Multi-omics analysis reveals a crosstalk between ferroptosis and peroxisomes on steatotic graft failure after liver transplantation
To identify the mechanism underlying macrosteatosis (MaS)-related graft failure (GF) in liver transplantation (LT) by multi-omics network analysis. The transcriptome and metabolome were assayed in graft and recipient plasma in discovery (n = 68) and validation (n = 89) cohorts. Differentially expressed molecules were identified by MaS and GF status. Transcriptional regulatory networks were generated to explore the mechanism for MaS-related inferior post-transplant prognosis. The differentially expressed molecules associated with MaS and GF were enriched in ferroptosis and peroxisome-related pathways. Core features of MaS-related GF were presented on decreased transferrin and impaired anti-oxidative capacity dependent upon dysregulation of transcription factors hepatocyte nuclear factor 4A (HNF4A) and hypoxia-inducible factor 1A (HIF1A). Furthermore, miR-362-3p and miR-299-5p inhibited transferrin and HIF1A expression, respectively. Lower M2 macrophages but higher memory CD4 T cells were observed in MaS-related GF cases. These results were validated in clinical specimens and cellular models. Systemic analysis of multi-omics data depicted a panorama of biological pathways deregulated in MaS-related GF. Transcriptional regulatory networks centered on transferrin and anti-oxidant responses were associated with poor MaS graft quality, qualifying as potential targets to improve prognosis of patients after LT.
liver transplantation / macrosteatosis / mechanism / metabonomic / prognosis / transcriptomics
1 | A Zarrinpar, RW Busuttil. Liver transplantation: past, present and future. Nat Rev Gastroenterol Hepatol. 2013;10(7):434-440. |
2 | AN Carrier, A Verma, M Mohiuddin, et al. Xenotransplantation: a new era. Front Immunol. 2022;13:900594. |
3 | JF Trotter. Liver transplantation around the world. Curr Opin Organ Transplant. 2017;22(2):123-127. |
4 | ES Orman, ME Mayorga, SB Wheeler, et al. Declining liver graft quality threatens the future of liver transplantation in the United States. Liver Transpl. 2015;21(8):1040-1050. |
5 | N Goldaracena, JM Cullen, D-S Kim, B Ekser, KJ Halazun. Expanding the donor pool for liver transplantation with marginal donors. Int J Surg. 2020;82:30-35. |
6 | JA Steggerda, MB Bloom, M Noureddin, et al. Higher thresholds for the utilization of steatotic allografts in liver transplantation: analysis from a US national database. PLoS One. 2020;15(4):e0230995. |
7 | KP Croome, DD Lee, S Croome, et al. The impact of postreperfusion syndrome during liver transplantation using livers with significant macrosteatosis. Am J Transplant. 2019;19(9):2550-2559. |
8 | J Schleicher, U Dahmen. Computational modeling of oxidative stress in fatty livers elucidates the underlying mechanism of the increased susceptibility to ischemia/reperfusion injury. Comput Struct Biotechnol J. 2018;16:511-522. |
9 | M Nordgren, M Fransen. Peroxisomal metabolism and oxidative stress. Biochimie. 2014;98:56-62. |
10 | X Tian, L Wu, X Li, W Zheng, H Zuo, H Song. Exosomes derived from bone marrow mesenchymal stem cells alleviate biliary ischemia reperfusion injury in fatty liver transplantation by inhibiting ferroptosis. Mol Cell Biochem. 2024;479(4):881-894. |
11 | R Cavill, D Jennen, J Kleinjans, JJ Briedé. Transcriptomic and metabolomic data integration. Briefings Bioinf. 2016;17(5):891-901. |
12 | O ?eda, M Cahová, I Míková, et al. Hepatic gene expression profiles differentiate steatotic and non-steatotic grafts in liver transplant recipients. Front Endocrinol. 2019;10:270. |
