1
|
Stapleton CP, Lord GM, Conlon PJ, Cavalleri GL. The relationship between donor-recipient genetic distance and long-term kidney transplant outcome. HRB Open Res 2020; 3:47. [PMID: 33655195 PMCID: PMC7888353 DOI: 10.12688/hrbopenres.13021.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
Background: We set out to quantify shared genetic ancestry between unrelated kidney donor-recipient pairs and test it as a predictor of time to graft failure. Methods: In a homogenous, unrelated, European cohort of deceased-donor kidney transplant pairs (n pairs = 1,808), we calculated, using common genetic variation, shared ancestry at the genic (n loci=40,053) and genomic level. We conducted a sub-analysis focused on transmembrane protein coding genes (n transcripts=8,637) and attempted replication of a previously published nonsynonymous transmembrane mismatch score. Measures of shared genetic ancestry were tested in a survival model against time to death-censored graft failure. Results: Shared ancestry calculated across the human leukocyte antigen (HLA) significantly associated with graft survival in individuals who had a high serological mismatch (n pairs = 186) with those who did not have any HLA mismatches indicating that shared ancestry calculated specific loci can capture known associations with genes impacting graft outcome. None of the other measures of shared ancestry at a genic level, genome-wide scale, transmembrane subset or nonsynonymous transmembrane mismatch score analysis were significant predictors of time to graft failure. Conclusions: In a large unrelated, deceased-donor European ancestry renal transplant cohort, shared donor-recipient genetic ancestry, calculated using common genetic variation, has limited value in predicting transplant outcome both on a genomic scale and at a genic level (other than at the HLA loci).
Collapse
Affiliation(s)
- Caragh P. Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Graham M. Lord
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | - UK and Ireland Renal Transplant Consortium
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
- Department of Nephrology, Beaumont Hospital, Dublin, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J. Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
2
|
Stapleton CP, Chang B, Keating BJ, Conlon PJ, Cavalleri GL. Polygenic risk score of non‐melanoma skin cancer predicts post‐transplant skin cancer across multiple organ types. Clin Transplant 2020; 34:e13904. [DOI: 10.1111/ctr.13904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 01/21/2023]
Affiliation(s)
- Caragh P. Stapleton
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin Ireland
| | - Bao‐Li Chang
- Penn Transplant Institute University of Pennsylvania Philadelphia PA USA
| | - Brendan J. Keating
- Penn Transplant Institute University of Pennsylvania Philadelphia PA USA
| | - Peter J. Conlon
- Department of Nephrology Beaumont Hospital Dublin Ireland
- Department of Medicine Royal College of Surgeons in Ireland Dublin Ireland
| | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin Ireland
| |
Collapse
|
3
|
Stapleton CP, Kennedy C, Fennelly NK, Murray SL, Connaughton DM, Dorman AM, Doyle B, Cavalleri GL, Conlon PJ. An Exome Sequencing Study of 10 Families with IgA Nephropathy. Nephron Clin Pract 2019; 144:72-83. [PMID: 31865346 DOI: 10.1159/000503564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 09/18/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Immunoglobulin A nephropathy (IgAN) is a heterogeneous disorder with a strong genetic component. The advent of whole exome sequencing (WES) has accelerated the discovery of genetic risk factors underlying familial disorders. OBJECTIVES We set out to test whether damaging variants in known kidney disease genes explain a proportion of IgAN cases recruited in Ireland. METHODS We performed WES in 10 Irish families with multiple affected members having kidney disease where at least one member had biopsy confirmed IgAN. Candidate variants were identified based on being shared between affected family members, minor allele frequency, function and predicted pathogenicity. Pathogenicity of variants was determined according to American College of Medical Genetics and Genomics guidelines. RESULTS We detected candidate variants in 3 of 10 families. We identified a likely pathogenic variant in COL4A5 in one family and a variant of unknown significance (VUS) in COL4A3 in another. Variants in COL4A5 and COL4A3 are known to cause Alport syndrome. In the third family, we identified a VUS in LMX1B, a gene associated with Nail-patella syndrome. CONCLUSIONS We identified a number of cases of familial IgAN where the families harbored variants in known kidney disease-related genes indicating that potentially a number of cases of familial IgAN are mistaken for other familial kidney disorders. However, the majority of families studied did not carry a candidate variant in a known kidney disease causing gene indicating that there may be >1 underlying genetic mechanism present in these families.
