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Abdrakhimov B, Kayewa E, Wang Z. Prediction of Acute Cardiac Rejection Based on Gene Expression Profiles. J Pers Med 2024; 14:410. [PMID: 38673037 PMCID: PMC11051265 DOI: 10.3390/jpm14040410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 03/30/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Acute cardiac rejection remains a significant challenge in the post-transplant period, necessitating meticulous monitoring and timely intervention to prevent graft failure. Thus, the goal of the present study was to identify novel biomarkers involved in acute cardiac rejection, paving the way for personalized diagnostic, preventive, and treatment strategies. A total of 809 differentially expressed genes were identified in the GSE150059 dataset. We intersected genes selected by analysis of variance, recursive feature elimination, least absolute shrinkage and selection operator, and random forest classifier to identify the most relevant genes involved in acute cardiac rejection. Thus, HCP5, KLRD1, GZMB, PLA1A, GNLY, and KLRB1 were used to train eight machine learning models: random forest, logistic regression, decision trees, support vector machines, gradient boosting machines, K-nearest neighbors, XGBoost, and neural networks. Models were trained, tested, and validated on the GSE150059 dataset (MMDx-based diagnosis of rejection). Eight algorithms achieved great performance in predicting acute cardiac rejection. However, all machine learning models demonstrated poor performance in two external validation sets that had rejection diagnosis based on histology: merged GSE2596 and GSE4470 dataset and GSE9377 dataset, thus highlighting differences between these two methods. According to SHAP and LIME, KLRD1 and HCP5 were the most impactful genes.
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Affiliation(s)
- Bulat Abdrakhimov
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China;
| | - Emmanuel Kayewa
- School of Computer Science, Wuhan University, Wuhan 430072, China;
| | - Zhiwei Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China;
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Gong X, Chi H, Strohmer DF, Teichmann AT, Xia Z, Wang Q. Exosomes: A potential tool for immunotherapy of ovarian cancer. Front Immunol 2023; 13:1089410. [PMID: 36741380 PMCID: PMC9889675 DOI: 10.3389/fimmu.2022.1089410] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
Ovarian cancer is a malignant tumor of the female reproductive system, with a very poor prognosis and high mortality rates. Chemotherapy and radiotherapy are the most common treatments for ovarian cancer, with unsatisfactory results. Exosomes are a subpopulation of extracellular vesicles, which have a diameter of approximately 30-100 nm and are secreted by many different types of cells in various body fluids. Exosomes are highly stable and are effective carriers of immunotherapeutic drugs. Recent studies have shown that exosomes are involved in various cellular responses in the tumor microenvironment, influencing the development and therapeutic efficacy of ovarian cancer, and exhibiting dual roles in inhibiting and promoting tumor development. Exosomes also contain a variety of genes related to ovarian cancer immunotherapy that could be potential biomarkers for ovarian cancer diagnosis and prognosis. Undoubtedly, exosomes have great therapeutic potential in the field of ovarian cancer immunotherapy. However, translation of this idea to the clinic has not occurred. Therefore, it is important to understand how exosomes could be used in ovarian cancer immunotherapy to regulate tumor progression. In this review, we summarize the biomarkers of exosomes in different body fluids related to immunotherapy in ovarian cancer and the potential mechanisms by which exosomes influence immunotherapeutic response. We also discuss the prospects for clinical application of exosome-based immunotherapy in ovarian cancer.
