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Giraudi PJ, Laraño AA, Monego SD, Pravisani R, Bonazza D, Gondolesi G, Tiribelli C, Baralle F, Baccarani U, Licastro D. Genome-wide DNA methylation and transcriptomic analysis of liver tissues subjected to early ischemia/reperfusion injury upon human liver transplantation. Ann Hepatol 2024; 29:101506. [PMID: 38710471 DOI: 10.1016/j.aohep.2024.101506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 05/08/2024]
Abstract
INTRODUCTION AND OBJECTIVES Epigenetic changes represent a mechanism connecting external stresses with long-term modifications of gene expression programs. In solid organ transplantation, ischemia-reperfusion injury (IRI) appears to induce epigenomic changes in the graft, although the currently available data are extremely limited. The present study aimed to characterize variations in DNA methylation and their effects on the transcriptome in liver transplantation from brain-dead donors. PATIENTS AND METHODS 12 liver grafts were evaluated through serial biopsies at different timings in the procurement-transplantation process: T0 (warm procurement, in donor), T1 (bench surgery), and T2 (after reperfusion, in recipient). DNA methylation (DNAm) and transcriptome profiles of biopsies were analyzed using microarrays and RNAseq. RESULTS Significant variations in DNAm were identified, particularly between T2 and T0. Functional enrichment of the best 1000 ranked differentially methylated promoters demonstrated that 387 hypermethylated and 613 hypomethylated promoters were involved in spliceosomal assembly and response to biotic stimuli, and inflammatory immune responses, respectively. At the transcriptome level, T2 vs. T0 showed an upregulation of 337 and downregulation of 61 genes, collectively involved in TNF-α, NFKB, and interleukin signaling. Cell enrichment analysis individuates macrophages, monocytes, and neutrophils as the most significant tissue-cell type in the response. CONCLUSIONS In the process of liver graft procurement-transplantation, IRI induces significant epigenetic changes that primarily act on the signaling pathways of inflammatory responses dependent on TNF-α, NFKB, and interleukins. Our DNAm datasets are the early IRI methylome literature and will serve as a launch point for studying the impact of epigenetic modification in IRI.
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Affiliation(s)
- Pablo J Giraudi
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy.
| | - Allen A Laraño
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy; Research Institute for Tropical Medicine, Department of Health, Muntinlupa City, Philippines
| | | | - Riccardo Pravisani
- Liver-Kidney Transplant Unit, Department of Medicine, University of Udine, Italy
| | - Deborah Bonazza
- Anatomia ed Istologia Patologica, Cattinara Hospital, ASUGI, Trieste, Italy
| | - Gabriel Gondolesi
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería, Universidad Favaloro, Buenos Aires, Argentina
| | - Claudio Tiribelli
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy
| | - Francisco Baralle
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy
| | - Umberto Baccarani
- Liver-Kidney Transplant Unit, Department of Medicine, University of Udine, Italy
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LaHue SC, Fuentealba M, Roa Diaz S, Seetharaman S, Garcia T, Furman D, Lai JC, Newman JC. Association of biological aging with frailty and post-transplant outcomes among adults with cirrhosis. GeroScience 2024; 46:3287-3295. [PMID: 38246968 PMCID: PMC11009173 DOI: 10.1007/s11357-024-01076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
Frailty is classically associated with advanced age but is also an important predictor of clinical outcomes in comparatively young adults with cirrhosis. We examined the association of biological aging with frailty and post-transplant outcomes in a pilot of adults with cirrhosis undergoing liver transplantation (LT). Frailty was measured via the Liver Frailty Index (LFI). The primary epigenetic clock DNA methylation (DNAm) PhenoAge was calculated from banked peripheral blood mononuclear cells; we secondarily explored two first-generation clocks (Hannum; Horvath) and two additional second-generation clocks (GrimAge; GrimAge2). Twelve adults were included: seven frail (LFI ≥ 4.4, mean age 55 years) and five robust (LFI < 3.2, mean age 55 years). Mean PhenoAge age acceleration (AgeAccel) was + 2.5 years (P = 0.23) for frail versus robust subjects. Mean PhenoAge AgeAccel was + 2.7 years (P = 0.19) for subjects who were readmitted or died within 30 days of discharge post-LT versus those without this outcome. When compared with first-generation clocks, the second-generation clocks demonstrated greater average AgeAccel for subjects with frailty or poor post-LT outcomes. Measuring biological age using DNAm-derived epigenetic clocks is feasible in adults undergoing LT. While frail and robust subjects had the same average chronological age, average biological age as measured by second-generation epigenetic clocks tended to be accelerated among those who were frail or experienced a poor post-LT outcome. These results suggest that frailty in these relatively young subjects with cirrhosis may involve similar aging mechanisms as frailty classically observed in chronologically older adults and warrant validation in a larger cohort.
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Affiliation(s)
- Sara C LaHue
- Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA.
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, 505 Parnassus Ave, Box 0114, San Francisco, CA, 94143, USA.
