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7. 130 Low Gene Copy Numbers (GCN) of complement C4 and C4A deficiency are highly significant genetic risk factors for idiopathic inflammatory myopathies and its major subgroups

Author

Zhou, Danlei, primary, King, Emily, additional, Rothwell, Simon, additional, Kryštůfková, Olga, additional, Notarnicola, Antonella, additional, Coss, Samantha, additional, Aziz, Rabheh, additional, Miller, Katherine, additional, Dang, Amanda, additional, Yu, Richard, additional, Drew, Joanne, additional, Lundstrom, Emeli, additional, Pachman, Lauren, additional, Mamyrova, Gulnara, additional, Curiel, Rodolfo, additional, De Paepe, Boel, additional, De Bleecker, Jan, additional, Payton, Antony, additional, Ollier, William, additional, O'Hanlon, Terrance, additional, Targoff, Ira, additional, Flegel, Willy, additional, Sivaraman, Vidya, additional, Obele, Edward, additional, Akoghlanian, Shoghik, additional, Driest, Kyla, additional, Spencer, Charles, additional, Ling Wu, Yee, additional, Nagaraja, Haikady, additional, Ardoin, Stacy, additional, Chinoy, Hector, additional, Rider, Lisa, additional, Miller, Frederick, additional, Lundberg, Ingrid, additional, Padyukov, Leonid, additional, Vencovský, Jiří, additional, Lamb, Janine, additional, and Yu, Chack-Yung, additional

Published
2023
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9. Fine mapping of Xq28: both MECP2 and IRAK1 contribute to risk for systemic lupus erythematosus in multiple ancestral groups

Author

Kaufman, Kenneth M, Zhao, Jian, Kelly, Jennifer A, Hughes, Travis, Adler, Adam, Sanchez, Elena, Ojwang, Joshua O, Langefeld, Carl D, Ziegler, Julie T, Williams, Adrienne H, Comeau, Mary E, Marion, Miranda C, Glenn, Stuart B, Cantor, Rita M, Grossman, Jennifer M, Hahn, Bevra H, Song, Yeong Wook, Yu, Chack-Yung, James, Judith A, Guthridge, Joel M, Brown, Elizabeth E, Alarcón, Graciela S, Kimberly, Robert P, Edberg, Jeffrey C, Ramsey-Goldman, Rosalind, Petri, Michelle A, Reveille, John D, Vilá, Luis M, Anaya, Juan-Manuel, Boackle, Susan A, Stevens, Anne M, Freedman, Barry I, Criswell, Lindsey A, Group, Bernardo A Pons-Estel on behalf of the Argentine Collaborative, Lee, Joo-Hyun, Lee, Ji-Seon, Chang, Deh-Ming, Scofield, R Hal A, Gilkeson, Gary S, Merrill, Joan T, Niewold, Timothy B, Vyse, Timothy James, Bae, Sang-Cheol, network, Marta E Alarcón-Riquelme on behalf of the BIOLUPUS, Jacob, Chaim O, Sivils, Kathy Moser, Gaffney, Patrick M, Harley, John B, Sawalha, Amr H, and Tsao, Betty P

Subjects
Human Genome, Autoimmune Disease, Lupus, Genetics, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Base Sequence, Chromosome Mapping, Chromosomes, Human, X, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Interleukin-1 Receptor-Associated Kinases, Lupus Erythematosus, Systemic, Methyl-CpG-Binding Protein 2, Molecular Sequence Data, Polymorphism, Single Nucleotide, Racial Groups, Real-Time Polymerase Chain Reaction, Risk Factors, Argentine Collaborative Group, BIOLUPUS network, Clinical Sciences, Immunology, Public Health and Health Services, Arthritis & Rheumatology
Abstract

ObjectivesThe Xq28 region containing IRAK1 and MECP2 has been identified as a risk locus for systemic lupus erythematosus (SLE) in previous genetic association studies. However, due to the strong linkage disequilibrium between IRAK1 and MECP2, it remains unclear which gene is affected by the underlying causal variant(s) conferring risk of SLE.MethodsWe fine-mapped ≥136 SNPs in a ∼227 kb region on Xq28, containing IRAK1, MECP2 and seven adjacent genes (L1CAM, AVPR2, ARHGAP4, NAA10, RENBP, HCFC1 and TMEM187), for association with SLE in 15 783 case-control subjects derived from four different ancestral groups.ResultsMultiple SNPs showed strong association with SLE in European Americans, Asians and Hispanics at p