13 | Z Liu, J Jia, H Ning, S Que, L Zhou, S Zheng. Systematic evaluation of the safety threshold for allograft macrovesicular steatosis in cadaveric liver transplantation. Front Physiol. 2019;10:429. |
14 | KR Jackson, JD Motter, CE Haugen, et al. Temporal trends in utilization and outcomes of steatotic donor livers in the United States. Am J Transplant. 2020;20(3):855-863. |
15 | SJ Dixon, KM Lemberg, MR Lamprecht, et al. Ferroptosis: an iron-dependent form of nonapoptotic cell death. Cell. 2012;149(5):1060-1072. |
16 | M Gao, P Monian, N Quadri, R Ramasamy, X Jiang. Glutaminolysis and transferrin regulate ferroptosis. Mol Cell. 2015;59(2):298-308. |
17 | JD Ryan, AE Armitage, JF Cobbold, et al. Hepatic iron is the major determinant of serum ferritin in NAFLD patients. Liver Int. 2018;38(1):164-173. |
18 | B Angoro, M Motshakeri, C Hemmaway, D Svirskis, M Sharma. Non-transferrin bound iron. Clin Chim Acta. 2022;531:157-167. |
19 | W Liu, SS Baker, R D Baker, L Zhu. Antioxidant mechanisms in nonalcoholic fatty liver disease. Curr Drug Targets. 2015;16(12):1301-1314. |
20 | NA Bonekamp, A V?lkl, HD Fahimi, M Schrader. Reactive oxygen species and peroxisomes: struggling for balance. Biofactors. 2009;35(4):346-355. |
21 | G-H Chen, C-C Song, K Pantopoulos, X-L Wei, H Zheng, Z Luo. Mitochondrial oxidative stress mediated Fe-induced ferroptosis via the NRF2?ARE pathway. Free Radic Biol Med. 2022;180:95-107. |
22 | JK Reddy, M Sambasiva Rao. Lipid metabolism and liver inflammation. II. Fatty liver disease and fatty acid oxidation. Am J Physiol Gastrointest Liver Physiol. 2006;290(5):G852-G858. |
23 | Z Liu, H Zhu, W Wang, et al. Metabonomic profile of macrosteatotic allografts for orthotopic liver transplantation in patients with initial poor function: mechanistic investigation and prognostic prediction. Front Cell Dev Biol. 2020;8:826. |
24 | A Alisi, G Carpino, FL Oliveira, N Panera, V Nobili, E Gaudio. The role of tissue macrophage-mediated inflammation on NAFLD pathogenesis and its clinical implications. Mediators Inflamm. 2017;2017:8162421. |
25 | UJ Tietge, MJ Bahr, MP Manns, KH B?ker. Plasma amino acids in cirrhosis and after liver transplantation: influence of liver function, hepatic hemodynamics and circulating hormones. Clin Transplant. 2002;16(1):9-17. |
26 | C Baciu, E Pasini, M Angeli, et al. Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis. PLoS One. 2017;12(12):e0189223. |
27 | K-W Huang, V Reebye, K Czysz, et al. Liver activation of hepatocellular nuclear factor-4α by small activating RNA rescues dyslipidemia and improves metabolic profile. Mol Ther Nucleic Acids. 2020;19:361-370. |
28 | Z Luo, M Tian, G Yang, et al. Hypoxia signaling in human health and diseases: implications and prospects for therapeutics. Signal Transduct Target Ther. 2022;7(1):218. |
29 | K Nakanishi, F Tajima, A Nakamura, et al. Effects of hypobaric hypoxia on antioxidant enzymes in rats. J Physiol. 1995;489(3):869-876. |
30 | Z Khan, GK Michalopoulos, DB Stolz. Peroxisomal localization of hypoxia-inducible factors and hypoxia-inducible factor regulatory hydroxylases in primary rat hepatocytes exposed to hypoxia-reoxygenation. Am J Pathol. 2006;169(4):1251-1269. |
31 | SG Khoei, H Manoochehri, M Saidijam. Systemic biological study for identification of miR-299-5p target genes in cancer. Meta Gene. 2020;24:100655. |
32 | Y Zhang, M Luo, X Cui, D O'Connell, Y Yang. Long noncoding RNA NEAT1 promotes ferroptosis by modulating the miR-362-3p/MIOX axis as a ceRNA. Cell Death Differ. 2022;29(9):1850-1863. |
33 | Z Liu, W Wang, S Que, Y He, S Zheng. Presence of macrosteatosis in vivo determined the survival status of rats after liver transplantation. Liver Transpl. 2021;27(3):459-460. |
