Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients

Cristina M. Lanata, Joanne Nititham, Kimberly E. Taylor, Sharon A. Chung, Dara G. Torgerson, Michael F. Seldin, Bernardo A. Pons-Estel, Teresa Tusié-Luna, Betty P. Tsao, Eric F. Morand, Marta E. Alarcón-Riquelme, Lindsey A. Criswell

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Abstract

Objective African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. Methods In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. Results We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7%). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). Conclusion Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.

Original languageEnglish
Article numbere0199003
Number of pages15
JournalPLoS ONE
Volume13
Issue number6
DOIs
Publication statusPublished - 1 Jun 2018

Cite this

Lanata, C. M., Nititham, J., Taylor, K. E., Chung, S. A., Torgerson, D. G., Seldin, M. F., ... Criswell, L. A. (2018). Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients. PLoS ONE, 13(6), [e0199003]. https://doi.org/10.1371/journal.pone.0199003
Lanata, Cristina M. ; Nititham, Joanne ; Taylor, Kimberly E. ; Chung, Sharon A. ; Torgerson, Dara G. ; Seldin, Michael F. ; Pons-Estel, Bernardo A. ; Tusié-Luna, Teresa ; Tsao, Betty P. ; Morand, Eric F. ; Alarcón-Riquelme, Marta E. ; Criswell, Lindsey A. / Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients. In: PLoS ONE. 2018 ; Vol. 13, No. 6.
@article{9878fe57f43542ec909a1ce906edf9df,
title = "Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients",
abstract = "Objective African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. Methods In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. Results We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7{\%}). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). Conclusion Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.",
author = "Lanata, {Cristina M.} and Joanne Nititham and Taylor, {Kimberly E.} and Chung, {Sharon A.} and Torgerson, {Dara G.} and Seldin, {Michael F.} and Pons-Estel, {Bernardo A.} and Teresa Tusi{\'e}-Luna and Tsao, {Betty P.} and Morand, {Eric F.} and Alarc{\'o}n-Riquelme, {Marta E.} and Criswell, {Lindsey A.}",
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Lanata, CM, Nititham, J, Taylor, KE, Chung, SA, Torgerson, DG, Seldin, MF, Pons-Estel, BA, Tusié-Luna, T, Tsao, BP, Morand, EF, Alarcón-Riquelme, ME & Criswell, LA 2018, 'Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients', PLoS ONE, vol. 13, no. 6, e0199003. https://doi.org/10.1371/journal.pone.0199003

Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients. / Lanata, Cristina M.; Nititham, Joanne; Taylor, Kimberly E.; Chung, Sharon A.; Torgerson, Dara G.; Seldin, Michael F.; Pons-Estel, Bernardo A.; Tusié-Luna, Teresa; Tsao, Betty P.; Morand, Eric F.; Alarcón-Riquelme, Marta E.; Criswell, Lindsey A.

In: PLoS ONE, Vol. 13, No. 6, e0199003, 01.06.2018.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients

AU - Lanata, Cristina M.

AU - Nititham, Joanne

AU - Taylor, Kimberly E.

AU - Chung, Sharon A.

AU - Torgerson, Dara G.

AU - Seldin, Michael F.

AU - Pons-Estel, Bernardo A.

AU - Tusié-Luna, Teresa

AU - Tsao, Betty P.

AU - Morand, Eric F.

AU - Alarcón-Riquelme, Marta E.

AU - Criswell, Lindsey A.

PY - 2018/6/1

Y1 - 2018/6/1

N2 - Objective African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. Methods In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. Results We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7%). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). Conclusion Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.

AB - Objective African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. Methods In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. Results We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7%). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). Conclusion Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.

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DO - 10.1371/journal.pone.0199003

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Lanata CM, Nititham J, Taylor KE, Chung SA, Torgerson DG, Seldin MF et al. Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients. PLoS ONE. 2018 Jun 1;13(6). e0199003. https://doi.org/10.1371/journal.pone.0199003