Collapse
Affiliation(s)
- Caragh P Stapleton
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Claire Kennedy
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | | | - Susan L Murray
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Dervla M Connaughton
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Brendan Doyle
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland.,Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
4
|
Murray SL, Dorman A, Benson KA, Connaughton DM, Stapleton CP, Fennelly NK, Kennedy C, McDonnell CA, Kidd K, Cormican SM, Ryan LA, Lavin P, Little MA, Bleyer AJ, Doyle B, Cavalleri GL, Hildebrandt F, Conlon PJ. Utility of Genomic Testing after Renal Biopsy. Am J Nephrol 2019; 51:43-53. [PMID: 31822006 DOI: 10.1159/000504869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/16/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Renal biopsy is the mainstay of renal pathological diagnosis. Despite sophisticated diagnostic techniques, it is not always possible to make a precise pathological diagnosis. Our aim was to identify a genetic cause of disease in patients who had undergone renal biopsy and determine if genetic testing altered diagnosis or treatment. METHODS Patients with suspected familial kidney disease underwent a variety of next-generation sequencing (NGS) strategies. The subset of these patients who had also undergone native kidney biopsy was identified. Histological specimens were reviewed by a consultant pathologist, and genetic and pathological diagnoses were compared. RESULTS Seventy-five patients in 47 families underwent genetic sequencing and renal biopsy. Patients were grouped into 5 diagnostic categories based on pathological diagnosis: tubulointerstitial kidney disease (TIKD; n = 18); glomerulonephritis (GN; n = 15); focal segmental glomerulosclerosis and Alport Syndrome (n = 11); thrombotic microangiopathy (TMA; n = 17); and nonspecific pathological changes (n = 14). Thirty-nine patients (52%) in 21 families (45%) received a genetic diagnosis; 13 cases (72%) with TIKD, 4 (27%) with GN, 6 (55%) with focal segmental glomerulosclerosis/Alport syndrome, and 10 (59%) with TMA and 6 cases (43%) with nonspecific features. Genetic testing resulted in changes in understanding of disease mechanism in 21 individuals (54%) in 12 families (57%). Treatment would have been altered in at least 26% of cases (10/39). CONCLUSIONS An accurate genetic diagnosis can result in changes in clinical diagnosis, understanding of pathological mechanism, and treatment. NGS should be considered as a complementary diagnostic technique to kidney biopsy in the evaluation of patients with kidney disease.
Collapse
Affiliation(s)
- Susan L Murray
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland,
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - Anthony Dorman
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
- Department of Pathology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine A Benson
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Dervla M Connaughton
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caragh P Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Claire Kennedy
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Ciara A McDonnell
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Kendrah Kidd
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Sarah M Cormican
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Louise A Ryan
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Peter Lavin
- Department of Nephrology, Tallaght Hospital, Dublin, Ireland
| | - Mark A Little
- Trinity Health Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Anthony J Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Brendan Doyle
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
5
|
Stapleton CP, Heinzel A, Guan W, van der Most PJ, van Setten J, Lord GM, Keating BJ, Israni AK, de Borst MH, Bakker SJ, Snieder H, Weale ME, Delaney F, Hernandez‐Fuentes MP, Reindl-Schwaighofer R, Oberbauer R, Jacobson PA, Mark PB, Chapman FA, Phelan PJ, Kennedy C, Sexton D, Murray S, Jardine A, Traynor JP, McKnight AJ, Maxwell AP, Smyth LJ, Oetting WS, Matas AJ, Mannon RB, Schladt DP, Iklé DN, Cavalleri GL, Conlon PJ. The impact of donor and recipient common clinical and genetic variation on estimated glomerular filtration rate in a European renal transplant population. Am J Transplant 2019; 19:2262-2273. [PMID: 30920136 PMCID: PMC6989089 DOI: 10.1111/ajt.15326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/22/2019] [Accepted: 02/11/2019] [Indexed: 01/25/2023]
Abstract
Genetic variation across the human leukocyte antigen loci is known to influence renal-transplant outcome. However, the impact of genetic variation beyond the human leukocyte antigen loci is less clear. We tested the association of common genetic variation and clinical characteristics, from both the donor and recipient, with posttransplant eGFR at different time-points, out to 5 years posttransplantation. We conducted GWAS meta-analyses across 10 844 donors and recipients from five European ancestry cohorts. We also analyzed the impact of polygenic risk scores (PRS), calculated using genetic variants associated with nontransplant eGFR, on posttransplant eGFR. PRS calculated using the recipient genotype alone, as well as combined donor and recipient genotypes were significantly associated with eGFR at 1-year posttransplant. Thirty-two percent of the variability in eGFR at 1-year posttransplant was explained by our model containing clinical covariates (including weights for death/graft-failure), principal components and combined donor-recipient PRS, with 0.3% contributed by the PRS. No individual genetic variant was significantly associated with eGFR posttransplant in the GWAS. This is the first study to examine PRS, composed of variants that impact kidney function in the general population, in a posttransplant context. Despite PRS being a significant predictor of eGFR posttransplant, the effect size of common genetic factors is limited compared to clinical variables.
