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2. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop

Author

Creary, Lisa E., Guerra, Sandra G., Chong, Winnie, Brown, Colin J., Turner, Thomas R., Robinson, James, Bultitude, Will P., Mayor, Neema P., Marsh, Steven G.E., Saito, Katsuyuki, Lam, Kevin, Duke, Jamie L., Mosbruger, Timothy L., Ferriola, Deborah, Monos, Dimitrios, Willis, Amanda, Askar, Medhat, Fischer, Gottfried, Saw, Chee Loong, Ragoussis, Jiannis, Petrek, Martin, Serra-Pagés, Carles, Juan, Manel, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Ameen, Reem, Al Shemmari, Salem, Spierings, Eric, Gendzekhadze, Ketevan, Morris, Gerald P., Zhang, Qiuheng, Kashi, Zahra, Hsu, Susan, Gangavarapu, Sridevi, Mallempati, Kalyan C., Yamamoto, Fumiko, Osoegawa, Kazutoyo, Vayntrub, Tamara, Chang, Chia-Jung, Hansen, John A., and Fernández-Viňa, Marcelo A.

Published
2019
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3. Identification of IL12RB1 as a Novel Systemic Sclerosis Susceptibility Locus

Author

López-Isac, Elena, Bossini-Castillo, Lara, Guerra, Sandra G., Denton, Christopher, Fonseca, Carmen, Assassi, Shervin, Zhou, Xiaodong, Mayes, Maureen D., Simeón, Carmen Pilar, Ortego-Centeno, Norberto, Castellví, Iván, Carreira, Patricia, Gorlova, Olga, Beretta, Lorenzo, Santaniello, Alessandro, Lunardi, Claudio, Hesselstrand, Roger, Nordin, Annika, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jörg H. W., Voskuyl, Alexandre E., de Vries-Bouwstra, Jeska, Koeleman, Bobby P., Herrick, Ariane, Worthington, Jane, Radstake, Timothy R. D. J., and Martin, Javier

Published
2014
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8. Analysis of Anti-RNA Polymerase III Antibody-positive Systemic Sclerosis and Altered GPATCH2L and CTNND2 Expression in Scleroderma Renal Crisis

Author

Stern, Edward P., primary, Guerra, Sandra G., additional, Chinque, Harry, additional, Acquaah, Vanessa, additional, González-Serna, David, additional, Ponticos, Markella, additional, Martin, Javier, additional, Ong, Voon H., additional, Khan, Korsa, additional, Nihtyanova, Svetlana I., additional, Harber, Mark, additional, Burns, Aine, additional, Mayes, Maureen D., additional, Assassi, Shervin, additional, Fonseca, Carmen, additional, and Denton, Christopher P., additional

Published
2020
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9. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-Lymphoblastoid cell lines : report from the 17th International HLA and Immunogenetics Workshop

Author

Creary, Lisa E, Guerra, Sandra G, Chong, Winnie, Brown, Colin J, Turner, Thomas R, Robinson, James, Bultitude, Will P, Mayor, Neema P, Marsh, Steven G E, Saito, Katsuyuki, Lam, Kevin, Duke, Jamie L, Mosbruger, Timothy L, Ferriola, Deborah, Monos, Dimitrios, Willis, Amanda, Askar, Medhat, Fischer, Gottfried, Loong Saw, Chee, Ragoussis, Ioannis, Petrek, Martin, Serra-Pagés, Carles, Juan Otero, Manel, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Ameen, Reem, Al Shemmari, Salem, Spierings, Eric, Gendzekhadze, Ketevan, Morris, Gerald P, Zhang, Quiheng, Kashi, Zahra, Hsu, Susan, Gangavarapu, Sridevi, Mallempati, Kalyan C, Yamamoto, Fumiko, Osoegawa, Kazutoyo, Vayntrub, Tamara, Chang, Chia-Jung, Hansen, John A, Fernández-Viňa, Marcelo A, Creary, Lisa E, Guerra, Sandra G, Chong, Winnie, Brown, Colin J, Turner, Thomas R, Robinson, James, Bultitude, Will P, Mayor, Neema P, Marsh, Steven G E, Saito, Katsuyuki, Lam, Kevin, Duke, Jamie L, Mosbruger, Timothy L, Ferriola, Deborah, Monos, Dimitrios, Willis, Amanda, Askar, Medhat, Fischer, Gottfried, Loong Saw, Chee, Ragoussis, Ioannis, Petrek, Martin, Serra-Pagés, Carles, Juan Otero, Manel, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Ameen, Reem, Al Shemmari, Salem, Spierings, Eric, Gendzekhadze, Ketevan, Morris, Gerald P, Zhang, Quiheng, Kashi, Zahra, Hsu, Susan, Gangavarapu, Sridevi, Mallempati, Kalyan C, Yamamoto, Fumiko, Osoegawa, Kazutoyo, Vayntrub, Tamara, Chang, Chia-Jung, Hansen, John A, and Fernández-Viňa, Marcelo A

