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Gerges D, Abd El-Ghany K, Hevesi Z, Aiad M, Omic H, Baumgartner C, Winnicki W, Eder M, Schmidt A, Eskandary F, Wagner L. Shedding Light on Viral Shedding: Novel Insights into Nuclear Assembly, Cytoplasmic Transformation and Extracellular Vesicle Release of the BK Virus. Int J Mol Sci 2024; 25:9130. [PMID: 39201816 PMCID: PMC11354704 DOI: 10.3390/ijms25169130] [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: 06/20/2024] [Revised: 08/13/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Despite the high prevalence of BK polyomavirus (BKPyV) and the associated risk for BKPyV-associated nephropathy (BKPyVAN) in kidney transplant (KTX) recipients, many details on viral processes such as replication, maturation, assembly and virion release from host cells have not been fully elucidated. VP1 is a polyomavirus-specific protein that is expressed in the late phase of its replicative cycle with important functions in virion assembly and infectious particle release. This study investigated the localization and time-dependent changes in the distribution of VP1-positive viral particles and their association within the spectrum of differing cell morphologies that are observed in the urine of KTX patients upon active BKPyV infection. We found highly differing recognition patterns of two anti-VP1 antibodies with respect to intracellular and extracellular VP1 localization, pointing towards independent binding sites that were seemingly associated with differing stages of virion maturation. Cells originating from single clones were stably cultured out of the urine sediment of KTX recipients with suspected BKPyVAN. The cell morphology, polyploidy, virus replication and protein production were investigated by confocal microscopy using both a monoclonal (mAb 4942) and a polyclonal rabbit anti-VP1-specific antibody (RantiVP1 Ab). Immunoblotting was performed to investigate changes in the VP1 protein. Both antibodies visualized VP1 and the mAb 4942 recognized VP1 in cytoplasmic vesicles exhibiting idiomorphic sizes when released from the cells. In contrast, the polyclonal antibody detected VP1 within the nucleus and in cytoplasm in colocalization with the endoplasmic reticulum marker CNX. At the nuclear rim, VP1 was recognized by both antibodies. Immunoblotting revealed two smaller versions of VP1 in urinary decoy cell extracts, potentially from different translation start sites as evaluated by in silico analysis. Oxford Nanopore sequencing showed integration of BKPyV DNA in chromosomes 3, 4 and 7 in one of the five tested primary cell lines which produced high viral copies throughout four passages before transcending into senescence. The different staining with two VP1-specific antibodies emphasizes the modification of VP1 during the process of virus maturation and cellular exit. The integration of BKPyV into the human genome leads to high virus production; however, this alone does not transform the cell line into a permanently cycling and indefinitely replicating one.
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Affiliation(s)
- Daniela Gerges
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Karim Abd El-Ghany
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
- Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria;
| | - Zsofia Hevesi
- Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria;
| | - Monika Aiad
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Haris Omic
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Clemens Baumgartner
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
- Division of Endocrinology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Winnicki
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Michael Eder
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Alice Schmidt
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
| | - Ludwig Wagner
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (K.A.E.-G.); (M.A.); (H.O.); (C.B.); (W.W.); (M.E.); (A.S.); (L.W.)
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Hinze C, Lovric S, Halloran PF, Barasch J, Schmidt-Ott KM. Epithelial cell states associated with kidney and allograft injury. Nat Rev Nephrol 2024; 20:447-459. [PMID: 38632381 DOI: 10.1038/s41581-024-00834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
The kidney epithelium, with its intricate arrangement of highly specialized cell types, constitutes the functional core of the organ. Loss of kidney epithelium is linked to the loss of functional nephrons and a subsequent decline in kidney function. In kidney transplantation, epithelial injury signatures observed during post-transplantation surveillance are strong predictors of adverse kidney allograft outcomes. However, epithelial injury is currently neither monitored clinically nor addressed therapeutically after kidney transplantation. Several factors can contribute to allograft epithelial injury, including allograft rejection, drug toxicity, recurrent infections and postrenal obstruction. The injury mechanisms that underlie allograft injury overlap partially with those associated with acute kidney injury (AKI) and chronic kidney disease (CKD) in the native kidney. Studies using advanced transcriptomic analyses of single cells from kidney or urine have identified a role for kidney injury-induced epithelial cell states in exacerbating and sustaining damage in AKI and CKD. These epithelial cell states and their associated expression signatures are also observed in transplanted kidney allografts, suggesting that the identification and characterization of transcriptomic epithelial cell states in kidney allografts may have potential clinical implications for diagnosis and therapy.
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Affiliation(s)
- Christian Hinze
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Svjetlana Lovric
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan Barasch
- Division of Nephrology, Columbia University, New York City, NY, USA
| | - Kai M Schmidt-Ott
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany.
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Nast CC. Polyomavirus nephropathy: diagnosis, histologic features, and differentiation from acute rejection. CLINICAL TRANSPLANTATION AND RESEARCH 2024; 38:71-89. [PMID: 38725187 PMCID: PMC11228385 DOI: 10.4285/ctr.24.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 06/29/2024]
Abstract
Polyomaviruses, particularly BK virus, are ubiquitous latent infections that may reactivate with immunosuppression during kidney transplantation, resulting in polyomavirus nephropathy (PVN). The levels of viruria and viremia serve as tools for screening and making a presumptive diagnosis of PVN, respectively, while a definitive diagnosis requires a kidney biopsy. There are histologic classifications of PVN based on the extent of tubular cell viral infection, interstitial fibrosis, and interstitial inflammation. These classifications correlate to some degree with graft function and loss, aiding in determining treatment efficacy and prognostication. PVN has histologic overlap with acute cell-mediated rejection, making the differential diagnosis challenging, although there are suggestive features for these different causes of graft dysfunction. This article reviews the diagnosis, histologic findings, and classifications of PVN, and discusses how to differentiate viral nephropathy from acute rejection.
