. 890-902
[12]
F. Sampaziotis, D. Muraro, O.C. Tysoe, S. Sawiak, T.E. Beach, E.M. Godfrey, et al.. Cholangiocyte organoids can repair bile ducts after transplantation in the human liver. Science, 371 (6531) ( 2021), pp. 839-846
[13]
Y. Shan, D. Qi, L. Zhang, L. Wu, W. Li, H. Liu, et al.. Single-cell RNA-seq revealing the immune features of donor liver during liver transplantation. Front Immunol, 14 ( 2023), p. 1096733
[14]
X. Li, S. Li, B. Wu, Q. Xu, D. Teng, T. Yang, et al.. Landscape of immune cells heterogeneity in liver transplantation by single-cell RNA sequencing analysis. Front Immunol, 13 ( 2022), Article 890019
[15]
X. Yang, D. Lu, R. Wang, Z. Lian, Z. Lin, J. Zhuo, et al.. Single-cell profiling reveals distinct immune phenotypes that contribute to ischaemia-reperfusion injury after steatotic liver transplantation. Cell Proliferation, 54 (10) ( 2021), Article e13116
[16]
Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, et al. Comprehensive integration of single-cell data. Cell 2019 ;177(7):1888-902.
[17]
X. Shao, H. Yang, X. Zhuang, J. Liao, P. Yang, J. Cheng, et al.. scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network. Nucleic Acids Res, 49 (21) ( 2021), p. e122
[18]
X. Shao, J. Liao, X. Lu, R. Xue, N. Ai, X. Fan. scCATCH: automatic annotation on cell types of clusters from single-cell RNA sequencing data. iScience, 23 (3) ( 2020), Article 100882
[19]
G. La Manno, R. Soldatov, A. Zeisel, E. Braun, H. Hochgerner, V. Petukhov, et al.. RNA velocity of single cells. Nature, 560 (7719) ( 2018), pp. 494-498
[20]
V. Bergen, M. Lange, S. Peidli, F.A. Wolf, F.J. Theis. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol, 38 (12) ( 2020), pp. 1408-1414
[21]
J. Cao, M. Spielmann, X. Qiu, X. Huang, D.M. Ibrahim, A.J. Hill, et al.. The single-cell transcriptional landscape of mammalian organogenesis. Nature, 566 (7745) ( 2019), pp. 496-502
[22]
X. Qiu, Q. Mao, Y. Tang, L. Wang, R. Chawla, H.A. Pliner, et al.. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods, 14 (10) ( 2017), pp. 979-982
[23]
Y. Zhou, B. Zhou, L. Pache, M. Chang, A.H. Khodabakhshi, O. Tanaseichuk, et al.. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun, 10 (1) ( 2019), p. 1523
[24]
T. Wu, E. Hu, S. Xu, M. Chen, P. Guo, Z. Dai, et al.. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation, 2 (3) ( 2021), Article 100141
[25]
L. Wang, J. Li, S. He, Y. Liu, H. Chen, S. He, et al.. Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution. Cell Death Dis, 12 (6) ( 2021), p. 589
[26]
H. Hirao, K. Nakamura, J.W. Kupiec-Weglinski. Liver ischaemia-reperfusion injury: a new understanding of the role of innate immunity. Nat Rev Gastroenterol Hepatol, 19 (4) ( 2022), pp. 239-256
[27]
A. Aubert, M. Lane, K. Jung, D.J. Granville. Granzyme B as a therapeutic target: an update in 2022. Expert Opin Ther Targets, 26 (11) ( 2022), pp. 979-993
[28]
M. Rucevic, L.D. Fast, G.D. Jay, F.M. Trespalcios, A. Sucov, E. Siryaporn, et al.. Altered levels and molecular forms of granzyme K in plasma from septic patients. Shock, 27 (5) ( 2007), pp. 488-493
[29]
M.J. Smyth, M.D. O’Connor, J.A. Trapani. Granzymes: a variety of serine protease specificities encoded by genetically distinct subfamilies. J Leukocyte Biol, 60 (5) ( 1996), pp. 555-562
[30]
J. Roth, T. Vogl, C. Sorg, C. Sunderkotter. Phagocyte-specific S100 proteins: a novel group of proinflammatory molecules. Trends Immunol, 24 (4) ( 2003), pp. 155-158
[31]
C. Silvestre-Roig, Z.G. Fridlender, M. Glogauer, P. Scapini. Neutrophil diversity in health and disease. Trends Immunol, 40 (7) ( 2019), pp. 565-583
[32]
S. Tang, J. Wang, J. Liu, Y. Huang, Y. Zhou, S. Yang, et al.. Niban protein regulates apoptosis in HK-2 cells via caspase-dependent pathway. Ren Failure, 41 (1) ( 2019), pp. 455-466
[33]
