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Wojciuk B, Salabura A, Grygorcewicz B, Kędzierska K, Ciechanowski K, Dołęgowska B. Urobiome: In Sickness and in Health. Microorganisms 2019; 7:microorganisms7110548. [PMID: 31717688 PMCID: PMC6921077 DOI: 10.3390/microorganisms7110548] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/16/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022] Open
Abstract
The human microbiome has been proven to contribute to the human condition, both in health and in disease. The metagenomic approach based on next-generation sequencing has challenged the dogma of urine sterility. The human urobiome consists of bacteria and eukaryotic viruses as well as bacteriophages, which potentially represent the key factor. There have been several significant findings with respect to the urobiome in the context of urological disorders. Still, the research on the urobiome in chronic kidney disease and kidney transplantation remains underrepresented, as does research on the role of the virome in the urinary microbiota. In this review, we present recent findings on the urobiome with a particular emphasis on chronic kidney disease and post-kidney transplantation status. Challenges and opportunities arising from the research on the human urobiome will also be discussed.
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Affiliation(s)
- Bartosz Wojciuk
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland
- Correspondence: ; Tel.: +48-914-661-654
| | - Agata Salabura
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Bartłomiej Grygorcewicz
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (B.G.); (B.D.)
| | - Karolina Kędzierska
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Kazimierz Ciechanowski
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (B.G.); (B.D.)
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Freedman BI, Kistler AL, Skewes-Cox P, Ganem D, Spainhour M, Turner J, Divers J, Langefeld CD, Murea M, Hicks PJ, Hemal AK, Snipes JA, Zhao L, Abend JR, Lyles DS, Ma L, Skorecki KL. JC polyoma viruria associates with protection from chronic kidney disease independently from apolipoprotein L1 genotype in African Americans. Nephrol Dial Transplant 2019; 33:1960-1967. [PMID: 29420808 DOI: 10.1093/ndt/gfx368] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background Viral infections can trigger chronic kidney disease (CKD) and the urine virome may inform risk. The Natural History of APOL1-Associated Nephropathy Study (NHAANS) reported that urine JC polyomavirus (JCPyV) associated with a lower risk of APOL1-associated nephropathy in African Americans. Herein, association was assessed between urine JCPyV with CKD in African Americans independent from the APOL1 genotype. Methods Quantitative polymerase chain reaction was performed for urinary detection of JCPyV and BK polyoma virus (BKPyV) in 200 newly recruited nondiabetic African Americans. A combined analysis was performed in these individuals plus 300 NHAANS participants. Results In the 200 new participants, urine JCPyV was present in 8.8% of CKD cases and 45.8% of nonnephropathy controls (P = 3.0 × 10-8). In those with APOL1 renal-risk genotypes, JCPyV was detected in 5.1% of cases and 40.0% of controls (P = 0.0002). In those lacking APOL1 renal-risk genotypes, JCPyV was detected in 12.2% of cases and 48.8% of controls (P = 8.5 × 10-5). BKPyV was detected in 1.3% of cases and 0.8% of controls (P = 0.77). In a combined analysis with 300 NHAANS participants (n = 500), individuals with urine JCPyV had a 63% lower risk of CKD compared with those without urine JCPyV (odds ratio 0.37; P = 4.6 × 10-6). RNA fluorescence in situ hybridization confirmed the presence of JCPyV genomic DNA and JCPyV messenger RNA (mRNA) in nondiseased kidney. Conclusions Inverse relationships exist between JCPyV viruria and non-diabetic CKD. Future studies should determine whether renal inflammation associated with CKD is less permissive for JCPyV reactivation/replication or whether JCPyV is a marker of reduced host immune responsiveness that diminishes immune pathologic contributions to CKD.
