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Ettenger RB, Seifert ME, Blydt-Hansen T, Briscoe DM, Holman J, Weng PL, Srivastava R, Fleming J, Malekzadeh M, Pearl M. Detection of Subclinical Rejection in Pediatric Kidney Transplantation: Current and Future Practices. Pediatr Transplant 2024; 28:e14836. [PMID: 39147695 DOI: 10.1111/petr.14836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024]
Abstract
INTRODUCTION The successes in the field of pediatric kidney transplantation over the past 60 years have been extraordinary. Year over year, there have been significant improvements in short-term graft survival. However, improvements in longer-term outcomes have been much less apparent. One important contributor has been the phenomenon of low-level rejection in the absence of clinical manifestations-so-called subclinical rejection (SCR). METHODS Traditionally, rejection has been diagnosed by changes in clinical parameters, including but not limited to serum creatinine and proteinuria. This review examines the shortcomings of this approach, the effects of SCR on kidney allograft outcome, the benefits and drawbacks of surveillance biopsies to identify SCR, and new urine and blood biomarkers that define the presence or absence of SCR. RESULTS Serum creatinine is an unreliable index of SCR. Surveillance biopsies are the method most utilized to detect SCR. However, these have significant drawbacks. New biomarkers show promise. These biomarkers include blood gene expression profiles and donor derived-cell free DNA; urine gene expression profiles; urinary cytokines, chemokines, and metabolomics; and other promising blood and urine tests. CONCLUSION Specific emphasis is placed on studies carried out in pediatric kidney transplant recipients. TRIAL REGISTRATION ClinicalTrials.gov: NCT03719339.
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Affiliation(s)
- Robert B Ettenger
- Division of Nephrology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Michael E Seifert
- Division of Pediatric Nephrology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tom Blydt-Hansen
- Multi-Organ Transplant Program, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - David M Briscoe
- Division of Nephrology, Department of Pediatrics Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John Holman
- Transplant Genomics Inc., Framingham, Massachusetts, USA
| | - Patricia L Weng
- Division of Nephrology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Rachana Srivastava
- Division of Nephrology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - James Fleming
- Transplant Genomics Inc., Framingham, Massachusetts, USA
| | - Mohammed Malekzadeh
- Division of Nephrology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Meghan Pearl
- Division of Nephrology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Falahat P, Scheidt U, Pörner D, Schwab S. Recent Insights in Noninvasive Diagnostic for the Assessment of Kidney and Cardiovascular Outcome in Kidney Transplant Recipients. J Clin Med 2024; 13:3778. [PMID: 38999343 PMCID: PMC11242869 DOI: 10.3390/jcm13133778] [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: 06/17/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Kidney transplantation improves quality of life and prolongs survival of patients with end-stage kidney disease. However, kidney transplant recipients present a higher risk for cardiovascular events compared to the general population. Risk assessment for graft failure as well as cardiovascular events is still based on invasive procedures. Biomarkers in blood and urine, but also new diagnostic approaches like genetic or molecular testing, can be useful tools to monitor graft function and to identify patients of high cardiovascular risk. Many biomarkers have been introduced, whereas most of these biomarkers have not been implemented in clinical routine. Here, we discuss recent developments in biomarkers and diagnostic models in kidney transplant recipients. Because many factors impact graft function and cardiovascular risk, it is most likely that no biomarker will meet the highest demands and standards. We advocate to shift focus to the identification of patients benefitting from molecular and genetic testing as well as from analysis of more specific biomarkers instead of finding one biomarker fitting to all patients.
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Affiliation(s)
- Peyman Falahat
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| | - Uta Scheidt
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| | - Daniel Pörner
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| | - Sebastian Schwab
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
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Masset C, Danger R, Degauque N, Dantal J, Giral M, Brouard S. Blood Gene Signature as a Biomarker for Subclinical Kidney Allograft Rejection: Where Are We? Transplantation 2024:00007890-990000000-00787. [PMID: 38867352 DOI: 10.1097/tp.0000000000005105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The observation decades ago that inflammatory injuries because of an alloimmune response might be present even in the absence of concomitant clinical impairment in allograft function conduced to the later definition of subclinical rejection. Many studies have investigated the different subclinical rejections defined according to the Banff classification (subclinical T cell-mediated rejection and antibody-mediated rejection), overall concluding that these episodes worsened long-term allograft function and survival. These observations led several transplant teams to perform systematic protocolar biopsies to anticipate treatment of rejection episodes and possibly prevent allograft loss. Paradoxically, the invasive characteristics and associated logistics of such procedures paved the way to investigate noninvasive biomarkers (urine and blood) of subclinical rejection. Among them, several research teams proposed a blood gene signature developed from cohort studies, most of which achieved excellent predictive values for the occurrence of subclinical rejection, mainly antibody-mediated rejection. Interestingly, although all identified genes relate to immune subsets and pathways involved in rejection pathophysiology, very few transcripts are shared among these sets of genes, highlighting the heterogenicity of such episodes and the difficult but mandatory need for external validation of such tools. Beyond this, their application and value in clinical practice remain to be definitively demonstrated in both biopsy avoidance and prevention of clinical rejection episodes. Their combination with other biomarkers, either epidemiological or biological, could contribute to a more accurate picture of a patient's risk of rejection and guide clinicians in the follow-up of kidney transplant recipients.
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Affiliation(s)
- Christophe Masset
- Institut de Transplantation-Urologie-Néphrologie (ITUN), Nantes University Hospital, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Richard Danger
- Institut de Transplantation-Urologie-Néphrologie (ITUN), Nantes University Hospital, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nicolas Degauque
- Institut de Transplantation-Urologie-Néphrologie (ITUN), Nantes University Hospital, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Jacques Dantal
- Institut de Transplantation-Urologie-Néphrologie (ITUN), Nantes University Hospital, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Magali Giral
- Institut de Transplantation-Urologie-Néphrologie (ITUN), Nantes University Hospital, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Sophie Brouard
- Institut de Transplantation-Urologie-Néphrologie (ITUN), Nantes University Hospital, Nantes, France
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, Nantes, France
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Laroche C, Engen RM. Immune monitoring in pediatric kidney transplant. Pediatr Transplant 2024; 28:e14785. [PMID: 38766986 DOI: 10.1111/petr.14785] [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: 03/09/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Long-term outcomes in pediatric kidney transplantation remain suboptimal, largely related to chronic rejection. Creatinine is a late marker of renal injury, and more sensitive, early markers of allograft injury are an active area of current research. METHODS This is an educational review summarizing existing strategies for monitoring for rejection in kidney transplant recipients. RESULTS We summarize supporting currently available clinical tests, including surveillance biopsy, donor specific antibodies, and donor-derived cell free DNA, as well as the potential limitations of these studies. In addition, we review the current avenues of active research, including transcriptomics, proteomics, metabolomics, and torque tenovirus levels. CONCLUSION Advancing the use of noninvasive immune monitoring will depend on well-designed multicenter trials that include patients with stable graft function, include biopsy results on all patients, and can demonstrate both association with a patient-relevant clinical endpoint such as graft survival or change in glomerular filtration rate and a potential timepoint for intervention.
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Affiliation(s)
| | - Rachel M Engen
- University of Wisconsin Madison, Madison, Wisconsin, USA
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Huang CF, Su P, Fisher TD, Levitsky J, Kelleher NL, Forte E. Mass spectrometry-based proteomics for advancing solid organ transplantation research. FRONTIERS IN TRANSPLANTATION 2023; 2:1286881. [PMID: 38993855 PMCID: PMC11235370 DOI: 10.3389/frtra.2023.1286881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/13/2023] [Indexed: 07/13/2024]
Abstract
Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called "bottom-up" proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, "Top-down" proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.
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Affiliation(s)
- Che-Fan Huang
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Pei Su
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Troy D. Fisher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Comprehensive Transplant Center Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
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6
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Chancharoenthana W, Traitanon O, Leelahavanichkul A, Tasanarong A. Molecular immune monitoring in kidney transplant rejection: a state-of-the-art review. Front Immunol 2023; 14:1206929. [PMID: 37675106 PMCID: PMC10477600 DOI: 10.3389/fimmu.2023.1206929] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Although current regimens of immunosuppressive drugs are effective in renal transplant recipients, long-term renal allograft outcomes remain suboptimal. For many years, the diagnosis of renal allograft rejection and of several causes of renal allograft dysfunction, such as chronic subclinical inflammation and infection, was mostly based on renal allograft biopsy, which is not only invasive but also possibly performed too late for proper management. In addition, certain allograft dysfunctions are difficult to differentiate from renal histology due to their similar pathogenesis and immune responses. As such, non-invasive assays and biomarkers may be more beneficial than conventional renal biopsy for enhancing graft survival and optimizing immunosuppressive drug regimens during long-term care. This paper discusses recent biomarker candidates, including donor-derived cell-free DNA, transcriptomics, microRNAs, exosomes (or other extracellular vesicles), urine chemokines, and nucleosomes, that show high potential for clinical use in determining the prognosis of long-term outcomes of kidney transplantation, along with their limitations.
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Affiliation(s)
- Wiwat Chancharoenthana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Tropical Immunology and Translational Research Unit (TITRU), Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Opas Traitanon
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Asada Leelahavanichkul
- Center of Excellence on Translational Research in Inflammation and Immunology (CETRII), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Adis Tasanarong
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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7
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Heilman RL, Fleming JN, Mai M, Smith B, Park WD, Holman J, Stegall MD. Multiple abnormal peripheral blood gene expression assay results are correlated with subsequent graft loss after kidney transplantation. Clin Transplant 2023; 37:e14987. [PMID: 37026820 DOI: 10.1111/ctr.14987] [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: 12/30/2022] [Revised: 03/16/2023] [Accepted: 03/26/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND The aim of this study was to correlate peripheral blood gene expression profile (GEP) results during the first post-transplant year with outcomes after kidney transplantation. METHODS We conducted a prospective, multicenter observational study of obtaining peripheral blood at five timepoints during the first post-transplant year to perform a GEP assay. The cohort was stratified based on the pattern of the peripheral blood GEP results: Tx-all GEP results normal, 1 Not-TX had one GEP result abnormal and >1 Not-TX two or more abnormal GEP results. We correlated the GEP results with outcomes after transplantation. RESULTS We enrolled 240 kidney transplant recipients. The cohort was stratified into the three groups: TX n = 117 (47%), 1 Not-TX n = 59 (25%) and >1 Not-TX n = 64 (27%). Compared to the TX group, the >1 Not-TX group had lower eGFR (p < .001) and more chronic changes on 1-year surveillance biopsy (p = .007). Death censored graft survival showed inferior graft survival in the >1 Not-TX group (p < .001) but not in the 1 Not-TX group. All graft losses in the >1 Not-TX group occurred after 1-year post-transplant. CONCLUSIONS We conclude that a pattern of persistently Not-TX GEP assay correlates with inferior graft survival.
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Affiliation(s)
| | - James N Fleming
- Medical Affairs, Transplant Genomics, Inc, Framingham, Massachusetts, USA
| | - Martin Mai
- Department of Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Byron Smith
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Walter D Park
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - John Holman
- Department of Surgery, University of Utah, Salt Lake City, Utah, USA
| | - Mark D Stegall
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
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Lima K, Ribas GT, Riella LV, Borges TJ. Inhibitory innate receptors and their potential role in transplantation. Transplant Rev (Orlando) 2023; 37:100776. [PMID: 37451057 DOI: 10.1016/j.trre.2023.100776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
The regulatory arm of the immune system plays a crucial role in maintaining immune tolerance and preventing excessive immune responses. Immune regulation comprises various regulatory cells and molecules that work together to suppress or regulate immune responses. The programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) are examples of inhibitory receptors that counteract activating signals and fine-tune immune responses. While most of the discoveries of immune regulation have been related to T cells and the adaptive immune system, the innate arm of the immune system also has a range of inhibitory receptors that can counteract activating signals and suppress the effector immune responses. Targeting these innate inhibitory receptors may provide a complementary therapeutic approach in several immune-related conditions, including transplantation. In this review, we will explore the potential role of innate inhibitory receptors in controlling alloimmunity during solid organ transplantation.
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Affiliation(s)
- Karina Lima
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Guilherme T Ribas
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Professional and Technological Education Sector, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Leonardo V Riella
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thiago J Borges
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Danger R, Le Berre L, Cadoux M, Kerleau C, Papuchon E, Mai HL, Nguyen TVH, Guérif P, Morelon E, Thaunat O, Legendre C, Anglicheau D, Lefaucheur C, Couzi L, Del Bello A, Kamar N, Le Quintrec M, Goutaudier V, Renaudin K, Giral M, Brouard S. Subclinical rejection-free diagnostic after kidney transplantation using blood gene expression. Kidney Int 2023; 103:1167-1179. [PMID: 36990211 DOI: 10.1016/j.kint.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/16/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023]
Abstract
We previously established a six-gene-based blood score associated with operational tolerance in kidney transplantation which was decreased in patients developing anti-HLA donor-specific antibodies (DSA). Herein, we aimed to confirm that this score is associated with immunological events and risk of rejection. We measured this using quantitative PCR (qPCR) and NanoString methods from an independent multicenter cohort of 588 kidney transplant recipients with paired blood samples and biopsies at one year after transplantation validating its association with pre-existing and de novo DSA. From 441 patients with protocol biopsy, there was a significant decrease of the score of tolerance in 45 patients with biopsy-proven subclinical rejection (SCR), a major threat associated with pejorative allograft outcomes that prompted an SCR score refinement. This refinement used only two genes, AKR1C3 and TCL1A, and four clinical parameters (previous experience of rejection, previous transplantation, sex of recipient and tacrolimus uptake). This refined SCR score was able to identify patients unlikely to develop SCR with a C-statistic of 0.864 and a negative predictive value of 98.3%. The SCR score was validated in an external laboratory, with two methods (qPCR and NanoString), and on 447 patients from an independent and multicenter cohort. Moreover, this score allowed reclassifying patients with discrepancies between the DSA presence and the histological diagnosis of antibody mediated rejection unlike kidney function. Thus, our refined SCR score could improve detection of SCR for closer and noninvasive monitoring, allowing early treatment of SCR lesions notably for patients DSA-positive and during lowering of immunosuppressive treatment.
