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Robertson H, Kim HJ, Li J, Robertson N, Robertson P, Jimenez-Vera E, Ameen F, Tran A, Trinh K, O'Connell PJ, Yang JYH, Rogers NM, Patrick E. Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas. Nat Med 2024:10.1038/s41591-024-03030-6. [PMID: 38890530 DOI: 10.1038/s41591-024-03030-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
The pathogenesis of allograft (dys)function has been increasingly studied using 'omics'-based technologies, but the focus on individual organs has created knowledge gaps that neither unify nor distinguish pathological mechanisms across allografts. Here we present a comprehensive study of human pan-organ allograft dysfunction, analyzing 150 datasets with more than 12,000 samples across four commonly transplanted solid organs (heart, lung, liver and kidney, n = 1,160, 1,241, 1,216 and 8,853 samples, respectively) that we leveraged to explore transcriptomic differences among allograft dysfunction (delayed graft function, acute rejection and fibrosis), tolerance and stable graft function. We identified genes that correlated robustly with allograft dysfunction across heart, lung, liver and kidney transplantation. Furthermore, we developed a transfer learning omics prediction framework that, by borrowing information across organs, demonstrated superior classifications compared to models trained on single organs. These findings were validated using a single-center prospective kidney transplant cohort study (a collective 329 samples across two timepoints), providing insights supporting the potential clinical utility of our approach. Our study establishes the capacity for machine learning models to learn across organs and presents a transcriptomic transplant resource that can be employed to develop pan-organ biomarkers of allograft dysfunction.
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Affiliation(s)
- Harry Robertson
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Hani Jieun Kim
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kinghorn Cancer Centre and Cancer Research Theme, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Jennifer Li
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Department of Renal and Transplantation Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Nicholas Robertson
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Paul Robertson
- Department of Renal and Transplantation Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Elvira Jimenez-Vera
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Farhan Ameen
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Andy Tran
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Katie Trinh
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Philip J O'Connell
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Department of Renal and Transplantation Medicine, Westmead Hospital, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Jean Y H Yang
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Natasha M Rogers
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Department of Renal and Transplantation Medicine, Westmead Hospital, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia.
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia.
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia.
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China.
- Centre for Cancer Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
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Duś-Szachniewicz K, Gdesz-Birula K, Zduniak K, Wiśniewski JR. Proteomic-Based Analysis of Hypoxia- and Physioxia-Responsive Proteins and Pathways in Diffuse Large B-Cell Lymphoma. Cells 2021; 10:cells10082025. [PMID: 34440794 PMCID: PMC8392495 DOI: 10.3390/cells10082025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/17/2023] Open
Abstract
Hypoxia is a common feature in most tumors, including hematological malignancies. There is a lack of studies on hypoxia- and physioxia-induced global proteome changes in lymphoma. Here, we sought to explore how the proteome of diffuse large B-cell lymphoma (DLBCL) changes when cells are exposed to acute hypoxic stress (1% of O2) and physioxia (5% of O2) for a long-time. A total of 8239 proteins were identified by LC–MS/MS, of which 718, 513, and 486 had significant changes, in abundance, in the Ri-1, U2904, and U2932 cell lines, respectively. We observed that changes in B-NHL proteome profiles induced by hypoxia and physioxia were quantitatively similar in each cell line; however, differentially abundant proteins (DAPs) were specific to a certain cell line. A significant downregulation of several ribosome proteins indicated a translational inhibition of new ribosome protein synthesis in hypoxia, what was confirmed in a pathway enrichment analysis. In addition, downregulated proteins highlighted the altered cell cycle, metabolism, and interferon signaling. As expected, the enrichment of upregulated proteins revealed terms related to metabolism, HIF1 signaling, and response to oxidative stress. In accordance to our results, physioxia induced weaker changes in the protein abundance when compared to those induced by hypoxia. Our data provide new evidence for understanding mechanisms by which DLBCL cells respond to a variable oxygen level. Furthermore, this study reveals multiple hypoxia-responsive proteins showing an altered abundance in hypoxic and physioxic DLBCL. It remains to be investigated whether changes in the proteomes of DLBCL under normoxia and physioxia have functional consequences on lymphoma development and progression.
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Affiliation(s)
- Kamila Duś-Szachniewicz
- Department of Clinical and Experimental Pathology, Institute of General and Experimental Pathology, Wrocław Medical University, Marcinkowskiego 1, 50-368 Wrocław, Poland; (K.G.-B.); (K.Z.)
- Correspondence:
| | - Katarzyna Gdesz-Birula
- Department of Clinical and Experimental Pathology, Institute of General and Experimental Pathology, Wrocław Medical University, Marcinkowskiego 1, 50-368 Wrocław, Poland; (K.G.-B.); (K.Z.)
| | - Krzysztof Zduniak
- Department of Clinical and Experimental Pathology, Institute of General and Experimental Pathology, Wrocław Medical University, Marcinkowskiego 1, 50-368 Wrocław, Poland; (K.G.-B.); (K.Z.)
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
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Bram Ednersson S, Stern M, Fagman H, Nilsson-Ehle H, Hasselblom S, Thorsell A, Andersson PO. Proteomic analysis in diffuse large B-cell lymphoma identifies dysregulated tumor microenvironment proteins in non-GCB/ABC subtype patients. Leuk Lymphoma 2021; 62:2360-2373. [PMID: 34114929 DOI: 10.1080/10428194.2021.1913147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The complexity of the activated B-cell like (ABC) diffuse large B-cell lymphoma (DLBCL) subtype is probably not only explained by genetic alterations and methods to measure global protein expression could bring new knowledge regarding the pathophysiology. We used quantitative proteomics to analyze the global protein expression of formalin-fixed paraffin-embedded (FFPE) tumor tissues from 202 DLBCL patients. We identified 6430 proteins and 498 were significantly regulated between the germinal center B-cell like (GCB) and non-GCB groups. A number of proteins previously not described to be upregulated in non-GCB or ABC DLBCL was found, e.g. CD64, CD85A, guanylate-binding protein 1 (GBP1), interferon-induced proteins with tetratricopeptide repeat (IFIT)2, and mixed lineage kinase domain-like protein (MLKL) and immunohistochemical staining showed higher expression of GBP1 and MLKL. A cluster analysis revealed that the most prominent cluster contained proteins involved in the tumor microenvironment and regulation of the immune system. Our data suggest that the therapeutic focus should be expanded toward the tumor microenvironment in non-GCB/ABC subtype patients.
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Affiliation(s)
- Susanne Bram Ednersson
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Mimmie Stern
- Department of Medicine, Section of Hematology, South Älvsborg Hospital, Borås, Sweden.,Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Henrik Fagman
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Herman Nilsson-Ehle
- Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Section of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sverker Hasselblom
- Department of Research, Development & Education, Region Halland, Halmstad, Sweden
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Medicine, Section of Hematology, South Älvsborg Hospital, Borås, Sweden.,Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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