Published
2019

10. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-Lymphoblastoid cell lines: report from the 17th International HLA and Immunogenetics Workshop

Author

CDL Patiëntenzorg MI, Infection & Immunity, Creary, Lisa E, Guerra, Sandra G, Chong, Winnie, Brown, Colin J, Turner, Thomas R, Robinson, James, Bultitude, Will P, Mayor, Neema P, Marsh, Steven G E, Saito, Katsuyuki, Lam, Kevin, Duke, Jamie L, Mosbruger, Timothy L, Ferriola, Deborah, Monos, Dimitrios, Willis, Amanda, Askar, Medhat, Fischer, Gottfried, Loong Saw, Chee, Ragoussis, Ioannis, Petrek, Martin, Serra-Pagés, Carles, Juan Otero, Manel, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Ameen, Reem, Al Shemmari, Salem, Spierings, Eric, Gendzekhadze, Ketevan, Morris, Gerald P, Zhang, Quiheng, Kashi, Zahra, Hsu, Susan, Gangavarapu, Sridevi, Mallempati, Kalyan C, Yamamoto, Fumiko, Osoegawa, Kazutoyo, Vayntrub, Tamara, Chang, Chia-Jung, Hansen, John A, Fernández-Viňa, Marcelo A, CDL Patiëntenzorg MI, Infection & Immunity, Creary, Lisa E, Guerra, Sandra G, Chong, Winnie, Brown, Colin J, Turner, Thomas R, Robinson, James, Bultitude, Will P, Mayor, Neema P, Marsh, Steven G E, Saito, Katsuyuki, Lam, Kevin, Duke, Jamie L, Mosbruger, Timothy L, Ferriola, Deborah, Monos, Dimitrios, Willis, Amanda, Askar, Medhat, Fischer, Gottfried, Loong Saw, Chee, Ragoussis, Ioannis, Petrek, Martin, Serra-Pagés, Carles, Juan Otero, Manel, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Ameen, Reem, Al Shemmari, Salem, Spierings, Eric, Gendzekhadze, Ketevan, Morris, Gerald P, Zhang, Quiheng, Kashi, Zahra, Hsu, Susan, Gangavarapu, Sridevi, Mallempati, Kalyan C, Yamamoto, Fumiko, Osoegawa, Kazutoyo, Vayntrub, Tamara, Chang, Chia-Jung, Hansen, John A, and Fernández-Viňa, Marcelo A

Published
2019

11. Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis

Author

Dritsoula, Athina, Papaioannou, Ioannis, Guerra, Sandra G., Fonseca, Carmen, Martin, Javier, Herrick, Ariane L., Abraham, David J., Denton, Christopher P., and Ponticos, Markella