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Affiliation(s)
- Richard Danger
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France.
| | - Ludmilla Le Berre
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France
| | - Marion Cadoux
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France
| | - Clarisse Kerleau
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France
| | - Emmanuelle Papuchon
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France; Centre d'Investigation Clinique en Biothérapie, Centre de Ressources Biologiques (CRB), CHU Nantes, Nantes, France
| | - Hoa Le Mai
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France
| | - Thi-Van-Ha Nguyen
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France
| | - Pierrick Guérif
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France
| | - Emmanuel Morelon
- Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital, Hospices Civils de Lyon, INSERM Unit 1111, Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Olivier Thaunat
- Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital, Hospices Civils de Lyon, INSERM Unit 1111, Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Christophe Legendre
- Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Institute, INSERM, Paris University, Paris, France
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Institute, INSERM, Paris University, Paris, France
| | - Carmen Lefaucheur
- Paris Translational Research Center for Organ Transplantation, INSERM UMR S970, Université Paris Cité, Kidney Transplant Department, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Lionel Couzi
- Department of Nephrology, Transplantation, Dialysis, and Apheresis, CHU Bordeaux, Bordeaux, France
| | - Arnaud Del Bello
- Department of Nephrology and Organ Transplantation, Centre Hospitalier Universitaire de Toulouse, INSERM UMR1291 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Nassim Kamar
- Department of Nephrology and Organ Transplantation, Centre Hospitalier Universitaire de Toulouse, INSERM UMR1291 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Moglie Le Quintrec
- Department of Nephrology, Dialysis and Renal Transplantation, University Hospital of Lapeyronie, Montpellier, France
| | - Valentin Goutaudier
- Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Institute, INSERM, Paris University, Paris, France; Université Paris Cité, INSERM U970, Paris Institute for Transplantation and Organ Regeneration, Paris, France
| | - Karine Renaudin
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France; CHU Nantes, Service d'Anatomie et Cytologie Pathologiques, Nantes, France
| | - Magali Giral
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France; Centre d'Investigation Clinique en Biothérapie, Centre de Ressources Biologiques (CRB), CHU Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes Université, Nantes, France
| | - Sophie Brouard
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology (CR2TI), UMR 1064, ITUN, Nantes, France; Centre d'Investigation Clinique en Biothérapie, Centre de Ressources Biologiques (CRB), CHU Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes Université, Nantes, France.
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10
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Huang E, Mengel M, Clahsen-van Groningen MC, Jackson AM. Diagnostic Potential of Minimally Invasive Biomarkers: A Biopsy-centered Viewpoint From the Banff Minimally Invasive Diagnostics Working Group. Transplantation 2023; 107:45-52. [PMID: 36508645 PMCID: PMC9746335 DOI: 10.1097/tp.0000000000004339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
With recent advances and commercial implementation of minimally invasive biomarkers in kidney transplantation, new strategies for the surveillance of allograft health are emerging. Blood and urine-based biomarkers can be used to detect the presence of rejection, but their applicability as diagnostic tests has not been studied. A Banff working group was recently formed to consider the potential of minimally invasive biomarkers for integration into the Banff classification for kidney allograft pathology. We review the existing data on donor-derived cell-free DNA, blood and urine transcriptomics, urinary protein chemokines, and next-generation diagnostics and conclude that the available data do not support their use as stand-alone diagnostic tests at this point. Future studies assessing their ability to distinguish complex phenotypes, differentiate T cell-mediated rejection from antibody-mediated rejection, and function as an adjunct to histology are needed to elevate these minimally invasive biomarkers from surveillance tests to diagnostic tests.
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Affiliation(s)
- Edmund Huang
- Division of Nephrology, Department of Medicine, Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Marian C. Clahsen-van Groningen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Institute of Experimental and Systems Biology, RWTH Aachen University, Aachen, Germany
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Vanhaverbeke M, Attard R, Bartekova M, Ben-Aicha S, Brandenburger T, de Gonzalo-Calvo D, Emanueli C, Farrugia R, Grillari J, Hackl M, Kalocayova B, Martelli F, Scholz M, Wettinger SB, Devaux Y. Peripheral blood RNA biomarkers for cardiovascular disease from bench to bedside: a position paper from the EU-CardioRNA COST action CA17129. Cardiovasc Res 2022; 118:3183-3197. [PMID: 34648023 PMCID: PMC9799060 DOI: 10.1093/cvr/cvab327] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/25/2023] Open
Abstract
Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners.
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Affiliation(s)
- Maarten Vanhaverbeke
- Department of Cardiovascular Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ritienne Attard
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Monika Bartekova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Dúbravská cesta 9, 84104 Bratislava, Slovakia
- Faculty of Medicine, Institute of Physiology, Comenius University, Sasinkova 2, 81372 Bratislava, Slovakia
| | - Soumaya Ben-Aicha
- Faculty of Medicine, Imperial College London, ICTEM Building, Du Cane Road, London W12 0NN, UK
| | - Timo Brandenburger
- Department of Anesthesiology, University Hospital Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Av. Alcalde Rovira Roure 80, 25198, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 28029, Madrid, Spain
| | - Costanza Emanueli
- Faculty of Medicine, Imperial College London, ICTEM Building, Du Cane Road, London W12 0NN, UK
| | - Rosienne Farrugia
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Johannes Grillari
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU - University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | | | - Barbora Kalocayova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Dúbravská cesta 9, 84104 Bratislava, Slovakia
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Milan 20097, Italy
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Stephanie Bezzina Wettinger
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, L-1445 Strassen, Luxembourg
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12
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Harrington C, Krishnan S, Mack CL, Cravedi P, Assis DN, Levitsky J. Noninvasive biomarkers for the diagnosis and management of autoimmune hepatitis. Hepatology 2022; 76:1862-1879. [PMID: 35611859 PMCID: PMC9796683 DOI: 10.1002/hep.32591] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/07/2023]
Abstract
Autoimmune hepatitis (AIH) is a rare disease of unclear etiology characterized by loss of self-tolerance that can lead to liver injury, cirrhosis, and acute liver failure. First-line treatment consists of systemic corticosteroids, or budesonide, and azathioprine, to which most patients are initially responsive, although predictors of response are lacking. Relapses are very common, correlate with histological activity despite normal serum transaminases, and increase hepatic fibrosis. Furthermore, current regimens lead to adverse effects and reduced quality of life, whereas medication titration is imprecise. Biomarkers that can predict the clinical course of disease, identify patients at elevated risk for relapse, and improve monitoring and medication dosing beyond current practice would have high clinical value. Herein, we review novel candidate biomarkers in adult and pediatric AIH based on prespecified criteria, including gene expression profiles, proteins, metabolites, and immune cell phenotypes in different stages of AIH. We also discuss biomarkers relevant to AIH from other immune diseases. We conclude with proposed future directions in which biomarker implementation into clinical practice could lead to advances in personalized therapeutic management of AIH.
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Affiliation(s)
- Claire Harrington
- Division of Gastroenterology & HepatologyNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Swathi Krishnan
- Medicine DepartmentYale School of MedicineNew HavenConnecticutUSA
| | - Cara L. Mack
- Section of Pediatric Gastroenterology, Hepatology & Nutrition, Children's Hospital ColoradoUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Paolo Cravedi
- Division of NephrologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - David N. Assis
- Section of Digestive DiseasesYale School of MedicineNew HavenConnecticutUSA
| | - Josh Levitsky
- Division of Gastroenterology & HepatologyNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
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13
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Hjortdal J, Griffin MD, Cadoux M, Armitage WJ, Bylesjo M, Gabhann PM, Murphy CC, Pleyer U, Tole D, Vabres B, Walkinshaw MD, Gourraud P, Karakachoff M, Brouard S, Degauque N. Peripheral blood immune cell profiling of acute corneal transplant rejection. Am J Transplant 2022; 22:2337-2347. [PMID: 35704290 PMCID: PMC9796948 DOI: 10.1111/ajt.17119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/17/2022] [Accepted: 06/09/2022] [Indexed: 01/25/2023]
Abstract
Acute rejection (AR) of corneal transplants (CT) has a profound effect on subsequent graft survival but detailed immunological studies in human CT recipients are lacking. In this multi-site, cross-sectional study, clinical details and blood samples were collected from adults with clinically diagnosed AR of full-thickness (FT)-CT (n = 35) and posterior lamellar (PL)-CT (n = 21) along with Stable CT recipients (n = 177) and adults with non-transplanted corneal disease (n = 40). For those with AR, additional samples were collected 3 months later. Immune cell analysis was performed by whole-genome microarrays (whole blood) and high-dimensional multi-color flow cytometry (peripheral blood mononuclear cells). For both, no activation signature was identified within the B cell and T cell repertoire at the time of AR diagnosis. Nonetheless, in FT- but not PL-CT recipients, AR was associated with differences in B cell maturity and regulatory CD4+ T cell frequency compared to stable allografts. These data suggest that circulating B cell and T cell subpopulations may provide insights into the regulation of anti-donor immune response in human CT recipients with differing AR risk. Our results suggest that, in contrast to solid organ transplants, genetic or cellular assays of peripheral blood are unlikely to be clinically exploitable for prediction or diagnosis of AR.
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Affiliation(s)
- Jesper Hjortdal
- Department of OphthalmologyAarhus University HospitalAarhusDenmark,Department of Clinical MedicineAarhus UniversityAarhusDenmark
| | - Matthew D. Griffin
- Regenerative Medicine Institute (REMEDI) at CÚRAM SFI Centre for Research in Medical DevicesSchool of Medicine, National University of Ireland GalwayGalwayIreland
| | - Marion Cadoux
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance
| | - W. John Armitage
- Translational Health SciencesUniversity of BristolBristolUK,Tissue and Eye ServicesNHS Blood and TransplantBristolUK
| | - Max Bylesjo
- Fios Genomics Ltd, Nine Edinburgh BioquarterEdinburghUK
| | | | - Conor C. Murphy
- Royal Victoria Eye and Ear HospitalDublinIreland,Royal College of Surgeons in Ireland University of Medicine and Health SciencesDublinIreland
| | - Uwe Pleyer
- Department of OphthalmologyCharité University HospitalBerlinGermany
| | - Derek Tole
- University Hospitals Bristol NHS Foundations TrustBristol Eye HospitalBristolUK
| | - Bertrand Vabres
- Nantes Université, CHU Nantes, Service OphtalmologieNantesFrance
| | - Malcolm D. Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Pierre‐Antoine Gourraud
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance,CHU de Nantes, INSERM, CIC 1413, Pôle Hospitalo‐Universitaire 11: Santé Publique, Clinique des donnéesNantesFrance
| | - Matilde Karakachoff
- CHU de Nantes, INSERM, CIC 1413, Pôle Hospitalo‐Universitaire 11: Santé Publique, Clinique des donnéesNantesFrance
| | - Sophie Brouard
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance
| | - Nicolas Degauque
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance
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14
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Alfaro R, Lorente S, Jimenez-Coll V, Martínez-Banaclocha H, Galián JA, Botella C, Moya-Quiles MR, Muro-Pérez M, de la Peña-Moral J, Minguela A, Legaz I, Muro M. Evaluating the Link between BAFF System Gene Expression and Acute Rejection Development in Kidney Transplantation. J Clin Med 2022; 11:jcm11143956. [PMID: 35887720 PMCID: PMC9319040 DOI: 10.3390/jcm11143956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
B-cell activating factor (BAFF) system signaling is critical for B-cell homeostasis, effector functions, and tolerance maintenance in transplants, but it has not been studied in kidney transplant recipients (KTRs). The aim was to analyze the changes in BAFF system expression in KTRs with/without acute rejection (AR/NAR). The BAFF system expression was analyzed by qPCR in 40 KTRs. A meta-analysis of BAFF system expression and histological renal damage was identified by the Chronic Allograft Damage Index (CADI) and performed from the GEO database. Proliferation-inducing ligand (APRIL) expression increased at three- and six-months post-KT (p = 0.014 and p < 0.001). B-cell maturation antigen (BCMA) expression increased at six-months post-KT (p = 0.038). BAFF expression remained stable in NAR-KTRs, but was increased in CADI concerning the No-CADI group at one year (p = 0.008). BCMA expression increased in the CADI group at one- (p = 0.001) and six-years post-KT (p = 0.024). At three months, the transmembrane activator and calcium modulator interactor (TACI) gene significantly elevated KTRs with DSAs (donor-specific antibody; p = 0.034). KTRs with DSAs significantly increase the B-cell activating factor receptor (R-BAFF; p = 0.021) and TACI (p = 0.018) between pre- and three-month post-KT. Changes in the expression of the BAFF system increase during post-KTR in the development of AR and chronic allograft damage, and could be an important pathological tool to detect and prevent kidney graft outcomes.
