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Thangamani Muthukumar - One of the best experts on this subject based on the ideXlab platform.
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foxp3 mrna profile prognostic of acute t cell mediated rejection and human Kidney Allograft survival
Transplantation, 2021Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:BACKGROUND T cell-mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes are nonresponsive to therapy, and molecular mechanisms for the nonresponsiveness are unknown. Our single-center study identified that urinary cell FOXP3 mRNA abundance predicts TCMR reversibility and Allograft survival. METHODS We developed PCR assays and measured absolute copy numbers of transcripts for FOXP3, CD25, CD3E, perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in the multicenter Clinical Trials in Organ Transplantation-04. In this replication study, we investigated the association between mRNA profile and TCMR diagnosis, TCMR reversibility, and Allograft survival. RESULTS 18S rRNA normalized levels of mRNA for FOXP3 (P = 0.01, Kruskal-Wallis test), CD25 (P = 0.01), CD3E (P < 0.0001), and perforin (P < 0.0001) were diagnostic of TCMR, but only FOXP3 mRNA level predicted TCMR reversibility (ROC AUC = 0.764; 95% confidence interval, 0.611-0.917; P = 0.008). Multivariable logistic regression analyses showed that urinary cell FOXP3 mRNA level predicted reversal, independent of clinical variables. A composite model of clinical variables and FOXP3 mRNA (AUC = 0.889; 95% CI, 0.781-0.997; P < 0.001) outperformed FOXP3 mRNA or clinical variables in predicting TCMR reversibility (P = 0.01, likelihood ratio test). Multivariable Cox proportional hazards regression analyses showed that FOXP3 mRNA level predicts Kidney Allograft survival (P = 0.047) but not after controlling for TCMR reversal (P = 0.477). CONCLUSIONS Urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts TCMR reversibility, and is prognostic of Kidney Allograft survival via a mechanism involving TCMR reversal.
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Kidney Allograft Function Is a Confounder of Urine Metabolite Profiles in Kidney Allograft Recipients
'MDPI AG', 2021Co-Authors: Karsten Suhre, Qiuying Chen, John R Lee, Thangamani Muthukumar, Darshana Dadhania, Steven S. Gross, Manikkam SuthanthiranAbstract:Noninvasive biomarkers of Kidney Allograft status can help minimize the need for standard of care Kidney Allograft biopsies. Metabolites that are measured in the urine may inform about Kidney function and health status, and potentially identify rejection events. To test these hypotheses, we conducted a metabolomics study of biopsy-matched urine cell-free supernatants from Kidney Allograft recipients who were diagnosed with two major types of acute rejections and no-rejection controls. Non-targeted metabolomics data for 674 metabolites and 577 unidentified molecules, for 192 biopsy-matched urine samples, were analyzed. Univariate and multivariate analyses identified metabolite signatures for Kidney Allograft rejection. The replicability of a previously developed urine metabolite signature was examined. Our study showed that metabolite profiles can serve as biomarkers for discriminating rejection biopsies from biopsies without rejection features, but also revealed a role of estimated Glomerular Filtration Rate (eGFR) as a major confounder of the metabolite signal
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Deep sequencing of DNA from urine of Kidney Allograft recipients to estimate donor/recipient-specific DNA fractions.
'Public Library of Science (PLoS)', 2021Co-Authors: Aziz Belkadi, Thangamani Muthukumar, Darshana Dadhania, John R Lee, Gaurav Thareja, Catherine Snopkowski, Anna Halama, Sara Abdelkader, Silvana AbdullaAbstract:Kidney transplantation is the treatment of choice for patients with end-stage Kidney failure, but transplanted Allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in Kidney transplants is Kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for Kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor Kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from Kidney Allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human Kidney Allograft
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foxp3 mrna profile prognostic of t cell mediated rejection and human Kidney Allograft survival
medRxiv, 2020Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:Background and objectives: T cell mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes fail to respond to anti-rejection therapy. FOXP3 is a specification factor for regulatory T cells and our single center study of 83 Kidney Allograft recipients showed that urinary cell FOXP3 mRNA level is diagnostic of TCMR and predicts TCMR reversibility and Allograft survival. The objective of the current study is to determine whether our original findings could be replicated in an independent cohort of 480 Kidney Allograft recipients enrolled in the multicenter Clinical Trials of Organ Transplantation (CTOT)-04. Design, setting, participants, and measurements: We measured levels of FOXP3 mRNA and levels of mRNA for CD25, CD3E, and perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in CTOT-04. RNA was isolated from the urinary cells and preamplification-enhanced real-time quantitative PCR assays were used to measure mRNAs. Results: 18S rRNA normalized levels of mRNA for FOXP3 (P=0.01, Kruskal-Wallis test), CD25 (P=0.01), CD3E (P<0.0001), and perforin (P<0.0001) distinguished patients with TCMR biopsies from those with No Rejection biopsies and those with stable graft function. FOXP3 mRNA level, but not the levels of mRNA for CD25, CD3E, or perforin, predicted TCMR reversal (AUC=0.764; 95% confidence interval, 0.611 to 0.917; P=0.008). Multivariable logistic regression analysis showed that FOXP3 mRNA level remains predictive after adjustment for potential cofounders. Kaplan-Meier survival curve analysis showed that FOXP3 mRNA level (P=0.0306) but not the levels of mRNA for CD25, CD3E, or perforin, is associated with Kidney Allograft survival. Conclusion: In the independent CTOT-04 cohort, we demonstrate that urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts its reversibility, and is prognostic of Kidney Allograft survival following an episode of TCMR.