A. Pedroza-Gonzalez, C. Verhoef, J.N.M. Ijzermans, M.P. Peppelenbosch, J. Kwekkeboom, J. Verheij, et al.. Activated tumor-infiltrating CD4+ regulatory T cells restrain antitumor immunity in patients with primary or metastatic liver cancer. Hepatology, 57 (1) ( 2013), pp. 183-194
[34]
D. Basavarajappa, M. Wan, A. Lukic, D. Steinhilber, B. Samuelsson, O. Rådmark. Roles of coactosin-like protein (CLP) and 5-lipoxygenase-activating protein (FLAP) in cellular leukotriene biosynthesis. Proc Natl Acad Sci USA, 111 (31) ( 2014), pp. 11371-11376
[35]
E.E.M. Bates, M.C. Dieu, O. Ravel, S.M. Zurawski, S. Patel, J.M. Bridon, et al.. CD40L activation of dendritic cells down-regulates DORA, a novel member of the immunoglobulin superfamily. Mol Immunol, 35 (9) ( 1998), pp. 513-524
[36]
Chu TY, Zheng-Gérard C, Huang KY, Chang YC, Chen YW, I KY, et al. GPR97 triggers inflammatory processes in human neutrophils via a macromolecular complex upstream of PAR2 activation. Nat Commun 2022;13(1):6385.
[37]
H. Sun, J. Feng, L. Tang. Function of TREM1 and TREM2 in liver-related diseases. Cells, 9 (12) ( 2020), p. 2626
[38]
C. Fondevila, J. Muñoz, J.J. Lozano, M.A. Loera, S. Jimenez-Galanes, O. Sanchez, et al.. Gene-expression profiles of human liver biopsies correlate with post-transplant allograft function and are determined by donor type. Liver Transplant, 15 (7) ( 2009), p. S73
[39]
X. Shao, C. Li, H. Yang, X. Lu, J. Liao, J. Qian, et al.. Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nat Commun, 13 (1) ( 2022), p. 4429
[40]
D.M. Cable, E. Murray, L.S. Zou, A. Goeva, E.Z. Macosko, F. Chen, et al.. Robust decomposition of cell type mixtures in spatial transcriptomics. Nat Biotechnol, 40 (4) ( 2021), pp. 517-526
[41]
X. Shao, J. Liao, C. Li, X. Lu, J. Cheng, X. Fan.CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice. Briefings Bioinf, 22 (4) ( 2021), Article bbaa269
[42]
A. Yoshido, G. Sudo, A. Takasawa, H. Aoki, H. Kitajima, E. Yamamoto, et al.. Serum amyloid A 1 recruits neutrophils to the invasive front of T1 colorectal cancers. J Gastroenterol Hepatol, 38 (2) ( 2023), pp. 301-310
[43]
Busch L al Taleb Z, Tsai YL, Nguyen VTT, Lu Q, Synatschke CV, et al. Amyloid beta and its naturally occurring N-terminal variants are potent activators of human and mouse formyl peptide receptor 1. J Biol Chem 2022 ;298(12):102642.
[44]
Q. Ma, R. Immler, M. Pruenster, M. Sellmayr, C. Li, A. von Brunn, et al.. Soluble uric acid inhibits β2 integrin-mediated neutrophil recruitment in innate immunity. Blood, 139 (23) ( 2022), pp. 3402-3417
[45]
R. González-Amaro, J.R. Cortés, F. Sánchez-Madrid, P. Martin. Is CD69 an effective brake to control inflammatory diseases?. Trends Mol Med, 19 (10) ( 2013), pp. 625-632
[46]
H. Ponta, L. Sherman, P.A. Herrlich. CD44: from adhesion molecules to signalling regulators. Nat Rev Mol Cell Biol, 4 (1) ( 2003), pp. 33-45
[47]
J.C. Hong, R.W. Busuttil. Cold ischemia time and liver graft survival. Am J Transplant, 8 (3) ( 2008), pp. 481-482
[48]
P. Sethi, M. Thillai, B.S. Thankamonyamma, S. Mallick, U. Gopalakrishnan, D. Balakrishnan, et al.. Living donor liver transplantation using small-for-size grafts: does size really matter?. J Clin Exp Hepatol, 8 (2) ( 2018), pp. 125-131
[49]
L.I. Mazilescu, S. Kotha, A. Ghanekar, L. Lilly, T.W. Reichman, Z. Galvin, et al.. Early allograft dysfunction after liver transplantation with donation after circulatory death and brain death grafts: does the donor type matter?. Transplant Direct, 7 (8) ( 2021), p. e727
[50]
G.K. Michalopoulos, B. Bhushan. Liver regeneration: biological and pathological mechanisms and implications. Nat Rev Gastroenterol Hepatol, 18 (1) ( 2021), pp. 40-55
[51]
T.A. Woreta, S.A. Alqahtani. Evaluation of abnormal liver tests. Med Clin North Am, 98 (1) ( 2014), pp. 1-16
PDF(8677 KB)

Accesses

Citation

Detail

段落导航
相关文章

/