Published
2013

10. Brief Report: Single‐nucleotide polymorphisms in VKORC1 are risk factors for systemic lupus erythematosus in Asians

Author

Kaiser, Rachel, Taylor, Kimberly E, Deng, Yun, Zhao, Jian, Li, Yonghong, Nititham, Joanne, Chang, Monica, Catanese, Joseph, Begovich, Ann B, Brown, Elizabeth E, Edberg, Jeffrey C, McGwin, Gerald, Alarcón, Graciela S, Ramsey‐Goldman, Rosalind, Reveille, John D, Vila, Luis M, Petri, Michelle, Kimberly, Robert P, Feng, Xuebing, Sun, Lingyun, Shen, Nan, Li, Wei, Lu, Jian‐Xin, Wakeland, Edward K, Li, Quan‐Zhen, Yang, Wanling, Lau, Yu‐Lung, Liu, Fei‐Lan, Chang, Deh‐Ming, Yu, Chack‐Yung, Song, Yeong W, Group, Hwee Siew Howe and the Tan Tock Seng Hospital Systemic Lupus Erythematosus Study, Tsao, Betty P, and Criswell, Lindsey A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Health Sciences, Genetics, Autoimmune Disease, Lupus, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Adult, Asian People, Case-Control Studies, Female, Genetic Predisposition to Disease, Genotype, Hemostasis, Humans, Lupus Erythematosus, Systemic, Male, Middle Aged, Mixed Function Oxygenases, Polymorphism, Single Nucleotide, Risk Factors, Venous Thrombosis, Vitamin K Epoxide Reductases, Hwee Siew Howe and the Tan Tock Seng Hospital Systemic Lupus Erythematosus Study Group, Clinical Sciences, Immunology, Public Health and Health Services, Arthritis & Rheumatology, Clinical sciences
Abstract

ObjectiveThe increased risk of thrombosis in systemic lupus erythematosus (SLE) may be partially explained by interrelated genetic pathways for thrombosis and SLE. The present study was undertaken to investigate whether 33 established and novel single-nucleotide polymorphisms (SNPs) in 20 genes involved in hemostasis pathways that have been associated with deep venous thrombosis (DVT) in the general population are risk factors for SLE among Asian subjects.MethodsPatients in the discovery cohort were enrolled in 1 of 2 North American SLE cohorts. Patients in the replication cohort were enrolled in 1 of 4 Asian or 2 North American cohorts. We first genotyped 263 Asian patients with SLE and 357 healthy Asian control subjects for 33 SNPs in the discovery phase, and then genotyped 5 SNPs in up to an additional 1,496 patients and 993 controls in the replication phase. Patients were compared to controls for bivariate association with minor alleles. Principal components analysis was used to control for intra-Asian ancestry in the replication cohort.ResultsTwo genetic variants in the gene VKORC1 were highly significant in both the discovery and replication cohorts: rs9934438 (in the discovery cohort, odds ratio [OR] 2.45, P=2×10(-9); in the replication cohort, OR 1.54, P=4×10(-6)) and rs9923231 (in the discovery cohort, OR 2.40, P=6×10(-9); in the replication cohort, OR 1.53, P=5×10(-6)). These associations were significant in the replication cohort after adjustment for intra-Asian ancestry: for rs9934438, OR 1.34, P=0.0029; for rs9923231, OR 1.34, P=0.0032.ConclusionGenetic variants in VKORC1, which are involved in vitamin K reduction and associated with DVT, correlate with SLE development in Asian subjects. These results suggest that there may be intersecting genetic pathways for the development of SLE and thrombosis.

Published
2013

12. Complement C4 gene copy number variations and polymorphisms, autoantibodies, and clinical manifestations of juvenile dermatomyositis– a multi-center study

Author

Coss, Samantha Lynn, primary, Aziz, Rabheh Abdul, additional, Zhou, Danlei, additional, Zhou, Bi, additional, Miller, Katherine, additional, Wu, Yee Ling, additional, Ardoin, Stacy, additional, Oberle, Edward, additional, Driest, Kyla, additional, Al Ahmed, Ohoud, additional, Patwardhan, Anjali, additional, Akoghlanian, Shoghik, additional, Sivaraman, Vidya, additional, Barbar-Smiley, Fatima, additional, Drew, Joanne, additional, Spencer, Charles, additional, Pachman, Lauren, additional, Morgan, Gabrielle, additional, Mamyrova, Gulnara, additional, Curiel, Rodolfo, additional, Jones, Olcay, additional, O’Hanlon, Terry, additional, Rider, Lisa, additional, Miller, Frederick, additional, Padyukov, Leonid, additional, Lundberg, Ingrid, additional, Notarnicola, Antonella, additional, Vencovský, Jiří, additional, Stibůrková, Blanka, additional, Kryštůfková, Olga, additional, and Yu, Chack-Yung, additional

Published
2023
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14. Complement in Rheumatic Diseases

Author

Yu, Chack Yung, Driest, Kyla, Wu, Yee Ling, Lintner, Katherine E., Patwardhan, Anjali, Spencer, Charles, Arnett, Frank C., Rigby, William F. C., Hebert, Lee A., Hauptmann, Georges, Mackay, Ian R., editor, Rose, Noel R., editor, Diamond, Betty, editor, and Davidson, Anne, editor

