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Pan X, Peng J, Zhu R, An N, Pei J. Non-invasive biomarkers of acute rejection in pediatric kidney transplantation: New targets and strategies. Life Sci 2024; 348:122698. [PMID: 38710278 DOI: 10.1016/j.lfs.2024.122698] [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: 02/01/2024] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Kidney transplantation is the preferred treatment for pediatric end-stage renal disease. However, pediatric recipients face unique challenges due to their prolonged need for kidney function to accommodate growth and development. The continual changes in the immune microenvironment during childhood development and the heightened risk of complications from long-term use of immunosuppressive drugs. The overwhelming majority of children may require more than one kidney transplant in their lifetime. Acute rejection (AR) stands as the primary cause of kidney transplant failure in children. While pathologic biopsy remains the "gold standard" for diagnosing renal rejection, its invasive nature raises concerns regarding potential functional impairment and the psychological impact on children due to repeated procedures. In this review, we outline the current research status of novel biomarkers associated with AR in urine and blood after pediatric kidney transplantation. These biomarkers exhibit superior diagnostic and prognostic performance compared to conventional ones, with the added advantages of being less invasive and highly reproducible for long-term graft monitoring. We also integrate the limitations of these novel biomarkers and propose a refined monitoring model to optimize the management of AR in pediatric kidney transplantation.
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Affiliation(s)
- Xingyu Pan
- Department of Pediatric surgrey, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Jinpu Peng
- Department of Pediatric surgrey, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Rong Zhu
- Department of Pediatric surgrey, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Nini An
- Department of Pediatric surgrey, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Jun Pei
- Department of Pediatric surgrey, Guizhou Provincial People's Hospital, Guiyang 550002, China.
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2
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Mizuno H, Murakami N. Multi-omics Approach in Kidney Transplant: Lessons Learned from COVID-19 Pandemic. CURRENT TRANSPLANTATION REPORTS 2023; 10:173-187. [PMID: 38152593 PMCID: PMC10751044 DOI: 10.1007/s40472-023-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 12/29/2023]
Abstract
Purpose of Review Multi-omics approach has advanced our knowledge on transplantation-associated clinical outcomes, such as acute rejection and infection, and emerging omics data are becoming available in kidney transplant and COVID-19. Herein, we discuss updated findings of multi-omics data on kidney transplant outcomes, as well as COVID-19 and kidney transplant. Recent Findings Transcriptomics, proteomics, and metabolomics revealed various inflammation pathways associated with kidney transplantation-related outcomes and COVID-19. Although multi-omics data on kidney transplant and COVID-19 is limited, activation of innate immune pathways and suppression of adaptive immune pathways were observed in the active phase of COVID-19 in kidney transplant recipients. Summary Multi-omics analysis has led us to a deeper exploration and a more comprehensive understanding of key biological pathways in complex clinical settings, such as kidney transplantation and COVID-19. Future multi-omics analysis leveraging multi-center biobank collaborative will further advance our knowledge on the precise immunological responses to allograft and emerging pathogens.
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Affiliation(s)
- Hiroki Mizuno
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
- Dvision of Nephrology and Rheumatology, Toranomon Hospital, Tokyo, Japan
| | - Naoka Murakami
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
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Rainey A, McKay GJ, English J, Thakkinstian A, Maxwell AP, Corr M. Proteomic analysis investigating kidney transplantation outcomes- a scoping review. BMC Nephrol 2023; 24:346. [PMID: 37993798 PMCID: PMC10666386 DOI: 10.1186/s12882-023-03401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Kidney transplantation is the optimal treatment option for most patients with end-stage kidney disease given the significantly lower morbidity and mortality rates compared to remaining on dialysis. Rejection and graft failure remain common in transplant recipients with limited improvement in long-term transplant outcomes despite therapeutic advances. There is an unmet need in the development of non-invasive biomarkers that specifically monitor graft function and predict transplant pathologies that affect outcomes. Despite the potential of proteomic investigatory approaches, up to now, no candidate biomarkers of sufficient sensitivity or specificity have translated into clinical use. The aim of this review was to collate and summarise protein findings and protein pathways implicated in the literature to date, and potentially flag putative biomarkers worth validating in independent patient cohorts. METHODS This review followed the Joanna Briggs' Institute Methodology for a scoping review. MedlineALL, Embase, Web of Science Core Collection, Scopus and Google Scholar databases were searched from inception until December 2022. Abstract and full text review were undertaken independently by two reviewers. Data was collated using a pre-designed data extraction tool. RESULTS One hundred one articles met the inclusion criteria. The majority were single-centre retrospective studies of small sample size. Mass spectrometry was the most used technique to evaluate differentially expressed proteins between diagnostic groups and studies identified various candidate biomarkers such as immune or structural proteins. DISCUSSION Putative immune or structural protein candidate biomarkers have been identified using proteomic techniques in multiple sample types including urine, serum and fluid used to perfuse donor kidneys. The most consistent findings implicated proteins associated with tubular dysfunction and immunological regulatory pathways such as leukocyte trafficking. However, clinical translation and adoption of candidate biomarkers is limited, and these will require comprehensive evaluation in larger prospective, multicentre trials.
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Affiliation(s)
- Anna Rainey
- Centre for Public Health- Queen's University Belfast, Belfast, UK
| | - Gareth J McKay
- Centre for Public Health- Queen's University Belfast, Belfast, UK
| | - Jane English
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Ammarin Thakkinstian
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Michael Corr
- Centre for Public Health- Queen's University Belfast, Belfast, UK.
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Abinti M, Favi E, Alfieri CM, Zanoni F, Armelloni S, Ferraresso M, Cantaluppi V, Castellano G. Update on current and potential application of extracellular vesicles in kidney transplantation. Am J Transplant 2023; 23:1673-1693. [PMID: 37517555 DOI: 10.1016/j.ajt.2023.07.010] [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: 05/02/2023] [Revised: 06/28/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
Kidney transplantation (KT) is the best treatment for end-stage kidney disease. However, early diagnosis of graft injury remains challenging, mainly because of the lack of accurate and noninvasive diagnostic techniques. Improving graft outcomes is equally demanding, as is the development of innovative therapies. Many research efforts are focusing on extracellular vesicles, cellular particles free in each body fluid that have shown promising results as precise markers of damage and potential therapeutic targets in many diseases, including the renal field. In fact, through their receptors and cargo, they act in damage response and immune modulation. In transplantation, they may be used to determine organ quality and aging, the presence of delayed graft function, rejection, and many other transplant-related pathologies. Moreover, their low immunogenicity and safe profile make them ideal for drug delivery and the development of therapies to improve KT outcomes. In this review, we summarize current evidence about extracellular vesicles in KT, starting with their characteristics and major laboratory techniques for isolation and characterization. Then, we discuss their use as potential markers of damage and as therapeutic targets, discussing their promising use in clinical practice as a form of liquid biopsy.
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Affiliation(s)
- Matteo Abinti
- Nephrology, Dialysis and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Evaldo Favi
- Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Carlo Maria Alfieri
- Nephrology, Dialysis and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Francesca Zanoni
- Nephrology, Dialysis and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Silvia Armelloni
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Mariano Ferraresso
- Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Vincenzo Cantaluppi
- Nephrology and Kidney Transplant Unit, Department of Translational Medicine (DIMET), University of Piemonte Orientale (UPO), "Maggiore della Carita" University Hospital, Novara, Italy
| | - Giuseppe Castellano
- Nephrology, Dialysis and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.
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5
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Ge Y, Ma S, Zhang J, Xiong Z, Li B, Ma S, Liu B, Yao X, Wang Z. Integrating bioinformatic analysis and detailed experiments reveal an EMT-related biomarker for clear cell renal cell carcinoma. Cancer Med 2023; 12:19320-19336. [PMID: 37676078 PMCID: PMC10557903 DOI: 10.1002/cam4.6504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) is associated with early recurrence and a poor prognosis in clear cell renal cell carcinoma (ccRCC). Studies have shown that EMT-related genes play an important regulatory role in tumor invasion, metastasis, and drug resistance, but the biological functions of EMT-related genes in ccRCC have not been specifically described. METHODS The mRNA and clinicopathological data of 532 ccRCC and 72 normal samples were downloaded from The Cancer Genome Atlas as a training set. The gene expression matrix and survival data of 91 and 101 ccRCC samples were obtained from the International Cancer Genome Consortium and the ArrayExpress databases as validation sets, respectively. Univariate Cox analysis was used to identify and cluster prognostic genes, and multivariate Cox was performed to construct a prognostic signature. Moreover, CIBERSORT and CellMiner were used to assess immune cell infiltration and prognostic gene-drug sensitivity of the signature, respectively. Most importantly, we performed detailed experiments to verify the oncogenic function of a significant gene, OLFML2B, in vitro and in vivo. RESULTS We constructed a prognostic signature including seven genes and divided patients into high-risk and low-risk groups. The prognosis of the high-risk group was significantly worse than that of the low-risk group through Kaplan-Meier survival analysis. Interestingly, significant differences were observed in clinical characteristics and immune cell infiltration between the two groups. In addition, a significant correlation was found between the expression of prognostic genes and the sensitivity of tumor cells to chemotherapeutics. Most importantly, OLFML2B was proved to contribute to the proliferation and metastasis of ccRCC through detailed functional experiments in vitro and in vivo, and its prognostic efficacy for ccRCC patients was affirmed. CONCLUSION We identified the prognostic signature of seven genes based on EMT-related genes as prognostic biomarkers for ccRCC. Besides, OLFML2B was validated as a potential diagnostic and therapeutic target for ccRCC by our detailed experiments.