Collapse
Affiliation(s)
- Caragh P. Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Peter J. van der Most
- Departments of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Graham M. Lord
- King’s College London, MRC Centre for Transplantation, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | - Brendan J. Keating
- Department of Surgery, Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ajay K. Israni
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Martin H. de Borst
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stephan J.L. Bakker
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Departments of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael E. Weale
- Division of Genetics & Molecular Medicine, King’s College London, London, UK
| | - Florence Delaney
- King’s College London, MRC Centre for Transplantation, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | | | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Patrick B. Mark
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Fiona A. Chapman
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Paul J. Phelan
- Department of Nephrology, Royal Infirmary of Edinburgh, NHS Lothian, UK
| | - Claire Kennedy
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Donal Sexton
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Susan Murray
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Alan Jardine
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Jamie P. Traynor
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | | | | | - Laura J. Smyth
- Centre for Public Health, Queen’s University of Belfast, Belfast, UK
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Roslyn B. Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | | | | | | | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J. Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
6
|
Stapleton CP, Birdwell KA, McKnight AJ, Maxwell AP, Mark PB, Sanders ML, Chapman FA, van Setten J, Phelan PJ, Kennedy C, Jardine A, Traynor JP, Keating B, Conlon PJ, Cavalleri GL. Polygenic risk score as a determinant of risk of non-melanoma skin cancer in a European-descent renal transplant cohort. Am J Transplant 2019; 19:801-810. [PMID: 30085400 PMCID: PMC6367067 DOI: 10.1111/ajt.15057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/26/2018] [Accepted: 07/26/2018] [Indexed: 01/25/2023]
Abstract
Renal transplant recipients have an increased risk of non-melanoma skin cancer (NMSC) compared to in the general population. Here, we show polygenic risk scores (PRS) calculated from genome-wide association studies (GWAS) of NMSC in a general, nontransplant setting, can predict risk of, and time to posttransplant skin cancer. Genetic variants, reaching predefined P-value thresholds were chosen from published squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) nontransplant GWAS. Using these GWAS, BCC and SCC PRS were calculated for each sample across three European ancestry renal transplant cohorts (n = 889) and tested as predictors of case:control status and time to NMSC posttransplant. BCC PRS calculated at P-value threshold 1 × 10-5 was the most significant predictor of case:control status of NMSC posttransplant (OR = 1.61; adjusted P = .0022; AUC [full model adjusted for clinical predictors and PRS] = 0.81). SCC PRS at P-value threshold 1 × 10-5 was the most significant predictor of time to posttransplant NMSC (adjusted P = 9.39 × 10-7 ; HR = 1.41, concordance [full model] = 0.74). PRS of nontransplant NMSC is predictive of case:control status and time to NMSC posttransplant. These results are relevant to how genomics can risk stratify patients to help develop personalized treatment regimens.