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Affiliation(s)
- Cynthia C Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Hirschhorn JW, Sasaki MM, Kegl A, Akter T, Dickerson T, Narlieva M, Nhan N, Liu T, Jim P, Young S, Orner E, Thwe P, Lucic D, Goldstein DY. Performance evaluation of the high-throughput quantitative Alinity m BK virus assay. J Clin Microbiol 2024; 62:e0135423. [PMID: 38526061 PMCID: PMC11005350 DOI: 10.1128/jcm.01354-23] [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: 10/13/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
BK virus (BKV) infection or reactivation in immunocompromised individuals can lead to adverse health consequences including BKV-associated nephropathy (BKVAN) in kidney transplant patients and BKV-associated hemorrhagic cystitis (BKV-HC) in allogeneic hematopoietic stem cell transplant recipients. Monitoring BKV viral load plays an important role in post-transplant patient care. This study evaluates the performance of the Alinity m BKV Investigational Use Only (IUO) assay. The linearity of the Alinity m BKV IUO assay had a correlation coefficient of 1.000 and precision of SD ≤ 0.25 Log IU/mL for all panel members tested (2.0-7.3 Log IU/mL). Detection rate at 50 IU/mL was 100%. Clinical plasma specimens tested comparing Alinity m BKV IUO to ELITech MGB Alert BKV lab-developed test (LDT) on the Abbott m2000 platform using specimen extraction protocols for DNA or total nucleic acid (TNA) resulted in coefficient of correlation of 0.900 and 0.963, respectively, and mean bias of 0.03 and -0.54 Log IU/mL, respectively. Alinity m BKV IUO compared with Altona RealStar BKV and Roche cobas BKV assays demonstrated coefficient of correlation of 0.941 and 0.980, respectively, and mean bias of -0.47 and -0.31 Log IU/mL, respectively. Urine specimens tested on Alintiy m BKV IUO and ELITech BKV LDT using TNA specimen extraction had a coefficient of correlation of 0.917 and mean bias of 0.29 Log IU/mL. The Alinity m BKV IUO assay was performed with high precision across the dynamic range and correlated well with other available BKV assays. IMPORTANCE BK virus (BKV) in transplant patients can lead to adverse health consequences. Viral load monitoring is important in post-transplant patient care. This study evaluates the Alinity m BKV assay with currently available assays.
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Affiliation(s)
- Julie W. Hirschhorn
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Mark M. Sasaki
- Molecular Diagnostics of Abbott, Des Plaines, Illinois, USA
| | - April Kegl
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tanjina Akter
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tanisha Dickerson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Momka Narlieva
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Nhi Nhan
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Tianxi Liu
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Patricia Jim
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Stephen Young
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Erika Orner
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Phyu Thwe
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Danijela Lucic
- Molecular Diagnostics of Abbott, Des Plaines, Illinois, USA
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Kumar S, Raman S, Sesham K, Gupta A, Yadav RK, Mridha AR, Yadav SC. Visual, rapid, and cost-effective BK virus detection system for renal transplanted patients using gold nanoparticle coupled loop-mediated isothermal amplification (nanoLAMP). J Virol Methods 2024; 325:114889. [PMID: 38290650 DOI: 10.1016/j.jviromet.2024.114889] [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: 10/25/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
A substantial percentage of kidney transplant recipients show transplant failure due to BK virus-induced nephropathy. This can be clinically controlled by the rapid and timely detection of BK virus infection in immune-compromised patients. We report a rapid (two hours from sample collection, processing, and detection), cost-effective (< 2$), highly sensitive and BKV-specific nanoLAMP (loop-mediated isothermal amplification) diagnostic methodology using novel primers and gold nanoparticles complex-based visual detection. The standardized nanoLAMP showed an analytical sensitivity of 25 copies/µl and did not cross-react with closely related JC and SV40 viruses. This nanoLAMP showed diagnostic sensitivity and specificity as 91% and 96%, respectively, taking 50 BK virus-negative (confirmed by qPCR from the plasma of healthy donors) and 57 positive BKV patient samples (confirmed by clinical parameters and qPCR assay). This simple two-step, low-cost, and quick (1-2 h/test) detection would be advantageous over the currently used diagnostic methodology. It may change the paradigm for polyomavirus infection-based failure of renal transplant.
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Affiliation(s)
- Sunil Kumar
- Nanobiology Lab, Electron Microscope Facility, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Srishty Raman
- Nanobiology Lab, Electron Microscope Facility, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Kishore Sesham
- Nanobiology Lab, Electron Microscope Facility, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Abhishek Gupta
- Nanobiology Lab, Electron Microscope Facility, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Raj Kanwar Yadav
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Asit Ranjan Mridha
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Subhash Chandra Yadav
- Nanobiology Lab, Electron Microscope Facility, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India.
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Li JJX, Ng JKM, Tang CY, Chan BCH, Chan SY, Law JHN, Teoh JY, VandenBussche CJ, Tse GM. Urine cytology in the detection of renal cell carcinomas - a territory-wide multi-institutional retrospective review of more than 2 decades. Cancer Cytopathol 2024; 132:186-192. [PMID: 38329359 DOI: 10.1002/cncy.22789] [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: 09/26/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 02/09/2024]
Abstract
INTRODUCTION Compared with urothelial lesions of the upper urinary tract, the diagnostic performance of urine cytology in detection of renal cell carcinomas is underreported. This study aims to establish the role of urine cytology in the assessment of renal carcinomas by a multi-institute review of urine cytology from nephrectomy confirmed renal cell carcinomas, referenced against renal urothelial and squamous cell carcinomas. METHODS Records of nephrectomy performed from the 1990s to 2020s at three hospitals were retrieved and matched to urine cytology specimens collected within 1 year prior. Patient demographics, specimen descriptors, and histology and staging parameters were reviewed and compared against cytologic diagnoses. RESULTS There were 1147 cases of urine cytology matched with renal cell carcinomas, with 666 renal urothelial/squamous carcinomas for comparison. The detection rate for urothelial/squamous (atypia or above [C3+]: 63.1%; suspicious or above [C4+]: 24.0%) were higher than renal cell carcinoma (C3+: 13.1%; C4+: 1.5%) (p < 0.001). The positive rate for upper tract urine exceeded other collection methods at 45.0% (C3+) and 10.0% (C4+) (p < .01). Other factors associated with increased positive rates were male sex, collecting duct carcinoma histology, nuclear grade, and renal/sinus involvement (p < .05). Multivariate analysis revealed additional positive correlations with presence of sarcomatoid tumor cells, lymphovascular invasion, and perinephric fat involvement (p < .05). Larger lesion size and higher urine volume did not improve detection rates (p < .05). CONCLUSIONS The detection rate of renal cell carcinomas is suboptimal compared with urothelial carcinomas, although urine samples collected from cystoscopy or percutaneous nephrostomy significantly outperformed voided urine specimens.
