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Zhang H, Haun RS, Collin F, Cassol C, Napier JOH, Wilson J, Hassen S, Ararat K, Boils C, Messias N, Caza TN, Cossey LN, Sharma S, Ambruzs JM, Agrawal N, Shekhtman G, Tian W, Srinivas T, Qu K, Woodward RN, Larsen CP, Stone S, Coley SM. Development and Validation of a Multiclass Model Defining Molecular Archetypes of Kidney Transplant Rejection: A Large Cohort Study of the Banff Human Organ Transplant Gene Expression Panel. J Transl Med 2024; 104:100304. [PMID: 38092179 DOI: 10.1016/j.labinv.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/19/2023] [Accepted: 12/06/2023] [Indexed: 01/15/2024] Open
Abstract
Gene expression profiling from formalin-fixed paraffin-embedded (FFPE) renal allograft biopsies is a promising approach for feasibly providing a molecular diagnosis of rejection. However, large-scale studies evaluating the performance of models using NanoString platform data to define molecular archetypes of rejection are lacking. We tested a diverse retrospective cohort of over 1400 FFPE biopsy specimens, rescored according to Banff 2019 criteria and representing 10 of 11 United Network of Organ Sharing regions, using the Banff Human Organ Transplant panel from NanoString and developed a multiclass model from the gene expression data to assign relative probabilities of 4 molecular archetypes: No Rejection, Antibody-Mediated Rejection, T Cell-Mediated Rejection, and Mixed Rejection. Using Least Absolute Shrinkage and Selection Operator regularized regression with 10-fold cross-validation fitted to 1050 biopsies in the discovery cohort and technically validated on an additional 345 biopsies, our model achieved overall accuracy of 85% in the discovery cohort and 80% in the validation cohort, with ≥75% positive predictive value for each class, except for the Mixed Rejection class in the validation cohort (positive predictive value, 53%). This study represents the technical validation of the first model built from a large and diverse sample of diagnostic FFPE biopsy specimens to define and classify molecular archetypes of histologically defined diagnoses as derived from Banff Human Organ Transplant panel gene expression profiling data.
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Affiliation(s)
| | | | | | | | | | - Jon Wilson
- Arkana Laboratories, Little Rock, Arkansas
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The Molecular Diagnosis Might Be Clinically Useful in Discrepant Kidney Allograft Biopsy Findings: An Analysis of Clinical Outcomes. Transplantation 2023; 107:485-494. [PMID: 36117252 PMCID: PMC9875837 DOI: 10.1097/tp.0000000000004284] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The Molecular Microscope Diagnostic System (MMDx) may overcome histology shortcomings. Previous studies have simply examined discrepant findings but have not attempted to determine clinical endpoints. To measure performance, clinical outcomes are strongly required. METHODS This single-center cohort study described discrepancies between MMDx and histology from 51 kidney transplant recipients (KTRs) and analyzed 72 indication biopsies, including 21 follow-up biopsies. Clinical performance was assessed by a combined endpoint of graft failure, rejection on follow-up biopsy, de novo donor-specific antibody, and improvement of kidney allograft function upon antirejection treatment. RESULTS MMDx agreed in 33 (65%) and differed in 18 (35%) of 51 KTRs. Most discrepancies occurred in biopsies called no rejection by MMDx and rejection by histology (15/24, 63%). In contrast, in biopsies called rejection by MMDx, 3 were classified as no rejection by histology (3/27, 11%). Discrepant findings between MMDx and histology occurred following delayed graft function and MMDx from biopsies with a low percentage of cortex. Among 15 biopsies classified as no rejection by MMDx but rejection by histology, the clinical course suggested no rejection in 9 cases. Six KTRs reached the endpoint, showing predominant t ≥ 2 lesions. CONCLUSIONS The most often occurring discrepancy is rejection by histology but no rejection by MMDx. As more KTRs do not meet the combined endpoint for rejection, MMDx might be clinically useful in these discrepant cases. Although strong histological findings have priority in indicating the treatment, clinical implementation of MMDx could strengthen treatment strategies.