- Buck Institute for Research On Aging, Novato, CA, USA.
| | | | - Stephanie Roa Diaz
- Buck Institute for Research On Aging, Novato, CA, USA
- Division of Geriatrics, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | - Srilakshmi Seetharaman
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Thelma Garcia
- Buck Institute for Research On Aging, Novato, CA, USA
- Division of Geriatrics, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | - David Furman
- Buck Institute for Research On Aging, Novato, CA, USA
- Instituto de Investigaciones en Medicina Traslacional, Universidad Austral, Consejo Nacional de Investigaciones Científicas y Técnicas, 1629, Pilar, Argentina
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer C Lai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - John C Newman
- Buck Institute for Research On Aging, Novato, CA, USA
- Division of Geriatrics, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
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Pradère P, Zajacova A, Bos S, Le Pavec J, Fisher A. Molecular monitoring of lung allograft health: is it ready for routine clinical use? Eur Respir Rev 2023; 32:230125. [PMID: 37993125 PMCID: PMC10663940 DOI: 10.1183/16000617.0125-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023] Open
Abstract
Maintenance of long-term lung allograft health in lung transplant recipients (LTRs) requires a fine balancing act between providing sufficient immunosuppression to reduce the risk of rejection whilst at the same time not over-immunosuppressing individuals and exposing them to the myriad of immunosuppressant drug side-effects that can cause morbidity and mortality. At present, lung transplant physicians only have limited and rather blunt tools available to assist them with this task. Although therapeutic drug monitoring provides clinically useful information about single time point and longitudinal exposure of LTRs to immunosuppressants, it lacks precision in determining the functional level of immunosuppression that an individual is experiencing. There is a significant gap in our ability to monitor lung allograft health and therefore tailor optimal personalised immunosuppression regimens. Molecular diagnostics performed on blood, bronchoalveolar lavage or lung tissue that can detect early signs of subclinical allograft injury, differentiate rejection from infection or distinguish cellular from humoral rejection could offer clinicians powerful tools in protecting lung allograft health. In this review, we look at the current evidence behind molecular monitoring in lung transplantation and ask if it is ready for routine clinical use. Although donor-derived cell-free DNA and tissue transcriptomics appear to be the techniques with the most immediate clinical potential, more robust data are required on their performance and additional clinical value beyond standard of care.
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Affiliation(s)
- Pauline Pradère
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Department of Respiratory Diseases, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph and Paris Saclay University, Paris, France
| | - Andrea Zajacova
- Prague Lung Transplant Program, Department of Pneumology, Motol University Hospital and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Saskia Bos
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Jérôme Le Pavec
- Department of Respiratory Diseases, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph and Paris Saclay University, Paris, France
| | - Andrew Fisher
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
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Chen D, Wang M, Guo Y, Wu W, Ji X, Dou X, Tang H, Zong Z, Zhang X, Xiong D. An aberrant DNA methylation signature for predicting the prognosis of head and neck squamous cell carcinoma. Cancer Med 2021; 10:5936-5947. [PMID: 34313009 PMCID: PMC8419750 DOI: 10.1002/cam4.4142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/28/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common malignancy worldwide with a poor prognosis. DNA methylation is an epigenetic modification that plays a critical role in the etiology and pathogenesis of HNSCC. The current study aimed to develop a predictive methylation signature based on bioinformatics analysis to improve the prognosis and optimize therapeutic outcome in HNSCC. Clinical information and methylation sequencing data of patients with HNSCC were downloaded from The Cancer Genome Atlas database. The R package was used to identify differentially methylated genes (DMGs) between HNSCC and adjacent normal tissues. We identified 22 DMGs associated with 246 differentially methylated sites. Patients with HNSCC were classified into training and test groups. Cox regression analysis was used to build a risk score formula based on the five methylation sites (cg26428455, cg13754259, cg17421709, cg19229344, and cg11668749) in the training group. The Kaplan–Meier survival curves showed that the overall survival (OS) rates were significantly different between the high‐ and low‐risk groups sorted by the signature in the training group (median: 1.38 vs. 1.57 years, log‐rank test, p < 0.001). The predictive power was then validated in the test group (median: 1.34 vs. 1.75 years, log‐rank test, p < 0.001). The area under the receiver operating characteristic curve (area under the curve) based on the signature for predicting the 5‐year survival rates, was 0.7 in the training and 0.73 in test groups, respectively. The results of multivariate Cox regression analysis showed that the riskscore (RS) signature based on the five methylation sites was an independent prognostic tool for OS prediction in patients. In addition, a predictive nomogram model that incorporated the RS signature and patient clinical information was developed. The innovative methylation signature‐based model developed in our study represents a robust prognostic tool for guiding clinical therapy and predicting the OS in patients with HNSCC.
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Affiliation(s)
- Dayang Chen
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Mengmeng Wang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Ying Guo
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wei Wu
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xiang Ji
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xiaowen Dou
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Huamei Tang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Zengyan Zong
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Dan Xiong
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
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Abstract
PURPOSE OF REVIEW DNA methylation is involved in gene transcription and as such important for cellular function. Here, the literature on DNA methylation in relation to acute rejection is summarized with a focus on the potential clinical utility of DNA methylation for monitoring transplant rejection. RECENT FINDINGS The tight transcriptional control of DNA methylation in immune cell function, e.g. demethylation in regulatory T-cell-specific genes for stable immunosuppressive capacities, suggests an important role for DNA methylation variations in the antidonor-directed immune response. Until today, differentially methylated DNA in immune cells, however, has not been described at the moment of allograft rejection. The ability to locus-specific modify DNA methylation could facilitate the generation of stable cells for cellular therapy purposes. The unique cell-specific characteristics of DNA methylation provide the opportunity to identify its cellular origin. Examining methylation of cell-free DNA in blood or urine may serve as a 'liquid biopsy' enabling minimally invasive detection of allograft rejection. SUMMARY Actual research publications on DNA methylation in relation to allograft rejection are scarce, which makes it challenging to determine its potential clinical value. Extensive research is needed to investigate the value of DNA methylation in early recognition, diagnosis, and/or successful treatment of allograft rejection.