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Affiliation(s)
- Joshua J X Li
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Joanna K M Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Cheuk-Yin Tang
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Bryan C H Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Sau Yee Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Jasmine H N Law
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Jeremy Y Teoh
- Department of Surgery, S.H. Ho Urology Centre, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | | | - Gary M Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
- Deparment of Pathology, North District Hospital, Hong Kong, Hong Kong
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Dolci M, Colico C, Ambrogi F, Favi E, Signorini L, Perego M, Campioli E, Maina KK, Ferrante P, Ferraresso M, Delbue S. Longitudinal study of human polyomaviruses viruria in kidney transplant recipients. Clin Exp Med 2024; 24:3. [PMID: 38231278 PMCID: PMC10794280 DOI: 10.1007/s10238-023-01290-z] [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: 09/17/2023] [Accepted: 11/03/2023] [Indexed: 01/18/2024]
Abstract
INTRODUCTION Immunosuppression after kidney transplantation (KTx) exposes recipients to Human Polyomaviruses (HPyVs) infections, whose natural history is still misunderstood. METHODS Allograft biopsies, and urine from 58 donor-recipient pairs were collected before KTx (T0) and 1 (T1), 15 (T2), 30 (T3), 60 (T4), 90 (T5), 180 (T6), 270 (T7), 360 (T8), and 540 (T9) days after transplant. Specimens were tested for JC (JCPyV) and BK (BKPyV), by quantitative Real-Time PCR. The course of post-KTx HPyVs viruria, and the association between JCPyV viruria in recipients and donors, were evaluated. RESULTS HPyVs were detected in 3/58 (5.2%) allograft biopsies. HPyVs viruria was present in 29/58 (50%) donors and 41/58 (70.7%) recipients. JCPyV DNA was detected in 26/58 (44.8%) donors and 25/58 recipients (43.1%), 19 of whom received kidney from JCPyV positive donor, whereas BKPyV genome was detected in 3 (5.2%) donors and 22 (37.9%) recipients. The median time of JCPyV, and BKPyV first episode of replication was 1, and 171 days post KTx, respectively. At T0, JCPyV viruria of donors was associated with increased risk of JCPyV replication post-KTx; recipients with JCPyV positive donors showed lower risk of BKPyV replication post-KTx. CONCLUSIONS The results suggested that JCPyV may be transmitted by allograft, and that its replication post KTx might prevent BKPyV reactivation. Future investigation regarding correlation between chronic exposure to immunosuppressive agents and HPyVs urinary replication are warranted.
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Affiliation(s)
- Maria Dolci
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via Carlo Pascal 36, 20133, Milan, Italy
| | - Caterina Colico
- Department of Emergency Surgery, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Federico Ambrogi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Evaldo Favi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- General Surgery and Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucia Signorini
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via Carlo Pascal 36, 20133, Milan, Italy
| | - Marta Perego
- General Surgery and Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Edoardo Campioli
- General Surgery and Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Kevin Kamau Maina
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via Carlo Pascal 36, 20133, Milan, Italy
| | - Pasquale Ferrante
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via Carlo Pascal 36, 20133, Milan, Italy
| | - Mariano Ferraresso
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- General Surgery and Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Serena Delbue
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via Carlo Pascal 36, 20133, Milan, Italy.
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Elsayed NS, Wolfe AJ, Burk RD. Urine microbiome in individuals with an impaired immune system. Front Cell Infect Microbiol 2024; 13:1308665. [PMID: 38274734 PMCID: PMC10808152 DOI: 10.3389/fcimb.2023.1308665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
With the advent of next generation sequencing, it is now appreciated that human urine is not sterile. Recent investigations of the urinary microbiome (urobiome) have provided insights into several urological diseases. Urobiome dysbiosis, defined as non-optimal urine microbiome composition, has been observed in many disorders; however, it is not clear whether this dysbiosis is the cause of urinary tract disorders or a consequence. In addition, immunologically altered disorders are associated with higher rates of urinary tract infections. These disorders include immunoproliferative and immunodeficiency diseases, cancer, and immunosuppressant therapy in transplant recipients. In this review, we examine the current state of knowledge of the urobiome in immunologically altered diseases, its composition and metabolomic consequences. We conclude that more data are required to describe the urobiome in immune altered states, knowledge that could facilitate understanding the role of the urobiome and its pathophysiological effects on urinary tract infections and other disorders of the urinary tract.
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Affiliation(s)
- Noha S. Elsayed
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Departments of Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, United States
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9
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Yuan J, Fei S, Gui Z, Wang Z, Chen H, Sun L, Tao J, Han Z, Ju X, Tan R, Gu M, Huang Z. Association of UGT1A Gene Polymorphisms with BKV Infection in Renal Transplantation Recipients. Curr Drug Metab 2024; 25:188-196. [PMID: 38509677 DOI: 10.2174/0113892002282727240307072255] [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: 11/28/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND BK virus (BKV) infection is an opportunistic infectious complication and constitutes a risk factor for premature graft failure in kidney transplantation. Our research aimed to identify associations and assess the impact of single-nucleotide polymorphisms (SNPs) on metabolism-related genes in patients who have undergone kidney transplantation with BKV infection. MATERIAL/METHODS The DNA samples of 200 eligible kidney transplant recipients from our center, meeting the inclusion criteria, have been collected and extracted. Next-generation sequencing was used to genotype SNPs on metabolism-associated genes (CYP3A4/5/7, UGT1A4/7/8/9, UGT2B7). A general linear model (GLM) was used to identify and eliminate confounding factors that may influence the outcome events. Multiple inheritance models and haplotype analyses were utilized to identify variation loci associated with infection caused by BKV and ascertain haplotypes, respectively. RESULTS A total of 141 SNPs located on metabolism-related genes were identified. After Hardy-Weinberg equilibrium (HWE) and minor allele frequency (MAF) analysis, 21 tagger SNPs were selected for further association analysis. Based on GLM results, no confounding factor was significant in predicting the incidence of BK polyomavirus-associated infection. Then, multiple inheritance model analyses revealed that the risk of BKV infection was significantly associated with rs3732218 and rs4556969. Finally, we detect significant associations between haplotype T-A-C of block 2 (rs4556969, rs3732218, rs12468274) and infection caused by BKV (P = 0.0004). CONCLUSION We found that genetic variants in the UGT1A gene confer BKV infection susceptibility after kidney transplantation.