Abstract

Objective: NKX2-5 is a homeobox transcription factor that is required for the formation of the heart and vessels during development, with significant postnatal down-regulation and reactivation in disease states, characterized by vascular remodeling. The purpose of this study was to investigate mechanisms that activate NKX2-5 expression in diseased vessels, such as systemic sclerosis (scleroderma; SSc)–associated pulmonary hypertension (PH), and to identify genetic variability that potentially underlies susceptibility to specific vascular complications. Methods: We explored NKX2-5 expression in biopsy samples from patients with SSc-associated PH and in pulmonary artery smooth muscle cells (PASMCs) from patients with scleroderma. Disease-associated putative functional single-nucleotide polymorphisms (SNPs) at the NKX2-5 locus were cloned and studied in reporter gene assays. SNP function was further examined through protein–DNA binding assays, chromatin immunoprecipitation assays, and RNA silencing analyses. Results: Increased NKX2-5 expression in biopsy samples from patients with SSc-associated PH was localized to remodeled vessels and PASMCs. Meta-analysis of 2 independent scleroderma cohorts revealed an association of rs3131917 with scleroderma (P = 0.029). We demonstrated that disease-associated SNPs are located in a novel functional enhancer, which increases NKX2-5 transcriptional activity through the binding of GATA-6, c-Jun, and myocyte-specific enhancer factor 2C. We also characterized an activator/coactivator transcription-enhancer factor domain 1 (TEAD1)/Yes-associated protein 1 (YAP1) complex, which was bound at rs3095870, another functional SNP, with TEAD1 binding the risk allele and activating the transcription of NKX2-5. Conclusion: NKX2-5 is genetically associated with scleroderma, pulmonary hypertension, and fibrosis. Functional evidence revealed a regulatory mechanism that results in NKX2-5 transcriptional activation in PASMCs through the interaction of an upstream promoter and a novel downstream enhancer. This mechanism can act as a model for NKX2-5 activation in cardiovascular disease characterized by vascular remodeling.

Published
2018

14. Contributors

Author

Ackerman, Paula M., Allen, Diane D., Allison, Leslie K., Atrice, Myrtice B., Ann, Joyce, Barredo, Ronald, Basco, Mark David, Bastian, Amy J., Beachy, Joanna C., Bezner, Janet R., Held Bradford, Elissa C., Burke-Doe, Annie, Byl, Nancy N., Campbell, Heather, Chaikin, Laurie Ruth, Chong, Doris, Claudel, Alain, D’Angelo, Elizabeth (Lisa), Dewane, Judith A., Diaz, Deborah S., Duff, Susan V., Embrey, Domenique Hendershot, Fuller, Kenda, Anne Galantino, Mary Lou, Garcia, Miguel, Garcia, William J., Godwin, Ellen M., Gorgon, Edward James, Grajo, Lenin C., Gutierrez, Teresa, Guzman, Julia M., Hammad, Rebecca, Heick, John D., Hiley, Janet A., Horn, Kristin, Hurt, Lauren F., Ikeda, Kristen, Keller, Jennifer L., Kiami, Sheri, Kietrys, David M., King, Laurie A., Lazaro, Rolando T., Lefmann, Sophie, Lopez, Rachel M., MacKay-Lyons, Marilyn, Mancini, Martina, Marinas, Rossniel, McAhren, Rachel, Mclaughlin, Rochelle, Melnick, Marsha, Miranda, Nicole, Moore, Brian M., Morton, Susanne M., Nair, Preeti, Nguyen, Emily, Oza, Preeti Deshpande, Pharo, Elizabeth, Philibert, Darbi Breath, Quiben, Myla U., Reina-Guerra, Sandra G., Roller, Margaret L., Rusher, Angela, Ryerson, Susan D., Salem, Yasser, Sasso-Lance, Elizabeth, Scalise-Smith, Dale, Schulte, Osa Jackson, Senesac, Claudia R., Chiu Shen, Eunice Yu, Smith, Timothy J., Sowers, Kerri, Stayner, Corrie J., Stephens, James, Stockert, Bradley W., Sweeney, Jane K., Szklut, Stacey E., Thompson, Marcia Hall, Truman, Heidi, Tuzzolino, Karla M., Umphred, Darcy A., Uy, Jeric, Vestal, Erin, Vitente, Arvie, Webber, Kristen, and Widener, Gail L.