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Affiliation(s)
- Rafael Alfaro
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - Santiago Lorente
- Nephrology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain;
| | - Víctor Jimenez-Coll
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - Helios Martínez-Banaclocha
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - José Antonio Galián
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - Carmen Botella
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - María Rosa Moya-Quiles
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - Manuel Muro-Pérez
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - Jesús de la Peña-Moral
- Pathology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain;
| | - Alfredo Minguela
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
| | - Isabel Legaz
- Department of Legal and Forensic Medicine, Faculty of Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
- Correspondence: (I.L.); (M.M.)
| | - Manuel Muro
- Immunology Services, University Clinical Hospital, Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), 30100 Murcia, Spain; (R.A.); (V.J.-C.); (H.M.-B.); (J.A.G.); (C.B.); (M.R.M.-Q.); (M.M.-P.); (A.M.)
- Correspondence: (I.L.); (M.M.)
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15
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Biological pathways and comparison with biopsy signals and cellular origin of peripheral blood transcriptomic profiles during kidney allograft pathology. Kidney Int 2022; 102:183-195. [PMID: 35526671 PMCID: PMC9231008 DOI: 10.1016/j.kint.2022.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 01/04/2023]
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16
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Levitsky J, Kandpal M, Guo K, Zhao L, Kurian S, Whisenant T, Abecassis M. Prediction of Liver Transplant Rejection With a Biologically Relevant Gene Expression Signature. Transplantation 2022; 106:1004-1011. [PMID: 34342962 PMCID: PMC9301991 DOI: 10.1097/tp.0000000000003895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Accepted: 05/31/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Noninvasive biomarkers distinguishing early immune activation before acute rejection (AR) could more objectively inform immunosuppression management in liver transplant recipients (LTRs). We previously reported a genomic profile distinguishing LTR with AR versus stable graft function. This current study includes key phenotypes with other causes of graft dysfunction and uses a novel random forest approach to augment the specificity of predicting and diagnosing AR. METHODS Gene expression results in LTRs with AR versus non-AR (combination of other causes of graft dysfunction and normal function) were analyzed from single and multicenter cohorts. A 70:30 approach (61 ARs; 162 non-ARs) was used for training and testing sets. Microarray data were normalized using a LT-specific vector. RESULTS Random forest modeling on the training set generated a 59-probe classifier distinguishing AR versus non-AR (area under the curve 0.83; accuracy 0.78, sensitivity 0.70, specificity 0.81, positive predictive value 0.54, negative predictive value [NPV] 0.89; F-score 0.61). Using a locked threshold, the classifier performed well on the testing set (accuracy 0.72, sensitivity 0.67, specificity 0.73, positive predictive value 0.48, NPV 0.86; F-score 0.56). Probability scores increased in samples preceding AR versus non-AR, when liver function tests were normal, and decreased following AR treatment (P < 0.001). Ingenuity pathway analysis of the genes revealed a high percentage related to immune responses and liver injury. CONCLUSIONS We have developed a blood-based biologically relevant biomarker that can be detected before AR-associated graft injury distinct from LTR never developing AR. Given its high NPV ("rule out AR"), the biomarker has the potential to inform precision-guided immunosuppression minimization in LTRs.
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Affiliation(s)
- Josh Levitsky
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Gastroenterology and Hepatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Manoj Kandpal
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Preventive Medicine, Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Kexin Guo
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Preventive Medicine, Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Lihui Zhao
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Preventive Medicine, Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Sunil Kurian
- Scripps Clinic Bio-Repository and Bio-Informatics Core, Scripps Green Hospital, La Jolla, CA
| | - Thomas Whisenant
- Center for Computational Biology and Bioinformatics, School of Medicine, University of California San Diego, San Diego, CA
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17
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Cheung R, Xu H, Jin X, Tian W, Pinney K, Bu L, Stone S, Woodward RN, Agrawal N, Dholakia S, Phan RT. Validation of a gene expression signature to measure immune quiescence in kidney transplant recipients in the CLIA setting. Biomark Med 2022; 16:647-661. [PMID: 35485169 DOI: 10.2217/bmm-2022-0113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Allograft rejection remains a major cause of graft failure in kidney transplantation. Here the authors report the validation of a non-invasive molecular diagnostic assay, AlloMap Kidney, using peripheral blood. Methods: The AlloMap Kidney test is a gene expression profile utilizing the RNA-seq platform to measure immune quiescence in kidney transplant patients. Results/Conclusions: Analytical validation showed robust performance characteristics with an accuracy correlation coefficient of 0.997 and a precision coefficient of variation of 0.049 across testing. Clinical validation from the prospective, multi-center studies of 235 samples (66 rejection and 169 quiescence specimens) demonstrated the sensitivity of 70% and specificity of 66% for allograft rejection, while the negative predictive value was 95% to discriminate rejection from quiescence at 10% prevalence of rejection.
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Affiliation(s)
| | - Hua Xu
- CareDx, Inc., Brisbane, CA 94005, USA
| | - Xia Jin
- CareDx, Inc., Brisbane, CA 94005, USA
| | | | | | - Lihong Bu
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
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18
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Filippone EJ, Gulati R, Farber JL. Noninvasive Assessment of the Alloimmune Response in Kidney Transplantation. Adv Chronic Kidney Dis 2021; 28:548-560. [PMID: 35367023 DOI: 10.1053/j.ackd.2021.08.002] [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: 04/09/2021] [Revised: 05/28/2021] [Accepted: 08/26/2021] [Indexed: 11/11/2022]
Abstract
Transplantation remains the optimal mode of kidney replacement therapy, but unfortunately long-term graft survival after 1 year remains suboptimal. The main mechanism of chronic allograft injury is alloimmune, and current clinical monitoring of kidney transplants includes measuring serum creatinine, proteinuria, and immunosuppressive drug levels. The most important biomarker routinely monitored is human leukocyte antigen (HLA) donor-specific antibodies (DSAs) with the frequency based on underlying immunologic risk. HLA-DSA should be measured if there is graft dysfunction, immunosuppression minimization, or nonadherence. Antibody strength is semiquantitatively estimated as mean fluorescence intensity, with titration studies for equivocal cases and for following response to treatment. Determination of in vitro C1q or C3d positivity or HLA-DSA IgG subclass analysis remains of uncertain significance, but we do not recommend these for routine use. Current evidence does not support routine monitoring of non-HLA antibodies except anti-angiotensin II type 1 receptor antibodies when the phenotype is appropriate. The monitoring of both donor-derived cell-free DNA in blood or gene expression profiling of serum and/or urine may detect subclinical rejection, although mainly as a supplement and not as a replacement for biopsy. The optimal frequency and cost-effectiveness of using these noninvasive assays remain to be determined. We review the available literature and make recommendations.
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19
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Park WD, Kim DY, Mai ML, Reddy KS, Gonwa T, Ryan MS, Herrera Hernandez LP, Smith ML, Geiger XJ, Turkevi-Nagy S, Cornell LD, Smith BH, Kremers WK, Stegall MD. Progressive decline of function in renal allografts with normal 1-year biopsies: Gene expression studies fail to identify a classifier. Clin Transplant 2021; 35:e14456. [PMID: 34717009 DOI: 10.1111/ctr.14456] [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: 04/30/2021] [Revised: 07/23/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
Histologic findings on 1-year biopsies such as inflammation with fibrosis and transplant glomerulopathy predict renal allograft loss by 5 years. However, almost half of the patients with graft loss have a 1-year biopsy that is either normal or has only interstitial fibrosis. The goal of this study was to determine if there was a gene expression profile in these relatively normal 1-year biopsies that predicted subsequent decline in renal function. Using transcriptome microarrays we measured intragraft mRNA levels in a retrospective Discovery cohort (170 patients with a normal/minimal fibrosis 1-year biopsy, 54 with progressive decline in function/graft loss and 116 with stable function) and developed a nested 10-fold cross-validated gene classifier that predicted progressive decline in renal function (positive predictive value = 38 ± 34%%; negative predictive value = 73 ± 30%, c-statistic = .59). In a prospective, multicenter Validation cohort (270 patients with Normal/Interstitial Fibrosis [IF]), the classifier had a 20% positive predictive value, 85% negative predictive value and .58 c-statistic. Importantly, the majority of patients with graft loss in the prospective study had 1-year biopsies scored as Normal or IF. We conclude predicting graft loss in many renal allograft recipients (i.e., those with a relatively normal 1-year biopsy and eGFR > 40) remains difficult.
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Affiliation(s)
| | - Dean Y Kim
- Henry Ford Hospital, Detroit, Michigan, USA
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20
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Park S, Guo K, Heilman RL, Poggio ED, Taber DJ, Marsh CL, Kurian SM, Kleiboeker S, Weems J, Holman J, Zhao L, Sinha R, Brietigam S, Rebello C, Abecassis MM, Friedewald JJ. Combining Blood Gene Expression and Cellfree DNA to Diagnose Subclinical Rejection in Kidney Transplant Recipients. Clin J Am Soc Nephrol 2021; 16:1539-1551. [PMID: 34620649 PMCID: PMC8499014 DOI: 10.2215/cjn.05530421] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/11/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVES Subclinical acute rejection is associated with poor outcomes in kidney transplant recipients. As an alternative to surveillance biopsies, noninvasive screening has been established with a blood gene expression profile. Donor-derived cellfree DNA (cfDNA) has been used to detect rejection in patients with allograft dysfunction but not tested extensively in stable patients. We hypothesized that we could complement noninvasive diagnostic performance for subclinical rejection by combining a donor-derived cfDNA and a gene expression profile assay. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We performed a post hoc analysis of simultaneous blood gene expression profile and donor-derived cfDNA assays in 428 samples paired with surveillance biopsies from 208 subjects enrolled in an observational clinical trial (Clinical Trials in Organ Transplantation-08). Assay results were analyzed as binary variables, and then, their continuous scores were combined using logistic regression. The performance of each assay alone and in combination was compared. RESULTS For diagnosing subclinical rejection, the gene expression profile demonstrated a negative predictive value of 82%, a positive predictive value of 47%, a balanced accuracy of 64%, and an area under the receiver operating curve of 0.75. The donor-derived cfDNA assay showed similar negative predictive value (84%), positive predictive value (56%), balanced accuracy (68%), and area under the receiver operating curve (0.72). When both assays were negative, negative predictive value increased to 88%. When both assays were positive, positive predictive value increased to 81%. Combining assays using multivariable logistic regression, area under the receiver operating curve was 0.81, significantly higher than the gene expression profile (P<0.001) or donor-derived cfDNA alone (P=0.006). Notably, when cases were separated on the basis of rejection type, the gene expression profile was significantly better at detecting cellular rejection (area under the receiver operating curve, 0.80 versus 0.62; P=0.001), whereas the donor-derived cfDNA was significantly better at detecting antibody-mediated rejection (area under the receiver operating curve, 0.84 versus 0.71; P=0.003). CONCLUSIONS A combination of blood-based biomarkers can improve detection and provide less invasive monitoring for subclinical rejection. In this study, the gene expression profile detected more cellular rejection, whereas donor-derived cfDNA detected more antibody-mediated rejection.
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Affiliation(s)
- Sookhyeon Park
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois,Division of Nephrology, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Kexin Guo
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois,Department of Preventive Medicine, Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Raymond L. Heilman
- Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Phoenix, Arizona
| | - Emilio D. Poggio
- Department of Nephrology and Hypertension, Cleveland Clinic, Cleveland, Ohio
| | - David J. Taber
- Division of Transplant Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Christopher L. Marsh
- Department of Medicine and Surgery, Scripps Clinic and Green Hospital, La Jolla, California
| | - Sunil M. Kurian
- Bio-Repository and Bio-Informatics Core, Scripps Health, La Jolla, California
| | | | - Juston Weems
- Eurofins US Clinical Diagnostics, Lee’s Summit, Missouri
| | - John Holman
- Transplant Genomics, Inc., Mansfield, Massachusetts
| | - Lihui Zhao
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois,Department of Preventive Medicine, Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rohita Sinha
- Eurofins US Clinical Diagnostics, Lee’s Summit, Missouri
| | - Susan Brietigam
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Christabel Rebello
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Michael M. Abecassis
- Department of Surgery, University of Arizona College of Medicine, Tucson, Arizona,Department of Immunobiology, University of Arizona College of Medicine, Tucson, Arizona
| | - John J. Friedewald
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois,Division of Nephrology, Department of Medicine, Northwestern University, Chicago, Illinois
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21
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Akalin E, Weir MR, Bunnapradist S, Brennan DC, Delos Santos R, Langone A, Djamali A, Xu H, Jin X, Dholakia S, Woodward RN, Bromberg JS. Clinical Validation of an Immune Quiescence Gene Expression Signature in Kidney Transplantation. KIDNEY360 2021; 2:1998-2009. [PMID: 35419538 PMCID: PMC8986041 DOI: 10.34067/kid.0005062021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023]
Abstract
Background Despite advances in immune suppression, kidney allograft rejection and other injuries remain a significant clinical concern, particularly with regards to long-term allograft survival. Evaluation of immune activity can provide information about rejection status and help guide interventions to extend allograft life. Here, we describe the validation of a blood gene expression classifier developed to differentiate immune quiescence from both T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR). Methods A five-gene classifier (DCAF12, MARCH8, FLT3, IL1R2, and PDCD1) was developed on 56 peripheral blood samples and validated on two sample sets independent of the training cohort. The primary validation set comprised 98 quiescence samples and 18 rejection samples: seven TCMR, ten ABMR, and one mixed rejection. The second validation set included eight quiescence and 11 rejection samples: seven TCMR, two ABMR, and two mixed rejection. AlloSure donor-derived cell-free DNA (dd-cfDNA) was also evaluated. Results AlloMap Kidney classifier scores in the primary validation set differed significantly between quiescence (median, 9.49; IQR, 7.68-11.53) and rejection (median, 13.09; IQR, 11.25-15.28), with P<0.001. In the second validation set, the cohorts were statistically different (P=0.03) and the medians were similar to the primary validation set. The AUC for discriminating rejection from quiescence was 0.786 for the primary validation and 0.800 for the second validation. AlloMap Kidney results were not significantly correlated with AlloSure, although both were elevated in rejection. The ability to discriminate rejection from quiescence was improved when AlloSure and AlloMap Kidney were used together (AUC, 0.894). Conclusion Validation of AlloMap Kidney demonstrated the ability to differentiate between rejection and immune quiescence using a range of scores. The diagnostic performance suggests that assessment of the mechanisms of immunologic activity is complementary to allograft injury information derived from AlloSure dd-cfDNA. Together, these biomarkers offer a more comprehensive assessment of allograft health and immune quiescence.