Published
2014
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15. Low copy numbers of complementC4andC4Adeficiency are risk factors for myositis, its subgroups and autoantibodies

Author

Zhou, Danlei, primary, King, Emily H, additional, Rothwell, Simon, additional, Krystufkova, Olga, additional, Notarnicola, Antonella, additional, Coss, Samantha, additional, Abdul-Aziz, Rabheh, additional, Miller, Katherine E, additional, Dang, Amanda, additional, Yu, G Richard, additional, Drew, Joanne, additional, Lundström, Emeli, additional, Pachman, Lauren M, additional, Mamyrova, Gulnara, additional, Curiel, Rodolfo V, additional, De Paepe, Boel, additional, De Bleecker, Jan L, additional, Payton, Antony, additional, Ollier, William, additional, O'Hanlon, Terrance P, additional, Targoff, Ira N, additional, Flegel, Willy A, additional, Sivaraman, Vidya, additional, Oberle, Edward, additional, Akoghlanian, Shoghik, additional, Driest, Kyla, additional, Spencer, Charles H, additional, Wu, Yee Ling, additional, Nagaraja, Haikady N, additional, Ardoin, Stacy P, additional, Chinoy, Hector, additional, Rider, Lisa G, additional, Miller, Frederick W, additional, Lundberg, Ingrid E, additional, Padyukov, Leonid, additional, Vencovský, Jiří, additional, Lamb, Janine A, additional, and Yu, Chack-Yung, additional

Published
2022
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16. Strong association of combined genetic deficiencies in the classical complement pathway with risk of systemic lupus erythematosus and primary Sjögren's syndrome

Author

Lundtoft, Christian, Sjöwall, Christopher, Rantapää-Dahlqvist, Solbritt, Bengtsson, Anders A., Jönsen, Andreas, Pucholt, Pascal, Wu, Yee Ling, Lundström, Emeli, Eloranta, Maija-Leena, Gunnarsson, Iva, Baecklund, Eva, Jonsson, Roland, Hammenfors, Daniel, Forsblad-d'Elia, Helena, Eriksson, Per, Mandl, Thomas, Bucher, Sara, Norheim, Katrine Brække, Johnsen, Svein Joar Auglæn, Omdal, Roald, Kvarnström, Marika, Wahren Herlenius, Marie Elisabeth, Truedsson, Lennart, Nilsson, Bo, Kozyrev, Sergey V., Bianchi, Matteo, Lindblad-Toh, Kerstin, Yu, Chack-Yung, Nordmark, Gunnel, Sandling, Johanna K., Svenungsson, Elisabet, Leonard, Dag, and Rönnblom, Lars

Subjects
Hereditary Complement Deficiency Diseases, Reumatologi och inflammation, DNA Copy Number Variations, Immunology, Complement C4, Complement System Proteins, Sjogren's Syndrome, Rheumatology, Humans, Lupus Erythematosus, Systemic, Immunology and Allergy, Complement Pathway, Classical, Medical Genetics, Medicinsk genetik, Rheumatology and Autoimmunity
Abstract

Objective Complete genetic deficiency of the complement component C2 is a strong risk factor for monogenic systemic lupus erythematosus (SLE), but whether heterozygous C2 deficiency adds to the risk of SLE or primary Sjogrens syndrome (SS) has not been studied systematically. This study was undertaken to investigate potential associations of heterozygous C2 deficiency and C4 copy number variation with clinical manifestations in patients with SLE and patients with primary SS. Methods The presence of the common 28-bp C2 deletion rs9332736 and C4 copy number variation was examined in Scandinavian patients who had received a diagnosis of SLE (n = 958) or primary SS (n = 911) and in 2,262 healthy controls through the use of DNA sequencing. The concentration of complement proteins in plasma and classical complement function were analyzed in a subgroup of SLE patients. Results Heterozygous C2 deficiency-when present in combination with a low C4A copy number-substantially increased the risk of SLE (odds ratio [OR] 10.2 [95% confidence interval (95% CI) 3.5-37.0]) and the risk of primary SS (OR 13.0 [95% CI 4.5-48.4]) when compared to individuals with 2 C4A copies and normal C2. For patients heterozygous for rs9332736 with 1 C4A copy, the median age at diagnosis was 7 years earlier in patients with SLE and 12 years earlier in patients with primary SS when compared to patients with normal C2. Reduced C2 levels in plasma (P = 2 x 10(-9)) and impaired function of the classical complement pathway (P = 0.03) were detected in SLE patients with heterozygous C2 deficiency. Finally, in a primary SS patient homozygous for C2 deficiency, we observed low levels of anti-Scl-70, which suggests a risk of developing systemic sclerosis or potential overlap between primary SS and other systemic autoimmune diseases. Conclusion We demonstrate that a genetic pattern involving partial deficiencies of C2 and C4A in the classical complement pathway is a strong risk factor for SLE and for primary SS. Our results emphasize the central role of the complement system in the pathogenesis of both SLE and primary SS. Funding Agencies|Swedish Research Council for Medicine and Health; Swedish Rheumatism Association; Swedish Heart-Lung Foundation; Swedish Society for Medical Research; Swedish Society of Medicine; Gustafsson Family Foundation; Wallenberg Scholarship; King Gustaf Vs 80-Year Foundation; Stockholm County and Region Ostergotland