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Affiliation(s)
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Dorothee Franziska Strohmer
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexander Tobias Teichmann
- Sichuan Provincial Center for Gynecology and Breast Diseases (Gynecology), Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany,*Correspondence: Zhijia Xia, ; Qin Wang,
| | - Qin Wang
- Sichuan Provincial Center for Gynecology and Breast Diseases (Gynecology), Affiliated Hospital of Southwest Medical University, Luzhou, China,*Correspondence: Zhijia Xia, ; Qin Wang,
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3
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Li X, Wei Y, Li J, Deng R, Fu Q, Nie W, Zhang H, Wu C, Su X, Wang J, Cao D, Liu X, Liu L, Wang C. Donor HLA genotyping of ex vivo expanded urine cells from kidney transplant recipients. HLA 2021; 98:431-447. [PMID: 34505410 DOI: 10.1111/tan.14426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/13/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
Antibody-mediated rejection (AMR) induced by donor-specific anti-HLA antibodies (DSA) remains a major cause of long-term graft loss after kidney transplantation. Currently, the presence of DSA cannot always be determined at a specific allele level, because existing donor HLA typing is low resolution and often incomplete, lacking HLA-DP, and occasionally HLA-C and HLA-DQ information and historical donor DNA samples are not available for HLA retyping. Here we present a novel, non-invasive technique for obtaining donor DNA from selectively expanded donor cells from urine of renal transplant recipients. Urine-derived cells were successfully expanded ex vivo from 31 of 32 enrolled renal transplant recipients, and with DNA obtained from these cells, donor HLA typing was unambiguously determined for HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1 and -DPB1 loci by next-generation sequencing. Our results showed 100% concordance of HLA typing data between donor peripheral blood and recipient urine-derived cells. In comparison, HLA typing showed that DNA derived from urine sediments mainly contained recipient-derived DNA. We also present the successful application of our novel technique in a clinical case of AMR in a renal transplant recipient. Urine-derived donor cells can be isolated from kidney transplant recipients and serve as a suitable source of donor material for reliable high-resolution HLA genotyping. Thus, this approach can aid the assessment of DSA specificity to support the diagnosis of AMR as well as the evaluation of treatment efficacy in kidney transplant recipients when complete donor HLA information and donor DNA are unavailable.
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Affiliation(s)
- Xirui Li
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yongcheng Wei
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Li
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ronghai Deng
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qian Fu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weijian Nie
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huanxi Zhang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chenglin Wu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaojun Su
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiali Wang
- Department of Nephrology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dajiang Cao
- BFR Clinical Diagnostics Lab, Beijing, China
| | | | - Longshan Liu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory on Organ Donation and Transplant Immunology, Guangzhou, China
| | - Changxi Wang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory on Organ Donation and Transplant Immunology, Guangzhou, China
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Bach C, Knaup KX, Herrmann M, Krumbiegel M, Pfister F, Büttner-Herold M, Steffen M, Zecher D, Lopau K, Schneider K, Dieterle A, Amann K, Reis A, Schiffer M, Spriewald BM, Wiesener MS. A noninvasive diagnostic approach to retrospective donor HLA typing in kidney transplant patients using urine. Transpl Int 2021; 34:1226-1238. [PMID: 33904183 DOI: 10.1111/tri.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/24/2021] [Accepted: 04/12/2021] [Indexed: 11/29/2022]
Abstract
Antibody-mediated rejection (AMR) is a major obstacle to long-term kidney transplantation. AMR is mostly caused by donor specific HLA antibodies, which can arise before or any time after transplantation. Incomplete donor HLA typing and unavailability of donor DNA regularly preclude the assessment of donor-specificity of circulating anti-HLA antibodies. In our centre, this problem arises in approximately 20% of all post-transplant HLA-antibody assessments. We demonstrate that this diagnostic challenge can be resolved by establishing donor renal tubular cell cultures from recipient´s urine as a source of high-quality donor DNA. DNA was then verified for genetic origin and purity by fluorescence in situ hybridization and short tandem repeat analysis. Two representative cases highlight the diagnostic value of this approach which is corroborated by analysis of ten additional patients. The latter were randomly sampled from routine clinical care patients with available donor DNA as controls. In all 12 cases, we were able to perform full HLA typing of the respective donors confirmed by cross-comparison to results from the stored 10 donor DNAs. We propose that this noninvasive diagnostic approach for HLA typing in kidney transplant patients is valuable to determine donor specificity of HLA antibodies, which is important in clinical assessment of suspected AMR.