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Affiliation(s)
- Enver Akalin
- Division of Nephrology, Kidney Transplant Program, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Matthew R. Weir
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Suphamai Bunnapradist
- Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California
| | - Daniel C. Brennan
- Comprehensive Transplant Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rowena Delos Santos
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Anthony Langone
- Vanderbilt University Medical Center, Medical Specialties Clinic, Veteran Affairs Hospital Renal Transplant Program, Nashville, Tennessee
| | - Arjang Djamali
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Hua Xu
- Research and Development, CareDx, Brisbane, California
| | - Xia Jin
- Research and Development, CareDx, Brisbane, California
| | - Sham Dholakia
- Medical Affairs, CareDx, South San Francisco, California
| | | | - Jonathan S. Bromberg
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
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22
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Buscher K, Heitplatz B, van Marck V, Song J, Loismann S, Rixen R, Hüchtmann B, Kurian S, Ehinger E, Wolf D, Ley K, Pavenstädt H, Reuter S. Data-Driven Kidney Transplant Phenotyping as a Histology-Independent Framework for Biomarker Discovery. J Am Soc Nephrol 2021; 32:1933-1945. [PMID: 34078665 PMCID: PMC8455252 DOI: 10.1681/asn.2020121685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/15/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND In transplant medicine, clinical decision making largely relies on histology of biopsy specimens. However, histology suffers from low specificity, sensitivity, and reproducibility, leading to suboptimal stratification of patients. We developed a histology-independent immune framework of kidney graft homeostasis and rejection. METHODS We applied tailored RNA deconvolution for leukocyte enumeration and coregulated gene network analysis to published bulk human kidney transplant RNA transcriptomes as input for unsupervised, high-dimensional phenotype clustering. We used framework-based graft survival analysis to identify a biomarker that was subsequently characterized in independent transplant biopsy specimens. RESULTS We found seven immune phenotypes that confirm known rejection types and uncovered novel signatures. The molecular phenotypes allow for improved graft survival analysis compared with histology, and identify a high-risk group in nonrejecting transplants. Two fibrosis-related phenotypes with distinct immune features emerged with reduced graft survival. We identified lysyl oxidase-like 2 (LOXL2)-expressing peritubular CD68+ macrophages as a framework-derived biomarker of impaired allograft function. These cells precede graft fibrosis, as demonstrated in longitudinal biopsy specimens, and may be clinically useful as a biomarker for early fibrogenesis. CONCLUSIONS This study provides a comprehensive, data-driven atlas of human kidney transplant phenotypes and demonstrates its utility to identify novel clinical biomarkers.
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Affiliation(s)
- Konrad Buscher
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany,Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California
| | - Barbara Heitplatz
- Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Veerle van Marck
- Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Jian Song
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sophie Loismann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Rebecca Rixen
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Birte Hüchtmann
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Sunil Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Erik Ehinger
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Dennis Wolf
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California,Department of Cardiology and Angiology I, University Heart Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California
| | - Hermann Pavenstädt
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Stefan Reuter
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
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23
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Integrative Analysis of Prognostic Biomarkers for Acute Rejection in Kidney Transplant Recipients. Transplantation 2021; 105:1225-1237. [PMID: 33148975 DOI: 10.1097/tp.0000000000003516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Noninvasive biomarkers may predict adverse events such as acute rejection after kidney transplantation and may be preferable to existing methods because of superior accuracy and convenience. It is uncertain how these biomarkers, often derived from a single study, perform across different cohorts of recipients. METHODS Using a cross-validation framework that evaluates the performance of biomarkers, the aim of this study was to devise an integrated gene signature set that predicts acute rejection in kidney transplant recipients. Inclusion criteria were publicly available datasets of gene signatures that reported acute rejection episodes after kidney transplantation. We tested the predictive probability for acute rejection using gene signatures within individual datasets and validated the set using other datasets. Eight eligible studies of 1454 participants, with a total of 512 acute rejections episodes were included. RESULTS All sets of gene signatures had good positive and negative predictive values (79%-96%) for acute rejection within their own cohorts, but the predictability reduced to <50% when tested in other independent datasets. By integrating signature sets with high specificity scores across all studies, a set of 150 genes (included CXCL6, CXCL11, OLFM4, and PSG9) which are known to be associated with immune responses, had reasonable predictive values (varied between 69% and 90%). CONCLUSIONS A set of gene signatures for acute rejection derived from a specific cohort of kidney transplant recipients do not appear to provide adequate prediction in an independent cohort of transplant recipients. However, the integration of gene signature sets with high specificity scores may improve the prediction performance of these markers.
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24
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Abstract
PURPOSE OF REVIEW Organ transplantation research has led to the discovery of several interesting individual mechanistic pathways, molecules and potential drug targets but there are still no comprehensive studies that have addressed how these varied mechanisms work in unison to regulate the posttransplant immune response that drives kidney rejection and dysfunction. RECENT FINDINGS Systems biology is a rapidly expanding field that aims to integrate existing knowledge of molecular concepts and large-scale genomic and clinical datasets into networks that can be used in cutting edge computational models to define disease mechanisms in a holistic manner. Systems biology approaches have brought a paradigm shift from a reductionist view of biology to a wider agnostic assessment of disease from several lines of evidence. Although the complex nature of the posttransplant immune response makes it difficult to pinpoint mechanisms, systems biology is enabling discovery of unknown biological interactions using the cumulative power of genomic data sets, clinical data and endpoints, and improved computational methods for the systematic deconvolution of this response. SUMMARY An integrative systems biology approach that leverages genomic data from varied technologies, such as DNA sequencing, copy number variation, RNA sequencing, and methylation profiles along with long-term clinical follow-up data has the potential to define a framework that can be mined to provide novel insights for developing therapeutic interventions in organ transplantation.
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25
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MicroRNA Expression Changes in Kidney Transplant: Diagnostic Efficacy of miR-150-5p as Potential Rejection Biomarker, Pilot Study. J Clin Med 2021; 10:jcm10132748. [PMID: 34206682 PMCID: PMC8268834 DOI: 10.3390/jcm10132748] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Background: The kidney allograft biopsy is considered the gold standard for rejection diagnosis but is invasive and could be indeterminate. Several publications point to the role of miRNA expression in suggesting its involvement in the acceptance or rejection of organ transplantation. This study aimed to analyze microRNAs involved in the differentiation and activation of B and T lymphocytes from kidney transplant (KT) patients’ peripheral blood leukocytes to be used as biomarkers of acute renal rejection (AR). Methods: A total of 15 KT patients with and without acute rejection (AR/NAR) were analyzed and quantified by miRNA PCR array. A total of 84 miRNAs related to lymphocyte differentiation and activation B and T were studied. The functions and biological pathways were analyzed to predict the potential targets of differential expressed miRNAs. Results: Six miRNA were increased in the AR group (miR-191-5p, miR-223-3p, miR-346, miR-423-5p, miR-574-3p, and miR-181d) and miR-150-5p was increased in the NAR group. In silico studies showed a total of 2603 target genes for the increased miRNAs in AR, while for the decrease miRNA, a total of 1107 target-potential genes were found. Conclusions: Our results show that KT with AR shows a decrease in miR-150-5p expression compared to NAR, suggesting that the decrease in miR-150-5p could be related to an increased MBD6 whose deregulation could have clinical consequences.
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26
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Wang Y, Zhang D, Hu X. A Three-Gene Peripheral Blood Potential Diagnosis Signature for Acute Rejection in Renal Transplantation. Front Mol Biosci 2021; 8:661661. [PMID: 34017855 PMCID: PMC8129004 DOI: 10.3389/fmolb.2021.661661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/21/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Acute rejection (AR) remains a major issue that negatively impacts long-term allograft survival in renal transplantation. The current study aims to apply machine learning methods to develop a non-invasive diagnostic test for AR based on gene signature in peripheral blood. Methods: We collected blood gene expression profiles of 251 renal transplant patients with biopsy-proven renal status from three independent cohorts in the Gene Expression Omnibus database. After differential expression analysis and machine learning algorithms, selected biomarkers were applied to the least absolute shrinkage and selection operator (LASSO) logistic regression to construct a diagnostic model in the training cohort. The diagnostic ability of the model was further tested in validation cohorts. Gene set enrichment analysis and immune cell assessment were also conducted for further investigation. Results: A novel diagnostic model based on three genes (TSEN15, CAPRIN1 and PRR34-AS1) was constructed in the training cohort (AUC = 0.968) and successfully verified in the validation cohort (AUC = 0.925) with high accuracy. Moreover, the diagnostic model also showed a promising value in discriminating T cell-mediated rejection (TCMR) (AUC = 0.786). Functional enrichment analysis and immune cell evaluation demonstrated that the AR model was significantly correlated with adaptive immunity, especially T cell subsets and dendritic cells. Conclusion: We identified and validated a novel three-gene diagnostic model with high accuracy for AR in renal transplant patients, and the model also performed well in distinguishing TCMR. The current study provided a promising tool to be used as a precise and cost-effective non-invasive test in clinical practice.
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Affiliation(s)
- Yicun Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Di Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
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27
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Gui Z, Suo C, Wang Z, Zheng M, Fei S, Chen H, Sun L, Han Z, Tao J, Ju X, Yang H, Gu M, Tan R. Impaired ATG16L-Dependent Autophagy Promotes Renal Interstitial Fibrosis in Chronic Renal Graft Dysfunction Through Inducing EndMT by NF-κB Signal Pathway. Front Immunol 2021; 12:650424. [PMID: 33927720 PMCID: PMC8076642 DOI: 10.3389/fimmu.2021.650424] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic renal graft dysfunction (CAD) is caused by multiple factors, including glomerular sclerosis, inflammation, interstitial fibrosis and tubular atrophy (IF/TA). However, the most prominent elements of CAD are IF/TA. Our studies have confirmed that endothelial-mesenchymal transition (EndMT) is an important source to allograft IF/TA. The characteristic of EndMT is the loss of endothelial marker and the acquisition of mesenchymal or fibroblastic phenotypes. Autophagy is an intracellular degradation pathway that is regulated by autophagy-related proteins and plays a vital role in many fibrotic conditions. However, whether or not autophagy contributes to fibrosis of renal allograft and how such mechanism occurs still remains unclear. Autophagy related 16 like gene (ATG16L) is a critical autophagy-related gene (ARG) necessary for autophagosome formation. Here, we first analyzed kidney transplant patient tissues from Gene Expression Omnibus (GEO) datasets and 60 transplant patients from our center. Recipients with stable kidney function were defined as non-CAD group and all patients in CAD group were histopathologically diagnosed with CAD. Results showed that ATG16L, as one significant differential ARG, was less expressed in CAD group compared to the non-CAD group. Furthermore, we found there were less autophagosomes and autolysosomes in transplanted kidneys of CAD patients, and downregulation of autophagy is a poor prognostic factor. In vitro, we found out that the knockdown of ATG16L enhanced the process of EndMT in human renal glomerular endothelial cells (HRGECs). In vivo, the changes of EndMT and autophagic flux were then detected in rat renal transplant models of CAD. We demonstrated the occurrence of EndMT, and indicated that abundance of ATG16L was accompanied by the dynamic autophagic flux change along different stages of kidney transplantation. Mechanistically, knockdown of ATG16L, specifically in endothelial cells, reduced of NF-κB degradation and excreted inflammatory cytokines (IL-1β, IL-6 and TNF-α), which could facilitate EndMT. In conclusion, ATG16L-dependent autophagic flux causing by transplant showed progressive loss increase over time. Inflammatory cytokines from this process promoted EndMT, thereby leading to progression of CAD. ATG16L served as a negative regulator of EndMT and development of renal graft fibrosis, and autophagy can be explored as a potential therapeutic target for chronic renal graft dysfunction.