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Vasco M, Benincasa G, Fiorito C, Faenza M, De Rosa P, Maiello C, Santangelo M, Vennarecci G, Napoli C. Clinical epigenetics and acute/chronic rejection in solid organ transplantation: An update. Transplant Rev (Orlando) 2021; 35:100609. [PMID: 33706201 DOI: 10.1016/j.trre.2021.100609] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 12/13/2022]
Abstract
The lack of a precise stratification algorithm for predicting patients at high risk of graft rejection challenges the current solid organ transplantation (SOT) clinical setting. In fact, the established biomarkers for transplantation outcomes are unable to accurately predict the onset time and severity of graft rejection (acute or chronic) as well as the individual response to immunosuppressive drugs. Thus, identifying novel molecular pathways underlying early immunological responses which can damage transplant integrity is needed to reach precision medicine and personalized therapy of SOT. Direct epigenetic-sensitive mechanisms, mainly DNA methylation and histone modifications, may play a relevant role for immune activation and long-term effects (e.g., activation of fibrotic processes) which may be translated in new non-invasive biomarkers and drug targets. In particular, the measure of DNA methylation by using the blood-based "epigenetic clock" system may be an added value to the donor eligibility criteria providing an estimation of the heart biological age as well as a predictive biomarkers. Besides, monitoring of DNA methylation changes may aid to predict acute vs chronic graft damage in kidney transplantation (KT) patients. For example, hypermethylation of genes belonging to the Notch and Wnt pathways showed a higher predictive value for chronic injury occurring at 12 months post-KT with respect to established clinical parameters. Detecting higher circulating cell-free DNA (cfDNA) fragments carrying hepatocyte-specific unmethylated loci in the inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), insulin like growth factor 2 receptor (IGF2R), and vitronectin (VTN) genes may be useful to predict acute graft injury after liver transplantation (LT) in serum samples. Furthermore, hypomethylation in the forkhead box P3 (FOXP3) gene may serve as a marker of infiltrating natural Treg percentage in the graft providing the ability to predict acute rejection events after heart transplantation (HTx). We aim to update on the possible clinical relevance of DNA methylation changes regulating immune-related pathways underlying acute or chronic graft rejection in KT, LT, and HTx which might be useful to prevent, monitor, and treat solid organ rejection at personalized level.
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Affiliation(s)
- Maria Vasco
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Carmela Fiorito
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Mario Faenza
- Multidisciplinary Department of Medical Surgical and Dental Sciences-Plastic Surgery Unit, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Paride De Rosa
- General Surgery and Transplantation Unit, "San Giovanni di Dio e Ruggi D'Aragona" University Hospital, Scuola Medica Salernitana, Salerno, Italy
| | - Ciro Maiello
- Department of Cardiovascular Surgery and Transplants, Monaldi Hospital, Azienda dei Colli, Naples, Italy
| | - Michele Santangelo
- General Surgery and Kidney Transplantation Unit, "Federico II" University Hospital, Naples, Italy
| | - Giovanni Vennarecci
- Division of General Surgery and Liver Transplantation, AO Cardarelli, Naples, Italy
| | - Claudio Napoli
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy; IRCCS SDN, Naples, Italy
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Zhang R, Li Y, Yu H, Liu L, Zhu C, Zuo S, Chen Z. An aberrant DNA methylation signature for predicting hepatocellular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1667. [PMID: 33490179 PMCID: PMC7812168 DOI: 10.21037/atm-20-7804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background By the time they are clinically diagnosed, patients with hepatocellular carcinoma (HCC) are often at the advanced stage. DNA methylation has become a useful predictor of prognosis for cancer patients. Research on DNA methylation as a biomarker for assessing the risk of occurrence in HCC patients is limited. The purpose of this study was to develop an efficient methylation site model for predicting survival in patients with HCC. Methods DNA methylation and gene expression profile data were extracted from The Cancer Genome Atlas (TCGA) database. Markers of DNA-methylated site in two subsets (the training subset and the test subset) were identified using a random survival forest algorithm and Cox proportional hazards regression. Then, Gene Ontology annotations were applied to investigate the functions of DNA methylation signatures. Results A total of 37 hub genes containing 713 methylated sites were identified among the differentially methylated genes (DMGs) and differentially expressed genes (DEGs). Finally, seven methylation sites (cg12824782, cg24871714, cg18683774, cg22796509, cg19450025, cg10474350, and cg06511917) were identified. In the training group and the test group, the area under the curve predicting the survival of patients with HCC was 0.750 and 0.742, respectively. The seven methylation sites signature could be used to divide the patients in the training group into high- and low-risk subgroups [overall survival (OS): 2.81 vs. 2.11 years; log-rank test, P<0.05]. Then, the prediction ability of the model was validated in the test dataset through risk stratification (OS: 2.04 vs. 2.88 years; log-rank test, P<0.05). Functional analysis demonstrated that these signature genes were related to the activity of DNA-binding transcription activator, RNA polymerase II distal enhancer sequence-specific DNA binding, and enhancer sequence-specific DNA binding. Conclusions The results of this study showed that the signature is useful for predicting the survival of HCC patients and thus, can facilitate treatment-related decision-making.