Published
2020
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15. Influence of TYK2 in systemic sclerosis susceptibility: a new locus in the IL-12 pathway

Author

López Isac, Elena, Campillo Davo, Diana, Bossini Castillo, Lara, Guerra, Sandra G., Assassi, Shervin, Simeón Aznar, Carmen Pilar, Carreira, Patricia, Ortego Centeno, Norberto, García de la Peña, Paloma, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemestaken, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jörg H.V., Voskuyl, Alexandre E., Vries-Bouwstra, Jeska de, Herrick, Ariane L., Worthington, Jane, Denton, Christopher P., Fonseca, Carmen, Radstake, Timothy R.D.J., Mayes, Maureen D., Martín, Javier, Spanish Scleroderma Study Group (SSSG), Espinosa Garriga, Gerard, Rheumatology, AII - Inflammatory diseases, and Universitat de Barcelona

Subjects
0301 basic medicine, Autoimmune diseases, Genome-wide association study, Logistic regression, Genètica mèdica, Human genetics, Medizinische Fakultät, Citoquines, Immunology and Allergy, Missense mutation, Genètica humana, Malalties autoimmunitàries, Medical genetics, Interleukin-12, Connective tissue disease, Cytokines, Signal Transduction, Immunology, Mutation, Missense, Locus (genetics), Systemic Sclerosis, Genetic polymorphisms, Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Rheumatology, Gene Polymorphism, Journal Article, medicine, Humans, Genetic Predisposition to Disease, ddc:610, Allele, TYK2 Kinase, Scleroderma, Systemic, business.industry, Polimorfisme genètic, Case-control study, medicine.disease, Treatment, 030104 developmental biology, Case-Control Studies, Gene polymorphism, business, Genome-Wide Association Study, Meta-Analysis
Abstract

OBJECTIVES: TYK2 is a common genetic risk factor for several autoimmune diseases. This gene encodes a protein kinase involved in interleukin 12 (IL-12) pathway, which is a well-known player in the pathogenesis of systemic sclerosis (SSc). Therefore, we aimed to assess the possible role of this locus in SSc. METHODS: This study comprised a total of 7103 patients with SSc and 12 220 healthy controls of European ancestry from Spain, USA, Germany, the Netherlands, Italy and the UK. Four TYK2 single-nucleotide polymorphisms (V362F (rs2304256), P1104A (rs34536443), I684S (rs12720356) and A928V (rs35018800)) were selected for follow-up based on the results of an Immunochip screening phase of the locus. Association and dependence analyses were performed by the means of logistic regression and conditional logistic regression. Meta-analyses were performed using the inverse variance method. RESULTS: Genome-wide significance level was reached for TYK2 V362F common variant in our pooled analysis ( p=3.08×10(−13), OR=0.83), while the association of P1104A, A928V and I684S rare and low-frequency missense variants remained significant with nominal signals ( p=2.28×10(−3), OR=0.80; p=1.27×10(−3), OR=0.59; p=2.63×10(−5), OR=0.83, respectively). Interestingly, dependence and allelic combination analyses showed that the strong association observed for V362F with SSc, corresponded to a synthetic association dependent on the effect of the three previously mentioned TYK2 missense variants. CONCLUSIONS: We report for the first time the association of TYK2 with SSc and reinforce the relevance of the IL-12 pathway in SSc pathophysiology.

Published
2015

16. Influence of TYK2 in systemic sclerosis susceptibility : a new locus in the IL-12 pathway

Author

López-Isac, Elena, Campillo-Davo, Diana, Bossini-Castillo, Lara, Guerra, Sandra G, Assassi, Shervin, Simeón, Carmen Pilar, Carreira, Patricia, Ortego-Centeno, Norberto, García de la Peña, Paloma, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jörg Hw, Voskuyl, Alexandre E, de Vries-Bouwstra, Jeska, Herrick, Ariane, Worthington, Jane, Denton, Christopher P, Fonseca, Carmen, Radstake, Timothy Rdj, Mayes, Maureen D, Martín, Javier, Spanish Scleroderma Group, López-Isac, Elena, Campillo-Davo, Diana, Bossini-Castillo, Lara, Guerra, Sandra G, Assassi, Shervin, Simeón, Carmen Pilar, Carreira, Patricia, Ortego-Centeno, Norberto, García de la Peña, Paloma, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jörg Hw, Voskuyl, Alexandre E, de Vries-Bouwstra, Jeska, Herrick, Ariane, Worthington, Jane, Denton, Christopher P, Fonseca, Carmen, Radstake, Timothy Rdj, Mayes, Maureen D, Martín, Javier, and Spanish Scleroderma Group