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Affiliation(s)
- Yue Ge
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Sheng Ma
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Junbiao Zhang
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Zezhong Xiong
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Beining Li
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Siquan Ma
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiangyang Yao
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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6
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Novacescu D, Latcu SC, Bardan R, Daminescu L, Cumpanas AA. Contemporary Biomarkers for Renal Transplantation: A Narrative Overview. J Pers Med 2023; 13:1216. [PMID: 37623466 PMCID: PMC10456039 DOI: 10.3390/jpm13081216] [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: 06/27/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Renal transplantation (RT) is the preferred treatment for end-stage renal disease. However, clinical challenges persist, i.e., early detection of graft dysfunction, timely identification of rejection episodes, personalization of immunosuppressive therapy, and prediction of long-term graft survival. Biomarkers have emerged as valuable tools to address these challenges and revolutionize RT patient care. Our review synthesizes the existing scientific literature to highlight promising biomarkers, their biological characteristics, and their potential roles in enhancing clinical decision-making and patient outcomes. Emerging non-invasive biomarkers seemingly provide valuable insights into the immunopathology of nephron injury and allograft rejection. Moreover, we analyzed biomarkers with intra-nephron specificities, i.e., glomerular vs. tubular (proximal vs. distal), which can localize an injury in different nephron areas. Additionally, this paper provides a comprehensive analysis of the potential clinical applications of biomarkers in the prediction, detection, differential diagnosis and assessment of post-RT non-surgical allograft complications. Lastly, we focus on the pursuit of immune tolerance biomarkers, which aims to reclassify transplant recipients based on immune risk thresholds, guide personalized immunosuppression strategies, and ultimately identify patients for whom immunosuppression may safely be reduced. Further research, validation, standardization, and prospective studies are necessary to fully harness the clinical utility of RT biomarkers and guide the development of targeted therapies.
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Affiliation(s)
- Dorin Novacescu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Silviu Constantin Latcu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Razvan Bardan
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Liviu Daminescu
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
| | - Alin Adrian Cumpanas
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
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Boada P, Fatou B, Belperron AA, Sigdel TK, Smolen KK, Wurie Z, Levy O, Ronca SE, Murray KO, Liberto JM, Rashmi P, Kerwin M, Montgomery RR, Bockenstedt LK, Steen H, Sarwal MM. Longitudinal serum proteomics analyses identify unique and overlapping host response pathways in Lyme disease and West Nile virus infection. Front Immunol 2022; 13:1012824. [PMID: 36569838 PMCID: PMC9784464 DOI: 10.3389/fimmu.2022.1012824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/07/2022] [Indexed: 12/14/2022] Open
Abstract
Advancement in proteomics methods for interrogating biological samples has helped identify disease biomarkers for early diagnostics and unravel underlying molecular mechanisms of disease. Herein, we examined the serum proteomes of 23 study participants presenting with one of two common arthropod-borne infections: Lyme disease (LD), an extracellular bacterial infection or West Nile virus infection (WNV), an intracellular viral infection. The LC/MS based serum proteomes of samples collected at the time of diagnosis and during convalescence were assessed using a depletion-based high-throughput shotgun proteomics (dHSP) pipeline as well as a non-depleting blotting-based low-throughput platform (MStern). The LC/MS integrated analyses identified host proteome responses in the acute and recovery phases shared by LD and WNV infections, as well as differentially abundant proteins that were unique to each infection. Notably, we also detected proteins that distinguished localized from disseminated LD and asymptomatic from symptomatic WNV infection. The proteins detected in both diseases with the dHSP pipeline identified unique and overlapping proteins detected with the non-depleting MStern platform, supporting the utility of both detection methods. Machine learning confirmed the use of the serum proteome to distinguish the infection from healthy control sera but could not develop discriminatory models between LD and WNV at current sample numbers. Our study is the first to compare the serum proteomes in two arthropod-borne infections and highlights the similarities in host responses even though the pathogens and the vectors themselves are different.
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Affiliation(s)
- Patrick Boada
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, CA, United States
| | - Benoit Fatou
- Department of Pathology, Boston Children’s Hospital - Harvard Medical School, Boston, MA, United States
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
| | - Alexia A. Belperron
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Tara K. Sigdel
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, CA, United States
| | - Kinga K. Smolen
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Division of Infectious Diseases, Boston Children’s Hospital – Harvard Medical School, Boston, MA, United States
| | - Zainab Wurie
- Department of Pathology, Boston Children’s Hospital - Harvard Medical School, Boston, MA, United States
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
| | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
- Division of Infectious Diseases, Boston Children’s Hospital – Harvard Medical School, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology & Harvard, Cambridge, MA, United States
| | - Shannon E. Ronca
- Division of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- William T. Shearer Center for Human Immunobiology, Texas Children’s Hospital, Houston, TX, United States
| | - Kristy O. Murray
- Division of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- William T. Shearer Center for Human Immunobiology, Texas Children’s Hospital, Houston, TX, United States
| | - Juliane M. Liberto
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, CA, United States
| | - Priyanka Rashmi
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, CA, United States
| | - Maggie Kerwin
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, CA, United States
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Linda K. Bockenstedt
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital - Harvard Medical School, Boston, MA, United States
- Precision Vaccines Program, Boston Children’s Hospital, Boston, MA, United States
| | - Minnie M. Sarwal
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, CA, United States
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Proteomics for Biomarker Discovery for Diagnosis and Prognosis of Kidney Transplantation Rejection. Proteomes 2022; 10:proteomes10030024. [PMID: 35893765 PMCID: PMC9326686 DOI: 10.3390/proteomes10030024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 02/07/2023] Open
Abstract
Renal transplantation is currently the treatment of choice for end-stage kidney disease, enabling a quality of life superior to dialysis. Despite this, all transplanted patients are at risk of allograft rejection processes. The gold-standard diagnosis of graft rejection, based on histological analysis of kidney biopsy, is prone to sampling errors and carries high costs and risks associated with such invasive procedures. Furthermore, the routine clinical monitoring, based on urine volume, proteinuria, and serum creatinine, usually only detects alterations after graft histologic damage and does not differentiate between the diverse etiologies. Therefore, there is an urgent need for new biomarkers enabling to predict, with high sensitivity and specificity, the rejection processes and the underlying mechanisms obtained from minimally invasive procedures to be implemented in routine clinical surveillance. These new biomarkers should also detect the rejection processes as early as possible, ideally before the 78 clinical outputs, while enabling balanced immunotherapy in order to minimize rejections and reducing the high toxicities associated with these drugs. Proteomics of biofluids, collected through non-invasive or minimally invasive analysis, e.g., blood or urine, present inherent characteristics that may provide biomarker candidates. The current manuscript reviews biofluids proteomics toward biomarkers discovery that specifically identify subclinical, acute, and chronic immune rejection processes while allowing for the discrimination between cell-mediated or antibody-mediated processes. In time, these biomarkers will lead to patient risk stratification, monitoring, and personalized and more efficient immunotherapies toward higher graft survival and patient quality of life.
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Abstract
The current standard of serum creatinine and biopsy to monitor allograft health has many limitations. The most significant drawback of the current standard is the lack of sensitivity and specificity to allograft injuries, which are diagnosed only after significant damage to the allograft. Thus, it is of critical need to identify a biomarker that is sensitive and specific to the early detection of allograft injuries. Urine, as the direct renal ultrafiltrate that can be obtained noninvasively, directly reflects intrarenal processes in the allograft at greater accuracy than analysis of peripheral blood. We review transcriptomic, metabolomic, genomic, and proteomic discovery-based approaches to identifying urinary biomarkers for the noninvasive detection of allograft injuries, as well as the use of urine cell-free DNA in the QSant urine assay as a sensitive surrogate for the renal allograft biopsy for rejection diagnosis.
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10
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Ashcroft J, Leighton P, Elliott TR, Hosgood SA, Nicholson ML, Kosmoliaptsis V. Extracellular vesicles in kidney transplantation: a state-of-the-art review. Kidney Int 2021; 101:485-497. [PMID: 34838864 DOI: 10.1016/j.kint.2021.10.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Kidney transplantation is the optimal treatment for patients with kidney failure; however, early detection and timely treatment of graft injury remain a challenge. Precise and noninvasive techniques of graft assessment and innovative therapeutics are required to improve kidney transplantation outcomes. Extracellular vesicles (EVs) are lipid bilayer-delimited particles with unique biosignatures and immunomodulatory potential, functioning as intermediaries of cell signalling. Promising evidence exists for the potential of EVs to develop precision diagnostics of graft dysfunction, and prognostic biomarkers for clinician decision making. The inherent targeting characteristics of EVs and their low immunogenic and toxicity profiles combined with their potential as vehicles for drug delivery make them ideal targets for development of therapeutics to improve kidney transplant outcomes. In this review, we summarize the current evidence for EVs in kidney transplantation, discuss common methodological principles of EV isolation and characterization, explore upcoming innovative approaches in EV research, and discuss challenges and opportunities to enable translation of research findings into clinical practice.
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Affiliation(s)
- James Ashcroft
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Philippa Leighton
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Tegwen R Elliott
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Sarah A Hosgood
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK
| | - Michael L Nicholson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK.
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11
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You R, Zheng H, Xu L, Ma T, Chen G, Xia P, Fan X, Ji P, Wang L, Chen L. Decreased urinary uromodulin is potentially associated with acute kidney injury: a systematic review and meta-analysis. J Intensive Care 2021; 9:70. [PMID: 34782019 PMCID: PMC8591828 DOI: 10.1186/s40560-021-00584-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 10/20/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Urinary uromodulin (uUMOD) is one of the novel biomarkers for predicting AKI. However, currently available publications showed inconsistent results. We designed this meta-analysis to evaluate the potential association between uUMOD and AKI. METHODS We searched research articles with no language restriction in Medline, Web of Science, Cochrane Library, Embase, and 3 Chinese datasets from inception to February 2021. We used random-effects models to estimate the standardized mean difference (SMD) between patients with AKI or not, while the leave-one-out method and random-effects meta-regression to evaluate the sensitivity and the impact of potential confounders such as age and surgery. RESULTS The meta-analysis comprising 3148 subjects from 11 studies showed that the uUMOD of the AKI group is significantly lower than the non-AKI group (SMD: - 0.71; 95% confidence interval (CI), - 1.00, - 0.42, P < 0. 001, I2 = 78.8%). Subgroup analysis revealed the difference is also significant in a different age, surgery condition, and assay time but not acute rejection (AR) group, especially in children (SMD: - 1.21, 95% CI: - 1.80, - 0.61; P < 0.001) and patients undergoing surgery (SMD: - 1.03, 95% CI: - 1.75, - 0.30; P < 0.001). Lower uromodulin is associated with higher odds for AKI incidence (odds ratio = 2.47, 95% CI: 1.12, 5.47; P < 0.001, I2 = 89%). Meta-reggression found that age was associated with the SMD of uUMOD. The study outcome was reliably confirmed by the sensitivity analysis. CONCLUSION The present study suggested a negative association between uUMOD and AKI especially in children and surgical patients.