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Affiliation(s)
- Renhua Zhang
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Yafei Li
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Hao Yu
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Lin Liu
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Changhao Zhu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi Zuo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zili Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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Zhang X, Zheng Y, Li G, Yu C, Ji T, Miao S. Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma. Transl Cancer Res 2020; 9:7299-7309. [PMID: 35117331 PMCID: PMC8798623 DOI: 10.21037/tcr-20-3204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Osteosarcoma (OS) is a common malignant bone tumor in children and adolescents. DNA methylation plays a crucial role in the prognosis prediction of cancer. Identification of novel DNA methylation sites biomarkers could be beneficial for the prognosis of OS patients. In this study, we aim to find an efficient methylated site model for predicting survival in OS. METHODS DNA methylation data were downloaded from the Cancer Genome Atlas database (TCGA) and the GEO database. Cox proportional hazard regression and random survival forest algorithm (RSFVH) were applied to identify DNA methylated site signature in the samples randomly assigned to the training subset and the other samples as the test subset. By randomizing 71 clinical samples into two individual groups and a series of statistical analyses between the two groups, a DNA methylation signature is verified. RESULTS This signature comprises four methylation sites (cg04533248, cg12401425, cg13997435, and cg15075357) associated with the patient training group from the univariate Cox proportional hazards regression analysis, RSFVH, and multivariate Cox regression analysis. Kaplan-Meier survival curves showed the OS patients in the high-risk group have a poor 5-year overall survival compared with the low-risk group, and this finding was identified in the test data set. A ROC analysis was performed in the current research. The results revealed that this signature was an independent predictor of patient survival by investigating the AUC of the four methylation sites signature in the training data set (AUC =0.861) and test data set, respectively (AUC =0.920). The nomogram described in the current study placed a great guiding value for predicting 1-, 2-, 3-year survival of the OS by combining age, gender, grade, and TNM stage as covariates with the RS of patients' methylation related signatures. CONCLUSIONS Our study proved that this signature might be a powerful prognostic tool for survival rate evaluation and guide tailored therapy for OS patients.
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Affiliation(s)
- Xijun Zhang
- Department of Laboratory of Jiayuguan City First People’s Hospital, Jiayuguan, China
| | - Yongjun Zheng
- The 984th Hospital of the People’s Liberation Army, Shangzhuang Township, Beijing, China
| | - Gaoshan Li
- Department of Orthopaedics, 968 Hospital of Joint Service Support Force of Chinese People’s Liberation Army, Jinzhou, China
| | - Changying Yu
- Department of Laboratory Medicine, the 965 Hospital of the PLA, Jilin, China
| | - Ting Ji
- Shenzhen Mindray Bio-Medical Electronics Co., Ltd, Shenzhen, China
| | - Shenghu Miao
- Department of Laboratory Medicine, Wuwei People’s Hospital, Wuwei, China
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The aging transplant population and immunobiology: any therapeutic implication? Curr Opin Organ Transplant 2020; 25:255-260. [PMID: 32374576 PMCID: PMC9366898 DOI: 10.1097/mot.0000000000000760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
PURPOSE OF REVIEW The aim of this review is to describe the latest investigations into the immunobiology of aging and the potential impact on outcomes after mechanical circulatory support implantation and heart transplantation. This information is relevant given the growing numbers of older patients with heart failure undergoing evaluation for mechanical circulatory support device (MCSD) or heart transplantation. RECENT FINDINGS A host of aging-associated aspects of immune dysfunction have been described in the general population including T-cell senescence, exhaustion, and terminal dedifferentiation, as well as impaired function of innate immune cells. Another important consequence of T-cell senescence is inflammation, which is known to have a strong relationship with both heart failure and frailty in older patients. Recent data on the association between T-cell and monocyte phenotypes as well as evaluation of gene expression and adverse outcomes after MCSD suggests the potential value of immunologic assessment of MCSD and heart transplant candidates and recipients. Measurement of physical frailty represents another avenue for patient evaluation that may complement immunologic assessment. Determination of immune dysfunction and frailty prior to transplantation may have implications for choice of induction and dosing of maintenance immunosuppression. SUMMARY As the age of transplant and MCSD candidates and recipients continues to increase, it is important for providers to recognize the potential impact of aging-associated immune dysfunction and how it may influence candidate selection, postintervention monitoring, and adjustment of immunosuppression.
