Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes

G. M. Hirschfield, G. Xie, E. Lu, Y. Sun, B. D. Juran, V. Chellappa, C. Coltescu, A. L. Mason, P. Milkiewicz, R. P. Myers, J. A. Odin, V. A. Luketic, B. Bacon, H. Bodenheimer, V. Liakina, C. Vincent, Cynthia Levy, S. Pillai, K. N. Lazaridis, C. I. AmosK. A. Siminovitch

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Abstract

We fine mapped two primary biliary cirrhosis (PBC) risk loci, CLEC16A (C-type lectin domain family 16 member A)-suppressor of cytokine signaling 1 (SOCS1) and Spi-B protein (SPIB) and sequenced a locus, sialic acid acetylesterase (SIAE), proposed to harbor autoimmunity-associated mutations. In all, 1450 PBC cases and 2957 healthy controls were genotyped for 84 single-nucleotide polymorphisms (SNPs) across the CLEC16A-SOCS1 and SPIB loci. All 10 exons of the SIAE gene were resequenced in 381 cases and point substitutions of unknown significance assayed for activity and secretion. Fine mapping identified 26 SNPs across the CLEC16A-SOCS1 and 11 SNPs across the SPIB locus with significant association to PBC, the strongest signals at the CLEC16A-SOCS1 locus emanating from a SOCS1 intergenic SNP (rs243325; P9.91 × 109) and at the SPIB locus from a SPIB intronic SNP (rs34944112; P3.65 × 109). Among the associated SNPs at the CLEC16A-SOCS1 locus, two within the CLEC16A gene as well as one SOCS1 SNP (rs243325) remained significant after conditional logistic regression and contributed independently to risk. Sequencing of the SIAE gene and functional assays of newly identified variants revealed six patients with functional non-synonymous SIAE mutations (Fisher's P9 × 104 vs controls) We demonstrate independent effects on risk of PBC for CLEC16A, SOCS1 and SPIB variants, while identifying functionally defective SIAE variants as potential factors in risk for PBC.

Original languageEnglish
Pages (from-to)328-335
Number of pages8
JournalGenes and Immunity
Volume13
Issue number4
DOIs
StatePublished - Jun 1 2012

Fingerprint

Acetylesterase
Biliary Liver Cirrhosis
N-Acetylneuraminic Acid
Single Nucleotide Polymorphism
Cytokines
Genes
C-Type Lectins
Mutation
IgA receptor
lambda Spi-1
Autoimmunity
Exons
Logistic Models

Keywords

  • Autoimmunity
  • fine mapping
  • primary biliary cirrhosis
  • sequence analysis

ASJC Scopus subject areas

  • Genetics(clinical)
  • Immunology
  • Genetics

Cite this

Hirschfield, G. M., Xie, G., Lu, E., Sun, Y., Juran, B. D., Chellappa, V., ... Siminovitch, K. A. (2012). Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes. Genes and Immunity, 13(4), 328-335. https://doi.org/10.1038/gene.2011.89

Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes. / Hirschfield, G. M.; Xie, G.; Lu, E.; Sun, Y.; Juran, B. D.; Chellappa, V.; Coltescu, C.; Mason, A. L.; Milkiewicz, P.; Myers, R. P.; Odin, J. A.; Luketic, V. A.; Bacon, B.; Bodenheimer, H.; Liakina, V.; Vincent, C.; Levy, Cynthia; Pillai, S.; Lazaridis, K. N.; Amos, C. I.; Siminovitch, K. A.

In: Genes and Immunity, Vol. 13, No. 4, 01.06.2012, p. 328-335.

Research output: Contribution to journalArticle

Hirschfield, GM, Xie, G, Lu, E, Sun, Y, Juran, BD, Chellappa, V, Coltescu, C, Mason, AL, Milkiewicz, P, Myers, RP, Odin, JA, Luketic, VA, Bacon, B, Bodenheimer, H, Liakina, V, Vincent, C, Levy, C, Pillai, S, Lazaridis, KN, Amos, CI & Siminovitch, KA 2012, 'Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes', Genes and Immunity, vol. 13, no. 4, pp. 328-335. https://doi.org/10.1038/gene.2011.89
Hirschfield, G. M. ; Xie, G. ; Lu, E. ; Sun, Y. ; Juran, B. D. ; Chellappa, V. ; Coltescu, C. ; Mason, A. L. ; Milkiewicz, P. ; Myers, R. P. ; Odin, J. A. ; Luketic, V. A. ; Bacon, B. ; Bodenheimer, H. ; Liakina, V. ; Vincent, C. ; Levy, Cynthia ; Pillai, S. ; Lazaridis, K. N. ; Amos, C. I. ; Siminovitch, K. A. / Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes. In: Genes and Immunity. 2012 ; Vol. 13, No. 4. pp. 328-335.
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AU - Hirschfield, G. M.

AU - Xie, G.

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AU - Sun, Y.

AU - Juran, B. D.

AU - Chellappa, V.

AU - Coltescu, C.

AU - Mason, A. L.

AU - Milkiewicz, P.

AU - Myers, R. P.

AU - Odin, J. A.

AU - Luketic, V. A.

AU - Bacon, B.

AU - Bodenheimer, H.

AU - Liakina, V.

AU - Vincent, C.

AU - Levy, Cynthia

AU - Pillai, S.

AU - Lazaridis, K. N.

AU - Amos, C. I.

AU - Siminovitch, K. A.

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N2 - We fine mapped two primary biliary cirrhosis (PBC) risk loci, CLEC16A (C-type lectin domain family 16 member A)-suppressor of cytokine signaling 1 (SOCS1) and Spi-B protein (SPIB) and sequenced a locus, sialic acid acetylesterase (SIAE), proposed to harbor autoimmunity-associated mutations. In all, 1450 PBC cases and 2957 healthy controls were genotyped for 84 single-nucleotide polymorphisms (SNPs) across the CLEC16A-SOCS1 and SPIB loci. All 10 exons of the SIAE gene were resequenced in 381 cases and point substitutions of unknown significance assayed for activity and secretion. Fine mapping identified 26 SNPs across the CLEC16A-SOCS1 and 11 SNPs across the SPIB locus with significant association to PBC, the strongest signals at the CLEC16A-SOCS1 locus emanating from a SOCS1 intergenic SNP (rs243325; P9.91 × 109) and at the SPIB locus from a SPIB intronic SNP (rs34944112; P3.65 × 109). Among the associated SNPs at the CLEC16A-SOCS1 locus, two within the CLEC16A gene as well as one SOCS1 SNP (rs243325) remained significant after conditional logistic regression and contributed independently to risk. Sequencing of the SIAE gene and functional assays of newly identified variants revealed six patients with functional non-synonymous SIAE mutations (Fisher's P9 × 104 vs controls) We demonstrate independent effects on risk of PBC for CLEC16A, SOCS1 and SPIB variants, while identifying functionally defective SIAE variants as potential factors in risk for PBC.

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