34 | Z Liu, J Lyu, X Li, et al. Graft-to-recipient weight ratio exerts nonlinear effects on prognosis by interacting with donor liver macrosteatosis. Front Surg. 2023;9:1075845. |
35 | M Fukai, T Hayashi, R Yokota, et al. Lipid peroxidation during ischemia depends on ischemia time in warm ischemia and reperfusion of rat liver. Free Radic Biol Med. 2005;38(10):1372-1381. |
36 | A Stamenkovic, KA O'Hara, DC Nelson, et al. Oxidized phosphatidylcholines trigger ferroptosis in cardiomyocytes during ischemia?reperfusion injury. Am J Physiol Heart Circ Physiol. 2021;320(3):H1170-H1184. |
37 | MJ Reiniers, RF van Golen, TM van Gulik, M Heger. Reactive oxygen and nitrogen species in steatotic hepatocytes: a molecular perspective on the pathophysiology of ischemia?reperfusion injury in the fatty liver. Antioxid Redox Signal. 2014;21(7):1119-1142. |
38 | RG Bardallo, I Company-Marin, E Folch-Puy, J Roselló-Catafau, A Panisello-Rosello, T Carbonell. PEG35 and glutathione improve mitochondrial function and reduce oxidative stress in cold fatty liver graft preservation. Antioxidants. 2022;11(1):158. |
39 | TM Seibt, B Proneth, M Conrad. Role of GPX4 in ferroptosis and its pharmacological implication. Free Radic Biol Med. 2019;133:144-152. |
40 | X Yang, D Lu, R Wang, et al. Single-cell profiling reveals distinct immune phenotypes that contribute to ischaemia?reperfusion injury after steatotic liver transplantation. Cell Prolif. 2021;54(10):e13116. |
41 | J Reimand, R Isserlin, V Voisin, et al. Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap. Nat Protoc. 2019;14(2):482-517. |
42 | B Chen, MS Khodadoust, CL Liu, AM Newman, AA Alizadeh. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243-259. |
43 | W Zhao, P Langfelder, T Fuller, J Dong, A Li, S Hovarth. Weighted gene coexpression network analysis: state of the art. J Biopharm Stat. 2010;20(2):281-300. |
44 | O Fornes, JA Castro-Mondragon, A Khan, et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2020;48(D1):D87-D92. |
45 | MD Goodyear, K Krleza-Jeric, T Lemmens. The Declaration of Helsinki. British Medical Journal Publishing Group; 2007:624-625. |
46 | ZD Goodman. Grading and staging systems for inflammation and fibrosis in chronic liver diseases. J Hepatol. 2007;47(4):598-607. |
47 | H Crowley, WD Lewis, F Gordon, R Jenkins, U Khettry. Steatosis in donor and transplant liver biopsies. Hum Pathol. 2000;31(10):1209-1213. |
48 | PS Kamath, RW Kim. The model for end-stage liver disease (MELD). Hepatology. 2007;45(3):797-805. |
49 | Z Liu, W Wang, L Zhuang, et al. Clear mortality gap caused by graft macrosteatosis in Chinese patients after cadaveric liver transplantation. Hepatobiliary Surg Nutr. 2020;9(6):739. |
50 | T Andersson, L Alfredsson, H K?llberg, S Zdravkovic, A Ahlbom. Calculating measures of biological interaction. Eur J Epidemiol. 2005;20:575-579. |
51 | ME Ritchie, B Phipson, D Wu, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47-e47. |
52 | Z Pang, G Zhou, J Ewald, et al. Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data. Nat Protoc. 2022;17(8):1735-1761. |
53 | P Langfelder, S Horvath. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 2008;9:1-13. |
54 | Z Liu, J Zhao, W Wang, et al. Integrative network analysis revealed genetic impact of pyruvate kinase L/R on hepatocyte proliferation and graft survival after liver transplantation. Oxid Med Cell Long. 2021;2021:7182914. |
55 | R Saito, ME Smoot, K Ono, et al. A travel guide to Cytoscape plugins. Nat Methods. 2012;9(11):1069-1076. |
56 | AM Newman, CL Liu, MR Green, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453-457. |
/
〈 | 〉 |