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urine metabolite profiles predictive of human Kidney Allograft status
Journal of The American Society of Nephrology, 2016Co-Authors: Karsten Suhre, Joseph E Schwartz, V K Sharma, Qiuying Chen, John R Lee, Thangamani Muthukumar, Darshana Dadhania, R Ding, David Ikle, Nancy D BridgesAbstract:Noninvasive diagnosis and prognostication of acute cellular rejection in the Kidney Allograft may help realize the full benefits of Kidney transplantation. To investigate whether urine metabolites predict Kidney Allograft status, we determined levels of 749 metabolites in 1516 urine samples from 241 Kidney graft recipients enrolled in the prospective multicenter Clinical Trials in Organ Transplantation-04 study. A metabolite signature of the ratio of 3-sialyllactose to xanthosine in biopsy specimen-matched urine supernatants best discriminated acute cellular rejection biopsy specimens from specimens without rejection. For clinical application, we developed a high-throughput mass spectrometry-based assay that enabled absolute and rapid quantification of the 3-sialyllactose-to-xanthosine ratio in urine samples. A composite signature of ratios of 3-sialyllactose to xanthosine and quinolinate to X-16397 and our previously reported urinary cell mRNA signature of 18S ribosomal RNA, CD3e mRNA, and interferon-inducible protein-10 mRNA outperformed the metabolite signatures and the mRNA signature. The area under the receiver operating characteristics curve for the composite metabolite-mRNA signature was 0.93, and the signature was diagnostic of acute cellular rejection with a specificity of 84% and a sensitivity of 90%. The composite signature, developed using solely biopsy specimen-matched urine samples, predicted future acute cellular rejection when applied to pristine samples taken days to weeks before biopsy. We conclude that metabolite profiling of urine offers a noninvasive means of diagnosing and prognosticating acute cellular rejection in the human Kidney Allograft, and that the combined metabolite and mRNA signature is diagnostic and prognostic of acute cellular rejection with very high accuracy.
Manikkam Suthanthiran - One of the best experts on this subject based on the ideXlab platform.
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Kidney Allograft Function Is a Confounder of Urine Metabolite Profiles in Kidney Allograft Recipients
'MDPI AG', 2021Co-Authors: Karsten Suhre, Qiuying Chen, John R Lee, Thangamani Muthukumar, Darshana Dadhania, Steven S. Gross, Manikkam SuthanthiranAbstract:Noninvasive biomarkers of Kidney Allograft status can help minimize the need for standard of care Kidney Allograft biopsies. Metabolites that are measured in the urine may inform about Kidney function and health status, and potentially identify rejection events. To test these hypotheses, we conducted a metabolomics study of biopsy-matched urine cell-free supernatants from Kidney Allograft recipients who were diagnosed with two major types of acute rejections and no-rejection controls. Non-targeted metabolomics data for 674 metabolites and 577 unidentified molecules, for 192 biopsy-matched urine samples, were analyzed. Univariate and multivariate analyses identified metabolite signatures for Kidney Allograft rejection. The replicability of a previously developed urine metabolite signature was examined. Our study showed that metabolite profiles can serve as biomarkers for discriminating rejection biopsies from biopsies without rejection features, but also revealed a role of estimated Glomerular Filtration Rate (eGFR) as a major confounder of the metabolite signal
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urine biomarkers informative of human Kidney Allograft rejection and tolerance
Human Immunology, 2018Co-Authors: Voravech Nissaisorakarn, John R Lee, Michelle Lubetzky, Manikkam SuthanthiranAbstract:We developed urinary cell messenger RNA (mRNA) profiling to monitor in vivo status of human Kidney Allografts based on our conceptualization that the Kidney Allograft may function as an in vivo flow cell sorter allowing access of graft infiltrating cells to the glomerular ultrafiltrate and that interrogation of urinary cells is informative of Allograft status. For the profiling urinary cells, we developed a two-step preamplification enhanced real-time quantitative PCR (RT-QPCR) assays with a customized amplicon; preamplification compensating for the low RNA yield from urine and the customized amplicon facilitating absolute quantification of mRNA and overcoming the inherent limitations of relative quantification widely used in RT-QPCR assays. Herein, we review our discovery and validation of urinary cell mRNAs as noninvasive biomarkers prognostic and diagnostic of acute cellular rejection (ACR) in Kidney Allografts. We summarize our results reflecting the utility of urinary cell mRNA profiling for predicting reversal of ACR with anti-rejection therapy; differential diagnosis of Kidney Allograft dysfunction; and noninvasive diagnosis and prognosis of BK virus nephropathy. Messenger RNA profiles associated with human Kidney Allograft tolerance are also summarized in this review. Altogether, data supporting the idea that urinary cell mRNA profiles are informative of Kidney Allograft status and tolerance are reviewed in this report.