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Affiliation(s)
- Zeping Gui
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuanjian Suo
- 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
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chen
- 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
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaobin Ju
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haiwei Yang
- 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
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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28
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Ang A, Schieve C, Rose S, Kew C, First MR, Mannon RB. Avoiding surveillance biopsy: Use of a noninvasive biomarker assay in a real-life scenario. Clin Transplant 2020; 35:e14145. [PMID: 33170974 DOI: 10.1111/ctr.14145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/29/2022]
Abstract
PURPOSE TruGraf™ blood test measures a specific gene expression signature in peripheral blood mononuclear cells for noninvasive assessment of kidney transplant recipients (KTRs) with stable renal function, excluding subclinical acute rejection (subAR) with high degree of confidence. Study objective was to correlate TruGraf™ test with 6-month surveillance biopsy (SBx). METHODS Prospective, single-center study of 116 consecutive KTRs with SBx performed at 6 months post-transplant..TruGraf™ done at time of SBx; results compared with histology (Banff 2017) for concordance. RESULTS Of 116 enrollees, 26 excluded, absent biopsy (n = 17), test quality control issues (n = 9), leaving 90 KTRs-66% deceased donor kidneys, 58% African American, and 59% male. TruGraf™ result negative in 67 subjects; 54 had normal biopsy, indicating SBx could have been avoided. Eight subjects had true positive result where biopsy justified. Unnecessary biopsy would have been performed in 15 subjects with false-positive TruGraf™, and subAR missed in 13 subjects with false-negative test. In overall population of 90 patients, SBx would have been avoided in 54 (60%). CONCLUSIONS Implementation of TruGraf™ testing in a "real-world" cohort at the time of SBx identified a significant proportion of KTRs that could have avoided SBx.
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Affiliation(s)
- Audrey Ang
- Division of Nephrology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Clifton Kew
- Division of Nephrology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Roy First
- Transplant Genomics Inc., Mansfield, MA, USA
| | - Roslyn B Mannon
- Division of Nephrology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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29
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Gray JN, Wolf-Doty T, Sulejmani N, Gaber O, Axelrod D, Abdalla B, Danovitch G. KidneyCare Guided Immuno-Optimization in Renal Allografts: The KIRA Protocol. Methods Protoc 2020; 3:E68. [PMID: 33007896 PMCID: PMC7712506 DOI: 10.3390/mps3040068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/20/2020] [Accepted: 09/25/2020] [Indexed: 01/09/2023] Open
Abstract
Immunosuppressant agents are essential in every transplant recipient's care yet walking the fine line of over- or under-immunosuppression is a constant struggle for both patients and transplant providers alike. Optimization and personalization of immunosuppression has been limited by the need for non-invasive graft surveillance methods that are specific enough to identify organ injury in real time. With this in mind, we propose a pilot study protocol utilizing both donor derived cell free DNA (dd-cfDNA, gene expression profiling (GEP), and machine learning (iBox), called KidneyCare, to assess the feasibility and safety in reducing immunosuppressant exposure without increasing the risk of clinical rejection, graft injury, or allograft loss. Patients randomized to the immunominimization arm will be enrolled in one of two protocols designed to eliminate one immunosuppressant and optimize the dose of the Calcineurin Inhibitors (CNIs) using the KidneyCare platform. All patients will be maintained on dual therapy of either steroids and a low dose CNI, or mycophenolate mofetil (MMF) and low dose CNI. Their outcomes will be compared to patients who have their immunosuppressants managed using standard clinical assessment and treatment protocols to determine the impact of immuno-optimization on graft function, complications, and patient reported outcomes.
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Affiliation(s)
- Jennifer N. Gray
- CareDx, 3260 Bayshore Blvd, Brisbane, CA 94005, USA; (T.W.-D.); (N.S.)
| | - Theresa Wolf-Doty
- CareDx, 3260 Bayshore Blvd, Brisbane, CA 94005, USA; (T.W.-D.); (N.S.)
| | - Nimisha Sulejmani
- CareDx, 3260 Bayshore Blvd, Brisbane, CA 94005, USA; (T.W.-D.); (N.S.)
| | - Osama Gaber
- Houston Methodist Hospital, 6565 Fannin St. Houston, TX 77030, USA;
| | - David Axelrod
- Department of Surgery, University of Iowa Medical Center, 200 Hawkins Dr, Iowa City, IA 52242, USA;
| | - Basmah Abdalla
- UCLA Medical Center, 757 Westwood Plaza, Los Angeles, CA 90095, USA; (B.A.); (G.D.)
| | - Gabriel Danovitch
- UCLA Medical Center, 757 Westwood Plaza, Los Angeles, CA 90095, USA; (B.A.); (G.D.)
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30
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Swanson KJ, Aziz F, Garg N, Mohamed M, Mandelbrot D, Djamali A, Parajuli S. Role of novel biomarkers in kidney transplantation. World J Transplant 2020; 10:230-255. [PMID: 32995319 PMCID: PMC7504189 DOI: 10.5500/wjt.v10.i9.230] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/21/2020] [Accepted: 08/26/2020] [Indexed: 02/05/2023] Open
Abstract
Clinical application of biomarkers is an integral component of transplant care. Clinicians and scientists alike are in search of better biomarkers than the current serologic (serum creatinine, donor-specific antibodies), urine-derived (urinalysis, urine protein), and histologic ones we now use. The science behind recent biomarker discovery spans across multiple molecular biologic disciplines, including transcriptomics, proteomics, and metabolomics. Innovative methodology and integration of basic and clinical approaches have allowed researchers to unearth molecular phenomena preceding clinical disease. Biomarkers can be classified in several ways. In this review, we have classified them via their origin and outcome: Primarily immunologic, i.e., representative of immune regulation and dysfunction and non-immunologic, pertaining to delayed graft function, cardiovascular events/mortality, infection, malignancy, post-transplant diabetes, graft, and patient survival. Novel biomarker uses to guide the diagnosis and management of transplant-related outcomes is a promising area of research. However, the use of biomarkers to predict outcomes after kidney transplantation is not well studied. In this review, we summarize the recent studies illustrating biomarker use and transplant outcomes.
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Affiliation(s)
- Kurtis J Swanson
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Fahad Aziz
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Neetika Garg
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Maha Mohamed
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Didier Mandelbrot
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Arjang Djamali
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Sandesh Parajuli
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
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31
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Levitsky J, Asrani SK, Schiano T, Moss A, Chavin K, Miller C, Guo K, Zhao L, Kandpal M, Bridges N, Brown M, Armstrong B, Kurian S, Demetris AJ, Abecassis M. Discovery and validation of a novel blood-based molecular biomarker of rejection following liver transplantation. Am J Transplant 2020; 20:2173-2183. [PMID: 32356368 PMCID: PMC7496674 DOI: 10.1111/ajt.15953] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/28/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023]
Abstract
Noninvasive biomarker profiles of acute rejection (AR) could affect the management of liver transplant (LT) recipients. Peripheral blood was collected following LT for discovery (Northwestern University [NU]) and validation (National Institute of Allergy and Infectious Diseases Clinical Trials in Organ Transplantation [CTOT]-14 study). Blood gene profiling was paired with biopsies showing AR or ADNR (acute dysfunction no rejection) as well as stable graft function samples (Transplant eXcellent-TX). CTOT-14 subjects had serial collections prior to AR, ADNR, TX, and after AR treatment. NU cohort gene expression (46 AR, 45 TX) was analyzed using random forest models to generate a classifier training set (36 gene probe) distinguishing AR vs TX (area under the curve 0.92). The algorithm and threshold were locked and tested on the CTOT-14 validation cohort (14 AR, 50 TX), yielding an accuracy of 0.77, sensitivity 0.57, specificity 0.82, positive predictive value (PPV) 0.47, and negative predictive value (NPV) 0.87 for AR vs TX. The probability score line slopes were positive preceding AR, and negative preceding TX and non-AR (TX + ADNR) (P ≤ .001) and following AR treatment. In conclusion, we have developed a blood biomarker diagnostic for AR that can be detected prior to AR-associated graft injury as well a normal graft function (non-AR). Further studies are needed to evaluate its utility in precision-guided immunosuppression optimization following LT.
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Affiliation(s)
- Josh Levitsky
- Comprehensive Transplant CenterNorthwestern University Feinberg School of MedicineChicagoIllinois,Division of Gastroenterology and HepatologyDepartment of MedicineNorthwestern University Feinberg School of MedicineChicagoIllinois
| | - Sumeet K. Asrani
- Annette C. and Harold C. Simmons Transplant InstituteBaylor University Medical CenterDallasTexas
| | | | | | | | | | - Kexin Guo
- Comprehensive Transplant CenterNorthwestern University Feinberg School of MedicineChicagoIllinois,Biostatistics Collaboration CenterDepartment of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinois
| | - Lihui Zhao
- Comprehensive Transplant CenterNorthwestern University Feinberg School of MedicineChicagoIllinois,Biostatistics Collaboration CenterDepartment of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinois
| | - Manoj Kandpal
- Comprehensive Transplant CenterNorthwestern University Feinberg School of MedicineChicagoIllinois,Biostatistics Collaboration CenterDepartment of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIllinois
| | - Nancy Bridges
- Division of Allergy, Immunology, and TransplantationNational Institute of Allergy and Infectious DiseasesBethesdaMaryland
| | - Merideth Brown
- Division of Allergy, Immunology, and TransplantationNational Institute of Allergy and Infectious DiseasesBethesdaMaryland
| | | | - Sunil Kurian
- The Scripps Research InstituteLa JollaCalifornia
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Pineda S, Sur S, Sigdel T, Nguyen M, Crespo E, Torija A, Meneghini M, Gomà M, Sirota M, Bestard O, Sarwal MM. Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection. Kidney Int Rep 2020; 5:1706-1721. [PMID: 33102963 PMCID: PMC7569686 DOI: 10.1016/j.ekir.2020.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Introduction Peripheral blood (PB) molecular patterns characterizing the different effector immune pathways driving distinct kidney rejection types remain to be fully elucidated. We hypothesized that transcriptome analysis using RNA sequencing (RNAseq) in samples of kidney transplant patients would enable the identification of unique protein-coding and noncoding genes that may be able to segregate different rejection phenotypes. Methods We evaluated 37 biopsy-paired PB samples from the discovery cohort, with stable (STA), antibody-mediated rejection (AMR), and T cell-mediated rejection (TCMR) by RNAseq. Advanced machine learning tools were used to perform 3-way differential gene expression analysis to identify gene signatures associated with rejection. We then performed functional in silico analysis and validation by Fluidigm (San Francisco, CA) in 62 samples from 2 independent kidney transplant cohorts. Results We found 102 genes (63 coding genes and 39 noncoding genes) associated with AMR (54 upregulated), TCMR (23 upregulated), and STA (25 upregulated) perfectly clustered with each rejection phenotype and highly correlated with main histologic lesions (ρ = 0.91). For the genes associated with AMR, we found enrichment in regulation of endoplasmic reticulum stress, adaptive immunity, and Ig class-switching. In the validation, we found that the SIGLEC17P pseudogene and 9 SIGLEC17P-related coding genes were highly expressed among AMR but not in TCMR and STA samples. Conclusions This analysis identifies a critical gene signature in PB in kidney transplant patients undergoing AMR, sufficient to differentiate them from patients with TCMR and immunologically quiescent kidney allografts. Our findings provide the basis for new studies dissecting the role of noncoding genes in the pathophysiology of kidney allograft rejection and their potential value as noninvasive biomarkers of the rejection process.
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Affiliation(s)
- Silvia Pineda
- Division of Transplant Surgery, University of California San Francisco, San Francisco, California, USA.,Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA
| | - Swastika Sur
- Division of Transplant Surgery, University of California San Francisco, San Francisco, California, USA
| | - Tara Sigdel
- Division of Transplant Surgery, University of California San Francisco, San Francisco, California, USA
| | - Mark Nguyen
- Division of Transplant Surgery, University of California San Francisco, San Francisco, California, USA
| | - Elena Crespo
- Laboratory of Experimental Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Alba Torija
- Laboratory of Experimental Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Maria Meneghini
- Laboratory of Experimental Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain.,Kidney Transplant Unit, Bellvitge University Hospital, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Montse Gomà
- Pathology Department, Bellvitge University Hospital, Barcelona University, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Oriol Bestard
- Division of Transplant Surgery, University of California San Francisco, San Francisco, California, USA.,Laboratory of Experimental Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Minnie M Sarwal
- Division of Transplant Surgery, University of California San Francisco, San Francisco, California, USA
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Abstract
Human corneal transplantation (keratoplasty) is typically considered to have superior short- and long-term outcomes and lower requirement for immunosuppression compared to solid organ transplants because of the inherent immune privilege and tolerogenic mechanisms associated with the anterior segment of the eye. However, in a substantial proportion of corneal transplants, the rates of acute rejection and/or graft failure are comparable to or greater than those of the commonly transplanted solid organs. Critically, while registry data and observational studies have helped to identify factors that are associated with increased risk of corneal transplant failure, the extent to which these risk factors operate through enhancing immune-mediated rejection is less clear. In this overview, we summarize a range of important recent clinical and basic insights related to high-risk corneal transplantation, the factors associated with graft failure, and the immunological basis of corneal allograft rejection. We highlight critical research areas from which continued progress is likely to drive improvements in the long-term survival of high-risk corneal transplants. These include further development and clinical testing of predictive risk scores and assays; greater use of multicenter clinical trials to optimize immunosuppressive therapy in high-risk recipients and robust clinical translation of novel, mechanistically-targeted immunomodulatory and regenerative therapies that are emerging from basic science laboratories. We also emphasize the relative lack of knowledge regarding transplant outcomes for infection-related corneal diseases that are common in the developing world and the potential for greater cross-pollination and synergy between corneal and solid organ transplant research communities.