Published
2016

17. Influence of TYK2 in systemic sclerosis susceptibility: a new locus in the IL-12 pathway

Author

Translationele immunologie, Infection & Immunity, López-Isac, Elena, Campillo-Davo, Diana, Bossini-Castillo, Lara, Guerra, Sandra G, Assassi, Shervin, Simeón, Carmen Pilar, Carreira, Patricia, Ortego-Centeno, Norberto, García de la Peña, Paloma, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jörg Hw, Voskuyl, Alexandre E, de Vries-Bouwstra, Jeska, Herrick, Ariane, Worthington, Jane, Denton, Christopher P, Fonseca, Carmen, Radstake, Timothy Rdj, Mayes, Maureen D, Martín, Javier, Spanish Scleroderma Group, Translationele immunologie, Infection & Immunity, López-Isac, Elena, Campillo-Davo, Diana, Bossini-Castillo, Lara, Guerra, Sandra G, Assassi, Shervin, Simeón, Carmen Pilar, Carreira, Patricia, Ortego-Centeno, Norberto, García de la Peña, Paloma, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jörg Hw, Voskuyl, Alexandre E, de Vries-Bouwstra, Jeska, Herrick, Ariane, Worthington, Jane, Denton, Christopher P, Fonseca, Carmen, Radstake, Timothy Rdj, Mayes, Maureen D, Martín, Javier, and Spanish Scleroderma Group

Published
2016

18. TYK2 and Systemic Sclerosis Susceptibility: a New Associated Locus in the IL-12 Pathway

Author

Lopez-Isac, Elena, Bossini-Castillo, Lara, Guerra, Sandra G., Assassi, Shervin, Simeon, Carmen P., Carreira, Patricia E., Ortego-Centeno, Norberto, de la Pena, Paloma Garcia, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jorg H. W., Voskuyl, Alexandre E., de Vries-Bouwstra, J. K., Herrick, Ariane L., Worthington, Jane, Denton, Christopher P., Fonseca, Carmen, Radstake, T. R. D. J., Mayes, Maureen D., Martin, Javier, Lopez-Isac, Elena, Bossini-Castillo, Lara, Guerra, Sandra G., Assassi, Shervin, Simeon, Carmen P., Carreira, Patricia E., Ortego-Centeno, Norberto, de la Pena, Paloma Garcia, Beretta, Lorenzo, Santaniello, Alessandro, Bellocchi, Chiara, Lunardi, Claudio, Moroncini, Gianluca, Gabrielli, Armando, Riemekasten, Gabriela, Witte, Torsten, Hunzelmann, Nicolas, Kreuter, Alexander, Distler, Jorg H. W., Voskuyl, Alexandre E., de Vries-Bouwstra, J. K., Herrick, Ariane L., Worthington, Jane, Denton, Christopher P., Fonseca, Carmen, Radstake, T. R. D. J., Mayes, Maureen D., and Martin, Javier

Published
2015

21. Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4

Author

Manku, Harinder, primary, Langefeld, Carl D., additional, Guerra, Sandra G., additional, Malik, Talat H., additional, Alarcon-Riquelme, Marta, additional, Anaya, Juan-Manuel, additional, Bae, Sang-Cheol, additional, Boackle, Susan A., additional, Brown, Elizabeth E., additional, Criswell, Lindsey A., additional, Freedman, Barry I., additional, Gaffney, Patrick M., additional, Gregersen, Peter A., additional, Guthridge, Joel M., additional, Han, Sang-Hoon, additional, Harley, John B., additional, Jacob, Chaim O., additional, James, Judith A., additional, Kamen, Diane L., additional, Kaufman, Kenneth M., additional, Kelly, Jennifer A., additional, Martin, Javier, additional, Merrill, Joan T., additional, Moser, Kathy L., additional, Niewold, Timothy B., additional, Park, So-Yeon, additional, Pons-Estel, Bernardo A., additional, Sawalha, Amr H., additional, Scofield, R. Hal, additional, Shen, Nan, additional, Stevens, Anne M., additional, Sun, Celi, additional, Gilkeson, Gary S., additional, Edberg, Jeff C., additional, Kimberly, Robert P., additional, Nath, Swapan K., additional, Tsao, Betty P., additional, and Vyse, Tim J., additional

Published
2013
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23. Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4.