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Affiliation(s)
- Christian Bach
- Department of Internal Medicine 5 - Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Karl X Knaup
- Department of Internal Medicine 4 - Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Markus Herrmann
- Department of Internal Medicine 4 - Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Mandy Krumbiegel
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Frederick Pfister
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Maike Büttner-Herold
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Martin Steffen
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Daniel Zecher
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Kai Lopau
- Department of Internal Medicine, University of Würzburg, Würzburg, Germany
| | - Karen Schneider
- Department of Internal Medicine 4 - Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Anne Dieterle
- Department of Internal Medicine 4 - Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Mario Schiffer
- Department of Internal Medicine 4 - Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Bernd M Spriewald
- Department of Internal Medicine 5 - Haematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Michael S Wiesener
- Department of Internal Medicine 4 - Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
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Pre-transplant donor-reactive IL-21 producing T cells as a tool to identify an increased risk for acute rejection. Sci Rep 2021; 11:12445. [PMID: 34127739 PMCID: PMC8203783 DOI: 10.1038/s41598-021-91967-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Pre-transplant screening focuses on the detection of anti-HLA alloantibodies. Previous studies have shown that IFN-γ and IL-21 producing T cells are associated with the development of acute rejection (AR). The aim of this study, was to assess whether pre-transplant donor-reactive T cells and/or B cells are associated with increased rejection risk. Samples from 114 kidney transplant recipients (transplanted between 2010 and 2013) were obtained pre-transplantation. The number of donor-reactive IFN-γ and IL-21 producing cells was analyzed by ELISPOT assay. The presence of donor specific antibodies (DSA) was also determined before transplantation. Numbers of donor-reactive IFN-γ producing cells were similar in patients with or without AR whereas those of IL-21 producing cells were higher in patients with AR (p = 0.03). Significantly more patients with AR [6/30(20%)] had detectable DSA compared to patients without AR [5/84(5.9%), p = 0.03]. Multivariate logistic regression showed that donor age (OR 1.06), pre-transplant DSA (OR 5.61) and positive IL-21 ELISPOT assay (OR 2.77) were independent predictors of an increased risk for the development of AR. Aside from an advanced donor-age and pre-transplant DSA, also pre-transplant donor-reactive IL-21 producing cells are associated with the development of AR after transplantation.
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Babel N, Anft M, Blazquez-Navarro A, Doevelaar AA, Seibert FS, Bauer F, Rohn BJ, Hoelzer B, Thieme CJ, Roch T, Meister TL, Pfaender S, Steinmann E, Dittmer U, Schenker P, Amann K, Viebahn R, Stervbo U, Westhoff TH. Immune monitoring facilitates the clinical decision in multifocal COVID-19 of a pancreas-kidney transplant patient. Am J Transplant 2020; 20:3210-3215. [PMID: 32777178 PMCID: PMC7436473 DOI: 10.1111/ajt.16252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 01/25/2023]
Abstract
The optimal management in transplant recipients with coronavirus disease 2019 (COVID-19) remains uncertain. The main concern is the ability of immunosuppressed patients to generate sufficient immunity for antiviral protection. Here, we report on immune monitoring facilitating a successful outcome of severe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated pneumonia, meningoencephalitis, gastroenteritis, and acute kidney and pancreas graft failure in a pancreas-kidney transplant recipient. Despite the very low numbers of circulating B, NK, and T cells identified in follow-up, a strong SARS-CoV-2 reactive T cell response was observed. Importantly, we detected T cells reactive to Spike, Membrane, and Nucleocapsid proteins of SARS-CoV-2 with majority of T cells showing polyfunctional proinflammatory Th1 phenotype at all analyzed time points. Antibodies against Spike protein were also detected with increasing titers in follow-up. Neutralization tests confirmed their antiviral protection. A correlation between cellular and humoral immunity was observed underscoring the specificity of demonstrated data. We conclude that analyzing the kinetics of nonspecific and SARS-CoV-2-reactive cellular and humoral immunity can facilitate the clinical decision on immunosuppression adjustment and allow successful outcome as demonstrated in the current clinical case. Although the antiviral protection of the detected SARS-CoV-2-reactive T cells requires further evaluation, our data prove an ability mounting a strong SARS-CoV-2-reactive T cell response with functional capacity in immunosuppressed patients.
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Affiliation(s)
- Nina Babel
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany,Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany,Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany,Correspondence Nina Babel
| | - Moritz Anft
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Arturo Blazquez-Navarro
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Adrian A.N. Doevelaar
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Felix S. Seibert
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Frederic Bauer
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Benjamin J. Rohn
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Bodo Hoelzer
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Constantin J. Thieme
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Toralf Roch
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany,Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Toni L. Meister
- Department of Molecular and Medical Virology, Ruhr-University, Bochum, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr-University, Bochum, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr-University, Bochum, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter Schenker
- Department of Surgery, University Hospital Knappschaftskrankenhaus Bochum, Ruhr-University, Bochum, Germany
| | - Kerstin Amann
- Department of Nephropathology, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Germany
| | - Richard Viebahn
- Department of Surgery, University Hospital Knappschaftskrankenhaus Bochum, Ruhr-University, Bochum, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Timm H. Westhoff
- Medical Department, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
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