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Affiliation(s)
- Jingwen Yuan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zeping Gui
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Xiaobing Ju
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Min Gu
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
- Department of Urology, The Second Affiliated Hospital with Nanjing Medical University, Nanjing, 210011, China
| | - Zhengkai Huang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
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Wang Y, Fang Y, Yan Z, Xia R, Zeng W, Deng W, Xu J, Feng X, Peng J, Miao Y. Fatal BK polyomavirus-associated pneumonia: report of two cases with literature review. BMC Infect Dis 2023; 23:592. [PMID: 37697264 PMCID: PMC10494412 DOI: 10.1186/s12879-023-08577-2] [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: 09/20/2022] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND In immunocompromised populations, such as patients with AIDS and recipients of solid organ and hematopoietic stem cell transplants, BK polyomavirus (BKPyV) can reactivate and cause several diseases, which can lead to death in their severe forms. Unlike hemorrhagic cystitis and BKPyV-associated nephropathy, BKPyV-associated pneumonia is rare, with only seven known cases worldwide. However, the disease can rapidly progress with extremely high mortality. CASE PRESENTATION Herein, we report two cases of BKPyV-associated pneumonia following hematopoietic stem cell transplantation. Both patients had consistent infectious pneumonia and graft-versus-host disease after stem cell transplantation. The diagnosis of BKPyV-associated pneumonia was confirmed by metagenomic next-generation sequencing and polymerase chain reaction after the sudden worsening of the pulmonary infection signs and symptoms concomitant with renal dysfunction and systemic immune weakening. Both patients eventually died of systemic multi-organ failure caused by severe pneumonia. CONCLUSIONS Currently, BKPyV reactivation cannot be effectively prevented. Immunocompromised patients must actively manage their primary lung infections, pay close attention to pulmonary signs and imaging changes. Especially during and after steroid pulse therapy or immunosuppressive therapy for graft versus host diseases, BKPyV load in blood/urine needs to be regularly measured, and the immunosuppressive intensity should be adjusted properly after the BKPyV reactivation diagnosis. Clinical trials of new antiviral drugs and therapies for BKPyV are urgently needed.
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Affiliation(s)
- Yuchen Wang
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Yiling Fang
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Ziyan Yan
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Renfei Xia
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Wenli Zeng
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Wenfeng Deng
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Jian Xu
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Xiaoqin Feng
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China.
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China.
| | - Yun Miao
- Department of Transplantation, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, China.
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Yang F, Chen X, Zhang H, Zhao GD, Yang H, Qiu J, Meng S, Wu P, Tao L, Wang Q, Huang G. Single-Cell Transcriptome Identifies the Renal Cell Type Tropism of Human BK Polyomavirus. Int J Mol Sci 2023; 24:ijms24021330. [PMID: 36674845 PMCID: PMC9861348 DOI: 10.3390/ijms24021330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
BK polyomavirus (BKPyV) infection is the main factor affecting the prognosis of kidney transplant recipients, as no antiviral agent is yet available. A better understanding of the renal-cell-type tropism of BKPyV can serve to develop new treatment strategies. In this study, the single-cell transcriptomic analysis demonstrated that the ranking of BKPyV tropism for the kidney was proximal tubule cells (PT), collecting duct cells (CD), and glomerular endothelial cells (GEC) according to the signature of renal cell type and immune microenvironment. In normal kidneys, we found that BKPyV infection-related transcription factors P65 and CEBPB were PT-specific transcription factors, and PT showed higher glycolysis/gluconeogenesis activities than CD and GEC. Furthermore, in the BKPyV-infected kidneys, the percentage of late viral transcripts in PT was significantly higher than in CD and GEC. In addition, PT had the smallest cell-cell interactions with immune cells compared to CD and GEC in both normal and BKPyV-infected kidneys. Subsequently, we indirectly demonstrated the ranking of BKPyV tropism via the clinical observation of sequential biopsies. Together, our results provided in-depth insights into the renal cell-type tropism of BKPyV in vivo at single-cell resolution and proposed a novel antiviral target.
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Affiliation(s)
- Feng Yang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Provincial International Cooperation Based of Science and Technology (Organ Transplantation), Sun Yat-Sen University, Guangzhou 510080, China
| | - Xutao Chen
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Hui Zhang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Guo-Dong Zhao
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Huifei Yang
- Department of Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Jiang Qiu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Siyan Meng
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Penghan Wu
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Liang Tao
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qin Wang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Correspondence: (Q.W.); (G.H.)
| | - Gang Huang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Provincial International Cooperation Based of Science and Technology (Organ Transplantation), Sun Yat-Sen University, Guangzhou 510080, China
- Correspondence: (Q.W.); (G.H.)
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12
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Zhao J, You X, Zeng X. Research progress of BK virus and systemic lupus erythematosus. Lupus 2022; 31:522-531. [PMID: 35264023 DOI: 10.1177/09612033221084259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: Systemic lupus erythematosus (SLE) is an autoimmune disease in which patients are often infected by viruses due to deficient immunity or immunosuppressant use. BK virus (BKV)mainly affects the kidney and can also cause multiple organ involvement throughout the body, which is similar to SLE. BKV is mostly a latent infection in vivo. The incidence of virus reactivation is higher in SLE patients. Reactivation of BKV can induce the production of autoantibodies, thereby promoting the occurrence and development of SLE.Purpose: Aim of this article is to review the prevalence and pathegenesis of BKV infection in SLE patients.Method: The literature search was conducted using four different databases including PubMed, Cochrane Library, Scopus and Web of Science.Results: BK virus is higher infection and reactivation in SLE patients. The "hapten carrier" mechanism may lead to the production of autoantibodies. Some immunosuppressive drugs, like leflumide and hydroxychloroquine, may show a protective effect.Conclusions: BKV infection plays a role in the occurrence and development of SLE, and its significance deserves further exploration.