Published
2022

17. Human Complement C4B Allotypes and Deficiencies in Selected Cases With Autoimmune Diseases

Author

Zhou, Danlei, primary, Rudnicki, Michael, additional, Chua, Gilbert T., additional, Lawrance, Simon K., additional, Zhou, Bi, additional, Drew, Joanne L., additional, Barbar-Smiley, Fatima, additional, Armstrong, Taylor K., additional, Hilt, Miranda E., additional, Birmingham, Daniel J., additional, Passler, Werner, additional, Auletta, Jeffrey J., additional, Bowden, Sasigarn A., additional, Hoffman, Robert P., additional, Wu, Yee Ling, additional, Jarjour, Wael N., additional, Mok, Chi Chiu, additional, Ardoin, Stacy P., additional, Lau, Yu Lung, additional, and Yu, Chack Yung, additional

Published
2021
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18. Four Systemic Lupus Erythematosus Subgroups, Defined by Autoantibodies Status, Differ Regarding HLA‐DRB1 Genotype Associations and Immunological and Clinical Manifestations

Author

Diaz‐Gallo, Lina‐Marcela, primary, Oke, Vilija, additional, Lundström, Emeli, additional, Elvin, Kerstin, additional, Ling Wu, Yee, additional, Eketjäll, Susanna, additional, Zickert, Agneta, additional, Gustafsson, Johanna T., additional, Jönsen, Andreas, additional, Leonard, Dag, additional, Birmingham, Daniel J., additional, Nordmark, Gunnel, additional, Bengtsson, Anders A., additional, Rönnblom, Lars, additional, Gunnarsson, Iva, additional, Yu, Chack‐Yung, additional, Padyukov, Leonid, additional, and Svenungsson, Elisabet, additional

Published
2021
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21. Four Systemic Lupus Erythematosus Subgroups, Defined by Autoantibodies Status, Differ Regarding HLA‐DRB1 Genotype Associations and Immunological and Clinical Manifestations.

Author

Diaz‐Gallo, Lina‐Marcela, Oke, Vilija, Lundström, Emeli, Elvin, Kerstin, Ling Wu, Yee, Eketjäll, Susanna, Zickert, Agneta, Gustafsson, Johanna T., Jönsen, Andreas, Leonard, Dag, Birmingham, Daniel J., Nordmark, Gunnel, Bengtsson, Anders A., Rönnblom, Lars, Gunnarsson, Iva, Yu, Chack‐Yung, Padyukov, Leonid, and Svenungsson, Elisabet

Subjects
SYSTEMIC lupus erythematosus, AUTOANTIBODIES, SJOGREN'S syndrome, SYMPTOMS, GENOTYPES
Abstract

Objective: The heterogeneity of systemic lupus erythematosus (SLE) constitutes clinical and therapeutical challenges. We therefore studied whether unrecognized disease subgroups can be identified by using autoantibody profiling together with HLA‐DRB1 alleles and immunological and clinical data. Methods: An unsupervised cluster analysis was performed based on detection of 13 SLE‐associated autoantibodies (double‐stranded DNA, nucleosomes, ribosomal P, ribonucleoprotein [RNP] 68, RNPA, Smith [Sm], Sm/RNP, Sjögren's syndrome antigen A [SSA]/Ro52, SSA/Ro60, Sjögren's syndrome antigen B [SSB]/La, cardiolipin [CL]‐Immunoglobulin G [IgG], CL–Immunoglobulin M [IgM], and β2 glycoprotein I [β2GPI]–IgG) in 911 patients with SLE from two cohorts. We evaluated whether each SLE subgroup is associated with HLA‐DRB1 alleles, clinical manifestations (n = 743), and cytokine levels in circulation (n = 446). Results: Our analysis identified four subgroups among the patients with SLE. Subgroup 1 (29.3%) was dominated by anti‐SSA/Ro60/Ro52/SSB autoantibodies and was strongly associated with HLA‐DRB1*03 (odds ratio [OR] = 4.73; 95% confidence interval [CI] = 4.52‐4.94). Discoid lesions were more common for this disease subgroup (OR = 1.71, 95% CI = 1.18‐2.47). Subgroup 2 (28.7%) was dominated by anti‐nucleosome/SmRNP/DNA/RNPA autoantibodies and associated with HLA‐DRB1*15 (OR = 1.62, 95% CI = 1.41‐1.84). Nephritis was most common in this subgroup (OR = 1.61, 95% CI = 1.14‐2.26). Subgroup 3 (23.8%) was characterized by anti‐ß2GPI‐IgG/anti‐CL–IgG/IgM autoantibodies and a higher frequency of HLA‐DRB1*04 compared with the other patients with SLE. Vascular events were more common in Subgroup 3 (OR = 1.74, 95% CI = 1.2‐2.5). Subgroup 4 (18.2%) was negative for the investigated autoantibodies, and this subgroup was not associated with HLA‐DRB1. Additionally, the levels of eight cytokines significantly differed among the disease subgroups. Conclusion: Our findings suggest that four fairly distinct subgroups can be identified on the basis of the autoantibody profile in SLE. These four SLE subgroups differ regarding associations with HLA‐DRB1 alleles and immunological and clinical features, suggesting dissimilar disease pathways. [ABSTRACT FROM AUTHOR]