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Complement component C5a induces aberrant epigenetic modifications in renal tubular epithelial cells accelerating senescence by Wnt4/βcatenin signaling after ischemia/reperfusion injury. Aging (Albany NY) 2020; 11:4382-4406. [PMID: 31284268 PMCID: PMC6660044 DOI: 10.18632/aging.102059] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/24/2019] [Indexed: 12/30/2022]
Abstract
Epigenetic mechanisms, such as DNA methylation, affect tubular maladaptive response after Acute Kidney Injury (AKI) and accelerate renal aging. Upon ischemia/reperfusion (I/R) injury, Complement activation leads to C5a release that mediates damage; however, little is known about the effect of C5a-C5a Receptor (C5aR) interaction in Renal Tubular Epithelial Cells (RTEC). Through a whole-genome DNA methylation analysis in cultured RTEC, we found that C5a induced aberrant methylation, particularly in regions involved in cell cycle control, DNA damage and Wnt signaling. The most represented genes were BCL9, CYP1B1 and CDK6. C5a stimulation of RTEC led to up-regulation of SA-β Gal and cell cycle arrest markers such as p53 and p21. C5a increased also IL-6, MCP-1 and CTGF gene expression, consistent with SASP development. In accordance, in a swine model of renal I/R injury, we found the increased expression of Wnt4 and βcatenin correlating with SA-β Gal, p21, p16 and IL-6 positivity. Administration of Complement Inhibitor (C1-Inh), antagonized SASP by reducing SA-β Gal, p21, p16, IL-6 and abrogating Wnt4/βcatenin activation. Thus, C5a affects the DNA methylation of genes involved in tubular senescence. Targeting epigenetic programs and Complement may offer novels strategies to protect tubular cells from accelerated aging and to counteract progression to Chronic Kidney Disease
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DNA Methylation Age Is More Closely Associated With Infection Risk Than Chronological Age in Kidney Transplant Recipients. Transplant Direct 2020; 6:e576. [PMID: 33134500 PMCID: PMC7581059 DOI: 10.1097/txd.0000000000001020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 11/26/2022] Open
Abstract
Older kidney transplant recipients demonstrate increased rates of infection but decreased rates of rejection compared with younger recipients, suggesting that older transplant patients are functionally overimmunosuppressed. We hypothesized that this is a consequence of reduction in immunological activity due to biological aging and that an immune biological age, as determined by DNA methylation (DNAm), would be associated more strongly with incidence of infection than chronological age. Methods DNAm analysis was performed on peripheral blood mononuclear cell collected from 60 kidney transplant recipients representing older (≥age 60 y) and younger (aged 30-59 y) patients 3 months after transplantation. DNAm age was calculated based on methylation status of a panel of CpG sites, which have been previously identified as indicative of biological age. Results Correlation was seen between chronological and DNAm age; however, there were many patients with significant differences (either acceleration or slowing) between DNAm age and chronological age. A statistically significant association was seen between increased DNAm age and incidence of infection in the first year after kidney transplantation, whereas no significant association was seen between chronological age and infection. Conclusions Assessment of DNAm age holds promise as an approach for patient evaluation and individualization of immune suppression regimens. This analysis may provide insights into the immunological mechanism behind increased incidence of infection observed in older transplant patients. The ability to measure biological age would allow for patient risk stratification and individualization of immunosuppression, improving outcomes for the growing numbers of older patients undergoing kidney transplantation.
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Zar G, Smith JG, Smith ML, Andersson B, Nilsson J. Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation. PLoS One 2019; 14:e0217747. [PMID: 31166960 PMCID: PMC6550412 DOI: 10.1371/journal.pone.0217747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) of heart transplant recipient- and donor-derived cardiac biopsies may facilitate organ matching, graft failure prediction, and immunotolerance research. The objective of this study was to determine the feasibility of WGS based on formalin-fixed paraffin-embedded endomyocardial biopsies. METHODS AND RESULTS The study included serial donor- and recipient samples from patients who had undergone heart transplantation at Skane University Hospital, Lund, Sweden, between 1988 and 2009. DNA extraction and WGS were conducted. Additional WGS sequencing quality metrics and coverage were obtained with the Genome Analysis Toolkit (GATK). 455 endomyocardial samples from 37 heart transplant recipients were acquired from routine rejection monitoring and stored as formalin-fixed paraffin-embedded samples. They were analyzed after 3-26 years of storage. DNA was extracted from 114 samples and WGS was run on 85 samples. DNA extraction yielded 313 ng (IQR 96-601) for all samples. A coverage of 11.3x (IQR 9.0-15.9) was recorded for all WGS samples. Three samples stored for > 25 years yielded a coverage of > 25x. Data were generated for 1.7 billion reads per sample (IQR 1.4-2.7). A Transition/Transversion (TiTv) ratio of 2.09 ± 0.05 was calculated for all WGS samples. No associations were found among storage time, DNA yield, or sequencing quality metrics. CONCLUSIONS The present study demonstrated the feasibility of whole-genome sequencing based on endomyocardial biopsies. This process could enable large-scale retrospective genomic studies using stored histopathological samples.