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Udomkarnjananun S, Francke MI, Dieterich M, van de Velde D, Verhoeven JGHP, Boer K, Clahsen-Van Groningen MC, De Winter BCM, Baan CC, Hesselink DA. Association Between the Intracellular Tacrolimus Concentration in CD3 + T Lymphocytes and CD14 + Monocytes and Acute Kidney Transplant Rejection. Ther Drug Monit 2022; 44:625-632. [PMID: 35358111 DOI: 10.1097/ftd.0000000000000982] [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: 12/20/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Intracellular tacrolimus concentration in peripheral blood mononuclear cells (PBMCs) (TAC [PBMC] ) has been proposed to better represent its active concentration than its whole blood concentration. As tacrolimus acts on T lymphocytes and other white blood cells, including monocytes, we investigated the association of tacrolimus concentration in CD3 + T lymphocytes (TAC [CD3] ) and CD14 + monocytes (TAC [CD14] ) with acute rejection after kidney transplantation. METHODS From a total of 61 samples in this case-control study, 28 samples were obtained during biopsy-proven acute rejection (rejection group), and 33 samples were obtained in the absence of rejection (control group). PBMCs were collected from both cryopreserved (retrospectively) and freshly obtained (prospectively) samples. CD3 + T lymphocytes and CD14 + monocytes were isolated from PBMCs, and their intracellular tacrolimus concentrations were measured. RESULTS The correlation between tacrolimus whole-blood and intracellular concentrations was poor. TAC [CD3] was significantly lower than TAC [CD14] (median 12.8 versus 81.6 pg/million cells; P < 0.001). No difference in TAC [PBMC] (48.5 versus 44.4 pg/million cells; P = 0.82), TAC [CD3] (13.4 versus 12.5 pg/million cells; P = 0.28), and TAC [CD14] (90.0 versus 72.8 pg/million cells; P = 0.27) was found between the rejection and control groups. However, freshly isolated PBMCs showed significantly higher TAC [PBMC] than PBMCs from cryopreserved samples. Subgroup analysis of intracellular tacrolimus concentrations from freshly isolated cells did not show a difference between rejectors and nonrejectors. CONCLUSIONS Differences in TAC [CD3] and TAC [CD14] between patients with and without rejection could not be demonstrated. However, further optimization of the cell isolation process is required because a difference in TAC [PBMC] between fresh and cryopreserved cells was observed. These results need to be confirmed in a study with a larger number of patients.
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Affiliation(s)
- Suwasin Udomkarnjananun
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Marith I Francke
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Marjolein Dieterich
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Daan van de Velde
- Department of Hospital Pharmacy, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; and
| | - Jeroen G H P Verhoeven
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Karin Boer
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Marian C Clahsen-Van Groningen
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Brenda C M De Winter
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
- Department of Hospital Pharmacy, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; and
| | - Carla C Baan
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Dennis A Hesselink
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Rotterdam, the Netherlands
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Zhou H, Lu H, Sun L, Wang Z, Zheng M, Hang Z, Zhang D, Tan R, Gu M. Diagnostic Biomarkers and Immune Infiltration in Patients With T Cell-Mediated Rejection After Kidney Transplantation. Front Immunol 2022; 12:774321. [PMID: 35058922 PMCID: PMC8764245 DOI: 10.3389/fimmu.2021.774321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
T cell-mediated rejection (TCMR) is an important rejection type in kidney transplantation, characterized by T cells and macrophages infiltration. The application of bioinformatic analysis in genomic research has been widely used. In the present study, Microarray data was analyzed to identify the potential diagnostic markers of TCMR in kidney transplantation. Cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT) was performed to determine the distribution of immune cell infiltration in the pathology. Totally 129 upregulated differently expressed genes (DEGs) and 378 downregulated DEGs were identified. The GO and KEGG results demonstrated that DEGs were mainly associated with pathways and diseases involved in immune response. The intersection of the two algorithms (PPI network and LASSO) contains three overlapping genes (CXCR6, CXCL13 and FCGR1A). After verification in GSE69677, only CXCR6 and CXCL13 were selected. Immune cells Infiltration analysis demonstrated that CXCR6 and CXCL13 were positively correlated with gamma delta T cells (p < 0.001), CD4+ memory activated T cells (p < 0.001), CD8+ T cells (p < 0.001) and M1 macrophages (p = 0.006), and negatively correlated with M2 macrophages (p < 0.001) and regulatory T cells (p < 0.001). Immunohistochemical staining and image analysis confirmed the overexpression of CXCR6 and CXCL13 in human allograft TCMR samples. CXCR6 and CXCL13 could be diagnostic biomarkers of TCMR and potential targets for immunotherapy in patients with TCMR.