Published
2022
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23. Association of PPP2CA polymorphisms with systemic lupus erythematosus susceptibility in multiple ethnic groups

Author

Tan, Wenfeng, Sunahori, Katsue, Zhao, Jian, Deng, Yun, Kaufman, Kenneth M., Kelly, Jennifer A., Langefeld, Carl D., Williams, Adrienne H., Comeau, Mary E., Ziegler, Julie T., Marion, Miranda C., Bae, Sang-Cheol, Lee, Joo Hyun, Lee, Ji-Seon, Chang, Deh-Ming, Song, Yeong Wook, Yu, Chack-Yung, Kimberly, Robert P., Edberg, Jeffrey C., Brown, Elizabeth E., Petri, Michelle A., Ramsey-Goldman, Rosalind, Vilá, Luis M., Reveille, John D., Alarcón-Riquelme, Marta E., Harley, John B., Boackle, Susan A., Stevens, Anne M., Scofield, Hal R., Merrill, Joan T., Freedman, Barry I., Anaya, Juan-Manuel, Criswell, Lindsey A., Jacob, Chaim O., Vyse, Timothy J., Niewold, Timothy B., Gaffney, Patrick M., Moser, Kathy L., Gilkeson, Gary S., Kamen, Diane L., James, Judith A., Grossman, Jennifer M., Hahn, Bevra H., Tsokos, George C., and Tsao, Betty P.

Published
2011
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26. The gene structure and the polymorphism of the human complement component C4

Author

Yu, Chack-yung, Porter, Rodney Robert, and Campbell, R. Duncan

Subjects
572.8, Complement (Immunology), Immunogenetics, Genetic polymorphisms
Abstract

1. The DNA sequence of the human complement C4A gene from a cosmid clone Cos 3A3 was determined and the complete exon-intron structure elucidated. The 5' flanking region of the C4 gene contains three TATA sequences and a transcriptional enhancer core sequence, which are >200 nucleotides (nt) and 60-70 nt upstream from the CAP site, respectively. The gene consists of 42 exons coding for a precursor protein of 1745 residues. The first exon codes for a 51 nt 5' untranslated sequence, a leader peptide of 19 residues, and the N-terminus of the β chain. The β-α and the α-γ chain junctions are encoded by exons 17 and 34, respectively. The anaphylatoxin C4a and the thiolester site are encoded by phase 1-1 symmetrical exons. Most of the amino acids encoded at the splice junctions are polar or charged. Between exons 10 and 11 is a 6-7 kb intron that is flanked by direct long terminal repeats and may be absent in some C4 genes located at the second C4 locus. The last exon codes for the C-terminus of the γ chain and a 140 bp 3' untranslated sequence. The intergenic region between the C4 gene and its neighbouring 21-hydroxylase (210Hase) gene is ~3028 bp. 2. Eighteen polymorphic amino acids on C4 have been identified through genomic DNA, cDNA and protein sequencing. Fourteen of them are located on the* chain (C4a: 2 changes; C4d: 12 changes). The rest are scattered on the β and the γ chains. There are potential size variations by one residue on the β chain, and by a tripeptide that contains a sulphation site on the α chain. 3. Four common and rare C4 alleles have been cloned from individuals whose C4 proteins were chemically and serologically characterised. Analysis of the sequences at the C4d regions has allowed the identification of the C4A/C4B isotypic residues at positions 1101-6: C4A has the sequence PCPVLD, while C4B has the sequence LSPVIH. Presumably these isotypic residues are the cause of the class-specific, differential chemical reactivates. Moreover, the probable locations for the two Eodgers (Kg) and the six Chido (Ch) antigenic determinants were deduced. The C4B isotypic residues may be involved in the expression of the Ch2 and the Ch4 epitopes, while the C4A isotypic residues may not be related to either of the Eg determinants. 4. Definitive restriction fragment length polymorphisms (RFLPs) representing the exact locations responsible for the isotypicity between C4A and C4B, and for their generally associated Rg1 and Ch1 antigenic determinants, have been designed. In combination with the Taq I polymorphic patterns specific for the C4 and for the 210Hase gene loci, it has been shown that the null allele of the HLA haplotype B44 DR6 C4A 3 C4B QO is not a C4B allele, but probably encodes another C4A 3 allotype at the second C4 locus.