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Affiliation(s)
- Gustav Zar
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - J. Gustav Smith
- Department of Clinical Sciences, Cardiology, Lund University and Skane University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Maya Landenhed Smith
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - Bodil Andersson
- Department of Clinical Sciences Lund, Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - Johan Nilsson
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
- * E-mail:
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Unveiling the Role of DNA Methylation in Kidney Transplantation: Novel Perspectives toward Biomarker Identification. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1602539. [PMID: 30766879 PMCID: PMC6350635 DOI: 10.1155/2019/1602539] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/30/2018] [Indexed: 12/13/2022]
Abstract
The burden of chronic kidney disease is dramatically rising, making it a major public health concern worldwide. Kidney transplantation is now the best treatment for patients with end-stage renal disease. Although kidney transplantation may improve survival and quality of life, its long-term results are hampered by immune- and/or non-immune-mediated complications. Thus, the identification of transplanted patients with a higher risk of posttransplant complications has become a big challenge for public health. However, current biomarkers of posttransplant complications have a poor predictive value, rising the need to explore novel approaches for the management of transplant patient. In this review we summarize the emerging literature about DNA methylation in kidney transplant complications, in order to highlight its perspectives toward biomarker identification. In the forthcoming future the monitoring of DNA methylation in kidney transplant patients could become a plausible strategy toward the prevention and/or treatment of kidney transplant complications.
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14
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Hubacek JA, Vymetalova J, Lanska V, Dlouha D. The fat mass and obesity related gene polymorphism influences the risk of rejection in heart transplant patients. Clin Transplant 2018; 32:e13443. [DOI: 10.1111/ctr.13443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslav A. Hubacek
- Centre for Experimental Medicine; Institute for Clinical and Experimental Medicine; Prague Czech Republic
| | - Jevgenija Vymetalova
- Cardio Centre; Institute for Clinical and Experimental Medicine; Prague Czech Republic
| | - Vera Lanska
- Statistic Unit; Institute for Clinical and Experimental Medicine; Prague Czech Republic
| | - Dana Dlouha
- Centre for Experimental Medicine; Institute for Clinical and Experimental Medicine; Prague Czech Republic
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15
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Díaz-Molina B, Diaz-Bulnes P, Carvajal Palao R, Bernardo MJ, Rodriguez RM, Corte-Iglesias V, Moris de la Tassa C, Lambert JL, Suarez-Alvarez B. Early Everolimus Initiation Fails to Counteract the Cytotoxic Response Mediated by CD8 + T and NK Cells in Heart Transplant Patients. Front Immunol 2018; 9:2181. [PMID: 30319636 PMCID: PMC6168668 DOI: 10.3389/fimmu.2018.02181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/04/2018] [Indexed: 12/22/2022] Open
Abstract
The positive long-term effects of conversion to everolimus (EVL) after heart transplantation (HT) have been evaluated in several studies. However, the timing of EVL initiation, the best way to combine it with other immunosuppressive treatments, and the impact of these combinations on the immune response are poorly understood aspects. Here, we analyzed the immune phenotype and function of HT patients (n = 56) at short and long terms (prospective and retrospective cohorts), taking into account the time of EVL initiation: early (3 months post-transplant, EVL-E group) or late (>1 year post-transplant, EVL-L group) compared with mycophenolate mofetil treatment (MMF group). We show that early EVL conversion from MMF allows the increase of cytotoxic (CD56dim CD16+) NK and effector-memory (EM, CD45RA− CCR7−) CD8+ T cell subsets, which show a significantly higher level of expression of cytotoxic molecules, IFN-γ production and degranulation ability under activation. NK cell expansion is accompanied by an altered balance of receptor expression, increasing the activation state, and lytic activity of those cells. Those changes are detected after as little as 1 month after EVL conversion in association with the expansion of regulatory T cells and the decrease in B cell frequency. However, no changes in the immune cells subsets were observed after late EVL initiation (EVL-L) compared with the MMF group. Our results imply that only early EVL conversion induces key changes in the post-transplant immune response, preserving an efficient anti-viral response, but simultaneously showing a limited ability to counteract the cytotoxic response to the allograft.
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Affiliation(s)
- Beatriz Díaz-Molina
- Advanced Heart Failure and Transplant Service, Department of Cardiology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Paula Diaz-Bulnes
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Reyes Carvajal Palao
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Maria José Bernardo
- Advanced Heart Failure and Transplant Service, Department of Cardiology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ramón M Rodriguez
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Viviana Corte-Iglesias
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Jose Luis Lambert
- Advanced Heart Failure and Transplant Service, Department of Cardiology, Hospital Universitario Central de Asturias, Oviedo, Spain.,Faculty of Health Sciences, Universidad Católica San Antonio de Murcia, Murcia, Spain
| | - Beatriz Suarez-Alvarez
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
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16
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Watanabe K, Karimpour-Fard A, Michael A, Miyamoto SD, Nakano SJ. Elevated serum vascular endothelial growth factor and development of cardiac allograft vasculopathy in children. J Heart Lung Transplant 2018; 37:1075-1082. [PMID: 29954686 PMCID: PMC6261433 DOI: 10.1016/j.healun.2018.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/19/2018] [Accepted: 04/25/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Cardiac allograft vasculopathy (CAV) is a leading cause of retransplantation and death in pediatric heart transplant recipients. Our aim was to evaluate the association between serum vascular endothelial growth factor-A (VEGF) and CAV development in the pediatric heart transplant population. METHODS In this retrospective study performed at a university hospital, VEGF concentrations were measured by enzyme-linked immunosorbent assay in banked serum from pediatric heart transplant recipients undergoing routine cardiac catheterization. In subjects with CAV (n = 29), samples were obtained at 2 time-points: before CAV diagnosis (pre-CAV) and at the time of initial CAV diagnosis (CAV). In subjects without CAV (no-CAV, n = 16), only 1 time-point was used. VEGF concentrations (n = 74) were assayed in duplicate. RESULTS Serum VEGF is elevated in pediatric heart transplant recipients before catheter-based diagnosis of CAV (no-CAV mean: 144.0 ± 89.05 pg/ml; pre-CAV mean: 316.2 ± 118.3 pg/ml; p = 0.0002). Receiver-operating characteristic curve analysis of pre-CAV VEGF levels demonstrated an area under the curve of 87.7% (p = 0.0002), with a VEGF level of 226.3 pg/ml predicting CAV development with 77.8% sensitivity and 91.7% specificity. VEGF is similarly elevated in subjects with angiographically diagnosed CAV and in those with normal angiography but intravascular ultrasound (IVUS) evidence of CAV. CONCLUSIONS The increase in serum VEGF before onset of detectable CAV is fundamental to its utility as a predictive biomarker and suggests further investigations of VEGF in the pathogenesis of CAV are warranted in the pediatric heart transplant population.