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Affiliation(s)
- Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Amy L Kistler
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Peter Skewes-Cox
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Don Ganem
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Mitzie Spainhour
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Jolyn Turner
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Jasmin Divers
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Mariana Murea
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Pamela J Hicks
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Ashok K Hemal
- Department of Urology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - James A Snipes
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Lihong Zhao
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Johanna R Abend
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Douglas S Lyles
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Lijun Ma
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Karl L Skorecki
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology and Department of Nephrology, Rambam Health Care Campus, Haifa, Israel
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Abstract
BACKGROUND An improved understanding of the pathogenesis in apolipoprotein L1 (APOL1) gene-associated chronic kidney disease (CKD) arose from observations in kidney transplantation. APOL1 genotyping could soon improve the safety of living kidney donation in individuals with recent African ancestry and alter the allocation of deceased donor kidneys. METHODS This article reviews the potential mechanisms that underlie development of APOL1-associated nephropathy. Roles for circulating APOL1 protein versus intrinsic renal expression of APOL1 are discussed, as well as the requirement for modifying genetic and/or environmental factors. RESULTS Abundant evidence supports local kidney production of APOL1 renal-risk variant protein in the development of nephropathy; this is true in both native kidney disease and after renal transplantation. Only a minority of kidneys from individuals with APOL1 high-risk genotypes will develop CKD or manifest shorter renal allograft survival after transplantation. Therefore, modifying factors that explain why only a subset of kidneys develops nephropathy remain critical to identify. It appears likely that environmental exposures, as opposed to major APOL1-second gene interactions, will prove to be stronger modifiers of the risk for nephropathy. CONCLUSIONS The evolving understanding of the pathogenesis in APOL1-associated nephropathy will identify biomarkers predicting nephropathy in individuals at high genetic risk and lead to novel therapies to prevent or slow native CKD progression and prolong survival of transplanted kidneys. In the interim, the National Institutes of Health-sponsored "APOL1 Long-term Kidney Transplantation Outcomes" Network will determine whether APOL1 genotyping in individuals with recent African ancestry improves outcomes and safety in kidney transplantation.
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Affiliation(s)
- Lijun Ma
- Department of Internal Medicine, Section on Nephrology; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jasmin Divers
- Division of Public Health Sciences, Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Divers J, Langefeld CD, Lyles DS, Ma L, Freedman BI. Protective association between JC polyoma viruria and kidney disease. Curr Opin Nephrol Hypertens 2019; 28:65-69. [PMID: 30320619 PMCID: PMC9070104 DOI: 10.1097/mnh.0000000000000464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PURPOSE OF REVIEW The presence of viruses in urine (urine virome) typically reflects infection in the kidneys and urinary tract. The urinary virome is associated with HIV-associated nephropathy and chronic glomerulosclerosis. There are many associations of this microbiome with human diseases that remain to be described. This manuscript reviews emerging data on relationships between kidney disease and urinary tract infection/colonization with JC polyomavirus (JCPyV). RECENT FINDINGS Approximately 30% of the adult population sheds JCPyV in the urine. Further, urinary tract infection with one polyomavirus strain appears to inhibit secondary infections. The presence of urinary JCPyV and BK polyomavirus (BKPyV) replication were measured with polymerase chain reaction in African Americans to assess relationships with apolipoprotein L1 gene (APOL1)-associated nephropathy. Urinary JCPyV was associated with paradoxically lower rates of nephropathy in those with APOL1 high-risk genotypes. Subsequent studies revealed African Americans with JCPyV viruria had lower rates of nondiabetic nephropathy independent from APOL1. SUMMARY Urinary tract JCPyV replication is common and associates with lower rates of nephropathy. This relationship is observed in diverse settings. Results support a host immune system that fails to eradicate nonnephropathic viruses and is also less likely to manifest renal parenchymal inflammation resulting in glomerulosclerosis.
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Affiliation(s)
- Jasmin Divers
- Division of Public Health Sciences, Department of Biostatistical Sciences, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Carl D. Langefeld
- Division of Public Health Sciences, Department of Biostatistical Sciences, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Douglas S. Lyles
- Department of Biochemistry, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Lijun Ma
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Rossi F, Li X, Jacobson L, Levine AJ, Chen Y, Palella FJ, Margolick J, Viscidi R. BK virus capsid antibodies are associated with protection against subsequent development of PML in HIV-infected patients. Virology 2015; 485:467-72. [PMID: 26356797 DOI: 10.1016/j.virol.2015.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 12/16/2022]
Abstract
Progressive multifocal leukoencephalopathy (PML) is caused by JC polyomavirus (JCPyV). Because a reciprocal relationship has been described between antibody levels to JCPyV and BK polyomavirus (BKPyV), we performed a nested case control study with pre-diagnostic serum samples from HIV infected subjects to examine the relationship between BKPyV capsid antibodies and the risk of PML. Serum samples collected 0.5-2 years before PML diagnosis from 25 cases (66 samples) and 80 matched controls (204 samples) were tested in ELISA for JCPyV, BKPyV type 1 and type 4 capsid antibodies. High levels of BKPyV 1 and 4 antibodies were associated with a lower risk of PML (BKPyV 1 OR, 0.56, 95% CI, 0.35-0.89; BKPyV 4 OR, 0.40, 95% CI, 0.24-0.0.67). Our study demonstrates that antibodies to BKPyV capsids are an immunological marker of protection against development of PML. Further studies are needed to define the mechanism.