Published
1987

33. Elevated serum complement levels and higher gene copy number of complement C4B are associated with hypertension and effective response to statin therapy in childhood-onset systemic lupus erythematosus (SLE)

Author

Mulvihill, Evan, primary, Ardoin, Stacy, additional, Thompson, Susan D, additional, Zhou, Bi, additional, Yu, Gakit Richard, additional, King, Emily, additional, Singer, Nora, additional, Levy, D M, additional, Brunner, Hermine, additional, Wu, Yee Ling, additional, Nagaraja, Haikady N, additional, Schanberg, Laura Eve, additional, and Yu, Chack-Yung, additional

Published
2019
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34. Opposite Profiles of Complement in Antiphospholipid Syndrome (APS) and Systemic Lupus Erythematosus (SLE) Among Patients With Antiphospholipid Antibodies (aPL)

Author

Savelli, Stephanie L., primary, Roubey, Robert A. S., additional, Kitzmiller, Kathryn J., additional, Zhou, Danlei, additional, Nagaraja, Haikady N., additional, Mulvihill, Evan, additional, Barbar-Smiley, Fatima, additional, Ardoin, Stacy P., additional, Wu, Yee Ling, additional, and Yu, Chack-Yung, additional

Published
2019
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35. 190 Opposite profiles of complement in antiphospholipid syndrome (APS) and systemic lupus erythematosus (SLE) among patients with antiphospholipid antibodies

Author

Yu, Chack-Yung, primary, Savelli, Stephanie, additional, Roubey, Robert, additional, Kitzmiller, Kathryn, additional, Zhou, Danlei, additional, Nagaraja, Haikady, additional, Mulvihill, Evan, additional, Barbar-Smiley, Fatima, additional, Ardoin, Stacy P, additional, and Wu, Yee-Ling, additional

Published
2019
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38. Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays

Author

Wenger Gail D, Yang Yan, Yu Chack-Yung, Singh Sunita, McHugh Kirk M, Nowak Norma J, Newsom David L, Auer Herbert, Gastier-Foster Julie M, and Kornacker Karl

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Array-based comparative genomic hybridization (aCGH) is a high-throughput method for measuring genome-wide DNA copy number changes. Current aCGH methods have limited resolution, sensitivity and reproducibility. Microarrays for aCGH are available only for a few organisms and combination of aCGH data with expression data is cumbersome. Results We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data. Conclusion A novel method of gene resolution analysis of copy number variation (graCNV) yields high-resolution maps of DNA copy number changes and is applicable to a broad range of organisms for which commercial oligonucleotide expression microarrays are available. Due to the standardization of oligonucleotide microarrays, graCNV results can reliably be compared between laboratories and can easily be combined with gene expression data using the same platform.

Published
2007
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42. The gene structure and the polymorphism of the human complement component C4