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Affiliation(s)
- Jiawei Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, 34732Peking Union Medical College, Beijing, China
| | - Xin You
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, 34732Peking Union Medical College, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, 34732Peking Union Medical College, Beijing, China
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BK Polyomavirus Activates HSF1 Stimulating Human Kidney Hek293 Cell Proliferation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9176993. [PMID: 34845419 PMCID: PMC8627348 DOI: 10.1155/2021/9176993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/14/2021] [Accepted: 10/30/2021] [Indexed: 11/21/2022]
Abstract
Objectives Some DNA viruses, such as BKPyV, are capable of inducing neoplastic transformation in human tissues through still unclear mechanisms. The goal of this study is to investigate the carcinogenic potential of BK polyomavirus (BKPyV) in human embryonic kidney 293 (Hek293) cells, dissecting the molecular mechanism that determines the neoplastic transformation. Materials and Methods BKPyV, isolated from urine samples of infected patients, was used to infect monolayers of Hek293 cells. Subsequently, intracellular redox changes, GSH/GSSH concentration by HPLC, and reactive oxygen/nitrogen species (ROS/RNS) production were monitored. Moreover, to understand the signaling pathway underlying the neoplastic transformation, the redox-sensitive HFS1-Hsp27 molecular axis was examined using the flavonoid quercetin and polishort hairpin RNA technologies. Results The data obtained show that while BKPyV replication is closely linked to the transcription factor p53, the increase in Hek293 cell proliferation is due to the activation of the signaling pathway mediated by HSF1-Hsp27. In fact, its inhibition blocks viral replication and cell growth, respectively. Conclusions The HSF1-Hsp27 signaling pathway is involved in BKPyV infection and cellular replication and its activation, which could be involved in cell transformation.
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14
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BK Polyomavirus-Biology, Genomic Variation and Diagnosis. Viruses 2021; 13:v13081502. [PMID: 34452367 PMCID: PMC8402805 DOI: 10.3390/v13081502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
The BK polyomavirus (BKPyV), a representative of the family Polyomaviridae, is widespread in the human population. While the virus does not cause significant clinical symptoms in immunocompetent individuals, it is activated in cases of immune deficiency, both pharmacological and pathological. Infection with the BKPyV is of particular importance in recipients of kidney transplants or HSC transplantation, in which it can lead to the loss of the transplanted kidney or to haemorrhagic cystitis, respectively. Four main genotypes of the virus are distinguished on the basis of molecular differentiation. The most common genotype worldwide is genotype I, with a frequency of about 80%, followed by genotype IV (about 15%), while genotypes II and III are isolated only sporadically. The distribution of the molecular variants of the virus is associated with the region of origin. BKPyV subtype Ia is most common in Africa, Ib-1 in Southeast Asia, and Ib-2 in Europe, while Ic is the most common variant in Northeast Asia. The development of molecular methods has enabled significant improvement not only in BKPyV diagnostics, but in monitoring the effectiveness of treatment as well. Amplification of viral DNA from urine by PCR (Polymerase Chain Reaction) and qPCR Quantitative Polymerase Chain Reaction) is a non-invasive method that can be used to confirm the presence of the genetic material of the virus and to determine the viral load. Sequencing techniques together with bioinformatics tools and databases can be used to determine variants of the virus, analyse their circulation in populations, identify relationships between them, and investigate the directions of evolution of the virus.
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15
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Orlowski S, Mourad JJ, Gallo A, Bruckert E. Coronaviruses, cholesterol and statins: Involvement and application for Covid-19. Biochimie 2021; 189:51-64. [PMID: 34153377 PMCID: PMC8213520 DOI: 10.1016/j.biochi.2021.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/01/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022]
Abstract
The infectious power of coronaviruses is dependent on cholesterol present in the membranes of their target cells. Indeed, the virus enters the infected cell either by fusion or by endocytosis, in both cases involving cholesterol-enriched membrane microdomains. These membrane domains can be disorganized in-vitro by various cholesterol-altering agents, including statins that inhibit cell cholesterol biosynthesis. As a consequence, numerous cell physiology processes, such as signaling cascades, can be compromised. Also, some examples of anti-bacterial and anti-viral effects of statins have been observed for infectious agents known to be cholesterol dependent. In-vivo, besides their widely-reported hypocholesterolemic effect, statins display various pleiotropic effects mediated, at least partially, by perturbation of membrane microdomains as a consequence of the alteration of endogenous cholesterol synthesis. It should thus be worth considering a high, but clinically well-tolerated, dose of statin to treat Covid-19 patients, in the early phase of infection, to inhibit virus entry into the target cells, in order to control the viral charge and hence avoid severe clinical complications. Based on its efficacy and favorable biodisposition, an option would be considering Atorvastatin, but randomized controlled clinical trials are required to test this hypothesis. This new therapeutic proposal takes benefit from being a drug repurposing, applied to a widely-used drug presenting a high efficiency-to-toxicity ratio. Additionally, this therapeutic strategy avoids any risk of drug resistance by viral mutation since it is host-targeted. Noteworthy, the same pharmacological approach could also be proposed to address different animal coronavirus endemic infections that are responsible for heavy economic losses.
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Affiliation(s)
- Stéphane Orlowski
- Institute for Integrative Biology of the Cell (I2BC), CNRS UMR 9198, and CEA / DRF / Institut des Sciences du Vivant Frédéric-Joliot / SB2SM, and Université Paris-Saclay, 91191, Gif-sur-Yvette, Cedex, France.
| | - Jean-Jacques Mourad
- Department of Internal Medicine and ESH Excellence Centre, Groupe Hospitalier Paris Saint-Joseph, Paris, France.
| | - Antonio Gallo
- Department of Endocrinology and Prevention of Cardiovascular Diseases, Institute of Cardiometabolism and Nutrition (ICAN), La Pitié-Salpêtrière Hospital, AP-HP, Paris, France.
| | - Eric Bruckert
- Department of Endocrinology and Prevention of Cardiovascular Diseases, Institute of Cardiometabolism and Nutrition (ICAN), La Pitié-Salpêtrière Hospital, AP-HP, Paris, France.