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acute rejection Kidney Allograft function and graft survival in patients with circulating pre transplant igg antibodies directed against donor hla a b or c locus determined antigens
Clinical Transplantation, 2016Co-Authors: Essa Abuhelaiqa, V K Sharma, Manikkam Suthanthiran, Meredith J Aull, Rex Friedlander, Prabhakar Putheti, Darshana DadhaniaAbstract:The relationship between circulating pre-transplant immunoglobulin G (IgG) antibodies to donor human leukocyte antigen (HLA) -C locus determined antigens alone and acute rejection, Kidney Allograft function, and graft survival is not fully defined. Also, the impact of circulating pre-transplant IgG antibodies to donor HLA-C locus antigens alone on these outcomes has not been compared with the impact of circulating pre-transplant IgG antibodies to donor HLA-A or -B locus antigens. We conducted a retrospective review of records of 1252 Kidney Allograft recipients transplanted at our center between January 2010 and January 2016 to identify patients with circulating pre-transplant IgG antibodies directed at Kidney donor HLA-A, -B, or -C locus determined antigens. Antibodies were detected and reported using the LABScreen Single Antigen Bead assay with microbeads coated with single HLA class I antigens. Pre-transplant and post-transplant data were collected and the graft outcomes of 16 Kidney graft recipients with antibodies to HLA-C locus antigens were compared to the outcomes in 56 recipients with antibodies to HLA-A or -B locus determined antigens. The one-year acute rejection rate was 6% in those with donor-specific antibodies (DSA) to HLA-C locus antigens and 20% in those with DSA to HLA-A or -B locus antigens. The graft survival rate was 100% in those with DSA to HLA-C locus antigens and 95% in those with DSA to HLA-A or -B locus antigens. None of the numerical differences were statistically significant (p>0.05). The presence of circulating pre-transplant IgG antibodies directed at Kidney donor HLA-C locus antigens alone may not be associated with an increased risk of acute rejection or a decreased graft survival rate. Our observations support the concept that circulating pre-transplant IgG antibodies directed at Kidney donor HLA-C locus antigens alone do not negatively impact Kidney Allograft outcomes and that the mean fluorescence intensities of the antibodies directed at HLA-C locus alone should not be used to list unacceptable HLA-C locus antigens for Kidney allocation. A study with a larger cohort is needed to investigate our hypothesis.
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circulating levels of 25 hydroxyvitamin d and acute cellular rejection in Kidney Allograft recipients
Transplantation, 2014Co-Authors: John R Lee, Darshana Dadhania, Manikkam Suthanthiran, Phyllis August, Jun B Lee, Thangamani MuthukumarAbstract:BACKGROUND Vitamin D, in addition to its established role in bone metabolism, may regulate the immune system and affect the outcome of Allografts. METHODS We identified 351 Kidney Allograft recipients who had serum levels of 25-hydroxyvitamin D (25[OH]D) measured within the first 30 days of transplantation. We evaluated the relationship between the circulating levels of 25(OH)D and acute cellular rejection (ACR), cytomegalovirus (CMV) disease, BK virus nephropathy, and Kidney graft function. RESULTS Vitamin D deficiency (circulating levels of 25[OH]D ≤20 ng/mL, defined using The Endocrine Society Clinical Practice 2011 Guideline) was observed in 216 (61.5%) of 351 Kidney graft recipients. Vitamin D deficiency was more frequent in female recipients (P=0.007, Fisher exact test) and African American recipients (P<0.001) and was less frequent in preemptive Kidney graft recipients (P=0.002). Biopsy-confirmed ACR was more frequent in the vitamin D-deficient group than in the sufficient group (10.2% vs. 3.7%, P=0.04). By multivariable Cox regression analysis, vitamin D deficiency was an independent risk factor for ACR (hazard ratio=3.3, P=0.02). Vitamin D deficiency was not associated with CMV disease, BK virus nephropathy, or Kidney Allograft function at 1 year. 1,25-Dihydroxyvitamin D3 supplementation initiated within the first 90 days of transplantation was associated with a lesser incidence of ACR compared to no treatment with 1,25-dihydroxyvitamin D3 (5.1% vs. 13.0%, P=0.099). CONCLUSIONS Vitamin D deficiency is an independent risk factor for development of ACR within the first year of Kidney transplantation and 1,25-dihydroxyvitamin D3 supplementation may help reduce the occurrence of ACR in the vitamin D-deficient group.