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Affiliation(s)
- Hai Zhou
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongcheng Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Zheng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhou Hang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dongliang Zhang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Gu
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Zhuang Q, Li H, Peng B, Liu Y, Zhang Y, Cai H, Liu S, Ming Y. Single-Cell Transcriptomic Analysis of Peripheral Blood Reveals a Novel B-Cell Subset in Renal Allograft Recipients With Accommodation. Front Pharmacol 2021; 12:706580. [PMID: 34658852 PMCID: PMC8514638 DOI: 10.3389/fphar.2021.706580] [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: 05/07/2021] [Accepted: 08/13/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Kidney transplantation (KTx) is a preeminent treatment for end-stage renal disease (ESRD). After the application of immunosuppressants (IS), renal allograft recipients could reach a state called accommodation which means they are neither rejected nor infected. This study aimed to describe the details of this immune accommodation and reveal a novel mechanism of IS on immune cell subpopulations. Methods: We analyzed multiple cell subgroups and their gene expression of peripheral T, B, myeloid, and NK cells from renal allograft recipients with accommodation and healthy control (HC) by single-cell transcriptomics sequencing (scRNA-seq) and flow cytometry. Results: A total of 8,272 cells were isolated and sequenced from three individuals, including 2,758 cells from HC, 2,550 cells from ESRD patient, and 2,964 cells from KTx patient, as well as 396 immune response–related genes were detected during sequencing. 5 T-cell, 4 NK-cell, 5 myeloid, and 4 B-cell clusters were defined. Among them, a B-cell subset (CD19+IGLC3lowIGKChighTCL1A-CD127+) of renal transplant recipients with accommodation was significantly lower than that of HC and verified by flow cytometry, and this B-cell subset showed an activated potential because of its high expression of CD127. Furthermore, we found that IL32 might be the key cytokine to induce the differentiation of this B-cell cluster. Conclusion: We found a novel B-cell subset (CD19+IGLC3lowIGKChighTCL1A-CD127+) which was inhibited and decreased in renal allograft recipients with accommodation. This study might reveal the effect of commonly used IS in clinical practice on B-cell subsets and related mechanism.
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Affiliation(s)
- Quan Zhuang
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China.,Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
| | - Hao Li
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Bo Peng
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China.,Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
| | - Yang Liu
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ying Zhang
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Haozheng Cai
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shu Liu
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China.,Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
| | - Yingzi Ming
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China.,Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
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Shi H, Gong Y, Liang Q, Li J, Xiang Y, Li G. Target-Initiated Great Change in Electrochemical Steric Hindrance for an Assay of Granzyme B Activity. Anal Chem 2021; 93:13382-13388. [PMID: 34549940 DOI: 10.1021/acs.analchem.1c03188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
To improve long-term graft patient outcomes and develop more effective antirejection therapies, noninvasive monitoring of acute cellular rejection (ACR) after organ transplantation is urgently needed. As a biomarker of ACR, Granzyme B (GrB) is expected to be applied in the noninvasive monitoring of ACR. Herein, we have developed a method for detecting the GrB activity based on the target-initiated great change in electrochemical steric hindrance by designing a nanoprobe. The nanoprobe is prepared by conjugating a specific peptide, which is responsive to GrB cleavage activity, to gold nanoparticles (AuNPs). Meanwhile, a piece of DNA sequence with G-quadruplex (G4) is attached at the distal end of the peptide. Upon exposure to GrB, the peptide substrate is cleaved to eliminate the steric hindrance between inter-nanoprobes as well as nanoprobe and DNA tetrahedron (TDN), allowing the released DNA strand to hybridize with TDN, giving sensitive signal output. The method can also be used to detect GrB activity in complex biological settings, so it has a great potential for monitoring GrB activity in the blood or urine of graft patients.
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Affiliation(s)
- Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Youjing Gong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Qizhi Liang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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Chronic-active Antibody-mediated Rejection: To Belatacept or Not, That Is the HOT Question. Transplantation 2021; 105:478-479. [PMID: 32732617 DOI: 10.1097/tp.0000000000003279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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The Use of Molecular Techniques to Distinguish BK Nephropathy from Acute Rejection - Close but not Quite. Transplantation 2021; 105:2346-2347. [PMID: 34288637 DOI: 10.1097/tp.0000000000003885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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