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Abstract
Single-cell RNA sequencing (scRNA-seq) allows the measurement of transcriptomes from individual cells providing new insights into complex biological systems. scRNA-seq has enabled the identification of rare cell types, new cell states, and intercellular communication networks that may be masked by traditional bulk transcriptional profiling. Researchers are increasingly using scRNA-seq to comprehensively characterize complex organs in health and disease. The diversity of immune cell types, some present at low frequency, in a transplanted organ undergoing rejection makes scRNA-seq ideally suited to characterize transplant pathologies because it can quantify subtle transcriptional differences between rare cell types. In this review, we discuss single-cell sequencing methods and their application in transplantation to date, current challenges, and future directions. We believe that the remarkably rapid pace of technological development in this field makes it likely that single-cell technologies such as scRNA-seq will have an impact on clinical transplantation within a decade.
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Shaw BI, Cheng DK, Acharya CR, Ettenger RB, Lyerly HK, Cheng Q, Kirk AD, Chambers ET. An age-independent gene signature for monitoring acute rejection in kidney transplantation. Theranostics 2020; 10:6977-6986. [PMID: 32550916 PMCID: PMC7295062 DOI: 10.7150/thno.42110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Acute rejection (AR) remains a significant problem that negatively impacts long-term renal allograft survival. Numerous therapies are used to prevent AR that differ by center and recipient age. This variability confounds diagnostic methods. Methods: To develop an age-independent gene signature for AR effective across a broad array of immunosuppressive regimens, we compiled kidney transplant biopsy (n=1091) and peripheral blood (n=392) gene expression profiles from 12 independent public datasets. After removing genes differentially expressed in pediatric and adult patients, we compared gene expression profiles from biopsy and peripheral blood samples of patients with AR to those who were stable (STA), using Mann-Whitney U Tests with validation in independent testing datasets. We confirmed this signature in pediatric and adult patients (42 AR and 47 STA) from our institutional biorepository. Results: We identified a novel age-independent gene network that identified AR from both kidney and blood samples. We developed a 90-probe set signature targeting 76 genes that differentiated AR from STA and found an 8 gene subset (DIP2C, ENOSF1, FBXO21, KCTD6, PDXDC1, REXO2, HLA-E, and RAB31) that was associated with AR. Conclusion: We used publicly available datasets to create a gene signature of AR that identified AR irrespective of immunosuppression regimen or recipient age. This study highlights a novel model to screen and validate biomarkers across multiple treatment regimens.
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Affiliation(s)
- Brian I Shaw
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Daniel K. Cheng
- Department of Pediatrics, Duke University Medical Center, Durham, United States
| | | | - Robert B Ettenger
- Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, United States
| | - Herbert Kim Lyerly
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Qing Cheng
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Allan D Kirk
- Department of Surgery, Duke University Medical Center, Durham, United States
- Department of Pediatrics, Duke University Medical Center, Durham, United States
| | - Eileen T Chambers
- Department of Surgery, Duke University Medical Center, Durham, United States
- Department of Pediatrics, Duke University Medical Center, Durham, United States
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Molecular Pathways Underlying Adaptive Repair of the Injured Kidney: Novel Donation After Cardiac Death and Acute Kidney Injury Platforms. Ann Surg 2020; 271:383-390. [PMID: 30048305 DOI: 10.1097/sla.0000000000002946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To test the hypothesis that gene expression profiling in peripheral blood from patients who have undergone kidney transplantation (KT) will provide mechanistic insights regarding graft repair and regeneration. BACKGROUND Renal grafts obtained from living donors (LD) typically function immediately, whereas organs from donation after cardiac death (DCD) or acute kidney injury (AKI) donors may experience delayed function with eventual recovery. Thus, recipients of LD, DCD, and AKI kidneys were studied to provide a more complete understanding of the molecular basis for renal recovery. METHODS Peripheral blood was collected from LD and DCD/AKI recipients before transplant and throughout the first 30 days thereafter. Total RNA was isolated and assayed on whole genome microarrays. RESULTS Comparison of longitudinal gene expression between LD and AKI/DCD revealed 2 clusters, representing 141 differentially expressed transcripts. A subset of 11 transcripts was found to be differentially expressed in AKI/DCD versus LD. In all recipients, the most robust gene expression changes were observed in the first day after transplantation. After day 1, gene expression profiles differed depending upon the source of the graft. In patients receiving LD grafts, the expression of most genes did not remain markedly elevated beyond the first day post-KT. In the AKI/DCD groups, elevations in gene expression were maintained for at least 5 days post-KT. In all recipients, the pattern of coordinate gene overexpression subsided by 28 to 30 days. CONCLUSIONS Gene expression in peripheral blood of AKI/DCD recipients offers a novel platform to understand the potential mechanisms and timing of kidney repair and regeneration after transplantation.
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37
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Song L, Fang F, Liu P, Zeng G, Liu H, Zhao Y, Xie X, Tseng G, Randhawa P, Xiao K. Quantitative Proteomics for Monitoring Renal Transplant Injury. Proteomics Clin Appl 2020; 14:e1900036. [PMID: 31999393 DOI: 10.1002/prca.201900036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 12/25/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE This study is aimed at developing a molecular diagnostics platform to enhance the interpretation of renal allograft biopsies using quantitative proteomic profiling of formalin-fixed and paraffin-embedded (FFPE) specimens. EXPERIMENTAL DESIGN A quantitative proteomics platform composed of 1) an optimized FFPE protein sample preparation method, 2) a tandem mass tag TMT10-plex-based proteomic workflow, and 3) a systematic statistical analysis pipeline to reveal differentially expressed proteins has been developed. This platform is then tested on a small sample set (five samples per phenotype) to reveal proteomic signatures that can differentiate T-cell mediated rejection (TCMR) and polyomavirus BK nephropathy (BKPyVN) from healthy functionally stable kidney tissue (STA). RESULTS Among 2798 quantified proteins, the expression levels of 740 BKPyVN and 638 TCMR associated proteins are significantly changed compared to STA specimens. Principal component analysis demonstrated good segregation of all three phenotypes investigated. Protein detection and quantitation are highly reproducible: replicate comparative analyses demonstrated 71-84% overlap of detected proteins, and the coefficient of variation for protein measurements is <15% in triplicate liquid chromatography-tandem mass spectrometry runs. CONCLUSIONS AND CLINICAL RELEVANCE Quantitative proteomics can be applied to archived FFPE specimens to differentiate different causes of renal allograft injury.
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Affiliation(s)
- Lei Song
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Department of Urological Organ Transplantation, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Fei Fang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Gang Zeng
- Department of Pathology, The Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Xubiao Xie
- Department of Urological Organ Transplantation, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Parmjeet Randhawa
- Department of Pathology, The Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kunhong Xiao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
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38
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Bioinformatics analyses on the immune status of renal transplant patients, a systemic research of renal transplantation. BMC Med Genomics 2020; 13:24. [PMID: 32046717 PMCID: PMC7014750 DOI: 10.1186/s12920-020-0673-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Kidney transplantation is the most effective treatment for end-stage renal disease. Allograft rejections severely affect survivals of allograft kidneys and recipients. METHODS Using bioinformatics approaches, the present study was designed to investigate immune status in renal transplant recipients. Fifteen datasets from Gene Expression Omnibus (GEO) were collected and analysed. Analysis of gene enrichment and protein-protein interactions were also used. RESULTS There were 40 differentially expressed genes (DEGs) identified in chronic rejection group when compared with stable recipients, which were enriched in allograft rejection module. There were 135 DEGs identified in acute rejection patients, compared with stable recipients, in which most genes were enriched in allograft rejection and immune deficiency. There were 288 DEGs identified in stable recipients when compared to healthy subjects. Most genes were related to chemokine signalling pathway. In integrated comparisons, expressions of MHC molecules and immunoglobulins were increased in both acute and chronic rejection; expressions of LILRB and MAP 4 K1 were increased in acute rejection patients, but not in stable recipients. There were no overlapping DEGs in blood samples of transplant recipients. CONCLUSION By performing bioinformatics analysis on the immune status of kidney transplant patients, the present study reports several DEGs in the renal biopsy of transplant recipients, which are requested to be validated in clinical practice.
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Jeon HJ, Lee JG, Kim K, Jang JY, Han SW, Choi J, Ryu JH, Koo TY, Jeong JC, Lee JW, Ishida H, Park JB, Lee SH, Ahn C, Yang J. Peripheral blood transcriptome analysis and development of classification model for diagnosing antibody-mediated rejection vs accommodation in ABO-incompatible kidney transplant. Am J Transplant 2020; 20:112-124. [PMID: 31373158 DOI: 10.1111/ajt.15553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/02/2019] [Accepted: 07/28/2019] [Indexed: 02/07/2023]
Abstract
The major obstacle to successful ABO blood group-incompatible kidney transplantation (ABOi KT) is antibody-mediated rejection (AMR). This study aimed to investigate transcriptional profiles through RNA sequencing and develop a minimally invasive diagnostic tool for discrimination between accommodation and early acute AMR in ABOi KT. Twenty-eight ABOi KT patients were selected: 18 with accommodation and 10 with acute AMR at the 10th day posttransplant protocol biopsy. Complete transcriptomes of their peripheral blood were analyzed by RNA sequencing. Candidate genes were selected by bioinformatics analysis, validated with quantitative polymerase chain reaction, and used to develop a classification model to diagnose accommodation. A total of 1385 genes were differentially expressed in accommodation compared with in AMR with P-adjusted < .05. Functional annotation and gene set enrichment analysis identified several immune-related and immunometabolic pathways. A 5-gene classification model including COX7A2L, CD69, CD14, CFD, and FOXJ3 was developed by logistic regression analysis. The model was further validated with an independent cohort and discriminated between accommodation and AMR with 92.7% sensitivity, 85.7% specificity, and 91.7% accuracy. Our study suggests that a classification model based on peripheral blood transcriptomics may allow minimally invasive diagnosis of acute AMR vs accommodation and subsequent patient-tailored immunosuppression in ABOi KT.
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Affiliation(s)
- Hee Jung Jeon
- Department of Internal Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Jae-Ghi Lee
- Transplantation Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Joon Young Jang
- Transplantation Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Won Han
- School of Industrial Management Engineering, Korea University, Seoul, Republic of Korea
| | - Jinwoo Choi
- School of Industrial Management Engineering, Korea University, Seoul, Republic of Korea
| | - Jung-Hwa Ryu
- Transplantation Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Tai Yeon Koo
- Transplantation Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jong Cheol Jeong
- Department of Nephrology, Ajou University School of Medicine, Suwon, Gyeonggi-do, Republic of Korea
| | - Jae Wook Lee
- Nephrology Clinic, National Cancer Center, Goyang, Gyeonggi-do, Republic of Korea
| | - Hideki Ishida
- Department of Urology, Tokyo Women's Medical University, Tokyo, Japan
| | - Jae Berm Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sang Ho Lee
- Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Curie Ahn
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jaeseok Yang
- Transplantation Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Transplantation Center, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Surgery, Seoul National University Hospital, Seoul, Republic of Korea
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Ventura CG, Whisenant T, Gelbart T, David DS, Agena F, Salomon DR, David-Neto E, Kurian SM. Discovery and cross-validation of peripheral blood and renal biopsy gene expression signatures from ethnically diverse kidney transplant populations. Am J Transplant 2019; 19:3356-3366. [PMID: 31152474 PMCID: PMC6883121 DOI: 10.1111/ajt.15482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/15/2019] [Accepted: 05/04/2019] [Indexed: 01/25/2023]
Abstract
We determined peripheral blood (PB) and biopsy (Bx) RNA expression signatures in a Brazilian and US cohort of kidney transplant patients. Phenotypes assigned by precise histology were: acute rejection (AR), interstitial fibrosis/tubular atrophy/chronic rejection (CR), excellent functioning transplants (TX), and glomerulonephritis recurrence (GN). Samples were analyzed on microarrays and profiles from each cohort were cross-validated on the other cohort with similar phenotypes. We discovered signatures for each tissue: (1) AR vs TX, (2) CR vs TX, and (3) GN vs TX using the Random Forests algorithm. We validated biopsies signatures of AR vs TX (area under the curve [AUC] 0.97) and CR vs TX (AUC 0.87). We also validated both PB and Bx signatures of AR vs TX and CR vs TX with varying degrees of accuracy. Several biological pathways were shared between AR and CR, suggesting similar rejection mechanisms in these 2 clinical phenotypes. Thus, we identified gene expression signatures for AR and CR in transplant patients and validated them in independent cohorts of significantly different racial/ethnic backgrounds. These results reveal that there are strong unifying immune mechanisms driving transplant diseases and identified in the signatures discovered in each cohort, suggesting that molecular diagnostics across populations are feasible despite ethnic and environmental differences.