Author

Yu, C, Yu, Chack-yung, Porter, R, Campbell, R, and Professor Rodney Porter, R

Subjects
Immunogenetics, Complement (Immunology), Genetic polymorphisms
Abstract

1. The DNA sequence of the human complement C4A gene from a cosmid clone Cos 3A3 was determined and the complete exon-intron structure elucidated. The 5' flanking region of the C4 gene contains three TATA sequences and a transcriptional enhancer core sequence, which are >200 nucleotides (nt) and 60-70 nt upstream from the CAP site, respectively. The gene consists of 42 exons coding for a precursor protein of 1745 residues. The first exon codes for a 51 nt 5' untranslated sequence, a leader peptide of 19 residues, and the N-terminus of the β chain. The β-α and the α-γ chain junctions are encoded by exons 17 and 34, respectively. The anaphylatoxin C4a and the thiolester site are encoded by phase 1-1 symmetrical exons. Most of the amino acids encoded at the splice junctions are polar or charged. Between exons 10 and 11 is a 6-7 kb intron that is flanked by direct long terminal repeats and may be absent in some C4 genes located at the second C4 locus. The last exon codes for the C-terminus of the γ chain and a 140 bp 3' untranslated sequence. The intergenic region between the C4 gene and its neighbouring 21-hydroxylase (210Hase) gene is ~3028 bp. 2. Eighteen polymorphic amino acids on C4 have been identified through genomic DNA, cDNA and protein sequencing. Fourteen of them are located on the* chain (C4a: 2 changes; C4d: 12 changes). The rest are scattered on the β and the γ chains. There are potential size variations by one residue on the β chain, and by a tripeptide that contains a sulphation site on the α chain. 3. Four common and rare C4 alleles have been cloned from individuals whose C4 proteins were chemically and serologically characterised. Analysis of the sequences at the C4d regions has allowed the identification of the C4A/C4B isotypic residues at positions 1101-6: C4A has the sequence PCPVLD, while C4B has the sequence LSPVIH. Presumably these isotypic residues are the cause of the class-specific, differential chemical reactivates. Moreover, the probable locations for the two Eodgers (Kg) and the six Chido (Ch) antigenic determinants were deduced. The C4B isotypic residues may be involved in the expression of the Ch2 and the Ch4 epitopes, while the C4A isotypic residues may not be related to either of the Eg determinants. 4. Definitive restriction fragment length polymorphisms (RFLPs) representing the exact locations responsible for the isotypicity between C4A and C4B, and for their generally associated Rg1 and Ch1 antigenic determinants, have been designed. In combination with the Taq I polymorphic patterns specific for the C4 and for the 210Hase gene loci, it has been shown that the null allele of the HLA haplotype B44 DR6 C4A 3 C4B QO is not a C4B allele, but probably encodes another C4A 3 allotype at the second C4 locus.

Published
2016

44. Long-read sequencing and de novo assembly of a Chinese genome

Author

Shi, Lingling, primary, Guo, Yunfei, additional, Dong, Chengliang, additional, Huddleston, John, additional, Yang, Hui, additional, Han, Xiaolu, additional, Fu, Aisi, additional, Li, Quan, additional, Li, Na, additional, Gong, Siyi, additional, Lintner, Katherine E., additional, Ding, Qiong, additional, Wang, Zou, additional, Hu, Jiang, additional, Wang, Depeng, additional, Wang, Feng, additional, Wang, Lin, additional, Lyon, Gholson J., additional, Guan, Yongtao, additional, Shen, Yufeng, additional, Evgrafov, Oleg V., additional, Knowles, James A., additional, Thibaud-Nissen, Francoise, additional, Schneider, Valerie, additional, Yu, Chack-Yung, additional, Zhou, Libing, additional, Eichler, Evan E., additional, So, Kwok-Fai, additional, and Wang, Kai, additional

Published
2016
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45. Effects of Complement C4 Gene Copy-Number Variations, Gene Size Dichotomy and C4A-Deficiency on Genetic Risk and Clinical Presentation of East-Asian and European Systemic Lupus Erythematosus (SLE)

Author

Yu, Chack Yung, primary, Chen, Ji Yih, additional, Wu, Yee Ling, additional, Mok, Mo Yin, additional, Wu, Yeong-Jian Jan, additional, Lintner, Katherine E., additional, Wang, Chin-Man, additional, Chung, Erwin K., additional, Yang, Yan, additional, Zhou, Bi, additional, Wang, Huanyu, additional, Yu, Denise J.H.C., additional, Alhomosh, Alaaedin, additional, Jones, Karla, additional, Spencer, Charles H., additional, Nagaraja, Haikady N., additional, Lau, Yu Long, additional, and Lau, Chak-Sing, additional

Published
2016
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46. Polymorphisms in α-Defensin–Encoding DEFA1A3 Associate with Urinary Tract Infection Risk in Children with Vesicoureteral Reflux

Author

Schwaderer, Andrew L., primary, Wang, Huanyu, additional, Kim, SungHwan, additional, Kline, Jennifer M., additional, Liang, Dong, additional, Brophy, Pat D., additional, McHugh, Kirk M., additional, Tseng, George C., additional, Saxena, Vijay, additional, Barr-Beare, Evan, additional, Pierce, Keith R., additional, Shaikh, Nader, additional, Manak, J. Robert, additional, Cohen, Daniel M., additional, Becknell, Brian, additional, Spencer, John D., additional, Baker, Peter B., additional, Yu, Chack-Yung, additional, and Hains, David S., additional

Published
2016
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47. Gene copy-number variations (CNVs) of complement C4 and C4A deficiency in genetic risk and pathogenesis of juvenile dermatomyositis

Author

Lintner, Katherine E, primary, Patwardhan, Anjali, additional, Rider, Lisa G, additional, Abdul-Aziz, Rabheh, additional, Wu, Yee Ling, additional, Lundström, Emeli, additional, Padyukov, Leonid, additional, Zhou, Bi, additional, Alhomosh, Alaaedin, additional, Newsom, David, additional, White, Peter, additional, Jones, Karla B, additional, O'Hanlon, Terrance P, additional, Miller, Frederick W, additional, Spencer, Charles H, additional, and Yu, Chack Yung, additional