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Affiliation(s)
- Francesca Rossi
- Department of Public Health Science and Infectious Diseases, "Sapienza" University of Rome, Rome, Italy
| | - Xiuhong Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lisa Jacobson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew J Levine
- Department of Neurology, University of California at Los Angeles, Los Angeles, USA
| | - Yue Chen
- University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, USA
| | - Frank J Palella
- Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Raphael Viscidi
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Kluba J, Linnenweber-Held S, Heim A, Ang AM, Raggub L, Broecker V, Becker JU, Schulz TF, Schwarz A, Ganzenmueller T. A rolling circle amplification screen for polyomaviruses other than BKPyV in renal transplant recipients confirms high prevalence of urinary JCPyV shedding. Intervirology 2015; 58:88-94. [PMID: 25677461 DOI: 10.1159/000369210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/20/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Multiple novel human polyomaviruses (HPyVs) have been discovered in the last few years. These or other, unknown, nephrotropic HPyVs may potentially be shed in urine. METHODS To search for known and unknown HPyVs we investigated BKPyV-negative urine samples from 105 renal transplant recipients (RTR) by rolling circle amplification (RCA) analysis and quantitative JCPyV PCR. Clinical data was analysed to identify risk factors for urinary polyomavirus shedding. RESULTS In 10% (11/105) of the urine samples RCA with subsequent sequencing revealed JCPyV, but no other HPyV sequences. Using quantitative JCPyV PCR, 24% (25/105) of the samples tested positive. Overall sensitivities of RCA of 44% (11/25) in detecting JCPyV in JCPyV DNA-positive urine and 67% (10/15) for samples with JCPyV loads >10,000 copies/ml can be assumed. Despite frequent detectable urinary shedding of JCPyV in our cohort, this could not be correlated with clinical risk factors. CONCLUSION Routine urinary JCPyV monitoring in BKPyV-negative RTR without suspected polyomavirus-associated nephropathy might be of limited diagnostic value. As RCA works in a sequence-independent manner, detection of novel and known polyomaviruses shed in sufficient quantities is feasible. High-level shedding of HPyVs other than BKPyV or JCPyV in the urine of RTR is unlikely to occur.
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Affiliation(s)
- Jeanette Kluba
- Institute of Virology, Hannover Medical School, Hannover, Germany
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Affiliation(s)
- Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jasmin Divers
- Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kevin P High
- Section on Infectious Diseases, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Freedman BI, Skorecki K. Gene-gene and gene-environment interactions in apolipoprotein L1 gene-associated nephropathy. Clin J Am Soc Nephrol 2014; 9:2006-13. [PMID: 24903390 DOI: 10.2215/cjn.01330214] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular genetics have revolutionized the understanding of susceptibility to the broad spectrum of kidney diseases with light microscopic appearance of FSGS, particularly in populations with recent African ancestry. These disorders include idiopathic FSGS, HIV-associated nephropathy, severe lupus nephritis, sickle cell nephropathy, and the primary kidney disorder focal global glomerulosclerosis, which had historically been ascribed to systemic hypertension. FSGS was once thought to include a multitude of unrelated disorders with similar histologic appearance. However, variation in the apolipoprotein L1 gene locus is now known to account for the vast majority of such cases in African Americans as well as nearly all the excess risk for FSGS and related forms of progressive nondiabetic nephropathy in populations with recent African ancestry, relative to European ancestry. Inheriting two coding apolipoprotein L1 gene nephropathy risk variants is necessary for susceptibility to CKD; however, these variants alone are insufficient to produce disease. This work reviews the evidence supporting second hits or modifying factors that affect risk for apolipoprotein L1 gene-associated nephropathy and produce the protean manifestations of this common and complex syndrome. Targeting modifiable second factors will lead to preventive therapies for slowing progression of nondiabetic nephropathy in many patients possessing two apolipoprotein L1 gene risk variants. This model of genetic risk coupled with modifiable second hits will serve as a paradigm applicable to patients with CKD of various etiologies as well as a host of other complex disorders.
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Affiliation(s)
- Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina; and
| | - Karl Skorecki
- Molecular Medicine Laboratory, Rambam Healthcare Campus, Haifa, Israel
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