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Shatizadeh Malekshahi S, Soleimanjahi H, Dorostkar F, Salimi V, Farahmand M. Survey of BK Virus in Renal Transplant Recipients in Iran: A Systematic Review and Meta-Analysis. Intervirology 2020; 64:1-9. [PMID: 33333504 DOI: 10.1159/000512132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 09/22/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION BK virus (BKV) infection in renal transplant (RT) recipients can cause hemorrhagic cystitis, transient renal dysfunction, and BKV nephropathy (BKVN). The prevalence and significance of BKV in RT recipients remain to be clarified in the Iranian population. The purpose of this review is to summarize the overall prevalence of BKV infection in RT recipients from previously published studies in Iran. METHODS We systematically reviewed articles through a comprehensive search of the main electronic and Persian national databases up to November 2019. RESULTS The overall pooled prevalence of BKV infection among the Iranian population was 23% (95% CI; 15-33%). Comparing these studies revealed that the prevalence of BKV in plasma samples ranges from 3 to 40%, in renal biopsies 1-13%, and in urine samples 10-49%. Due to substantial heterogeneity among reported studies (I2 = 93%, p < 0.01), random-effect meta-analysis was performed. BKV infection rate was slightly higher in women than men (16%, p = 0.04 vs. 14%, p < 0.01, respectively). The majority of the studies employed real-time PCR (24%, I2 = 93, p < 0.01) and analyzed plasma samples alone or in combination with other types of specimens. BKV prevalence from 5 cities among the Iranian population showed a higher prevalence rate in Guilan. CONCLUSION Our analysis provides a preliminary estimate of the epidemiology of BKV infection in RT recipients in Iran. These results arouse a need for more epidemiological studies of BKV infection in different unanalyzed regions in Iran. Early detection of BKV in RT recipients helps timely nephropathy diagnosis and prevents graft loss.
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Affiliation(s)
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
| | - Fariba Dorostkar
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Teheran, Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Teheran, Iran
| | - Mohammad Farahmand
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Teheran, Iran,
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Uhlorn BL, Jackson R, Li S, Bratton SM, Van Doorslaer K, Campos SK. Vesicular trafficking permits evasion of cGAS/STING surveillance during initial human papillomavirus infection. PLoS Pathog 2020; 16:e1009028. [PMID: 33253291 PMCID: PMC7728285 DOI: 10.1371/journal.ppat.1009028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 12/10/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022] Open
Abstract
Oncogenic human papillomaviruses (HPVs) replicate in differentiating epithelium, causing 5% of cancers worldwide. Like most other DNA viruses, HPV infection initiates after trafficking viral genome (vDNA) to host cell nuclei. Cells possess innate surveillance pathways to detect microbial components or physiological stresses often associated with microbial infections. One of these pathways, cGAS/STING, induces IRF3-dependent antiviral interferon (IFN) responses upon detection of cytosolic DNA. Virion-associated vDNA can activate cGAS/STING during initial viral entry and uncoating/trafficking, and thus cGAS/STING is an obstacle to many DNA viruses. HPV has a unique vesicular trafficking pathway compared to many other DNA viruses. As the capsid uncoats within acidic endosomal compartments, minor capsid protein L2 protrudes across vesicular membranes to facilitate transport of vDNA to the Golgi. L2/vDNA resides within the Golgi lumen until G2/M, whereupon vesicular L2/vDNA traffics along spindle microtubules, tethering to chromosomes to access daughter cell nuclei. L2/vDNA-containing vesicles likely remain intact until G1, following nuclear envelope reformation. We hypothesize that this unique vesicular trafficking protects HPV from cGAS/STING surveillance. Here, we investigate cGAS/STING responses to HPV infection. DNA transfection resulted in acute cGAS/STING activation and downstream IFN responses. In contrast, HPV infection elicited minimal cGAS/STING and IFN responses. To determine the role of vesicular trafficking in cGAS/STING evasion, we forced premature viral penetration of vesicular membranes with membrane-perturbing cationic lipids. Such treatment renders a non-infectious trafficking-defective mutant HPV infectious, yet susceptible to cGAS/STING detection. Overall, HPV evades cGAS/STING by its unique subcellular trafficking, a property that may contribute to establishment of infection.
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Affiliation(s)
- Brittany L. Uhlorn
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Robert Jackson
- School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Shuaizhi Li
- Department of Immunobiology, The University of Arizona, Tucson, Arizona, United States of America
| | - Shauna M. Bratton
- Department of Physiology, The University of Arizona, Tucson, Arizona, United States of America
| | - Koenraad Van Doorslaer
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, Arizona, United States of America
- School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, The University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, The University of Arizona, Tucson, Arizona, United States of America
- Genetics Graduate Interdisciplinary Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Samuel K. Campos
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, The University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, The University of Arizona, Tucson, Arizona, United States of America
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, Arizona, United States of America
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Cotiguala L, Masood A, Park JM, Samaniego-Picota MD, Kaul DR, Naik AS. Increasing net immunosuppression after BK polyoma virus infection. Transpl Infect Dis 2020; 23:e13472. [PMID: 32959930 DOI: 10.1111/tid.13472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/21/2020] [Accepted: 09/06/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Reducing immunosuppression can effectively treat BK viremia (BKV) and BK nephropathy, but has been associated with increased risks for acute rejection and development of donor-specific antibodies (DSA). To date there have been no systematic evaluations of re-escalating immunosuppression in transplant patients with resolving BKV. Importantly, the safety of this approach and impact on graft survival is unclear. METHODS We performed a single-center retrospective review of kidney transplant recipients between July 2011 and June 2013 who had immunosuppression reduction after developing BKV (plasma PCR ≥ 1000 copies/ml). Changes in immunosuppression and patient outcomes were tracked until occurrence of a complication event: biopsy-proven acute rejection (BPAR), detection of de novo DSA, or recurrent BKV. Patients were grouped according to whether or not net immunosuppression was eventually increased. RESULTS Out of 88 patients with BKV, 44 (50%) had net immunosuppression increased while the other 44 did not. Duration of viremia, peak viremia, induction, and sensitization status were similar between the two groups. In a Kaplan-Meier analysis, increasing immunosuppression was associated with less BPAR (P = .001) and a trend toward less de novo DSA development (P = .06). Death-censored graft survival (P = .27) was not different between the two groups. In the net immunosuppression increase group, recurrent BKV occurred in 22.7% without any BKV-related graft losses. CONCLUSION These findings support potential benefits of increasing immunosuppression in patients with low-level or resolved BKV, but prospective trials are needed to better understand such an approach.