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Affiliation(s)
- Carlucci Gualberto Ventura
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Thomas Whisenant
- University of California, San Diego, School of Medicine, Center for Computational Biology and Bioinformatics, La Jolla, California
| | - Terri Gelbart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Daisa S.R. David
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Fabiana Agena
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Elias David-Neto
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Sunil M. Kurian
- Scripps Center for Organ Transplantation, Scripps Green Hospital, La Jolla, California
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41
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Zhang H, Shi G, Hu Q, Zhang H, Zheng M, Jiang K, Gu M. Transcriptional dissection of differentially expressed long non-coding RNAs and messenger RNAs reveals the potential molecular mechanism after kidney transplantation. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:458. [PMID: 31700894 DOI: 10.21037/atm.2019.08.60] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Kidney transplantation has given benefits to patients, although the associated genetic mechanisms are unclear. The present study aimed to understand the changes in gene expression and genetic pathways after kidney transplantation with the administration of immunosuppressive drugs. Methods The transcriptome data of blood samples from kidney transplantation recipients, obtained by RNA-seq, were reannotated to a more complete human genome (GRCh38/hg38). We compared the differentially expressed genes (DEGs) at pretransplant and 1 week, 3 months and 6 months posttransplant; researched the temporal variation of the DEGs; and constructed a long non-coding RNA (lncRNA)-messenger RNA (mRNA) network. Results We found that compared to that at pretransplantation, 1,766 genes and 3,530 genes were upregulated and downregulated, respectively, at 1 week after kidney transplantation, and the number of DEGs declined over time. These DEGs were separated into 16 clusters, and the temporal variation expression was established by the average expression of the DEGs. A pathway analysis suggested that the immune reaction was attenuated and that the expression of ribosome-related proteins was reduced. Conclusions The lncRNA-mRNA network had 235 connections between 138 lncRNAs and 170 mRNAs. This work generated a gene profile based on temporal variation and revealed a significantly altered lncRNA-mRNA axis contributing to molecular regulation, suggesting the potential gene mechanism of kidney transplantation and the effects of immunosuppressive drugs.
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Affiliation(s)
- Hengcheng Zhang
- Department of Urology, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Guodong Shi
- Pancreas Center, Department of General Surgery, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.,Pancreas Institute of Nanjing Medical University, Nanjing 210029, China
| | - Qingqiao Hu
- Department of Nuclear Medicine, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Henglu Zhang
- Department of Endocrinology and Metabolism, Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian 223001, China
| | - Ming Zheng
- Department of Urology, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Kuirong Jiang
- Pancreas Center, Department of General Surgery, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.,Pancreas Institute of Nanjing Medical University, Nanjing 210029, China
| | - Min Gu
- Department of Urology, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Van Loon E, Gazut S, Yazdani S, Lerut E, de Loor H, Coemans M, Noël LH, Thorrez L, Van Lommel L, Schuit F, Sprangers B, Kuypers D, Essig M, Gwinner W, Anglicheau D, Marquet P, Naesens M. Development and validation of a peripheral blood mRNA assay for the assessment of antibody-mediated kidney allograft rejection: A multicentre, prospective study. EBioMedicine 2019; 46:463-472. [PMID: 31378695 PMCID: PMC6710906 DOI: 10.1016/j.ebiom.2019.07.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Background Antibody-mediated rejection, a leading cause of renal allograft graft failure, is diagnosed by histological assessment of invasive allograft biopsies. Accurate non-invasive biomarkers are not available. Methods In the multicentre, prospective BIOMARGIN study, blood samples were prospectively collected at time of renal allograft biopsies between June 2011 and August 2016 and analyzed in three phases. The discovery and derivation phases of the study (N = 117 and N = 183 respectively) followed a case-control design and included whole genome transcriptomics and targeted mRNA expression analysis to construct and lock a multigene model. The primary end point was the diagnostic accuracy of the locked multigene assay for antibody-mediated rejection in a third validation cohort of serially collected blood samples (N = 387). This trial is registered with ClinicalTrials.gov, number NCT02832661. Findings We identified and locked an 8-gene assay (CXCL10, FCGR1A, FCGR1B, GBP1, GBP4, IL15, KLRC1, TIMP1) in blood samples from the discovery and derivation phases for discrimination between cases with (N = 49) and without (N = 134) antibody-mediated rejection. In the validation cohort, this 8-gene assay discriminated between cases with (N = 41) and without antibody-mediated rejection (N = 346) with good diagnostic accuracy (ROC AUC 79·9%; 95% CI 72·6 to 87·2, p < 0·0001). The diagnostic accuracy of the 8-gene assay was retained both at time of stable graft function and of graft dysfunction, within the first year and also later after transplantation. The 8-gene assay is correlated with microvascular inflammation and transplant glomerulopathy, but not with the histological lesions of T-cell mediated rejection. Interpretation We identified and validated a novel 8-gene expression assay that can be used for non-invasive diagnosis of antibody-mediated rejection. Funding The Seventh Framework Programme (FP7) of the European Commission.
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Affiliation(s)
- Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium
| | - Stéphane Gazut
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, Gif-sur-Yvette, France
| | - Saleh Yazdani
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Evelyne Lerut
- University Hospitals Leuven, Department of Morphology and Molecular Pathology, Leuven, Belgium
| | - Henriette de Loor
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Maarten Coemans
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Laure-Hélène Noël
- Necker-Enfants Malades Institute, French National Institute of Health and Medical Research U1151, France
| | - Lieven Thorrez
- KU Leuven Department of Development and Regeneration, campus KULAK, Kortrijk, Belgium
| | - Leentje Van Lommel
- KU Leuven Gene Expression Unit, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frans Schuit
- KU Leuven Gene Expression Unit, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium; KU Leuven Laboratory of Molecular Immunology, Rega Institute, Leuven, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium
| | - Marie Essig
- CHU Limoges, Department of Nephrology, Dialysis and Transplantation, Univ. Limoges, U850 INSERM, Limoges, France
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Dany Anglicheau
- Paris Descartes, Sorbonne Paris Cité University, INSERM U1151, Paris, France; Department of Nephrology and Kidney Transplantation, RTRS Centaure, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pierre Marquet
- CHU Limoges, Univ. Limoges, U850 INSERM, Limoges, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium.
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43
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Paquot F, Weekers L, Bonvoisin C, Pottel H, Jouret F. "Acute kidney dysfunction with no rejection" is associated with poor renal outcomes at 2 years post kidney transplantation. BMC Nephrol 2019; 20:249. [PMID: 31288762 PMCID: PMC6617570 DOI: 10.1186/s12882-019-1444-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/01/2019] [Indexed: 01/08/2023] Open
Abstract
Background “Acute kidney dysfunction with no rejection” (ADNR) corresponds to acute kidney injury without histological evidence of acute rejection (AR) in kidney transplant recipients (KTR). The prognosis of ADNR is unknown. Methods From 2007 to 2015, we categorized KTR with for-cause kidney biopsy within the first 12 months post kidney transplantation (KTx) into ADNR (n = 93) and biopsy-proven AR (n = 22). Controls (C, n = 135) included KTR with no ADNR or AR within the first 24 months post-KTx. A piecewise linear regression with a single fixed-knot at 12 months served to establish intercepts and slopes of MDRD-eGFR variations from 12 to 24 months. The percentage of KTR with ≥30% reduction of eGFR from 12 to 24 months was calculated as a surrogate marker of future graft loss. Results The median time for for-cause biopsy was 22 [10–70] and 13 [7–43] days for ADNR and AR, respectively. At 12 months, eGFR was significantly higher in C (57.6 ± 14.9 mL/min/1.73m2) vs. ADNR (43.5 ± 15.4 mL/min/1.73m2, p < 0.0001) and vs. AR (46.5 ± 15.2 mL/min/1.73m2, p < 0.0065). The proportion of KTR with ≥30% reduction in eGFR from 12 to 24 months reached 16.3% in C vs. 29.9% in ADNR (p = 0.02) and vs. 15% in AR (not significant). Conclusions ADNR is associated with poor outcomes within 2 years post-KTx.
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Affiliation(s)
- François Paquot
- Division of Nephrology, Department of Internal Medicine, University of Liège Hospital, Avenue Hippocrate, 13 - B4000, Liège, Belgium.
| | - Laurent Weekers
- Division of Nephrology, Department of Internal Medicine, University of Liège Hospital, Avenue Hippocrate, 13 - B4000, Liège, Belgium
| | - Catherine Bonvoisin
- Division of Nephrology, Department of Internal Medicine, University of Liège Hospital, Avenue Hippocrate, 13 - B4000, Liège, Belgium
| | - Hans Pottel
- KU Leuven Kulak, Department of Public Health and Primary Care, University of Leuven, Kortrijk, Belgium
| | - François Jouret
- Division of Nephrology, Department of Internal Medicine, University of Liège Hospital, Avenue Hippocrate, 13 - B4000, Liège, Belgium.,Groupe Interdisciplinaire de Génoprotéomique Appliquée, Cardiovascular Sciences, University of Liège, Liège, Belgium
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44
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Zhang W, Yi Z, Keung KL, Shang H, Wei C, Cravedi P, Sun Z, Xi C, Woytovich C, Farouk S, Huang W, Banu K, Gallon L, Magee CN, Najafian N, Samaniego M, Djamali A, Alexander SI, Rosales IA, Smith RN, Xiang J, Lerut E, Kuypers D, Naesens M, O'Connell PJ, Colvin R, Menon MC, Murphy B. A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection. J Am Soc Nephrol 2019; 30:1481-1494. [PMID: 31278196 DOI: 10.1681/asn.2018111098] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/01/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In kidney transplant recipients, surveillance biopsies can reveal, despite stable graft function, histologic features of acute rejection and borderline changes that are associated with undesirable graft outcomes. Noninvasive biomarkers of subclinical acute rejection are needed to avoid the risks and costs associated with repeated biopsies. METHODS We examined subclinical histologic and functional changes in kidney transplant recipients from the prospective Genomics of Chronic Allograft Rejection (GoCAR) study who underwent surveillance biopsies over 2 years, identifying those with subclinical or borderline acute cellular rejection (ACR) at 3 months (ACR-3) post-transplant. We performed RNA sequencing on whole blood collected from 88 individuals at the time of 3-month surveillance biopsy to identify transcripts associated with ACR-3, developed a novel sequencing-based targeted expression assay, and validated this gene signature in an independent cohort. RESULTS Study participants with ACR-3 had significantly higher risk than those without ACR-3 of subsequent clinical acute rejection at 12 and 24 months, faster decline in graft function, and decreased graft survival in adjusted Cox analysis. We identified a 17-gene signature in peripheral blood that accurately diagnosed ACR-3, and validated it using microarray expression profiles of blood samples from 65 transplant recipients in the GoCAR cohort and three public microarray datasets. In an independent cohort of 110 transplant recipients, tests of the targeted expression assay on the basis of the 17-gene set showed that it identified individuals at higher risk of ongoing acute rejection and future graft loss. CONCLUSIONS Our targeted expression assay enabled noninvasive diagnosis of subclinical acute rejection and inflammation in the graft and may represent a useful tool to risk-stratify kidney transplant recipients.
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Affiliation(s)
- Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zhengzi Yi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Karen L Keung
- Department of Medicine, Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Huimin Shang
- Department of Microbiology and Immunology, Cornell Medical Center, New York, New York
| | - Chengguo Wei
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paolo Cravedi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zeguo Sun
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caixia Xi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Christopher Woytovich
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samira Farouk
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Weiqing Huang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Khadija Banu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lorenzo Gallon
- Department of Medicine-Nephrology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ciara N Magee
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Nader Najafian
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Milagros Samaniego
- Division of Nephrology, Department of Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Arjang Djamali
- Division of Nephrology, Department of Medicine, University of Wisconsin, Madison, Wisconsin
| | - Stephen I Alexander
- Department of Medicine, Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Ivy A Rosales
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rex Neal Smith
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jenny Xiang
- Department of Microbiology and Immunology, Cornell Medical Center, New York, New York
| | | | - Dirk Kuypers
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.,Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium; and
| | - Maarten Naesens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.,Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium; and
| | - Philip J O'Connell
- Department of Medicine, Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Madhav C Menon
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Barbara Murphy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York;
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45
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Hanssen O, Lovinfosse P, Weekers L, Hustinx R, Jouret F. [ 18F-FDG positron emission tomography in non-oncological renal pathology: Current indications and perspectives]. Nephrol Ther 2019; 15:430-438. [PMID: 30982747 DOI: 10.1016/j.nephro.2018.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022]
Abstract
Positron emission tomography combined with computed tomography (PET/CT) is a nuclear imaging technique which provides anatomical and functional information. PET/CT is increasingly used in non-oncological nephrology since conventional radiological approaches after injection of contrast agents are relatively contra-indicated in patients with chronic kidney disease (CKD). PET/CT after i.v. injection of 18F-fluoro-deoxy-glucose (FDG) is not toxic and is characterized by a high sensitivity. The level of irradiation (∼5mSv) is acceptable. CKD does not significantly influence tissue uptake of 18F-FDG. The purpose of the present review aims at detailing the non-oncological indications of 18F-FDG PET/CT in general nephrology and after kidney transplantation. Particularly, 18F-FDG PET/CT appears useful in the diagnosis of cyst infection in patients with autosomal dominant polycystic kidney disease, as well as in the characterization of retroperitoneal fibrosis. In kidney transplant recipients, 18F-FDG PET/CT may help in the diagnostic work-up of suspected acute rejection, thereby eventually avoiding unnecessary kidney transplant biopsy. Perspectives in 18F-FDG PET/CT imaging are discussed, including innovative approaches of image analysis.
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Affiliation(s)
- Oriane Hanssen
- Service de néphrologie, centre hospitalier universitaire de Liège, avenue Hippocrate 13, 4000 Liège, Belgique
| | - Pierre Lovinfosse
- Service de médecine nucléaire et imagerie oncologique, centre hospitalier universitaire de Liège, avenue Hippocrate 13, 4000 Liège, Belgique
| | - Laurent Weekers
- Service de médecine nucléaire et imagerie oncologique, centre hospitalier universitaire de Liège, avenue Hippocrate 13, 4000 Liège, Belgique
| | - Roland Hustinx
- Service de médecine nucléaire et imagerie oncologique, centre hospitalier universitaire de Liège, avenue Hippocrate 13, 4000 Liège, Belgique
| | - François Jouret
- Service de néphrologie, centre hospitalier universitaire de Liège, avenue Hippocrate 13, 4000 Liège, Belgique; Groupe interdisciplinaire de géno-protéomique appliquée (GIGA), sciences cardiovasculaires, université de Liège, Liège, Belgique.
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46
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Marsh CL, Kurian SM, Rice JC, Whisenant TC, David J, Rose S, Schieve C, Lee D, Case J, Barrick B, Peddi VR, Mannon RB, Knight R, Maluf D, Mandelbrot D, Patel A, Friedewald JJ, Abecassis MM, First MR. Application of TruGraf v1: A Novel Molecular Biomarker for Managing Kidney Transplant Recipients With Stable Renal Function. Transplant Proc 2019; 51:722-728. [PMID: 30979456 DOI: 10.1016/j.transproceed.2019.01.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/10/2018] [Accepted: 01/17/2019] [Indexed: 01/22/2023]
Abstract
TruGraf v1 is a laboratory-developed DNA microarray-based gene expression blood test to enable proactive noninvasive serial assessment of kidney transplant recipients with stable renal function. It has been previously validated in patients identified as Transplant eXcellence (TX: stable serum creatinine, normal biopsy results, indicative of immune quiescence), and not-TX (renal dysfunction and/or rejection on biopsy results). TruGraf v1 is intended for use in subjects with stable renal function to measure the immune status as an alternative to invasive, expensive, and risky surveillance biopsies. MATERIALS AND METHODS In this study, simultaneous blood tests and clinical assessments were performed in 192 patients from 7 transplant centers to evaluate TruGraf v1. The molecular testing laboratory was blinded to renal function and biopsy results. RESULTS Overall, TruGraf v1 accuracy (concordance between TruGraf v1 result and clinical and/or histologic assessment) was 74% (142/192), and a result of TX was accurate in 116 of 125 (93%). The negative predictive value for TruGraf v1 was 90%, with a sensitivity 74% and specificity of 73%. Results did not significantly differ in patients with a biopsy-confirmed diagnosis vs those without a biopsy. CONCLUSIONS TruGraf v1 can potentially support a clinical decision enabling unnecessary surveillance biopsies with high confidence, making it an invaluable addition to the transplant physician's tool kit for managing patients. TruGraf v1 testing can potentially avoid painful and risky invasive biopsies, reduce health care costs, and enable frequent assessment of patients with stable renal function to confirm the presence of immune quiescence in the peripheral blood.
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Affiliation(s)
- C L Marsh
- Scripps Center for Organ Transplantation, La Jolla, California, United States; Scripps Clinic Bio-Repository and Transplantation Research, La Jolla, California, United States.
| | - S M Kurian
- Scripps Clinic Bio-Repository and Transplantation Research, La Jolla, California, United States
| | - J C Rice
- Scripps Center for Organ Transplantation, La Jolla, California, United States
| | - T C Whisenant
- University of California, San Diego, School of Medicine, Center for Computational Biology and Bioinformatics, La Jolla, California, United States
| | - J David
- Transplant Genomics Inc, Mansfield, Massachusetts, United States
| | - S Rose
- Transplant Genomics Inc, Mansfield, Massachusetts, United States
| | - C Schieve
- Transplant Genomics Inc, Mansfield, Massachusetts, United States
| | - D Lee
- Transplant Genomics Inc, Mansfield, Massachusetts, United States
| | - J Case
- Scripps Clinic Bio-Repository and Transplantation Research, La Jolla, California, United States
| | - B Barrick
- Scripps Clinic Bio-Repository and Transplantation Research, La Jolla, California, United States
| | - V R Peddi
- California Pacific Medical Center, San Francisco, California, United States
| | - R B Mannon
- University of Alabama School of Medicine, Birmingham, Alabama, United States
| | - R Knight
- Houston Methodist Hospital, Houston, Texas, United States
| | - D Maluf
- University of Virginia, Charlottesville, Virginia, United States
| | - D Mandelbrot
- University of Wisconsin, Madison, Wisconsin, United States
| | - A Patel
- Henry Ford Hospital, Detroit, Michigan, United States
| | - J J Friedewald
- Comprehensive Transplant Center, Northwestern University, Chicago, Illionis, United States
| | - M M Abecassis
- Comprehensive Transplant Center, Northwestern University, Chicago, Illionis, United States
| | - M R First
- Transplant Genomics Inc, Mansfield, Massachusetts, United States; Comprehensive Transplant Center, Northwestern University, Chicago, Illionis, United States
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47
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Friedewald JJ, Kurian SM, Heilman RL, Whisenant TC, Poggio ED, Marsh C, Baliga P, Odim J, Brown MM, Ikle DN, Armstrong BD, charette JI, Brietigam SS, Sustento-Reodica N, Zhao L, Kandpal M, Salomon DR, Abecassis MM. Development and clinical validity of a novel blood-based molecular biomarker for subclinical acute rejection following kidney transplant. Am J Transplant 2019; 19:98-109. [PMID: 29985559 PMCID: PMC6387870 DOI: 10.1111/ajt.15011] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/12/2018] [Accepted: 07/03/2018] [Indexed: 01/25/2023]
Abstract
Noninvasive biomarkers are needed to monitor stable patients after kidney transplant (KT), because subclinical acute rejection (subAR), currently detectable only with surveillance biopsies, can lead to chronic rejection and graft loss. We conducted a multicenter study to develop a blood-based molecular biomarker for subAR using peripheral blood paired with surveillance biopsies and strict clinical phenotyping algorithms for discovery and validation. At a predefined threshold, 72% to 75% of KT recipients achieved a negative biomarker test correlating with the absence of subAR (negative predictive value: 78%-88%), while a positive test was obtained in 25% to 28% correlating with the presence of subAR (positive predictive value: 47%-61%). The clinical phenotype and biomarker independently and statistically correlated with a composite clinical endpoint (renal function, biopsy-proved acute rejection, ≥grade 2 interstitial fibrosis, and tubular atrophy), as well as with de novo donor-specific antibodies. We also found that <50% showed histologic improvement of subAR on follow-up biopsies despite treatment and that the biomarker could predict this outcome. Our data suggest that a blood-based biomarker that reduces the need for the indiscriminate use of invasive surveillance biopsies and that correlates with transplant outcomes could be used to monitor KT recipients with stable renal function, including after treatment for subAR, potentially improving KT outcomes.
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Affiliation(s)
| | | | | | - Thomas C. Whisenant
- UC San Diego Center for Computational Biology & Bioinformatics, San Diego, CA, USA
| | | | | | | | - Jonah Odim
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Merideth M. Brown
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | | | | | - jane I. charette
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | | | - Lihui Zhao
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Manoj Kandpal
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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48
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First MR, Peddi VR, Mannon R, Knight R, Marsh CL, Kurian SM, Rice JC, Maluf D, Mandelbrot D, Patel A, David J, Schieve C, Lee D, Lewis P, Friedewald JJ, Abecassis MM, Rose S. Investigator Assessment of the Utility of the TruGraf Molecular Diagnostic Test in Clinical Practice. Transplant Proc 2018; 51:729-733. [PMID: 30979457 DOI: 10.1016/j.transproceed.2018.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/14/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND TruGraf v1 is a well-validated DNA microarray-based test that analyzes blood gene expression profiles as an indicator of immune status in kidney transplant recipients with stable renal function. METHODS In this study, investigators assessed clinical utility of the TruGraf test in patient management. In a retrospective study, simultaneous blood tests and clinical assessments were performed in 192 patients at 7 transplant centers, and in a prospective observational study they were performed in 45 subjects at 5 transplant centers. RESULTS When queried regarding whether or not the TruGraf test result impacted their decision regarding patient management, in 168 of 192 (87.5%) cases the investigator responded affirmatively. The prospective study indicated that TruGraf results supported physicians' decisions on patient management 87% (39/45) of the time, and in 93% of cases physicians indicated that they would use serial TruGraf testing in future patient management. A total of 21 of 39 (54%) reported results confirmed their decision that no intervention was needed, and 17 of 39 (44%) reported that results specifically informed them that a decision not to perform a surveillance biopsy was correct. CONCLUSIONS TruGraf is the first and only noninvasive test to be evaluated for clinical utility in determining rejection status of patients with stable renal function and shows promise of providing support for clinical decisions to avoid unnecessary surveillance biopsies with a high degree of confidence. TruGraf is an invaluable addition to the transplant physician's tool kit for managing patient health by avoiding painful and invasive biopsies, reducing health care costs, and enabling frequent assessment of patients with stable renal function to confirm immune quiescence.
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Affiliation(s)
- M R First
- Transplant Genomics Inc, Mansfield, MA; Comprehensive Transplant Center, Northwestern University, Chicago, IL.
| | - V R Peddi
- California Pacific Medical Center, San Francisco, CA
| | - R Mannon
- University of Alabama at Birmingham, Birmingham, AL
| | - R Knight
- Houston Methodist Hospital, Houston, TX
| | - C L Marsh
- Scripps Center for Organ Transplantation, La Jolla, CA
| | - S M Kurian
- Scripps Center for Organ Transplantation, La Jolla, CA
| | - J C Rice
- Scripps Center for Organ Transplantation, La Jolla, CA
| | - D Maluf
- University of Virginia, Charlottesville, VA
| | | | - A Patel
- Henry Ford Hospital, Detroit, MI
| | - J David
- Transplant Genomics Inc, Mansfield, MA
| | - C Schieve
- Transplant Genomics Inc, Mansfield, MA
| | - D Lee
- Transplant Genomics Inc, Mansfield, MA
| | - P Lewis
- Transplant Genomics Inc, Mansfield, MA
| | - J J Friedewald
- Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - M M Abecassis
- Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - S Rose
- Transplant Genomics Inc, Mansfield, MA
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49
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Barner M, DeKoning J, Kashi Z, Halloran P. Recent Advancements in the Assessment of Renal Transplant Dysfunction with an Emphasis on Microarray Molecular Diagnostics. Clin Lab Med 2018; 38:623-635. [PMID: 30420057 DOI: 10.1016/j.cll.2018.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conventional assessment of renal transplant rejection and injury through use of histology, C4d staining, and HLA antibody testing, has been the standard approach to transplant management. By many measures, these methods of conventional assessment may be considered flawed, particularly with the subjective nature of histologic diagnoses. The Alberta Transplant Applied Genomics Center has developed the Molecular Microscope diagnostic system, which uses microarrays to measure gene expression. These data are analyzed using classifiers (weighted equations) that compare the tested biopsy to a proprietary reference set of biopsies to provide objective measures of the status of the renal transplant.
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Affiliation(s)
- Meagan Barner
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA
| | - Jenefer DeKoning
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA
| | - Zahra Kashi
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA.
| | - Phillip Halloran
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Alberta Transplant Applied Genomics Center, 250 Heritage Medical Research Centre, Edmonton, Alberta T6G 2S2, Canada; Transcriptome Sciences Inc, Edmonton, Alberta, Canada
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50
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Jamshaid F, Froghi S, Di Cocco P, Dor FJ. Novel non-invasive biomarkers diagnostic of acute rejection in renal transplant recipients: A systematic review. Int J Clin Pract 2018; 72:e13220. [PMID: 30011113 DOI: 10.1111/ijcp.13220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/07/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Acute rejection is a significant complication detrimental to kidney transplant function. Current accepted means of diagnosis is percutaneous renal biopsy, a costly and invasive procedure. There is an urgent need to detect and validate non-invasive biomarkers capable of replacing the biopsy. DESIGN, SETTING, PARTICIPANTS AND MEASUREMENTS Comprehensive literature searches of Medline, EMBASE and Cochrane Central Register of Controlled Trials databases were performed. Eligible studies were included as per inclusion criteria and assessed for quality using the GRADE quality of evidence tool. Outcomes evaluated included biomarker diagnostic performance, number of patients/samples, mean age and gender ratio, immunosuppression regime, in addition to clinical applications of the biomarker(s) tested. PRISMA guidelines were followed. Where possible, statistical analysis of comparative performance data was performed. RESULTS 23 studies were included in this review, including 19 adult, 3 paediatric and 1 mixed studies. A total of 2858 participants and 50 candidate non-invasive tests were identified. Sensitivity, specificity and area under the curve performance values ranged 36%-100%, 30%-100% and 0.55-0.98, respectively. CONCLUSIONS Although larger, more robust multi-centre validation studies are needed before non-invasive biomarkers can replace the biopsy, numerous candidate tests have demonstrated significant promise for various facets of postoperative management. Suggested uses include: ruling out patients with a low risk of acute rejection to avoid the need for biopsy, non-invasive testing where the biopsy is contraindicated and a prompt diagnosis is needed, and integration into a serial blood monitoring protocol in conjunction with serum creatinine.
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Affiliation(s)
- Faisal Jamshaid
- MRC Centre for Transplantation, Guy's Campus, Kings College London School of Medicine, London, UK
| | - Saied Froghi
- MRC Centre for Transplantation, Guy's Campus, Kings College London School of Medicine, London, UK
- Imperial College London, Imperial College Renal and Transplant Centre, Hammersmith Hospital, London, UK
| | - Pierpaolo Di Cocco
- Imperial College London, Imperial College Renal and Transplant Centre, Hammersmith Hospital, London, UK
| | - Frank Jmf Dor
- Imperial College London, Imperial College Renal and Transplant Centre, Hammersmith Hospital, London, UK
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