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Affiliation(s)
- Kae Watanabe
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA
| | - Anis Karimpour-Fard
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alix Michael
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA
| | - Shelley D Miyamoto
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA
| | - Stephanie J Nakano
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA.
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17
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Peters FS, Peeters AMA, Mandaviya PR, van Meurs JBJ, Hofland LJ, van de Wetering J, Betjes MGH, Baan CC, Boer K. Differentially methylated regions in T cells identify kidney transplant patients at risk for de novo skin cancer. Clin Epigenetics 2018; 10:81. [PMID: 29946375 PMCID: PMC6006560 DOI: 10.1186/s13148-018-0519-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/11/2018] [Indexed: 01/08/2023] Open
Abstract
Background Cutaneous squamous cell carcinoma (cSCC) occurs 65–200 times more in immunosuppressed organ transplant patients than in the general population. T cells, which are targeted by the given immunosuppressive drugs, are involved in anti-tumor immune surveillance and are functionally regulated by DNA methylation. Prior to kidney transplantation, we aim to discover differentially methylated regions (DMRs) in T cells involved in de novo post-transplant cSCC development. Methods We matched 27 kidney transplant patients with a future de novo cSCC after transplantation to 27 kidney transplant patients without cSCC and studied genome-wide DNA methylation of T cells prior to transplantation. From 11 out of the 27 cSCC patients, the DNA methylation of T cells after transplantation was also examined to assess stability of the observed differences in DNA methylation. Raw methylation values obtained with the 450k array were confirmed with pyrosequencing. Results We found 16 DMRs between patients with a future cSCC and those who do not develop this complication after transplantation. The majority of the DMRs were located in regulatory genomic regions such as flanking bivalent transcription start sites and bivalent enhancer regions, and most of the DMRs contained CpG islands. Examples of genes annotated to the DMRs are ZNF577, coding for a zinc-finger protein, and FLOT1, coding for a protein involved in T cell migration. The longitudinal analysis revealed that DNA methylation of 9 DMRs changed significantly after transplantation. DNA methylation of 5 out of 16 DMRs was relatively stable, with a variation in beta-value lower than 0.05 for at least 50% of the CpG sites within that region. Conclusions This is the first study demonstrating that DNA methylation of T cells from patients with a future de novo post-transplant cSCC is different from patients without cSCC. These results were obtained before transplantation, a clinically relevant time point for cSCC risk assessment. Several DNA methylation profiles remained relatively stable after transplantation, concluding that these are minimally affected by the transplantation and possibly have a lasting effect on post-transplant cSCC development. Electronic supplementary material The online version of this article (10.1186/s13148-018-0519-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fleur S Peters
- 1Neprology and Transplantation, Department of Internal Medicine, Rotterdam Transplant Group, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemiek M A Peeters
- 1Neprology and Transplantation, Department of Internal Medicine, Rotterdam Transplant Group, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pooja R Mandaviya
- 2Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce B J van Meurs
- 2Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leo J Hofland
- 3Endocrinology, Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jacqueline van de Wetering
- 1Neprology and Transplantation, Department of Internal Medicine, Rotterdam Transplant Group, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michiel G H Betjes
- 1Neprology and Transplantation, Department of Internal Medicine, Rotterdam Transplant Group, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carla C Baan
- 1Neprology and Transplantation, Department of Internal Medicine, Rotterdam Transplant Group, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karin Boer
- 1Neprology and Transplantation, Department of Internal Medicine, Rotterdam Transplant Group, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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18
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Peters FS, Peeters AMA, Hofland LJ, Betjes MGH, Boer K, Baan CC. Interferon-Gamma DNA Methylation Is Affected by Mycophenolic Acid but Not by Tacrolimus after T-Cell Activation. Front Immunol 2017; 8:822. [PMID: 28747916 PMCID: PMC5506181 DOI: 10.3389/fimmu.2017.00822] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/29/2017] [Indexed: 12/20/2022] Open
Abstract