Published
2015
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49. SNPs in VKORC1 are Risk Factors for Systemic Lupus Erythematosus in Asians: Genetic risk factors for Lupus

Author

Kaiser, Rachel, Taylor, Kimberly E., Deng, Yun, Zhao, Jian, Li, Yonghong, Nititham, Joanne, Chang, Monica, Catanese, Joseph, Begovich, Ann B., Brown, Elizabeth E., Edberg, Jeffrey C., McGwin, Gerald, Alarcón, Graciela S., Ramsey-Goldman, Rosalind, Reveille, John D., Vila, Luis M., Petri, Michelle, Kimberly, Robert P., Feng, Xuebing, Sun, Lingyun, Shen, Nan, Li, Wei, Lu, Jian-Xin, Wakeland, Edward K., Li, Quan-Zhen, Yang, Wanling, Lau, Yu-Lung, Liu, Fei-Lan, Chang, Deh-Ming, Yu, Chack-Yung, Song, Yeong W., Howe, Hwee Siew, Tsao, Betty P., and Criswell, Lindsey A.

Subjects
Adult, Male, Venous Thrombosis, Hemostasis, Genotype, Middle Aged, Polymorphism, Single Nucleotide, Article, Mixed Function Oxygenases, Asian People, Risk Factors, Case-Control Studies, Vitamin K Epoxide Reductases, Humans, Lupus Erythematosus, Systemic, Female, Genetic Predisposition to Disease
Abstract

The increased risk of thrombosis in systemic lupus erythematosus (SLE) may be partially explained by interrelated genetic pathways for thrombosis and SLE. The present study was undertaken to investigate whether 33 established and novel single-nucleotide polymorphisms (SNPs) in 20 genes involved in hemostasis pathways that have been associated with deep venous thrombosis (DVT) in the general population are risk factors for SLE among Asian subjects.Patients in the discovery cohort were enrolled in 1 of 2 North American SLE cohorts. Patients in the replication cohort were enrolled in 1 of 4 Asian or 2 North American cohorts. We first genotyped 263 Asian patients with SLE and 357 healthy Asian control subjects for 33 SNPs in the discovery phase, and then genotyped 5 SNPs in up to an additional 1,496 patients and 993 controls in the replication phase. Patients were compared to controls for bivariate association with minor alleles. Principal components analysis was used to control for intra-Asian ancestry in the replication cohort.Two genetic variants in the gene VKORC1 were highly significant in both the discovery and replication cohorts: rs9934438 (in the discovery cohort, odds ratio [OR] 2.45, P=2×10(-9); in the replication cohort, OR 1.54, P=4×10(-6)) and rs9923231 (in the discovery cohort, OR 2.40, P=6×10(-9); in the replication cohort, OR 1.53, P=5×10(-6)). These associations were significant in the replication cohort after adjustment for intra-Asian ancestry: for rs9934438, OR 1.34, P=0.0029; for rs9923231, OR 1.34, P=0.0032.Genetic variants in VKORC1, which are involved in vitamin K reduction and associated with DVT, correlate with SLE development in Asian subjects. These results suggest that there may be intersecting genetic pathways for the development of SLE and thrombosis.

Published
2013

50. Complement Components, C3 and C4, and the Metabolic Syndrome

Author

Copenhaver, Melanie, Yu, Chack-Yung, and Hoffman, Robert P.

Abstract

Introduction: Increased systemic inflammation plays a significant role in the development of adult cardiometabolic diseases such as insulin resistance, dyslipidemia, atherosclerosis, and hypertension. The complement system is a part of the innate immune system and plays a key role in the regulation of inflammation. Of particular importance is the activation of complement components C3 and C4. C3 is produced primarily by the liver but is also produced in adipocytes, macrophages and endothelial cells, all of which are present in adipose tissues. Dietary fat and chylomicrons stimulate C3 production. Adipocytes in addition to producing C3 also have receptors for activated C3 and other complement components and thus also respond to as well as produce a target for complement. C3adesArg, also known as acylation stimulation factor, increases adipocyte triglyceride synthesis and release. These physiological effects play a significant role in the development of metabolic syndrome. Epidemiologically, obese adults and non-obese adults with cardiometabolic disease who are not obese have been shown to have increased complement levels. C4 levels also correlate with body mass index. Genetically, specific C3 polymorphisms have been shown to predict future cardiovascular events and. D decreased C4 long gene copy number is associated with increased longevity. Conclusion: Future research is clearly needed to clarify the role of complement in the development of cardiovascular disease and mechanisms for its action. The complement system may provide a new area for intervention in the prevention of cardiometabolic diseases.

Published
2019
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