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Affiliation(s)
- Laura Cotiguala
- Department of Pharmacy Services, Michigan Medicine, Ann Arbor, MI, USA
| | - Ahmad Masood
- Nephrology Associates of Michigan, Ypsilanti, MI, USA
| | - Jeong M Park
- Department of Pharmacy Services, Michigan Medicine, Ann Arbor, MI, USA.,Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
| | | | - Daniel R Kaul
- Division of Infectious Diseases, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Abhijit S Naik
- Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA
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Korneffel K, Gehring B, Rospert D, Rees M, Ortiz J. BK Virus in Renal Transplant Patients Using Alemtuzumab for Induction Immunosuppression. EXP CLIN TRANSPLANT 2020; 18:557-563. [DOI: 10.6002/ect.2019.0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Alcendor DJ. BK Polyomavirus Virus Glomerular Tropism: Implications for Virus Reactivation from Latency and Amplification during Immunosuppression. J Clin Med 2019; 8:jcm8091477. [PMID: 31533282 PMCID: PMC6780320 DOI: 10.3390/jcm8091477] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022] Open
Abstract
BK polyomavirus (BKPyV), or BKV infection, is ubiquitous and usually non-pathogenic, with subclinical infections in 80–90% of adults worldwide. BKV infection is often associated with pathology in immunocompromised individuals. BKV infection often is associated with renal impairment, including ureteral stenosis, hemorrhagic cystitis, and nephropathy. BKV infection is less commonly associated with pneumonitis, retinitis, liver disease, and meningoencephalitis. BKV is known to replicate, establish latency, undergo reactivation, and induce clinical pathology in renal tubular epithelial cells. However, recent in vitro studies support the notion that BKV has expanded tropism-targeting glomerular parenchymal cells of the human kidney, which could impact glomerular function, enhance inflammation, and serve as viral reservoirs for reactivation from latency during immunosuppression. The implications of BKV expanded tropism in the glomerulus, and how specific host and viral factors that would contribute to glomerular inflammation, cytolysis, and renal fibrosis are related to BKV associated nephropathy (BKVAN), have not been explored. The pathogenesis of BKV in human glomerular parenchymal cells is poorly understood. In this review, I examine target cell populations for BKV infectivity in the human glomerulus. Specifically, I explore the implications of BKV expanded tropism in the glomerulus with regard viral entry, replication, and dissemination via cell types exposed to BKV trafficking in glomerulus. I also describe cellular targets shown to be permissive in vitro and in vivo for BKV infection and lytic replication, the potential role that glomerular parenchymal cells play in BKV latency and/or reactivation after immunosuppression, and the rare occurrence of BKV pathology in glomerular parenchymal cells in patients with BKVAN.
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Affiliation(s)
- Donald J Alcendor
- Center for AIDS Health Disparities Research, Meharry Medical College, 1005 Dr. D.B. Todd Jr. Blvd., Hubbard Hospital, 5th Floor, Rm. 5025, Nashville, TN 37208, USA.
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21
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Sigdel TK, Mercer N, Nandoe S, Nicora CD, Burnum-Johnson K, Qian WJ, Sarwal MM. Urinary Virome Perturbations in Kidney Transplantation. Front Med (Lausanne) 2018; 5:72. [PMID: 29725592 PMCID: PMC5916966 DOI: 10.3389/fmed.2018.00072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
The human microbiome is important for health and plays a role in essential metabolic functions and protection from certain pathogens. Conversely, dysbiosis of the microbiome is seen in the context of various diseases. Recent studies have highlighted that a complex microbial community containing hundreds of bacteria colonizes the healthy urinary tract, but little is known about the human urinary viruses in health and disease. To evaluate the human urinary virome in the context of kidney transplantation (tx), variations in the composition of the urinary virome were evaluated in urine samples from normal healthy volunteers as well as patients with kidney disease after they had undergone kidney tx. Liquid chromatography-mass spectrometry/mass spectrometry analysis was undertaken on a selected cohort of 142 kidney tx patients and normal healthy controls, from a larger biobank of 770 kidney biopsy matched urine samples. In addition to analysis of normal healthy control urine, the cohort of kidney tx patients had biopsy confirmed phenotype classification, coincident with the urine sample analyzed, of stable grafts (STA), acute rejection, BK virus nephritis, and chronic allograft nephropathy. We identified 37 unique viruses, 29 of which are being identified for the first time in human urine samples. The composition of the human urinary virome differs in health and kidney injury, and the distribution of viral proteins in the urinary tract may be further impacted by IS exposure, diet and environmental, dietary, or cutaneous exposure to various insecticides and pesticides.
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Affiliation(s)
- Tara K. Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Neil Mercer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Sharvin Nandoe
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
- Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin Burnum-Johnson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Minnie M. Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
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Abstract
Progressive multifocal leukoencephalopathy (PML) is a relatively common complication of HIV disease. In this chapter changes to the epidemiology are discussed along with an update in its pathogenesis and treatment. Immune reconstitution inflammatory syndrome is increasingly frequent in PML; accordingly management strategies and prognosis are detailed.
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Affiliation(s)
- Shaun Zhai
- Department of Neurology, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Bruce James Brew
- Department of Neurology, St. Vincent's Hospital, Sydney, NSW, Australia; Department of HIV Medicine and Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, St. Vincent's Hospital, Sydney, NSW, Australia.
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23
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Cui L, Markou A, Stratton CW, Lianidou E. Diagnosis and Assessment of Microbial Infections with Host and Microbial MicroRNA Profiles. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7119978 DOI: 10.1007/978-3-319-95111-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) encoded by viral genome or host have been found participating in host-microbe interactions. Differential expression profiles of miRNAs were shown linking to specific disease pathologies which indicated its potency as diagnostic/prognostic biomarkers of infectious disease. This was emphasized by the discovery of circulating miRNAs which were found to be remarkably stable in mammalian biofluids. Standardized methods of miRNA quantification including RNA isolation should be established before they will be ready for use in clinical practice.