Immunosuppressive drug therapy is required to treat patients with autoimmune disease and patients who have undergone organ transplantation. The main targets of the immunosuppressive drugs tacrolimus and mycophenolic acid (MPA; the active metabolite of mycophenolate mofetil) are T cells. It is currently unknown whether these immunosuppressive drugs have an effect on DNA methylation—an epigenetic regulator of cellular function. Here, we determined the effect of tacrolimus and MPA on DNA methylation of the gene promoter region of interferon gamma (IFNγ), a pro-inflammatory cytokine. Total T cells, naive T cells (CCR7+CD45RO−), and memory T cells (CD45RO+ and CCR7−CD45RO−) were isolated from CMV seropositive healthy controls and stimulated with α-CD3/CD28 in the presence or absence of tacrolimus or MPA. DNA methylation of the IFNγ promoter region was quantified by pyrosequencing at 4 h, days 1, 3, and 4 after stimulation. In parallel, T-cell differentiation, and IFNγ protein production were analyzed by flow cytometry at days 1 and 3 after stimulation. Our results show that MPA induced changes in IFNγ DNA methylation of naive T cells; MPA counteracted the decrease in methylation after stimulation. Tacrolimus did not affect IFNγ DNA methylation of naive T cells. In the memory T cells, both immunosuppressive drugs did not affect IFNγ DNA methylation. Differentiation of naive T cells into a central-memory-like phenotype (CD45RO+) was inhibited by both immunosuppressive drugs, while differentiation of memory T cells remained unaffected by both MPA and tacrolimus. IFNγ protein production was suppressed by tacrolimus. Our results demonstrate that MPA influenced IFNγ DNA methylation of naive T cells after stimulation of T cells, while tacrolimus had no effect. Both tacrolimus and MPA did not affect IFNγ DNA methylation of memory T cells.
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Affiliation(s)
- Fleur S Peters
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Annemiek M A Peeters
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Leo J Hofland
- Endocrinology, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Michiel G H Betjes
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Karin Boer
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
| | - Carla C Baan
- Nephrology and Transplantation, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Erasmus MC, Rotterdam, Netherlands
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19
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Boer K, de Wit LEA, Peters FS, Hesselink DA, Hofland LJ, Betjes MGH, Looman CWN, Baan CC. Variations in DNA methylation of interferon gamma and programmed death 1 in allograft rejection after kidney transplantation. Clin Epigenetics 2016; 8:116. [PMID: 27891189 PMCID: PMC5112717 DOI: 10.1186/s13148-016-0288-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/08/2016] [Indexed: 02/07/2023] Open
Abstract
Background The role of DNA methylation in the regulation of the anti-donor-directed immune response after organ transplantation is unknown. Here, we studied the methylation of two mediators of the immune response: the pro-inflammatory cytokine interferon γ (IFNγ) and the inhibitory receptor programmed death 1 (PD1) in naïve and memory CD8+ T cell subsets in kidney transplant recipients receiving immunosuppressive medication. Both recipients experiencing an episode of acute allograft rejection (rejectors) as well as recipients without rejection (non-rejectors) were included. Results CpGs in the promoter regions of both IFNγ and PD1 were significantly (p < 0.001) higher methylated in the naïve CD8+ T cells compared to the memory T cell subsets. The methylation status of both IFNγ and PD1 inversely correlated with the percentage of IFNγ or PD1-producing cells. Before transplantation, the methylation status of both IFNγ and PD1 was not significantly different from healthy donors. At 3 months after transplantation, irrespective of rejection and subsequent anti-rejection therapy, the IFNy methylation was significantly higher in the differentiated effector memory CD45RA+ (EMRA) CD8+ T cells (p = 0.01) whereas the PD1 methylation was significantly higher in all memory CD8+ T cell subsets (CD27+ memory; p = 0.02: CD27− memory; p = 0.02: EMRA; p = 0.002). Comparing the increase in methylation in the first 3 months after transplantation between rejectors and non-rejectors demonstrated a significantly more prominent increase in the PD1 methylation in the CD27− memory CD8+ T cells in rejectors (increase in rejectors 14%, increase in non-rejectors 1.9%, p = 0.04). The increase in DNA methylation in the other memory CD8+ T cells was not significantly different between rejectors and non-rejectors. At 12 months after transplantation, the methylation of both IFNγ and PD1 returned to baseline levels. Conclusions The DNA methylation of both IFNγ and PD1 increases the first 3 months after transplantation in memory CD8+ T cells in kidney transplant recipients. This increase was irrespective of a rejection episode indicating that general factors of the kidney transplantation procedure, including the use of immunosuppressive medication, contribute to these variations in DNA methylation.
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Affiliation(s)
- Karin Boer
- Department of Internal Medicine, Section Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na520, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - L Elly A de Wit
- Department of Internal Medicine, Section Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na520, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Fleur S Peters
- Department of Internal Medicine, Section Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na520, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Dennis A Hesselink
- Department of Internal Medicine, Section Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na520, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Leo J Hofland
- Department of Internal Medicine, Section Endocrinology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michiel G H Betjes
- Department of Internal Medicine, Section Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na520, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Caspar W N Looman
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carla C Baan
- Department of Internal Medicine, Section Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na520, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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