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Affiliation(s)
- Ruilian You
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Hua Zheng
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Lubin Xu
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Tiantian Ma
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Gang Chen
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Peng Xia
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Xiaohong Fan
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Peili Ji
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China
| | - Li Wang
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Limeng Chen
- Department of Nephrology, Peking Union Medical College Hospital, No 1, Shuaifuyuan, Wangfujing St, Beijing, 100730, China.
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12
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Lai X, Zheng X, Mathew JM, Gallon L, Leventhal JR, Zhang ZJ. Tackling Chronic Kidney Transplant Rejection: Challenges and Promises. Front Immunol 2021; 12:661643. [PMID: 34093552 PMCID: PMC8173220 DOI: 10.3389/fimmu.2021.661643] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023] Open
Abstract
Despite advances in post-transplant management, the long-term survival rate of kidney grafts and patients has not improved as approximately forty percent of transplants fails within ten years after transplantation. Both immunologic and non-immunologic factors contribute to late allograft loss. Chronic kidney transplant rejection (CKTR) is often clinically silent yet progressive allogeneic immune process that leads to cumulative graft injury, deterioration of graft function. Chronic active T cell mediated rejection (TCMR) and chronic active antibody-mediated rejection (ABMR) are classified as two principal subtypes of CKTR. While significant improvements have been made towards a better understanding of cellular and molecular mechanisms and diagnostic classifications of CKTR, lack of early detection, differential diagnosis and effective therapies continue to pose major challenges for long-term management. Recent development of high throughput cellular and molecular biotechnologies has allowed rapid development of new biomarkers associated with chronic renal injury, which not only provide insight into pathogenesis of chronic rejection but also allow for early detection. In parallel, several novel therapeutic strategies have emerged which may hold great promise for improvement of long-term graft and patient survival. With a brief overview of current understanding of pathogenesis, standard diagnosis and challenges in the context of CKTR, this mini-review aims to provide updates and insights into the latest development of promising novel biomarkers for diagnosis and novel therapeutic interventions to prevent and treat CKTR.
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Affiliation(s)
- Xingqiang Lai
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Organ Transplant Center, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Zheng
- Department of Urology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - James M. Mathew
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lorenzo Gallon
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Medicine, Nephrology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Joseph R. Leventhal
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Zheng Jenny Zhang
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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13
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Belkadi A, Thareja G, Dadhania D, Lee JR, Muthukumar T, Snopkowski C, Li C, Halama A, Abdelkader S, Abdulla S, Mahmoud Y, Malek J, Suthanthiran M, Suhre K. Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions. PLoS One 2021; 16:e0249930. [PMID: 33857204 PMCID: PMC8049329 DOI: 10.1371/journal.pone.0249930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/27/2021] [Indexed: 11/19/2022] Open
Abstract
Kidney transplantation is the treatment of choice for patients with end-stage kidney failure, but transplanted allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in kidney transplants is kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from kidney allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human kidney allograft.
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Affiliation(s)
- Aziz Belkadi
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Darshana Dadhania
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - John R. Lee
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Thangamani Muthukumar
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Catherine Snopkowski
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Anna Halama
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Sara Abdelkader
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Silvana Abdulla
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yasmin Mahmoud
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Joel Malek
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Manikkam Suthanthiran
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
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14
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Swensen AC, He J, Fang AC, Ye Y, Nicora CD, Shi T, Liu AY, Sigdel TK, Sarwal MM, Qian WJ. A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer. Front Med (Lausanne) 2021; 8:548212. [PMID: 33928097 PMCID: PMC8076675 DOI: 10.3389/fmed.2021.548212] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 03/18/2021] [Indexed: 01/10/2023] Open
Abstract
Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.
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Affiliation(s)
- Adam C Swensen
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Jingtang He
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Alexander C Fang
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Yinyin Ye
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Carrie D Nicora
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Tujin Shi
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Alvin Y Liu
- Department of Urology, University of Washington, Seattle, WA, United States
| | - Tara K Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Wei-Jun Qian
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
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15
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Heidari SS, Nafar M, Kalantari S, Tavilani H, Karimi J, Foster L, Moon KM, Khodadadi I. Urinary epidermal growth factor is a novel biomarker for early diagnosis of antibody mediated kidney allograft rejection: A urinary proteomics analysis. J Proteomics 2021; 240:104208. [PMID: 33785428 DOI: 10.1016/j.jprot.2021.104208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/27/2021] [Accepted: 03/24/2021] [Indexed: 12/27/2022]
Abstract
Although antibody mediated rejection (AMR) accounts for 20-30% of all acute renal allograft rejections, introducing biomarkers for a timely detection of allograft rejection has been remained challenging. This study investigated novel diagnostic biomarkers of AMR by examining of urine proteome in renal transplant patients. Thirty-six patients with kidney transplantation including 22 AMR patients and 14 patients with stable renal function (control group) were enrolled in this study. Urinary samples were collected and Label free quantification (LFQ) proteomics technique was applied on urine samples and data was subjected to Random Forest (RF) algorithm to predict main candidate proteins contributing in AMR. Finally, applicability of candidate diagnostic biomarkers was evaluated in new sets of AMR subjects, stable patients and healthy volunteers. A total of 1020 proteins were detected in urine proteome. RF algorithm predicted 20 differentially expressed proteins with the highest sensitivity and specificity and combination of EGF, COL6A, and NID-1 was identified as possible panel for early diagnosis of AMR. Applicability of EGF as diagnostic biomarker was validated in urine samples of independent set of AMR subjects. This is the first urinary proteomics study in AMR patients demonstrating that urinary EGF might be used as early diagnostic biomarker for AMR. SIGNIFICANCE: Renal antibody mediated rejection (AMR) accounts for 20-30% of all acute rejections of allografted kidneys. Although several possible biomarkers have been proposed to predict AMR, ineffectiveness of current urinary biomarkers in early diagnosing of AMR patients and in distinguishing AMR subjects from patients with stable kidney function casts doubts on their applicability in clinic. Here for the first time and based on the analysis of urinary proteome we showed that uEGF and uEGF/Cr might be candidate biomarkers to predict AMR with high diagnostic power.
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Affiliation(s)
- Somaye-Sadat Heidari
- Department of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohsen Nafar
- Chronic Kidney Disease Research Center, Shahid Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shiva Kalantari
- Chronic Kidney Disease Research Center, Shahid Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Molecular Biology, Umeå University, Umeå, Sweden.
| | - Heidar Tavilani
- Department of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Jamshid Karimi
- Department of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Leonard Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
| | - Iraj Khodadadi
- Department of Clinical Biochemistry, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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16
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Sigdel TK, Schroeder AW, Yang JYC, Sarwal RD, Liberto JM, Sarwal MM. Targeted Urine Metabolomics for Monitoring Renal Allograft Injury and Immunosuppression in Pediatric Patients. J Clin Med 2020; 9:jcm9082341. [PMID: 32707952 PMCID: PMC7465632 DOI: 10.3390/jcm9082341] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
Despite new advancements in surgical tools and therapies, exposure to immunosuppressive drugs related to non-immune and immune injuries can cause slow deterioration and premature failure of organ transplants. Diagnosis of these injuries by non-invasive urine monitoring would be a significant clinical advancement for patient management, especially in pediatric cohorts. We investigated the metabolomic profiles of biopsy matched urine samples from 310 unique kidney transplant recipients using gas chromatography-mass spectrometry (GC-MS). Focused metabolite panels were identified that could detect biopsy confirmed acute rejection with 92.9% sensitivity and 96.3% specificity (11 metabolites) and could differentiate BK viral nephritis (BKVN) from acute rejection with 88.9% sensitivity and 94.8% specificity (4 metabolites). Overall, targeted metabolomic analyses of biopsy-matched urine samples enabled the generation of refined metabolite panels that non-invasively detect graft injury phenotypes with high confidence. These urine biomarkers can be rapidly assessed for non-invasive diagnosis of specific transplant injuries, opening the window for precision transplant medicine.
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17
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Abstract
Early detection of graft injury after kidney transplantation is key to maintaining long-term good graft function. Graft injury could be due to a multitude of factors including ischaemia reperfusion injury, cell or antibody-mediated rejection, progressive interstitial fibrosis and tubular atrophy, infections and toxicity from the immunosuppressive drugs themselves. The current gold standard for assessing renal graft dysfunction is renal biopsy. However, biopsy is usually late when triggered by a change in serum creatinine and of limited utility in diagnosis of early injury when histological changes are equivocal. Therefore, there is a need for timely, objective and non-invasive diagnostic techniques with good early predictive value to determine graft injury and provide precision in titrating immunosuppression. We review potential novel plasma and urine biomarkers that offer sensitive new strategies for early detection and provide major insights into mechanisms of graft injury. This is a rapidly expanding field, but it is likely that a combination of biomarkers will be required to provide adequate sensitivity and specificity for detecting graft injury.
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18
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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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19
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Paul P, Antonydhason V, Gopal J, Haga SW, Hasan N, Oh JW. Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. Int J Mol Sci 2020; 21:E961. [PMID: 32024005 PMCID: PMC7038205 DOI: 10.3390/ijms21030961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023] Open
Abstract
The clinical sampling of urine is noninvasive and unrestricted, whereby huge volumes can be easily obtained. This makes urine a valuable resource for the diagnoses of diseases. Urinary and renal proteomics have resulted in considerable progress in kidney-based disease diagnosis through biomarker discovery and treatment. This review summarizes the bioinformatics tools available for this area of proteomics and the milestones reached using these tools in clinical research. The scant research publications and the even more limited bioinformatic tool options available for urinary and renal proteomics are highlighted in this review. The need for more attention and input from bioinformaticians is highlighted, so that progressive achievements and releases can be made. With just a handful of existing tools for renal and urinary proteomic research available, this review identifies a gap worth targeting by protein chemists and bioinformaticians. The probable causes for the lack of enthusiasm in this area are also speculated upon in this review. This is the first review that consolidates the bioinformatics applications specifically for renal and urinary proteomics.
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Affiliation(s)
- Piby Paul
- St. Jude Childrens Cancer Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Vimala Antonydhason
- Department of Microbiology and Immunology, Institute for Biomedicine, Gothenburg University, 413 90 Gothenburg, Sweden;
| | - Judy Gopal
- Department of Environmental Health Sciences, Konkuk University, Seoul 143-701, Korea;
| | - Steve W. Haga
- Department of Computer Science and Engineering, National Sun Yat Sen University, Kaohsiung 804, Taiwan;
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
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20
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Sirolli V, Pieroni L, Di Liberato L, Urbani A, Bonomini M. Urinary Peptidomic Biomarkers in Kidney Diseases. Int J Mol Sci 2019; 21:E96. [PMID: 31877774 PMCID: PMC6982248 DOI: 10.3390/ijms21010096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of disease, lack accuracy, and are not connected with molecular pathophysiology. Analysis of urine peptide content (urinary peptidomics) has emerged as one of the most attractive areas in disease biomarker discovery. Urinary peptidome analysis allows the detection of short and long-term physiological or pathological changes occurring within the kidney. Urinary peptidomics has been applied extensively for several years now in renal patients, and may greatly improve kidney disease management by supporting earlier and more accurate detection, prognostic assessment, and prediction of response to treatment. It also promises better understanding of kidney disease pathophysiology, and has been proposed as a "liquid biopsy" to discriminate various types of renal disorders. Furthermore, proteins being the major drug targets, peptidome analysis may allow one to evaluate the effects of therapies at the protein signaling pathway level. We here review the most recent findings on urinary peptidomics in the setting of the most common kidney diseases.
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Affiliation(s)
- Vittorio Sirolli
- Nephrology and Dialysis Unit, Department of Medicine, G. d’Annunzio University, Chieti-Pescara, SS.Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy; (V.S.); (L.D.L.)
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy;
| | - Lorenzo Di Liberato
- Nephrology and Dialysis Unit, Department of Medicine, G. d’Annunzio University, Chieti-Pescara, SS.Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy; (V.S.); (L.D.L.)
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Mario Bonomini
- Nephrology and Dialysis Unit, Department of Medicine, G. d’Annunzio University, Chieti-Pescara, SS.Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy; (V.S.); (L.D.L.)
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21
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Tetz V, Tetz G. Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma. Sci Rep 2019; 9:17995. [PMID: 31784694 PMCID: PMC6884558 DOI: 10.1038/s41598-019-54618-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/14/2019] [Indexed: 02/08/2023] Open
Abstract
Our study demonstrated for the first time that bacterial extracellular DNA (eDNA) can change the thermal behavior of specific human plasma proteins, leading to an elevation of the heat-resistant protein fraction, as well as to de novo acquisition of heat-resistance. In fact, the majority of these proteins were not known to be heat-resistant nor do they possess any prion-like domain. Proteins found to become heat-resistant following DNA exposure were named "Tetz-proteins". Interestingly, plasma proteins that become heat-resistant following treatment with bacterial eDNA are known to be associated with cancer. In pancreatic cancer, the proportion of proteins exhibiting eDNA-induced changes in thermal behavior was found to be particularly elevated. Therefore, we analyzed the heat-resistant proteome in the plasma of healthy subjects and in patients with pancreatic cancer and found that exposure to bacterial eDNA made the proteome of healthy subjects more similar to that of cancer patients. These findings open a discussion on the possible novel role of eDNA in disease development following its interaction with specific proteins, including those involved in multifactorial diseases such as cancer.
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Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10027, USA.,Tetz Laboratories, New York, NY, 10027, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10027, USA. .,Tetz Laboratories, New York, NY, 10027, USA.
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22
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Al-Nedawi K, Haas-Neill S, Gangji A, Ribic CM, Kapoor A, Margetts P. Circulating microvesicle protein is associated with renal transplant outcome. Transpl Immunol 2019; 55:101210. [PMID: 31226423 DOI: 10.1016/j.trim.2019.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/13/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022]
Abstract
Renal transplantation is an effective therapy with improved long-term outcomes compared with other therapies for end stage renal disease. Present methods for evaluating kidney allograft function, such as serum creatinine or allograft biopsy, are not sensitive and identify pathological changes only after any potential intervention would be effective. Thus, there is a necessity for biomarkers that would provide early prognostic information about kidney transplant outcomes. Circulating microvesicles represent an attractive source of biomarkers for different diseases including renal failure. We have studied the proteins of the circulating microvesicles from two populations of kidney transplant recipients (n = 20) with poor transplant outcomes (n = 10) or good transplant outcome (n = 10), according to their estimated glomerular filtration rate (eGFR). Microvesicles from age-matched healthy subjects (n = 10) were used as a control. Also, we performed a pilot study to assess the microvesicle protein in kidney transplant recipients before and six months after kidney transplant (n = 6), compared to healthy subjects. Proteomic analysis of microvesicles could discriminate between transplant recipients and healthy subjects, and between transplant patients based on eGFR. Our results shed light on the potential of blood microvesicles to provide a novel tool for the prediction of the outcome of kidney transplants.
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Affiliation(s)
- Khalid Al-Nedawi
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada; St. Joseph's Healthcare Research Institute & Hamilton Center for Kidney Research, Canada.
| | - Sandor Haas-Neill
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada; St. Joseph's Healthcare Research Institute & Hamilton Center for Kidney Research, Canada
| | - Azim Gangji
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada; St. Joseph's Healthcare Research Institute & Hamilton Center for Kidney Research, Canada
| | - Christine M Ribic
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada; St. Joseph's Healthcare Research Institute & Hamilton Center for Kidney Research, Canada
| | - Anil Kapoor
- St. Joseph's Healthcare Research Institute & Hamilton Center for Kidney Research, Canada; Department of Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Peter Margetts
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada; St. Joseph's Healthcare Research Institute & Hamilton Center for Kidney Research, Canada
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Watson D, Yang JYC, Sarwal RD, Sigdel TK, Liberto JM, Damm I, Louie V, Sigdel S, Livingstone D, Soh K, Chakraborty A, Liang M, Lin PC, Sarwal MM. A Novel Multi-Biomarker Assay for Non-Invasive Quantitative Monitoring of Kidney Injury. J Clin Med 2019; 8:E499. [PMID: 31013714 PMCID: PMC6517941 DOI: 10.3390/jcm8040499] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022] Open
Abstract
The current standard of care measures for kidney function, proteinuria, and serum creatinine (SCr) are poor predictors of early-stage kidney disease. Measures that can detect chronic kidney disease in its earlier stages are needed to enable therapeutic intervention and reduce adverse outcomes of chronic kidney disease. We have developed the Kidney Injury Test (KIT) and a novel KIT Score based on the composite measurement and validation of multiple biomarkers across a unique set of 397 urine samples. The test is performed on urine samples that require no processing at the site of collection and without target sequencing or amplification. We sought to verify that the pre-defined KIT test, KIT Score, and clinical thresholds correlate with established chronic kidney disease (CKD) and may provide predictive information on early kidney injury status above and beyond proteinuria and renal function measurements alone. Statistical analyses across six DNA, protein, and metabolite markers were performed on a subset of residual spot urine samples with CKD that met assay performance quality controls from patients attending the clinical labs at the University of California, San Francisco (UCSF) as part of an ongoing IRB-approved prospective study. Inclusion criteria included selection of patients with confirmed CKD and normal healthy controls; exclusion criteria included incomplete or missing information for sample classification, logistical delays in transport/processing of urine samples or low sample volume, and acute kidney injury. Multivariate logistic regression of kidney injury status and likelihood ratio statistics were used to assess the contribution of the KIT Score for prediction of kidney injury status and stage of CKD as well as assess the potential contribution of the KIT Score for detection of early-stage CKD above and beyond traditional measures of renal function. Urine samples were processed by a proprietary immunoprobe for measuring cell-free DNA (cfDNA), methylated cfDNA, clusterin, CXCL10, total protein, and creatinine. The KIT Score and stratified KIT Score Risk Group (high versus low) had a sensitivity and specificity for detection of kidney injury status (healthy or CKD) of 97.3% (95% CI: 94.6-99.3%) and 94.1% (95% CI: 82.3-100%). In addition, in patients with normal renal function (estimated glomerular filtration rate (eGFR) ≥ 90), the KIT Score clearly identifies those with predisposing risk factors for CKD, which could not be detected by eGFR or proteinuria (p < 0.001). The KIT Score uncovers a burden of kidney injury that may yet be incompletely recognized, opening the door for earlier detection, intervention and preservation of renal function.
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Affiliation(s)
- Drew Watson
- KIT Bio, 665 3rd Street, San Francisco, CA 94107, USA.
| | - Joshua Y C Yang
- KIT Bio, 665 3rd Street, San Francisco, CA 94107, USA.
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Reuben D Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Juliane M Liberto
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Izabella Damm
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Victoria Louie
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Shristi Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Devon Livingstone
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Katherine Soh
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Arjun Chakraborty
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Michael Liang
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Pei-Chen Lin
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Minnie M Sarwal
- KIT Bio, 665 3rd Street, San Francisco, CA 94107, USA.
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
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24
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Urine Angiotensin II Signature Proteins as Markers of Fibrosis in Kidney Transplant Recipients. Transplantation 2019; 103:e146-e158. [PMID: 30801542 DOI: 10.1097/tp.0000000000002676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Interstitial fibrosis/tubular atrophy (IFTA) is an important cause of kidney allograft loss; however, noninvasive markers to identify IFTA or guide antifibrotic therapy are lacking. Using angiotensin II (AngII) as the prototypical inducer of IFTA, we previously identified 83 AngII-regulated proteins in vitro. We developed mass spectrometry-based assays for quantification of 6 AngII signature proteins (bone marrow stromal cell antigen 1, glutamine synthetase [GLNA], laminin subunit beta-2, lysophospholipase I, ras homolog family member B, and thrombospondin-I [TSP1]) and hypothesized that their urine excretion will correlate with IFTA in kidney transplant patients. METHODS Urine excretion of 6 AngII-regulated proteins was quantified using selected reaction monitoring and normalized by urine creatinine. Immunohistochemistry was used to assess protein expression of TSP1 and GLNA in kidney biopsies. RESULTS The urine excretion rates of AngII-regulated proteins were found to be increased in 15 kidney transplant recipients with IFTA compared with 20 matched controls with no IFTA (mean log2[fmol/µmol of creatinine], bone marrow stromal cell antigen 1: 3.8 versus 3.0, P = 0.03; GLNA: 1.2 versus -0.4, P = 0.03; laminin subunit beta-2: 6.1 versus 5.4, P = 0.06; lysophospholipase I: 2.1 versus 0.6, P = 0.002; ras homolog family member B: 1.2 versus -0.1, P = 0.006; TSP1_GGV: 2.5 versus 1.9; P = 0.15; and TSP1_TIV: 2.0 versus 0.6, P = 0.0006). Receiver operating characteristic curve analysis demonstrated an area under the curve = 0.86 for the ability of urine AngII signature proteins to discriminate IFTA from controls. Urine excretion of AngII signature proteins correlated strongly with chronic IFTA and total inflammation. In a separate cohort of 19 kidney transplant recipients, the urine excretion of these 6 proteins was significantly lower following therapy with AngII inhibitors (P < 0.05). CONCLUSIONS AngII-regulated proteins may represent markers of IFTA and guide antifibrotic therapies.
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Marx D, Metzger J, Olagne J, Belczacka I, Faguer S, Colombat M, Husi H, Mullen W, Gwinner W, Caillard S. Proteomics in Kidney Allograft Transplantation—Application of Molecular Pathway Analysis for Kidney Allograft Disease Phenotypic Biomarker Selection. Proteomics Clin Appl 2019; 13:e1800091. [DOI: 10.1002/prca.201800091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/10/2019] [Indexed: 02/06/2023]
Affiliation(s)
- David Marx
- Nephrology – Transplantation DepartmentUMR_S. INSERM UMR_S 1109ImmunoRhumatologie MoléculaireFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de StrasbourgInstitut d'Immunologie et d'Hématologie 67085 Strasbourg France
- Laboratoire de Spectrométrie de Masse BioOrganiqueUniversity of StrasbourgCentre National de la Recherche ScientifiqueInstitut Pluridisciplinaire Hubert Curien UMR 7178 67037 Strasbourg France
| | | | - Jérôme Olagne
- Nephrology – Transplantation DepartmentUMR_S. INSERM UMR_S 1109ImmunoRhumatologie MoléculaireFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de StrasbourgInstitut d'Immunologie et d'Hématologie 67085 Strasbourg France
- Department of PathologyUniversity Hospital of Strasbourg 67091 Strasbourg France
| | | | - Stanislas Faguer
- Department of Nephrology and Organ TransplantationUniversity Hospital of Toulouse 31059 Toulouse France
- Institut National de la Santé et de la Recherche Médicale (INSERM)Institut of Cardiovascular and Metabolic Disease U1048 31432 Toulouse France
- Université Toulouse III Paul‐Sabatier 31330 Toulouse France
| | - Magali Colombat
- Department of PathologyCancer University Institute of Toulouse 31100 Toulouse France
| | - Holger Husi
- Division of Biomedical SciencesCentre for Health ScienceUniversity of the Highlands and Islands Inverness IV2 3JH UK
| | - William Mullen
- Institute of Cardiovascular and Medical SciencesUniversity of Glasgow Glasgow G12 8TA United Kingdom
| | - Wilfried Gwinner
- Department of NephrologyHannover Medical School 30625 Hannover Germany
| | - Sophie Caillard
- Nephrology – Transplantation DepartmentUMR_S. INSERM UMR_S 1109ImmunoRhumatologie MoléculaireFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de StrasbourgInstitut d'Immunologie et d'Hématologie 67085 Strasbourg France
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Abstract
PURPOSE OF REVIEW Despite modern immunosuppression, renal allograft rejection remains a major contributor to graft loss. Novel biomarkers may help improve posttransplant outcomes through the early detection and treatment of rejection. Our objective is to provide an overview of proteomics, review recent discovery-based rejection studies, and explore innovative approaches in biomarker development. RECENT FINDINGS Urine MMP7 was identified as a biomarker of subclinical and clinical rejection using two-dimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) and improved the overall diagnostic discrimination of urine CXCL10 : Cr alone for renal allograft inflammation. A novel peptide signature to classify stable allografts from acute rejection, chronic allograft injury, and polyoma virus (BKV) nephropathy was identified using isobaric tag for relative and absolute quantitation (TRAQ) and label-free MS, with independent validation by selected reaction monitoring mass spectrometry (SRM-MS). Finally, an in-depth exploration of peripheral blood mononuclear cells identified differential proteoform expression in healthy transplants versus rejection. SUMMARY There is still much in the human proteome that remains to be explored, and further integration of renal, urinary, and exosomal data may offer deeper insight into the pathophysiology of rejection. Functional proteomics may be more biologically relevant than protein/peptide quantity alone, such as assessment of proteoforms or activity-based protein profiling. Discovery-based studies have identified potential biomarker candidates, but external validation studies are required.
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Caterino M, Zacchia M, Costanzo M, Bruno G, Arcaniolo D, Trepiccione F, Siciliano R, Mazzeo M, Ruoppolo M, Capasso G. Urine Proteomics Revealed a Significant Correlation Between Urine-Fibronectin Abundance and Estimated-GFR Decline in Patients with Bardet-Biedl Syndrome. Kidney Blood Press Res 2018. [DOI: 10.1159/000488096] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Chen L, Su W, Chen H, Chen DQ, Wang M, Guo Y, Zhao YY. Proteomics for Biomarker Identification and Clinical Application in Kidney Disease. Adv Clin Chem 2018; 85:91-113. [PMID: 29655463 DOI: 10.1016/bs.acc.2018.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Treatment effectiveness for kidney disease is limited by lack of accuracy, sensitivity, specificity of diagnostic, prognostic, and therapeutic biomarkers. The gold standard test renal biopsy along with serum creatinine and proteinuria is often necessary to establish a diagnosis, particularly in glomerular disease. Proteomics has become a powerful tool for novel biomarker discovery in kidney disease. Novel proteomics offer earlier and more accurate diagnosis of renal pathology than possible with traditional biomarkers such as serum creatinine and urine protein. In addition, proteomic biomarkers could also be useful to choose the most suitable therapeutic targets. This review focuses on the current status of proteomic biomarkers from animal models (5/6 nephrectomy, unilateral ureteral obstruction, and diabetic nephropathy) and human studies (chronic kidney disease, glomerular diseases, transplantation, dialysis, acute and drug-induced kidney injury) to assess relevant findings and clinical usefulness. Current issues and problems related to the discovery, validation, and clinical application of proteomic biomarkers are discussed. We also describe several proteomic strategies highlighting technologic advancements, specimen selection, data processing and analysis. This review might provide help in future proteomic studies to improve the diagnosis and management of kidney disease.
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Affiliation(s)
- Lin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Wei Su
- Baoji Central Hospital, Baoji, China
| | - Hua Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Dan-Qian Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Ming Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Yan Guo
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, United States
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China.
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29
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Dias Bastos PA, Vlahou A, Leite-Moreira A, Santos LL, Ferreira R, Vitorino R. Deciphering the disease-related molecular networks using urine proteomics. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Rhodes DCJ. Human Tamm-Horsfall protein, a renal specific protein, serves as a cofactor in complement 3b degradation. PLoS One 2017; 12:e0181857. [PMID: 28742158 PMCID: PMC5524369 DOI: 10.1371/journal.pone.0181857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 07/07/2017] [Indexed: 11/18/2022] Open
Abstract
Tamm-Horsfall protein (THP) is an abundant urinary protein of renal origin. We hypothesize that THP can act as an inhibitor of complement since THP binds complement 1q (C1q) of the classical complement pathway, inhibits activation of this pathway, and is important in decreasing renal ischemia-reperfusion injury (a complement-mediated condition). In this study, we began to investigate whether THP interacted with the alternate complement pathway via complement factor H (CFH). THP was shown to bind CFH using ligand blots and in an ELISA (KD of 1 × 10−6 M). Next, the ability of THP to alter CFH’s normal action as it functioned as a cofactor in complement factor I (CFI)–mediated complement 3b (C3b) degradation was investigated. Unexpectedly, control experiments in these in vitro assays suggested that THP, without added CFH, could act as a cofactor in CFI-mediated C3b degradation. This cofactor activity was present equally in THP isolated from 10 different individuals. While an ELISA demonstrated small amounts of CFH contaminating THP samples, these CFH amounts were insufficient to explain the degree of cofactor activity present in THP. An ELISA demonstrated that THP directly bound C3b (KD ~ 5 × 10−8m), a prerequisite for a protein acting as a C3b degradation cofactor. The cofactor activity of THP likely resides in the protein portion of THP since partially deglycosylated THP still retained cofactor activity. In conclusion, THP appears to participate directly in complement inactivation by its ability to act as a cofactor for C3b degradation, thus adding support to the hypothesis that THP might act as an endogenous urinary tract inhibitor of complement.
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Affiliation(s)
- Diana C. J. Rhodes
- Department of Anatomy, Pacific Northwest University of Health Sciences, Yakima, Washington, United States of America
- * E-mail:
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31
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Salvadori M, Tsalouchos A. Biomarkers in renal transplantation: An updated review. World J Transplant 2017; 7:161-178. [PMID: 28698834 PMCID: PMC5487307 DOI: 10.5500/wjt.v7.i3.161] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/07/2017] [Accepted: 04/19/2017] [Indexed: 02/05/2023] Open
Abstract
Genomics, proteomics and molecular biology lead to tremendous advances in all fields of medical sciences. Among these the finding of biomarkers as non invasive indicators of biologic processes represents a useful tool in the field of transplantation. In addition to define the principal characteristics of the biomarkers, this review will examine the biomarker usefulness in the different clinical phases following renal transplantation. Biomarkers of ischemia-reperfusion injury and of delayed graft function are extremely important for an early diagnosis of these complications and for optimizing the treatment. Biomarkers predicting or diagnosing acute rejection either cell-mediated or antibody-mediated allow a risk stratification of the recipient, a prompt diagnosis in an early phase when the histology is still unremarkable. The kidney solid organ response test detects renal transplant recipients at high risk for acute rejection with a very high sensitivity and is also able to make diagnosis of subclinical acute rejection. Other biomarkers are able to detect chronic allograft dysfunction in an early phase and to differentiate the true chronic rejection from other forms of chronic allograft nephropathies no immune related. Finally biomarkers recently discovered identify patients tolerant or almost tolerant. This fact allows to safely reduce or withdrawn the immunosuppressive therapy.
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32
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The Use of Genomics and Pathway Analysis in Our Understanding and Prediction of Clinical Renal Transplant Injury. Transplantation 2017; 100:1405-14. [PMID: 26447506 DOI: 10.1097/tp.0000000000000943] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development and application of high-throughput molecular profiling have transformed the study of human diseases. The problem of handling large, complex data sets has been facilitated by advances in complex computational analysis. In this review, the recent literature regarding the application of transcriptional genomic information to renal transplantation, with specific reference to acute rejection, acute kidney injury in allografts, chronic allograft injury, and tolerance is discussed, as is the current published data regarding other "omics" strategies-proteomics, metabolomics, and the microRNA transcriptome. These data have shed new light on our understanding of the pathogenesis of specific disease conditions after renal transplantation, but their utility as a biomarker of disease has been hampered by study design and sample size. This review aims to highlight the opportunities and obstacles that exist with genomics and other related technologies to better understand and predict renal allograft outcome.
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33
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Choi YW, Kim YG, Song MY, Moon JY, Jeong KH, Lee TW, Ihm CG, Park KS, Lee SH. Potential urine proteomics biomarkers for primary nephrotic syndrome. Clin Proteomics 2017; 14:18. [PMID: 28522940 PMCID: PMC5434615 DOI: 10.1186/s12014-017-9153-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/06/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Nephrotic syndrome (NS) is a nonspecific kidney disorder, commonly caused by minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and membranous nephropathy (MN). Here we analyzed urinary protein profiles, aiming to discover disease-specific biomarkers of these three common diseases in NS. METHODS Sixteen urine samples were collected from patients with biopsy-proven NS and healthy controls. After removal of high-abundance proteins, the urinary protein profile was analyzed by LC-MS/MS to generate a discovery set. For validation, ELISA was used to analyze the selected proteins in 61 urine samples. RESULTS The discovery set included 228 urine proteins, of which 22 proteins were differently expressed in MCD, MN, and FSGS. Among these, C9, CD14, and SERPINA1 were validated by ELISA. All three proteins were elevated in MCD, MN, and FSGS groups compared with in IgA nephropathy and healthy controls. When a regression model was applied, receiver operating characteristic analysis clearly discriminated MCD from the other causative diseases in NS. CONCLUSIONS We developed a disease-specific protein panel that discriminated between three main causes of NS. Through this pilot study, we suggest that urine proteomics could be a non-invasive and clinically available tool to discriminate MCD from MN and FSGS.
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Affiliation(s)
- Young Wook Choi
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
| | - Yang Gyun Kim
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
| | - Min-Young Song
- Department of Physiology, Kyung Hee University School of Medicine, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Korea
| | - Ju-Young Moon
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
| | - Kyung-Hwan Jeong
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
| | - Tae-Won Lee
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
| | - Chun-Gyoo Ihm
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
| | - Kang-Sik Park
- Department of Physiology, Kyung Hee University School of Medicine, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Korea
| | - Sang-Ho Lee
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University School of Medicine, 892 Dongnam-ro, Gangdong-gu, Seoul, Korea
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Menon MC, Murphy B, Heeger PS. Moving Biomarkers toward Clinical Implementation in Kidney Transplantation. J Am Soc Nephrol 2017; 28:735-747. [PMID: 28062570 DOI: 10.1681/asn.2016080858] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Long-term kidney transplant outcomes remain suboptimal, delineating an unmet medical need. Although current immunosuppressive therapy in kidney transplant recipients is effective, dosing is conventionally adjusted empirically on the basis of time after transplant or altered in response to detection of kidney dysfunction, histologic evidence of allograft damage, or infection. Such strategies tend to detect allograft rejection after significant injury has already occurred, fail to detect chronic subclinical inflammation that can negatively affect graft survival, and ignore specific risks and immune mechanisms that differentially contribute to allograft damage among transplant recipients. Assays and biomarkers that reliably quantify and/or predict the risk of allograft injury have the potential to overcome these deficits and thereby, aid clinicians in optimizing immunosuppressive regimens. Herein, we review the data on candidate biomarkers that we contend have the highest potential to become clinically useful surrogates in kidney transplant recipients, including functional T cell assays, urinary gene and protein assays, peripheral blood cell gene expression profiles, and allograft gene expression profiles. We identify barriers to clinical biomarker adoption in the transplant field and suggest strategies for moving biomarker-based individualization of transplant care from a research hypothesis to clinical implementation.
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Affiliation(s)
- Madhav C Menon
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Barbara Murphy
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter S Heeger
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
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35
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Analytical Aspects of the Implementation of Biomarkers in Clinical Transplantation. Ther Drug Monit 2016; 38 Suppl 1:S80-92. [PMID: 26418704 DOI: 10.1097/ftd.0000000000000230] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In response to the urgent need for new reliable biomarkers to complement the guidance of the immunosuppressive therapy, a huge number of biomarker candidates to be implemented in clinical practice have been introduced to the transplant community. This includes a diverse range of molecules with very different molecular weights, chemical and physical properties, ex vivo stabilities, in vivo kinetic behaviors, and levels of similarity to other molecules, etc. In addition, a large body of different analytical techniques and assay protocols can be used to measure biomarkers. Sometimes, a complex software-based data evaluation is a prerequisite for appropriate interpretation of the results and for their reporting. Although some analytical procedures are of great value for research purposes, they may be too complex for implementation in a clinical setting. Whereas the proof of "fitness for purpose" is appropriate for validation of biomarker assays used in exploratory drug development studies, a higher level of analytical validation must be achieved and eventually advanced analytical performance might be necessary before diagnostic application in transplantation medicine. A high level of consistency of results between laboratories and between methods (if applicable) should be obtained and maintained to make biomarkers effective instruments in support of therapeutic decisions. This overview focuses on preanalytical and analytical aspects to be considered for the implementation of new biomarkers for adjusting immunosuppression in a clinical setting and highlights critical points to be addressed on the way to make them suitable as diagnostic tools. These include but are not limited to appropriate method validation, standardization, education, automation, and commercialization.
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36
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Dwivedi RC, Navarrete M, Choi N, Spicer V, Rigatto C, Arora RC, Krokhin O, Ho J, Wilkins JA. A proteomic evaluation of urinary changes associated with cardiopulmonary bypass. Clin Proteomics 2016; 13:17. [PMID: 27528862 PMCID: PMC4983784 DOI: 10.1186/s12014-016-9118-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/04/2016] [Indexed: 01/31/2023] Open
Abstract
Background The urinary proteome of patients undergoing cardiopulmonary bypass (CPB) may provide important insights into systemic and renal changes associated with the procedure. Such information may ultimately provide a basis to differentiate changes or properties associated with the development of acute kidney injury. While mass spectrometry (MS) analysis offers the potential for in-depth compositional analysis it is often limited in coverage and relative quantitation capacity. The aim of this study was to develop a process flow for the preparation and comparison of the intraoperative urinary proteome. Methods Urines were collected from patients at the start of CPB and 1-h into CPB. Pooled samples (n = 5) from each time point were processed using a modified Filter Assisted Sample Preparation protocol. The resulting peptides were analyzed by 2D-LC–MS/MS and by 1D-LC–MS/MS SWATH (Sequential Window acquisition of All Theoretical fragment ion spectra). Results The 2D-LC–MS/MS analysis identified 1324 proteins in the two pools, of which 744 were quantifiable. The SWATH approach provided quantitation for 730 proteins, 552 of which overlapped with the common population from the 2D-IDA results. Intensity correlation filtering between the two methods gave 475 proteins for biological interpretation. Proteins displaying greater than threefold changes (>log2 1.59) at 1-hour CPB relative to the initiation of CPB (26 down-regulated and 22 up-regulated) were selected for further analysis. Up-regulated proteins were enriched in GO terms related to humoral immune response, predominantly innate immunity (C4b, lactotransferrin, protein S100-A8, cathelicidin, myeloperoxidase) and extracellular matrix reorganization (e.g. MMP-9). Conclusions This study describes a scheme for processing urine from patients undergoing CPB for mass spectrometry-based analysis. The introduction of SWATH into the workflow offers a sample and instrument sparing approach to obtaining consistent in-depth sample analysis. The design of the methodology is such that it can be readily applied to large numbers of clinical samples with the potential for automation. The results also suggest that activation of the innate immune responses occur during cardiac bypass surgery. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9118-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ravi C Dwivedi
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada
| | - Mario Navarrete
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada
| | - Nora Choi
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada ; Cardiac Sciences Program, St. Boniface Hospital Research Centre, Winnipeg, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada
| | - Claudio Rigatto
- Department of Internal Medicine, Section of Nephrology, University of Manitoba, Winnipeg, MB Canada
| | - Rakesh C Arora
- Department of Surgery, University of Manitoba, Winnipeg, MB Canada ; Cardiac Sciences Program, St. Boniface Hospital Research Centre, Winnipeg, Canada
| | - Oleg Krokhin
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada
| | - Julie Ho
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada ; Department of Internal Medicine, Section of Nephrology, University of Manitoba, Winnipeg, MB Canada ; Department of Immunology, University of Manitoba, Winnipeg, MB Canada
| | - John A Wilkins
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba and Health Sciences Centre, Room 799, John Buhler Research Center, 715 Mc Dermot Avenue, Winnipeg, MB R3E 3P4 Canada ; Department of Internal Medicine, Section of Biomedical Proteomics, University of Manitoba, Winnipeg, MB Canada
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Perez JD, Sakata MM, Colucci JA, Spinelli GA, Felipe CR, Carvalho VM, Cardozo KHM, Medina-Pestana JO, Tedesco-Silva H, Schor N, Casarini DE. Plasma proteomics for the assessment of acute renal transplant rejection. Life Sci 2016; 158:111-20. [PMID: 27393492 DOI: 10.1016/j.lfs.2016.06.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/08/2016] [Accepted: 06/28/2016] [Indexed: 12/13/2022]
Abstract
UNLABELLED Renal transplant is the best treatment for patients with chronical kidney disease however acute graft rejection is the major impediment to success in renal transplantation leading to loss of the organ the first year after transplantation. The aim of this study was to identify plasma proteins that may be early biomarkers of acute rejection of renal allograft, developing a diagnostic model that avoids the loss of the transplanted organ. Shotgun proteomics (LC-MS/MS) method was used to analyze a set of thirty-one plasma samples, including 06 from patients with acute graft rejection after transplantation (rejection group/Rej-group) and twenty-five from renal transplant patients with stable renal graft function (control group/Ct-group). As results nineteen proteins were upregulated in the rejection group compared to the control group, and two proteins were downregulated; and three were present exclusively in the rejection group. After analysis, we selected four proteins that were related to the acute phase response and that were strongly associated with each other: they are alpha-1 antitrypsin (A1AT), alpha-2 antiplasmin (A2AP), serum amyloid A (SAA) and apolipoprotein CIII (APOC3). We think that simultaneous monitoring of SAA and APOC3 can provide insights into a broad profile of signaling proteins and is highly valuable for the early detection of a possible acute renal graft rejection. STATEMENT OF SIGNIFICANCE OF THE STUDY In this study we did plasma shotgun patients with and without acute rejection of renal allograft. In a clinical setting an acute rejection is typically suspected upon an increase in plasma creatinine and renal biopsy. But these methods are late and unspecific; sometimes the rejection process is already advanced when there is an increase in serum creatinine. Therefore, it is necessary to find proteins that can predict the allograft rejection process. In our study were able to identify changes in the concentration of plasma protein belonging to a network of protein interaction processes the acute phase response. We believe, therefore, that development of a routine diagnosis of these proteins can detect early acute rejection of renal allograft process, thus preventing its loss.
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Affiliation(s)
- Juliana D Perez
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maísa M Sakata
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Juliana A Colucci
- Universidade de Santo Amaro, Programa em Medicina Populacional, São Paulo, Brazil
| | - Gláucio A Spinelli
- Nephrology Division, Hospital do Rim e Hipertensão, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudia R Felipe
- Nephrology Division, Hospital do Rim e Hipertensão, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | | | - José O Medina-Pestana
- Nephrology Division, Hospital do Rim e Hipertensão, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Hélio Tedesco-Silva
- Nephrology Division, Hospital do Rim e Hipertensão, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Nestor Schor
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Dulce E Casarini
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo, São Paulo, Brazil.
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Gwinner W, Metzger J, Husi H, Marx D. Proteomics for rejection diagnosis in renal transplant patients: Where are we now? World J Transplant 2016; 6:28-41. [PMID: 27011903 PMCID: PMC4801803 DOI: 10.5500/wjt.v6.i1.28] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/14/2015] [Accepted: 01/05/2016] [Indexed: 02/05/2023] Open
Abstract
Rejection is one of the key factors that determine the long-term allograft function and survival in renal transplant patients. Reliable and timely diagnosis is important to treat rejection as early as possible. Allograft biopsies are not suitable for continuous monitoring of rejection. Thus, there is an unmet need for non-invasive methods to diagnose acute and chronic rejection. Proteomics in urine and blood samples has been explored for this purpose in 29 studies conducted since 2003. This review describes the different proteomic approaches and summarizes the results from the studies that examined proteomics for the rejection diagnoses. The potential limitations and open questions in establishing proteomic markers for rejection are discussed, including ongoing trials and future challenges to this topic.
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Mining the human urine proteome for monitoring renal transplant injury. Kidney Int 2016; 89:1244-52. [PMID: 27165815 DOI: 10.1016/j.kint.2015.12.049] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/09/2015] [Accepted: 12/30/2015] [Indexed: 12/13/2022]
Abstract
The human urinary proteome provides an assessment of kidney injury with specific biomarkers for different kidney injury phenotypes. In an effort to fully map and decipher changes in the urine proteome and peptidome after kidney transplantation, renal allograft biopsy matched urine samples were collected from 396 kidney transplant recipients. Centralized and blinded histology data from paired graft biopsies was used to classify urine samples into diagnostic categories of acute rejection, chronic allograft nephropathy, BK virus nephritis, and stable graft. A total of 245 urine samples were analyzed by liquid chromatography-mass spectrometry using isobaric Tags for Relative and Absolute Quantitation (iTRAQ) reagents. From a group of over 900 proteins identified in transplant injury, a set of 131 peptides were assessed by selected reaction monitoring for their significance in accurately segregating organ injury causation and pathology in an independent cohort of 151 urine samples. Ultimately, a minimal set of 35 proteins were identified for their ability to segregate the 3 major transplant injury clinical groups, comprising the final panel of 11 urinary peptides for acute rejection (93% area under the curve [AUC]), 12 urinary peptides for chronic allograft nephropathy (99% AUC), and 12 urinary peptides for BK virus nephritis (83% AUC). Thus, urinary proteome discovery and targeted validation can identify urine protein panels for rapid and noninvasive differentiation of different causes of kidney transplant injury, without the requirement of an invasive biopsy.
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Zapf A, Gwinner W, Karch A, Metzger J, Haller H, Koch A. Non-invasive diagnosis of acute rejection in renal transplant patients using mass spectrometry of urine samples - a multicentre phase 3 diagnostic accuracy study. BMC Nephrol 2015; 16:153. [PMID: 26374548 PMCID: PMC4570292 DOI: 10.1186/s12882-015-0146-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/29/2015] [Indexed: 12/20/2022] Open
Abstract
Background Reliable and timely detection of acute rejection in renal transplant patients is important to preserve the allograft function and to prevent premature allograft failure. The current gold standard for the rejection diagnosis is an allograft biopsy which is usually performed upon an unexplained decline in allograft function. Because of the invasiveness of the biopsy, non-invasive tests have been suggested to diagnose acute rejection including mass spectrometry analysis of urine samples. Design and methods The aim of this study is to examine the diagnostic accuracy of mass spectrometry analysis in urine for the diagnosis of acute rejections using the biopsy as gold-standard. The study is an ongoing prospective, single-arm, multicentre, phase 3 diagnostic accuracy study. It started in October 2011 and will be concluded in December 2015. Patient within the first year after transplantation who are scheduled for a biopsy to clarify unexplained impairment of the allograft are consecutively recruited into the study. The overall sample size (n = 600) was calculated to demonstrate a sensitivity of 83 % and a specificity of 70 % for a one-sided type one error of 2.5 % and a power of 80 % per hypothesis. Biopsy evaluation and mass spectrometry analysis of urine samples (obtained immediately before biopsy) are performed independently by different readers without knowledge from the respective other assessment. The follow-up observation period is 6 months. For the primary analysis, the lower limits of the two-sided 95 % Wald confidence intervals for sensitivity and specificity will be compared with the pre-specified thresholds (83 % for sensitivity and 70 % for specificity). In secondary analyses the predictive values, the diagnostic measures in subgroups, and the clinical course will be assessed. Discussion Previous phase 2 diagnostic accuracy studies (in small selected study populations) provided sufficient evidence to suggest mass spectrometry on urine samples as a promising approach to detect acute rejections. This study determines the diagnostic performance of the test in the routine setting of post-transplant patient care, compared to the biopsy-based rejection diagnosis. The next step would be a randomized trial to compare the two diagnostic strategies (including the urine test or not) in relation to patient relevant endpoints. Trial registration NCT01315067; March 14, 2011 Electronic supplementary material The online version of this article (doi:10.1186/s12882-015-0146-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonia Zapf
- Institute for Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073, Göttingen, Germany.
| | - Wilfried Gwinner
- Department of Nephrology, Medical School Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Annika Karch
- Institute for Biostatistics, Medical School Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Jochen Metzger
- Mosaiques Diagnostics and Therapeutics, Rotenburger Str. 20, 30659, Hannover, Germany.
| | - Hermann Haller
- Department of Nephrology, Medical School Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Armin Koch
- Institute for Biostatistics, Medical School Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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A Computational Gene Expression Score for Predicting Immune Injury in Renal Allografts. PLoS One 2015; 10:e0138133. [PMID: 26367000 PMCID: PMC4569485 DOI: 10.1371/journal.pone.0138133] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/25/2015] [Indexed: 12/13/2022] Open
Abstract
Background Whole genome microarray meta-analyses of 1030 kidney, heart, lung and liver allograft biopsies identified a common immune response module (CRM) of 11 genes that define acute rejection (AR) across different engrafted tissues. We evaluated if the CRM genes can provide a molecular microscope to quantify graft injury in acute rejection (AR) and predict risk of progressive interstitial fibrosis and tubular atrophy (IFTA) in histologically normal kidney biopsies. Methods Computational modeling was done on tissue qPCR based gene expression measurements for the 11 CRM genes in 146 independent renal allografts from 122 unique patients with AR (n = 54) and no-AR (n = 92). 24 demographically matched patients with no-AR had 6 and 24 month paired protocol biopsies; all had histologically normal 6 month biopsies, and 12 had evidence of progressive IFTA (pIFTA) on their 24 month biopsies. Results were correlated with demographic, clinical and pathology variables. Results The 11 gene qPCR based tissue CRM score (tCRM) was significantly increased in AR (5.68 ± 0.91) when compared to STA (1.29 ± 0.28; p < 0.001) and pIFTA (7.94 ± 2.278 versus 2.28 ± 0.66; p = 0.04), with greatest significance for CXCL9 and CXCL10 in AR (p <0.001) and CD6 (p<0.01), CXCL9 (p<0.05), and LCK (p<0.01) in pIFTA. tCRM was a significant independent correlate of biopsy confirmed AR (p < 0.001; AUC of 0.900; 95% CI = 0.705–903). Gene expression modeling of 6 month biopsies across 7/11 genes (CD6, INPP5D, ISG20, NKG7, PSMB9, RUNX3, and TAP1) significantly (p = 0.037) predicted the development of pIFTA at 24 months. Conclusions Genome-wide tissue gene expression data mining has supported the development of a tCRM-qPCR based assay for evaluating graft immune inflammation. The tCRM score quantifies injury in AR and stratifies patients at increased risk of future pIFTA prior to any perturbation of graft function or histology.
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Wang A, Sarwal MM. Computational Models for Transplant Biomarker Discovery. Front Immunol 2015; 6:458. [PMID: 26441963 PMCID: PMC4561798 DOI: 10.3389/fimmu.2015.00458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/24/2015] [Indexed: 01/11/2023] Open
Abstract
Translational medicine offers a rich promise for improved diagnostics and drug discovery for biomedical research in the field of transplantation, where continued unmet diagnostic and therapeutic needs persist. Current advent of genomics and proteomics profiling called "omics" provides new resources to develop novel biomarkers for clinical routine. Establishing such a marker system heavily depends on appropriate applications of computational algorithms and software, which are basically based on mathematical theories and models. Understanding these theories would help to apply appropriate algorithms to ensure biomarker systems successful. Here, we review the key advances in theories and mathematical models relevant to transplant biomarker developments. Advantages and limitations inherent inside these models are discussed. The principles of key -computational approaches for selecting efficiently the best subset of biomarkers from high--dimensional omics data are highlighted. Prediction models are also introduced, and the integration of multi-microarray data is also discussed. Appreciating these key advances would help to accelerate the development of clinically reliable biomarker systems.
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Affiliation(s)
- Anyou Wang
- Department of Surgery, Division of MultiOrgan Transplantation, University of California San Francisco, San Francisco, CA, USA
| | - Minnie M. Sarwal
- Department of Surgery, Division of MultiOrgan Transplantation, University of California San Francisco, San Francisco, CA, USA
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Gopal J, Muthu M, Chun SC, Wu HF. State-of-the-art nanoplatform-integrated MALDI-MS impacting resolutions in urinary proteomics. Proteomics Clin Appl 2015; 9:469-81. [PMID: 25736343 DOI: 10.1002/prca.201400182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/26/2014] [Accepted: 02/26/2015] [Indexed: 12/17/2022]
Abstract
Urine proteomics has become a subject of interest, since it has led to a number of breakthroughs in disease diagnostics. Urine contains information not only from the kidney and the urinary tract but also from other organs, thus urinary proteome analysis allows for identification of biomarkers for both urogenital and systemic diseases. The following review gives a brief overview of the analytical techniques that have been in practice for urinary proteomics. MALDI-MS technique and its current application status in this area of clinical research have been discussed. The review comments on the challenges facing the conventional MALDI-MS technique and the upgradation of this technique with the introduction of nanotechnology. This review projects nano-based techniques such as nano-MALDI-MS, surface-assisted laser desorption/ionization, and nanostructure-initiator MS as the platforms that have the potential in trafficking MALDI-MS from the lab to the bedside.
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Affiliation(s)
- Judy Gopal
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Manikandan Muthu
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Se-Chul Chun
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University and Academia Sinica, Kaohsiung, Taiwan.,Center for Nanosciences and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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Vaidyanathan K. Urinary proteomics and metabolomics in the diagnosis of pediatric disorders. Proteomics Clin Appl 2015; 9:482-9. [PMID: 25631340 DOI: 10.1002/prca.201400093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/24/2014] [Accepted: 01/27/2015] [Indexed: 12/17/2022]
Abstract
Proteomics is the study of structures and functions of proteins, while metabolomics is the study of small-molecule metabolites in the cells, tissues, and organs of the organism. Proteomic technologies have wide applications in medical field. The current revolution in proteomics has led to the discovery of several new protein markers for various disorders. Urinary proteomics and metabolomics have also evolved in the recent years, for the diagnosis of both renal and nonrenal disorders. The urinary proteome varies in normal and abnormal conditions. Different techniques are employed for the analysis of pediatric urinary proteome, the commonest being MS. Before introduction into clinical use, there is the need for careful standardization. Available data suggest that there are differences in urinary proteome between adult and pediatric populations. It is noted that infant urine contains proteins involved in translation and transcription, cellular growth, and metabolic processes, which are not predominant in adult urine. Available data on urinary proteomic and metabolomic profile in common pediatric disorders are also reviewed here.
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Affiliation(s)
- Kannan Vaidyanathan
- Department of Biochemistry, Pushpagiri Institute of Medical Science & Research Center, Tiruvalla, India
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Abstract
The effectiveness of treatment of renal diseases is limited because the lack of diagnostic, prognostic and therapeutic markers. Despite the more than a decade of intensive investigation of urinary biomarkers, no new clinical biomarkers were approved. This is in part because the early expectations toward proteomics in biomarkers discovery were significantly higher than the capability of technology at the time. However, during the last decade, proteomic technology has made dramatic progress in both the hardware and software methods. In this review we are discussing modern quantitative methods of mass-spectrometry and providing several examples of their applications for discovery and validation of renal disease biomarkers. We are optimistic about future prospects for the development of novel of specific clinical urinary biomarkers.
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Affiliation(s)
- Marina Jerebtsova
- Department of Microbiology, Howard University College of Medicine, 520 W Street N.W., Washington, DC 20059, USA
| | - Sergei Nekhai
- Department of Medicine, Howard University College of Medicine, 520 W Street N.W., Washington, DC 20059, USA ; Center for Sickle Cell Disease, Howard University College of Medicine, 520 W Street N.W., Washington, DC 20059, USA
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Ong S, Mannon RB. Genomic and proteomic fingerprints of acute rejection in peripheral blood and urine. Transplant Rev (Orlando) 2014; 29:60-7. [PMID: 25542607 DOI: 10.1016/j.trre.2014.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 12/06/2014] [Indexed: 12/13/2022]
Abstract
Acute dysfunction of a kidney transplant can be the result of many different etiologies and an allograft biopsy is frequently necessary to diagnose acute rejection. This invasive procedure, while generally safe, is time consuming, costly and inconvenient. We summarize recent advances in genomic and proteomic techniques using peripheral blood and urine for the diagnosis of acute rejection. While much progress has been made, validation of these new molecular tests in the clinical setting is still required.
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Affiliation(s)
- Song Ong
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Roslyn B Mannon
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA; Division of Transplantation, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA.
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Abstract
Proteomics and biochemical profiling have emerged as exciting and powerful tools in clinical biomarker research. In the field of transplantation, proteomics aims not only at developing noninvasive means for immune monitoring but also to gain mechanistic insights into the pathophysiology of the alloimmune response and hence defining new therapeutic targets. This chapter provides an overview of proteomic biomarker-driven approaches and its underlying concepts and discusses the advantages, clinical implications, challenges, and limitations of this novel modality as it relates to solid organ transplantation.
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Affiliation(s)
- Katrin Kienzl-Wagner
- Center of Operative Medicine, Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Gerald Brandacher
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation (VCA) Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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Segawa T, Nomura KH, Villanueva SYAM, Saito M, Nomura K, Gloriani NG, Yoshida SI. Identification of leptospiral 3-hydroxyacyl-CoA dehydrogenase released in the urine of infected hamsters. BMC Microbiol 2014; 14:132. [PMID: 24884439 PMCID: PMC4036750 DOI: 10.1186/1471-2180-14-132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/07/2014] [Indexed: 01/03/2023] Open
Abstract
Background Leptospirosis is a global zoonosis caused by pathogenic Leptospira. The non-specific clinical signs and symptoms of leptospirosis lead to its misdiagnosis. To date, there is still no reliable rapid test kit that can accurately diagnose leptospirosis at bedside or in field. In this research, with the ultimate goal of formulating a rapid and accurate diagnostic tool for leptospirosis, we aimed to identify leptospiral proteins excreted in urine of infected hamsters, which are thought to mimic Weil’s disease. Results Hamsters were subcutaneously infected with leptospires, and the general attributes of urine as well as the proteins excreted in it were examined. Some leptospiral proteins were found to be excreted in the urine from the early phase of infection. The most important finding of this study was the detection of the lipid-metabolizing enzyme, 3-hydroxyacyl-CoA dehydrogenase (HADH), before the onset of illness, when leptospires were not yet detected in the urine of infected hamsters. Conclusions This is the first report on the detection of leptospiral HADH in the host urine, which may be a possible candidate leptospiral antigen that can be used in the early diagnosis of human and animal leptospirosis.
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Affiliation(s)
- Takaya Segawa
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
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Rodríguez-Suárez E, Siwy J, Zürbig P, Mischak H. Urine as a source for clinical proteome analysis: From discovery to clinical application. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:884-98. [DOI: 10.1016/j.bbapap.2013.06.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/10/2013] [Accepted: 06/20/2013] [Indexed: 01/03/2023]
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50
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Albalat A, Mischak H, Mullen W. Clinical application of urinary proteomics/peptidomics. Expert Rev Proteomics 2014; 8:615-29. [DOI: 10.1586/epr.11.46] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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