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Alloimmunity But Not Viral Immunity Promotes Allograft Loss in a Mouse Model of Polyomavirus-Associated Allograft Injury. Transplant Direct 2017; 3:e161. [PMID: 28620645 PMCID: PMC5464780 DOI: 10.1097/txd.0000000000000677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/15/2017] [Indexed: 11/30/2022] Open
Abstract
Background The interplay between viral infection and alloimmunity is known to influence the fate of transplanted organs. Clarifying how local virus-associated inflammation/injury and antiviral immunity can alter host alloimmune responses in transplantation remains a critical question. Methods We used a mouse model of polyomavirus (PyV) infection and kidney transplantation to investigate the roles of direct viral pathology, the antiviral immune response, and alloimmunity in the pathogenesis of PyV-associated allograft injury. We have previously shown that an effective primary T cell response is required in PyV-associated graft injury. Results Here we show that the transfer of primed antidonor, but not antiviral, T cells results in PyV-associated allograft injury. In further studies, we use a surrogate minor antigen model (ovalbumin) and show that only antidonor specific T cells and not antiviral specific T cells are sufficient to mediate injury. Lastly, we demonstrate that local but not systemic virus-mediated inflammation and injury within the graft itself are required. Conclusions These data suggest that in this mouse model, the predominant mechanism of allograft injury in PyV-associated injury is due to an augmented alloimmune T cell response driven by virus-induced inflammation/injury within the graft. These studies highlight the important interplay between viral infection and alloimmunity in a model system.
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25
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MOURA ELVIANIB, PETZHOLD SILVIAV, AMARAL AUGUSTOR, DEBONI LUCIANEM, FRANÇA PAULOHDE. Evaluation of the predisposition and clinical impact of BK virus replication in kidney transplant patients. ACTA ACUST UNITED AC 2017; 89:675-684. [DOI: 10.1590/0001-3765201720160470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/19/2017] [Indexed: 12/29/2022]
Affiliation(s)
- ELVIANI B. MOURA
- Universidade da Região de Joinville, Brazil; Fundação Pró-Rim, Brazil
| | | | | | | | - PAULO H.C. DE FRANÇA
- Universidade da Região de Joinville, Brazil; Universidade da Região de Joinville, Brazil
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26
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Radtke J, Dietze N, Fischer L, Achilles EG, Li J, Scheidat S, Thaiss F, Nashan B, Koch M. Incidence of BK polyomavirus infection after kidney transplantation is independent of type of immunosuppressive therapy. Transpl Infect Dis 2016; 18:850-855. [PMID: 27639176 DOI: 10.1111/tid.12611] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 05/06/2016] [Accepted: 07/04/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND BK polyomavirus (BKV) infection and BKV nephropathy (BKVN) are risk factors for allograft function and survival. METHODS We retrospectively analyzed BK viremia and BKVN in 348 patients who received a kidney transplantation donated after brain death (n=232) or living donation (n=116) between 2008 and 2013. A total of 266 patients were treated with standard immunosuppression consisting of basiliximab induction, calcineurin inhibitor (CNI), and mycophenolic acid (MPA, n=219) or everolimus (n=47); 82 patients received more intense immunosuppression with lymphocyte depletion, CNI and MPA (n=38) or everolimus (n=44). RESULTS BK viremia occurred in 33 (9.5%) patients in the first year and in 7 (2.0%) recipients in the second year after transplantation. BKVN occurred in 4 (1.1%) patients in the first year. Donor and recipient age, diabetes, previous transplantation, and type of transplantation (donated after brain death vs living donation) were not risk factors (P>.05). BK incidence did not differ depending on induction or maintenance immunosuppression. CONCLUSION Incidence of BK viremia is independent of recipient characteristics, type of transplantation as well as induction and maintenance immunosuppression.
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Affiliation(s)
- Josephine Radtke
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Nina Dietze
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Lutz Fischer
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Eike-Gert Achilles
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Jun Li
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Silke Scheidat
- Department of Internal Medicine III, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Friedrich Thaiss
- Department of Internal Medicine III, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Bjoern Nashan
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
| | - Martina Koch
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf UKE, University Transplantation-Center UTC, Hamburg, Germany
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27
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Drouin A, Giguère S, Déraspe M, Marchand M, Tyers M, Loo VG, Bourgault AM, Laviolette F, Corbeil J. Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons. BMC Genomics 2016; 17:754. [PMID: 27671088 PMCID: PMC5037627 DOI: 10.1186/s12864-016-2889-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 07/06/2016] [Indexed: 12/14/2022] Open
Abstract
Background The identification of genomic biomarkers is a key step towards improving diagnostic tests and therapies. We present a reference-free method for this task that relies on a k-mer representation of genomes and a machine learning algorithm that produces intelligible models. The method is computationally scalable and well-suited for whole genome sequencing studies. Results The method was validated by generating models that predict the antibiotic resistance of C. difficile, M. tuberculosis, P. aeruginosa, and S. pneumoniae for 17 antibiotics. The obtained models are accurate, faithful to the biological pathways targeted by the antibiotics, and they provide insight into the process of resistance acquisition. Moreover, a theoretical analysis of the method revealed tight statistical guarantees on the accuracy of the obtained models, supporting its relevance for genomic biomarker discovery. Conclusions Our method allows the generation of accurate and interpretable predictive models of phenotypes, which rely on a small set of genomic variations. The method is not limited to predicting antibiotic resistance in bacteria and is applicable to a variety of organisms and phenotypes. Kover, an efficient implementation of our method, is open-source and should guide biological efforts to understand a plethora of phenotypes (http://github.com/aldro61/kover/). Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2889-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandre Drouin
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada.
| | - Sébastien Giguère
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Maxime Déraspe
- Department of Molecular Medicine, Université Laval, Québec, Canada
| | - Mario Marchand
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada.,Big Data Research Centre, Université Laval, Québec, Canada
| | - Michael Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Vivian G Loo
- Division of Infectious Diseases, Departments of Medicine and Microbiology, McGill University Health Centre, Montréal, Canada.,Department of Medicine, McGill University, Montréal, Canada
| | - Anne-Marie Bourgault
- Division of Infectious Diseases, Departments of Medicine and Microbiology, McGill University Health Centre, Montréal, Canada.,Department of Medicine, McGill University, Montréal, Canada
| | - François Laviolette
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada.,Big Data Research Centre, Université Laval, Québec, Canada
| | - Jacques Corbeil
- Department of Molecular Medicine, Université Laval, Québec, Canada.,Big Data Research Centre, Université Laval, Québec, Canada
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