Collapse
Affiliation(s)
- Caragh P. Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kelly A. Birdwell
- Department of Medicine, Vanderbilt University Medical Centre, Tennessee, USA
| | | | | | - Patrick B. Mark
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | | | - Fiona A. Chapman
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Jessica van Setten
- Department of Cardiology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Paul J. Phelan
- Department of Nephrology, Royal Infirmary of Edinburgh, NHS Lothian, UK
| | - Claire Kennedy
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Alan Jardine
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Jamie P. Traynor
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Brendan Keating
- Department of Surgery, Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter J. Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
7
|
Affiliation(s)
- Maria Hernandez‐Fuentes
- MRC Centre for Transplantation and NIHR Biomedical Research Centre at Guy's and St Thomas'NHS Foundation Trust and King's College LondonLondonUK
| | - Caragh P. Stapleton
- Department of Molecular and Cellular TherapeuticsThe Royal College of Surgeons of Ireland and Beaumont HospitalDublinIreland
| | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular TherapeuticsThe Royal College of Surgeons of Ireland and Beaumont HospitalDublinIreland
| | - Peter Conlon
- Department of Molecular and Cellular TherapeuticsThe Royal College of Surgeons of Ireland and Beaumont HospitalDublinIreland
| | - Michael E. Weale
- MRC Centre for Transplantation and NIHR Biomedical Research Centre at Guy's and St Thomas'NHS Foundation Trust and King's College LondonLondonUK
| | - Graham M. Lord
- MRC Centre for Transplantation and NIHR Biomedical Research Centre at Guy's and St Thomas'NHS Foundation Trust and King's College LondonLondonUK
| | | |
Collapse
|
8
|
Snoek R, van Setten J, Keating BJ, Israni AK, Jacobson PA, Oetting WS, Matas AJ, Mannon RB, Zhang Z, Zhang W, Hao K, Murphy B, Reindl-Schwaighofer R, Heinzl A, Oberbauer R, Viklicky O, Conlon PJ, Stapleton CP, Bakker SJL, Snieder H, Peters EDJ, van der Zwaag B, Knoers NVAM, de Borst MH, van Eerde AM. NPHP1 (Nephrocystin-1) Gene Deletions Cause Adult-Onset ESRD. J Am Soc Nephrol 2018; 29:1772-1779. [PMID: 29654215 DOI: 10.1681/asn.2017111200] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/19/2018] [Indexed: 11/03/2022] Open
Abstract
Background Nephronophthisis (NPH) is the most prevalent genetic cause for ESRD in children. However, little is known about the prevalence of NPH in adult-onset ESRD. Homozygous full gene deletions of the NPHP1 gene encoding nephrocystin-1 are a prominent cause of NPH. We determined the prevalence of NPH in adults by assessing homozygous NPHP1 full gene deletions in adult-onset ESRD.Methods Adult renal transplant recipients from five cohorts of the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN) underwent single-nucleotide polymorphism genotyping. After quality control, we determined autosomal copy number variants (such as deletions) on the basis of median log2 ratios and B-allele frequency patterns. The findings were independently validated in one cohort. Patients were included in the analysis if they had adult-onset ESRD, defined as start of RRT at ≥18 years old.Results We included 5606 patients with adult-onset ESRD; 26 (0.5%) showed homozygous NPHP1 deletions. No donor controls showed homozygosity for this deletion. Median age at ESRD onset was 30 (range, 18-61) years old for patients with NPH, with 54% of patients age ≥30 years old. Notably, only three (12%) patients were phenotypically classified as having NPH, whereas most patients were defined as having CKD with unknown etiology (n=11; 42%).Conclusions Considering that other mutation types in NPHP1 or mutations in other NPH-causing genes were not analyzed, NPH is a relatively frequent monogenic cause of adult-onset ESRD. Because 88% of patients had not been clinically diagnosed with NPH, wider application of genetic testing in adult-onset ESRD may be warranted.
Collapse
Affiliation(s)
- Rozemarijn Snoek
- Departments of Genetics and.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Brendan J Keating
- Department of Surgery, Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ajay K Israni
- Department of Medicine, Hennepin County Medical Center
| | | | | | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Roslyn B Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences.,Icahn Institute for Genomics and Multiscale Biology, and
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ke Hao
- Department of Genetics and Genomic Sciences.,Icahn Institute for Genomics and Multiscale Biology, and
| | - Barbara Murphy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzl
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Ondrej Viklicky
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Peter J Conlon
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons, Dublin, Ireland.,Department of Nephrology, Beaumont Hospital, Dublin, Ireland; and
| | - Caragh P Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons, Dublin, Ireland
| | | | | | - Edith D J Peters
- Departments of Genetics and.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Nine V A M Knoers
- Departments of Genetics and.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Genetica, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Albertien M van Eerde
- Departments of Genetics and .,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
9
|
Stapleton CP, Conlon PJ, Phelan PJ. Using omics to explore complications of kidney transplantation. Transpl Int 2017; 31:251-262. [PMID: 28892567 DOI: 10.1111/tri.13067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/26/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022]
Abstract
The importance of genetic and biochemical variation in renal transplant outcomes has been clear since the discovery of the HLA in the 1950s. Since that time, there have been huge advancements in both transplantation and omics. In recent years, there has seen an increased number of genome-, proteome- and transcriptome-wide studies in the field of transplantation moving away from the earlier candidate gene/protein approaches. These areas have the potential to lead to the development of personalized treatment depending on individual molecular risk profiles. Here, we discuss recent progress and the current literature surrounding omics and renal transplant complications.
Collapse
Affiliation(s)
- Caragh P Stapleton
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland.,Department of Medicine, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Paul J Phelan
- Department of Nephrology, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| |
Collapse
|
10
|
|