Author

Manku, Harinder, Langefeld, Carl D., Guerra, Sandra G., Malik, Talat H., Alarcon-Riquelme, Marta, Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Criswell, Lindsey A., Freedman, Barry I., Gaffney, Patrick M., Gregersen, Peter A., Guthridge, Joel M., Han, Sang-Hoon, Harley, John B., Jacob, Chaim O., James, Judith A., Kamen, Diane L., and Kaufman, Kenneth M.

Subjects
AUTOIMMUNE diseases, LYMPHOCYTES, INFLAMMATION, ATHEROSCLEROSIS, ISCHEMIA
Abstract

We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P = 1.71×10−34, OR = 1.43[1.26–1.60]) and rs1234317-T (P = 1.16×10−28, OR = 1.38[1.24–1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5′ region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5′ risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait. [ABSTRACT FROM AUTHOR]

Published
2013
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24. Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4.

Author

Manku, Harinder, Langefeld, Carl D., Guerra, Sandra G., Malik, Talat H., Alarcon-Riquelme, Marta, Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Criswell, Lindsey A., Freedman, Barry I., Gaffney, Patrick M., Gregersen, Peter A., Guthridge, Joel M., Han, Sang-Hoon, Harley, John B., Jacob, Chaim O., James, Judith A., Kamen, Diane L., and Kaufman, Kenneth M.

Subjects
*AUTOIMMUNE diseases, *LYMPHOCYTES, *INFLAMMATION, *ATHEROSCLEROSIS, *ISCHEMIA
Abstract

We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P = 1.71×10−34, OR = 1.43[1.26–1.60]) and rs1234317-T (P = 1.16×10−28, OR = 1.38[1.24–1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5′ region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5′ risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait. [ABSTRACT FROM AUTHOR]

Published
2013
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25. Influence of TYK2 in systemic sclerosis susceptibility: a new locus in the IL-12 pathway.

Author

López-Isac E, Campillo-Davo D, Bossini-Castillo L, Guerra SG, Assassi S, Simeón CP, Carreira P, Ortego-Centeno N, García de la Peña P, Beretta L, Santaniello A, Bellocchi C, Lunardi C, Moroncini G, Gabrielli A, Riemekasten G, Witte T, Hunzelmann N, Kreuter A, Distler JH, Voskuyl AE, de Vries-Bouwstra J, Herrick A, Worthington J, Denton CP, Fonseca C, Radstake TR, Mayes MD, and Martín J

Subjects
Case-Control Studies, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Mutation, Missense, Scleroderma, Systemic immunology, Signal Transduction genetics, Signal Transduction immunology, Interleukin-12 physiology, Polymorphism, Single Nucleotide, Scleroderma, Systemic genetics, TYK2 Kinase genetics
Abstract

Objectives: TYK2 is a common genetic risk factor for several autoimmune diseases. This gene encodes a protein kinase involved in interleukin 12 (IL-12) pathway, which is a well-known player in the pathogenesis of systemic sclerosis (SSc). Therefore, we aimed to assess the possible role of this locus in SSc., Methods: This study comprised a total of 7103 patients with SSc and 12 220 healthy controls of European ancestry from Spain, USA, Germany, the Netherlands, Italy and the UK. Four TYK2 single-nucleotide polymorphisms (V362F (rs2304256), P1104A (rs34536443), I684S (rs12720356) and A928V (rs35018800)) were selected for follow-up based on the results of an Immunochip screening phase of the locus. Association and dependence analyses were performed by the means of logistic regression and conditional logistic regression. Meta-analyses were performed using the inverse variance method., Results: Genome-wide significance level was reached for TYK2 V362F common variant in our pooled analysis (p=3.08×10(-13), OR=0.83), while the association of P1104A, A928V and I684S rare and low-frequency missense variants remained significant with nominal signals (p=2.28×10(-3), OR=0.80; p=1.27×10(-3), OR=0.59; p=2.63×10(-5), OR=0.83, respectively). Interestingly, dependence and allelic combination analyses showed that the strong association observed for V362F with SSc, corresponded to a synthetic association dependent on the effect of the three previously mentioned TYK2 missense variants., Conclusions: We report for the first time the association of TYK2 with SSc and reinforce the relevance of the IL-12 pathway in SSc pathophysiology., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/)

Published
2016
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