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independent risk factors for urinary tract infection and for subsequent bacteremia or acute cellular rejection a single center report of 1166 Kidney Allograft recipients
Transplantation, 2013Co-Authors: John R Lee, Darshana Dadhania, Manikkam Suthanthiran, Phyllis August, Heejung Bang, Choli Hartono, Meredith J Aull, Michael J Satlin, Thangamani MuthukumarAbstract:Background Urinary tract infection (UTI) is a frequent, serious complication in Kidney Allograft recipients.
John R Lee - One of the best experts on this subject based on the ideXlab platform.
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foxp3 mrna profile prognostic of acute t cell mediated rejection and human Kidney Allograft survival
Transplantation, 2021Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:BACKGROUND T cell-mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes are nonresponsive to therapy, and molecular mechanisms for the nonresponsiveness are unknown. Our single-center study identified that urinary cell FOXP3 mRNA abundance predicts TCMR reversibility and Allograft survival. METHODS We developed PCR assays and measured absolute copy numbers of transcripts for FOXP3, CD25, CD3E, perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in the multicenter Clinical Trials in Organ Transplantation-04. In this replication study, we investigated the association between mRNA profile and TCMR diagnosis, TCMR reversibility, and Allograft survival. RESULTS 18S rRNA normalized levels of mRNA for FOXP3 (P = 0.01, Kruskal-Wallis test), CD25 (P = 0.01), CD3E (P < 0.0001), and perforin (P < 0.0001) were diagnostic of TCMR, but only FOXP3 mRNA level predicted TCMR reversibility (ROC AUC = 0.764; 95% confidence interval, 0.611-0.917; P = 0.008). Multivariable logistic regression analyses showed that urinary cell FOXP3 mRNA level predicted reversal, independent of clinical variables. A composite model of clinical variables and FOXP3 mRNA (AUC = 0.889; 95% CI, 0.781-0.997; P < 0.001) outperformed FOXP3 mRNA or clinical variables in predicting TCMR reversibility (P = 0.01, likelihood ratio test). Multivariable Cox proportional hazards regression analyses showed that FOXP3 mRNA level predicts Kidney Allograft survival (P = 0.047) but not after controlling for TCMR reversal (P = 0.477). CONCLUSIONS Urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts TCMR reversibility, and is prognostic of Kidney Allograft survival via a mechanism involving TCMR reversal.
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Deep sequencing of DNA from urine of Kidney Allograft recipients to estimate donor/recipient-specific DNA fractions.
'Public Library of Science (PLoS)', 2021Co-Authors: Aziz Belkadi, Thangamani Muthukumar, Darshana Dadhania, John R Lee, Gaurav Thareja, Catherine Snopkowski, Anna Halama, Sara Abdelkader, Silvana AbdullaAbstract:Kidney transplantation is the treatment of choice for patients with end-stage Kidney failure, but transplanted Allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in Kidney transplants is Kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for Kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor Kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from Kidney Allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human Kidney Allograft
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foxp3 mrna profile prognostic of t cell mediated rejection and human Kidney Allograft survival
medRxiv, 2020Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:Background and objectives: T cell mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes fail to respond to anti-rejection therapy. FOXP3 is a specification factor for regulatory T cells and our single center study of 83 Kidney Allograft recipients showed that urinary cell FOXP3 mRNA level is diagnostic of TCMR and predicts TCMR reversibility and Allograft survival. The objective of the current study is to determine whether our original findings could be replicated in an independent cohort of 480 Kidney Allograft recipients enrolled in the multicenter Clinical Trials of Organ Transplantation (CTOT)-04. Design, setting, participants, and measurements: We measured levels of FOXP3 mRNA and levels of mRNA for CD25, CD3E, and perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in CTOT-04. RNA was isolated from the urinary cells and preamplification-enhanced real-time quantitative PCR assays were used to measure mRNAs. Results: 18S rRNA normalized levels of mRNA for FOXP3 (P=0.01, Kruskal-Wallis test), CD25 (P=0.01), CD3E (P<0.0001), and perforin (P<0.0001) distinguished patients with TCMR biopsies from those with No Rejection biopsies and those with stable graft function. FOXP3 mRNA level, but not the levels of mRNA for CD25, CD3E, or perforin, predicted TCMR reversal (AUC=0.764; 95% confidence interval, 0.611 to 0.917; P=0.008). Multivariable logistic regression analysis showed that FOXP3 mRNA level remains predictive after adjustment for potential cofounders. Kaplan-Meier survival curve analysis showed that FOXP3 mRNA level (P=0.0306) but not the levels of mRNA for CD25, CD3E, or perforin, is associated with Kidney Allograft survival. Conclusion: In the independent CTOT-04 cohort, we demonstrate that urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts its reversibility, and is prognostic of Kidney Allograft survival following an episode of TCMR.
