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1. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits

Author

Lili Liu, Atlas Khan, Elena Sanchez-Rodriguez, Francesca Zanoni, Yifu Li, Nicholas Steers, Olivia Balderes, Junying Zhang, Priya Krithivasan, Robert A. LeDesma, Clara Fischman, Scott J. Hebbring, John B. Harley, Halima Moncrieffe, Leah C. Kottyan, Bahram Namjou-Khales, Theresa L. Walunas, Rachel Knevel, Soumya Raychaudhuri, Elizabeth W. Karlson, Joshua C. Denny, Ian B. Stanaway, David Crosslin, Thomas Rauen, Jürgen Floege, Frank Eitner, Zina Moldoveanu, Colin Reily, Barbora Knoppova, Stacy Hall, Justin T. Sheff, Bruce A. Julian, Robert J. Wyatt, Hitoshi Suzuki, Jingyuan Xie, Nan Chen, Xujie Zhou, Hong Zhang, Lennart Hammarström, Alexander Viktorin, Patrik K. E. Magnusson, Ning Shang, George Hripcsak, Chunhua Weng, Tatjana Rundek, Mitchell S. V. Elkind, Elizabeth C. Oelsner, R. Graham Barr, