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Rroji M, Figurek A, Spasovski G. Advancing kidney transplant outcomes: the role of urinary proteomics in graft function monitoring and rejection detection. Expert Rev Proteomics 2024; 21:297-316. [PMID: 39133121 DOI: 10.1080/14789450.2024.2389829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/15/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Kidney transplantation significantly improves the lives of those with end-stage kidney disease, offering best alternative to dialysis. However, transplant success is threatened by the acute and chronic rejection mechanisms due to complex immune responses against the new organ. AREAS COVERED The ongoing research into biomarkers holds promise for revolutionizing the early detection and monitoring of the graft health. Liquid biopsy techniques offer a new avenue, with several diagnostic, predictive, and prognostic biomarkers showing promise in detecting and monitoring kidney diseases and an early and chronic allograft rejection. EXPERT OPINION Evaluating the protein composition related to kidney transplant results could lead to identifying biomarkers that provide insights into the graft functionality. Non-invasive proteomic biomarkers can drastically enhance clinical outcomes and change the way how kidney transplants are evaluated for patients and physicians if they succeed in this transition. Hence, the advancement in proteomic technologies, leads toward a significant improvement in understanding of the protein markers and molecular mechanisms linked to the outcomes of kidney transplants. However, the road from discovery to the use of such proteins in clinical practice is long, with a need for continuous validation and beyond the singular research team with comprehensive infrastructure and across research groups collaboration.
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Affiliation(s)
- Merita Rroji
- Faculty of Medicine, University Department of Nephrology, University of Medicine Tirana, Tirana, Albania
| | - Andreja Figurek
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Goce Spasovski
- Medical Faculty, University Department of Nephrology, University of Skopje, Skopje, Macedonia
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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: 13] [Impact Index Per Article: 4.3] [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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Zhang Y, Ou M, Lin H, Lai L, Chen H, Chen J, Sui W, Xue W, Zhang R, Gan Q, Tang D, Sun X, Dong J, Yan Q, Dai Y. Proteomic analysis of differentially expressed proteins in the serum of patients with acute renal allograft rejection using iTRAQ labelling technology. Mol Med Rep 2020; 22:2329-2341. [PMID: 32705285 PMCID: PMC7411402 DOI: 10.3892/mmr.2020.11299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 04/07/2020] [Indexed: 12/24/2022] Open
Abstract
Transplantation is currently the best treatment for patients with end‑stage renal disease. However, acute rejection (AR) is the major source of failure in renal transplantation. The current best practice for the diagnosis of AR involves renal biopsy, but it is invasive, time‑consuming, costly and inconvenient. Sensitive and less invasive detection of AR episodes in renal transplant patients is essential to preserve allograft function. The present study applied isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry to analyze serum protein expression in patients with AR and healthy controls. Overall, 1,399 proteins were identified. Using a cut‑off of Q<0.05 and a fold change of >1.2 for the variation in expression, 109 proteins were identified to be differentially expressed between the AR and control groups, 72 of which were upregulated and 37 were downregulated. Several proteins, including properdin, keratin 1, lipoprotein(a) and vitamin D‑binding protein, may have roles in the pathogenesis of AR. The present study focused on iTRAQ‑based proteomic profiling of serum samples in AR. Insight from the present study may help advance the understanding of the molecular mechanisms of AR and identify potential novel biomarkers of AR for further characterization.
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Affiliation(s)
- Yue Zhang
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Hua Lin
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Liusheng Lai
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Huaizhou Chen
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Jiejing Chen
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Weiguo Sui
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Wen Xue
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Ruohan Zhang
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Qing Gan
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Donge Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Xuyong Sun
- Department of Organ Transplantation, Institute of Transplant Medicine, No. 923 Hospital of People's Liberation Army, Guangxi Key Laboratory for Transplantation Medicine, Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi 530021, P.R. China
| | - Jianhui Dong
- Department of Organ Transplantation, Institute of Transplant Medicine, No. 923 Hospital of People's Liberation Army, Guangxi Key Laboratory for Transplantation Medicine, Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi 530021, P.R. China
| | - Qiang Yan
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
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Chen J, Cui X, Qian Z, Li Y, Kang K, Qu J, Li L, Gou D. Multi-omics analysis reveals regulators of the response to PDGF-BB treatment in pulmonary artery smooth muscle cells. BMC Genomics 2016; 17:781. [PMID: 27716141 PMCID: PMC5053085 DOI: 10.1186/s12864-016-3122-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 09/26/2016] [Indexed: 12/18/2022] Open
Abstract
Background Pulmonary arterial hypertension (PAH) is a lethal disease with pronounced narrowing of pulmonary vessels due to abnormal cell proliferation. The platelet-derived growth factor BB (PDGF-BB) is well known as a potent mitogen for smooth muscle cell proliferation. To better understand how this growth factor regulates pulmonary arterial smooth muscle cells (PASMCs) proliferation, we sought to characterize the response to PDGF-BB stimulation at system-wide levels, including the transcriptome and proteome. Results In this study, we identified 1611 mRNAs (transcriptome), 207 proteins (proteome) differentially expressed in response to PDGF-BB stimulation in PASMCs based on RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ) assay. Transcription factor (TF)-target network analysis revealed that PDGF-BB regulated gene expression potentially via TFs including HIF1A, JUN, EST1, ETS1, SMAD1, FOS, SP1, STAT1, LEF1 and CEBPB. Among them, SMAD1-involved BMPR2/SMADs axis plays a significant role in PAH development. Interestingly, we observed that the expression of BMPR2 was decreased in both mRNA and protein level in response to PDGF-BB. Further study revealed that BMPR2 is the direct target of miR-376b that is up-regulated upon PDGF-BB treatment. Finally, EdU incorporation assay showed that miR-376b promoted proliferation of PASMCs. Conclusion This integrated analysis of PDGF-BB-regulated transcriptome and proteome was performed for the first time in normal PASMCs, which revealed a crosstalk between PDGF signaling and BMPR2/SMADs axis. Further study demonstrated that PDGF-BB-induced miR-376b upregulation mediated the downregulation of BMPR2, which led to expression change of its downstream targets and promoted proliferation of PASMCs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3122-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jidong Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xiaolei Cui
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China
| | - Zhengjiang Qian
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Yanjiao Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Kang Kang
- Department of Physiology, Shenzhen University Health Science Center, Shenzhen, Guangdong, 518060, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Li Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.
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Dai M, Feng M, Ye Y, Wu X, Liu D, Liao M, Cao W. Exogenous avian leukosis virus-induced activation of the ERK/AP1 pathway is required for virus replication and correlates with virus-induced tumorigenesis. Sci Rep 2016; 6:19226. [PMID: 26754177 PMCID: PMC4709637 DOI: 10.1038/srep19226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/03/2015] [Indexed: 12/13/2022] Open
Abstract
A proteomics approach was used to reveal the up-regulated proteins involved in the targeted mitogen-activated protein kinase (MAPK) signal transduction pathway in DF-1 cells after ALV subgroup J (ALV-J) infection. Next, we found that ALV-J CHN06 strain infection of DF-1 cells correlated with extracellular signal-regulated kinase 2 (ERK2) activation, which was mainly induced within 15 min, a very early stage of infection, and at a late infection stage, from 108 h to 132 h post-infection. Infection with other ALV subgroup (A/B) strains also triggered ERK/MAPK activation. Moreover, when activating ERK2, ALV subgroups A, B and J simultaneously induced the phosphorylation of c-Jun, an AP1 family member and p38 activation but had no obvious effect on JNK activation at either 15 min or 120 h. Interestingly, only PD98059 inhibited the ALV-induced c-Jun phosphorylation while SP600125 or SB203580 had no influence on c-Jun activation. Furthermore, the viral gp85 and gag proteins were found to contribute to ERK2/AP1 activation. Additionally, the specific ERK inhibitor, PD980509, significantly suppressed ALV replication, as evidenced by extremely low levels of ALV promoter activity and ALV-J protein expression. In vivo analysis of ERK2 activation in tumor cells derived from ALV-J-infected chicken demonstrated a strong correlation between ERK/MAPK activation and virus-associated tumorigenesis.
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Affiliation(s)
- Manman Dai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
| | - Min Feng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
| | - Yu Ye
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
| | - Xiaochan Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
| | - Di Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture
- South China Collaborative innovation Center for Prevention and Control of poultry Infectious diseases and Safety of Poultry Products.
| | - Weisheng Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People’s Republic of China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture
- South China Collaborative innovation Center for Prevention and Control of poultry Infectious diseases and Safety of Poultry Products.
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