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circulating levels of 25 hydroxyvitamin d and acute cellular rejection in Kidney Allograft recipients
Transplantation, 2014Co-Authors: John R Lee, Darshana Dadhania, Manikkam Suthanthiran, Phyllis August, Jun B Lee, Thangamani MuthukumarAbstract:BACKGROUND Vitamin D, in addition to its established role in bone metabolism, may regulate the immune system and affect the outcome of Allografts. METHODS We identified 351 Kidney Allograft recipients who had serum levels of 25-hydroxyvitamin D (25[OH]D) measured within the first 30 days of transplantation. We evaluated the relationship between the circulating levels of 25(OH)D and acute cellular rejection (ACR), cytomegalovirus (CMV) disease, BK virus nephropathy, and Kidney graft function. RESULTS Vitamin D deficiency (circulating levels of 25[OH]D ≤20 ng/mL, defined using The Endocrine Society Clinical Practice 2011 Guideline) was observed in 216 (61.5%) of 351 Kidney graft recipients. Vitamin D deficiency was more frequent in female recipients (P=0.007, Fisher exact test) and African American recipients (P<0.001) and was less frequent in preemptive Kidney graft recipients (P=0.002). Biopsy-confirmed ACR was more frequent in the vitamin D-deficient group than in the sufficient group (10.2% vs. 3.7%, P=0.04). By multivariable Cox regression analysis, vitamin D deficiency was an independent risk factor for ACR (hazard ratio=3.3, P=0.02). Vitamin D deficiency was not associated with CMV disease, BK virus nephropathy, or Kidney Allograft function at 1 year. 1,25-Dihydroxyvitamin D3 supplementation initiated within the first 90 days of transplantation was associated with a lesser incidence of ACR compared to no treatment with 1,25-dihydroxyvitamin D3 (5.1% vs. 13.0%, P=0.099). CONCLUSIONS Vitamin D deficiency is an independent risk factor for development of ACR within the first year of Kidney transplantation and 1,25-dihydroxyvitamin D3 supplementation may help reduce the occurrence of ACR in the vitamin D-deficient group.
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independent risk factors for urinary tract infection and for subsequent bacteremia or acute cellular rejection a single center report of 1166 Kidney Allograft recipients
Transplantation, 2013Co-Authors: John R Lee, Darshana Dadhania, Manikkam Suthanthiran, Phyllis August, Heejung Bang, Choli Hartono, Meredith J Aull, Michael J Satlin, Thangamani MuthukumarAbstract:Background Urinary tract infection (UTI) is a frequent, serious complication in Kidney Allograft recipients.
Phyllis August - One of the best experts on this subject based on the ideXlab platform.
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foxp3 mrna profile prognostic of acute t cell mediated rejection and human Kidney Allograft survival
Transplantation, 2021Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:BACKGROUND T cell-mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes are nonresponsive to therapy, and molecular mechanisms for the nonresponsiveness are unknown. Our single-center study identified that urinary cell FOXP3 mRNA abundance predicts TCMR reversibility and Allograft survival. METHODS We developed PCR assays and measured absolute copy numbers of transcripts for FOXP3, CD25, CD3E, perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in the multicenter Clinical Trials in Organ Transplantation-04. In this replication study, we investigated the association between mRNA profile and TCMR diagnosis, TCMR reversibility, and Allograft survival. RESULTS 18S rRNA normalized levels of mRNA for FOXP3 (P = 0.01, Kruskal-Wallis test), CD25 (P = 0.01), CD3E (P < 0.0001), and perforin (P < 0.0001) were diagnostic of TCMR, but only FOXP3 mRNA level predicted TCMR reversibility (ROC AUC = 0.764; 95% confidence interval, 0.611-0.917; P = 0.008). Multivariable logistic regression analyses showed that urinary cell FOXP3 mRNA level predicted reversal, independent of clinical variables. A composite model of clinical variables and FOXP3 mRNA (AUC = 0.889; 95% CI, 0.781-0.997; P < 0.001) outperformed FOXP3 mRNA or clinical variables in predicting TCMR reversibility (P = 0.01, likelihood ratio test). Multivariable Cox proportional hazards regression analyses showed that FOXP3 mRNA level predicts Kidney Allograft survival (P = 0.047) but not after controlling for TCMR reversal (P = 0.477). CONCLUSIONS Urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts TCMR reversibility, and is prognostic of Kidney Allograft survival via a mechanism involving TCMR reversal.
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foxp3 mrna profile prognostic of t cell mediated rejection and human Kidney Allograft survival
medRxiv, 2020Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:Background and objectives: T cell mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes fail to respond to anti-rejection therapy. FOXP3 is a specification factor for regulatory T cells and our single center study of 83 Kidney Allograft recipients showed that urinary cell FOXP3 mRNA level is diagnostic of TCMR and predicts TCMR reversibility and Allograft survival. The objective of the current study is to determine whether our original findings could be replicated in an independent cohort of 480 Kidney Allograft recipients enrolled in the multicenter Clinical Trials of Organ Transplantation (CTOT)-04. Design, setting, participants, and measurements: We measured levels of FOXP3 mRNA and levels of mRNA for CD25, CD3E, and perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in CTOT-04. RNA was isolated from the urinary cells and preamplification-enhanced real-time quantitative PCR assays were used to measure mRNAs. Results: 18S rRNA normalized levels of mRNA for FOXP3 (P=0.01, Kruskal-Wallis test), CD25 (P=0.01), CD3E (P<0.0001), and perforin (P<0.0001) distinguished patients with TCMR biopsies from those with No Rejection biopsies and those with stable graft function. FOXP3 mRNA level, but not the levels of mRNA for CD25, CD3E, or perforin, predicted TCMR reversal (AUC=0.764; 95% confidence interval, 0.611 to 0.917; P=0.008). Multivariable logistic regression analysis showed that FOXP3 mRNA level remains predictive after adjustment for potential cofounders. Kaplan-Meier survival curve analysis showed that FOXP3 mRNA level (P=0.0306) but not the levels of mRNA for CD25, CD3E, or perforin, is associated with Kidney Allograft survival. Conclusion: In the independent CTOT-04 cohort, we demonstrate that urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts its reversibility, and is prognostic of Kidney Allograft survival following an episode of TCMR.
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circulating levels of 25 hydroxyvitamin d and acute cellular rejection in Kidney Allograft recipients
Transplantation, 2014Co-Authors: John R Lee, Darshana Dadhania, Manikkam Suthanthiran, Phyllis August, Jun B Lee, Thangamani MuthukumarAbstract:BACKGROUND Vitamin D, in addition to its established role in bone metabolism, may regulate the immune system and affect the outcome of Allografts. METHODS We identified 351 Kidney Allograft recipients who had serum levels of 25-hydroxyvitamin D (25[OH]D) measured within the first 30 days of transplantation. We evaluated the relationship between the circulating levels of 25(OH)D and acute cellular rejection (ACR), cytomegalovirus (CMV) disease, BK virus nephropathy, and Kidney graft function. RESULTS Vitamin D deficiency (circulating levels of 25[OH]D ≤20 ng/mL, defined using The Endocrine Society Clinical Practice 2011 Guideline) was observed in 216 (61.5%) of 351 Kidney graft recipients. Vitamin D deficiency was more frequent in female recipients (P=0.007, Fisher exact test) and African American recipients (P<0.001) and was less frequent in preemptive Kidney graft recipients (P=0.002). Biopsy-confirmed ACR was more frequent in the vitamin D-deficient group than in the sufficient group (10.2% vs. 3.7%, P=0.04). By multivariable Cox regression analysis, vitamin D deficiency was an independent risk factor for ACR (hazard ratio=3.3, P=0.02). Vitamin D deficiency was not associated with CMV disease, BK virus nephropathy, or Kidney Allograft function at 1 year. 1,25-Dihydroxyvitamin D3 supplementation initiated within the first 90 days of transplantation was associated with a lesser incidence of ACR compared to no treatment with 1,25-dihydroxyvitamin D3 (5.1% vs. 13.0%, P=0.099). CONCLUSIONS Vitamin D deficiency is an independent risk factor for development of ACR within the first year of Kidney transplantation and 1,25-dihydroxyvitamin D3 supplementation may help reduce the occurrence of ACR in the vitamin D-deficient group.
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independent risk factors for urinary tract infection and for subsequent bacteremia or acute cellular rejection a single center report of 1166 Kidney Allograft recipients
Transplantation, 2013Co-Authors: John R Lee, Darshana Dadhania, Manikkam Suthanthiran, Phyllis August, Heejung Bang, Choli Hartono, Meredith J Aull, Michael J Satlin, Thangamani MuthukumarAbstract:Background Urinary tract infection (UTI) is a frequent, serious complication in Kidney Allograft recipients.
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independent risk factors for urinary tract infection and for subsequent bacteremia or acute cellular rejection a single center report of 1166 Kidney Allograft recipients
Transplantation, 2013Co-Authors: John R Lee, Manikkam Suthanthiran, Phyllis August, Heejung Bang, Choli Hartono, Meredith J Aull, Michael J Satlin, Darshana Dadhania, Thangamani MuthukumarAbstract:BACKGROUND Urinary tract infection (UTI) is a frequent, serious complication in Kidney Allograft recipients. METHODS We reviewed the records of 1166 Kidney Allograft recipients who received their Allografts at our institution between January 2005 and December 2010 and determined the incidence of UTI during the first 3 months after transplantation (early UTI). We used Cox proportional hazards models to determine the risk factors for early UTI and whether early UTI was an independent risk factor for subsequent bacteremia or acute cellular rejection (ACR). RESULTS UTI, defined as 10 or more bacterial colony-forming units/mL urine, developed in 247 (21%) of the 1166 recipients. Independent risk factors for the first episode of UTI were female gender (hazard ratio [HR], 2.9; 95% confidence intervals [CI], 2.2-3.7; P<0.001), prolonged use of Foley catheter (HR, 3.9; 95% CI, 2.8-5.4; P <0.001), ureteral stent (HR, 1.4; 95% CI, 1.1-1.8; P=0.01), age (HR, 1.1; 95% CI, 1.0-1.2; P=0.03), and delayed graft function (HR, 1.4; 95% CI, 1.0-1.9; P=0.06). Trimethoprim/sulfamethoxazole prophylaxis was associated with a reduced risk of UTI (HR, 0.6; 95% CI, 0.3-0.9; P=0.02). UTI was an independent risk factor for subsequent bacteremia (HR, 2.4; 95% CI, 1.2-4.8; P=0.01). Untreated UTI, but not treated UTI, was associated with an increased risk of ACR (HR, 2.8; 95% CI, 1.3-6.2; P=0.01). CONCLUSIONS Female gender, prolonged use of Foley catheter, ureteral stent, age, and delayed graft function are independent risk factors for early UTI. UTI is independently associated with the development of bacteremia, and untreated UTI is associated with subsequent ACR.
Darshana Dadhania - One of the best experts on this subject based on the ideXlab platform.
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foxp3 mrna profile prognostic of acute t cell mediated rejection and human Kidney Allograft survival
Transplantation, 2021Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:BACKGROUND T cell-mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes are nonresponsive to therapy, and molecular mechanisms for the nonresponsiveness are unknown. Our single-center study identified that urinary cell FOXP3 mRNA abundance predicts TCMR reversibility and Allograft survival. METHODS We developed PCR assays and measured absolute copy numbers of transcripts for FOXP3, CD25, CD3E, perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in the multicenter Clinical Trials in Organ Transplantation-04. In this replication study, we investigated the association between mRNA profile and TCMR diagnosis, TCMR reversibility, and Allograft survival. RESULTS 18S rRNA normalized levels of mRNA for FOXP3 (P = 0.01, Kruskal-Wallis test), CD25 (P = 0.01), CD3E (P < 0.0001), and perforin (P < 0.0001) were diagnostic of TCMR, but only FOXP3 mRNA level predicted TCMR reversibility (ROC AUC = 0.764; 95% confidence interval, 0.611-0.917; P = 0.008). Multivariable logistic regression analyses showed that urinary cell FOXP3 mRNA level predicted reversal, independent of clinical variables. A composite model of clinical variables and FOXP3 mRNA (AUC = 0.889; 95% CI, 0.781-0.997; P < 0.001) outperformed FOXP3 mRNA or clinical variables in predicting TCMR reversibility (P = 0.01, likelihood ratio test). Multivariable Cox proportional hazards regression analyses showed that FOXP3 mRNA level predicts Kidney Allograft survival (P = 0.047) but not after controlling for TCMR reversal (P = 0.477). CONCLUSIONS Urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts TCMR reversibility, and is prognostic of Kidney Allograft survival via a mechanism involving TCMR reversal.
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Kidney Allograft Function Is a Confounder of Urine Metabolite Profiles in Kidney Allograft Recipients
'MDPI AG', 2021Co-Authors: Karsten Suhre, Qiuying Chen, John R Lee, Thangamani Muthukumar, Darshana Dadhania, Steven S. Gross, Manikkam SuthanthiranAbstract:Noninvasive biomarkers of Kidney Allograft status can help minimize the need for standard of care Kidney Allograft biopsies. Metabolites that are measured in the urine may inform about Kidney function and health status, and potentially identify rejection events. To test these hypotheses, we conducted a metabolomics study of biopsy-matched urine cell-free supernatants from Kidney Allograft recipients who were diagnosed with two major types of acute rejections and no-rejection controls. Non-targeted metabolomics data for 674 metabolites and 577 unidentified molecules, for 192 biopsy-matched urine samples, were analyzed. Univariate and multivariate analyses identified metabolite signatures for Kidney Allograft rejection. The replicability of a previously developed urine metabolite signature was examined. Our study showed that metabolite profiles can serve as biomarkers for discriminating rejection biopsies from biopsies without rejection features, but also revealed a role of estimated Glomerular Filtration Rate (eGFR) as a major confounder of the metabolite signal
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Deep sequencing of DNA from urine of Kidney Allograft recipients to estimate donor/recipient-specific DNA fractions.
'Public Library of Science (PLoS)', 2021Co-Authors: Aziz Belkadi, Thangamani Muthukumar, Darshana Dadhania, John R Lee, Gaurav Thareja, Catherine Snopkowski, Anna Halama, Sara Abdelkader, Silvana AbdullaAbstract:Kidney transplantation is the treatment of choice for patients with end-stage Kidney failure, but transplanted Allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in Kidney transplants is Kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for Kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor Kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from Kidney Allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human Kidney Allograft
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foxp3 mrna profile prognostic of t cell mediated rejection and human Kidney Allograft survival
medRxiv, 2020Co-Authors: Danny Luan, Thangamani Muthukumar, Darshana Dadhania, R Ding, Michelle Lubetzky, John R Lee, Vijay K Sharma, Phyllis August, Franco B Mueller, Joseph E SchwartzAbstract:Background and objectives: T cell mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with Kidney Allograft failure. Almost 40% of TCMR episodes fail to respond to anti-rejection therapy. FOXP3 is a specification factor for regulatory T cells and our single center study of 83 Kidney Allograft recipients showed that urinary cell FOXP3 mRNA level is diagnostic of TCMR and predicts TCMR reversibility and Allograft survival. The objective of the current study is to determine whether our original findings could be replicated in an independent cohort of 480 Kidney Allograft recipients enrolled in the multicenter Clinical Trials of Organ Transplantation (CTOT)-04. Design, setting, participants, and measurements: We measured levels of FOXP3 mRNA and levels of mRNA for CD25, CD3E, and perforin, and 18S rRNA in 3559 urines from 480 Kidney Allograft recipients prospectively enrolled in CTOT-04. RNA was isolated from the urinary cells and preamplification-enhanced real-time quantitative PCR assays were used to measure mRNAs. Results: 18S rRNA normalized levels of mRNA for FOXP3 (P=0.01, Kruskal-Wallis test), CD25 (P=0.01), CD3E (P<0.0001), and perforin (P<0.0001) distinguished patients with TCMR biopsies from those with No Rejection biopsies and those with stable graft function. FOXP3 mRNA level, but not the levels of mRNA for CD25, CD3E, or perforin, predicted TCMR reversal (AUC=0.764; 95% confidence interval, 0.611 to 0.917; P=0.008). Multivariable logistic regression analysis showed that FOXP3 mRNA level remains predictive after adjustment for potential cofounders. Kaplan-Meier survival curve analysis showed that FOXP3 mRNA level (P=0.0306) but not the levels of mRNA for CD25, CD3E, or perforin, is associated with Kidney Allograft survival. Conclusion: In the independent CTOT-04 cohort, we demonstrate that urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts its reversibility, and is prognostic of Kidney Allograft survival following an episode of TCMR.
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urine metabolite profiles predictive of human Kidney Allograft status
Journal of The American Society of Nephrology, 2016Co-Authors: Karsten Suhre, Joseph E Schwartz, V K Sharma, Qiuying Chen, John R Lee, Thangamani Muthukumar, Darshana Dadhania, R Ding, David Ikle, Nancy D BridgesAbstract:Noninvasive diagnosis and prognostication of acute cellular rejection in the Kidney Allograft may help realize the full benefits of Kidney transplantation. To investigate whether urine metabolites predict Kidney Allograft status, we determined levels of 749 metabolites in 1516 urine samples from 241 Kidney graft recipients enrolled in the prospective multicenter Clinical Trials in Organ Transplantation-04 study. A metabolite signature of the ratio of 3-sialyllactose to xanthosine in biopsy specimen-matched urine supernatants best discriminated acute cellular rejection biopsy specimens from specimens without rejection. For clinical application, we developed a high-throughput mass spectrometry-based assay that enabled absolute and rapid quantification of the 3-sialyllactose-to-xanthosine ratio in urine samples. A composite signature of ratios of 3-sialyllactose to xanthosine and quinolinate to X-16397 and our previously reported urinary cell mRNA signature of 18S ribosomal RNA, CD3e mRNA, and interferon-inducible protein-10 mRNA outperformed the metabolite signatures and the mRNA signature. The area under the receiver operating characteristics curve for the composite metabolite-mRNA signature was 0.93, and the signature was diagnostic of acute cellular rejection with a specificity of 84% and a sensitivity of 90%. The composite signature, developed using solely biopsy specimen-matched urine samples, predicted future acute cellular rejection when applied to pristine samples taken days to weeks before biopsy. We conclude that metabolite profiling of urine offers a noninvasive means of diagnosing and prognosticating acute cellular rejection in the human Kidney Allograft, and that the combined metabolite and mRNA signature is diagnostic and prognostic of acute cellular rejection with very high accuracy.
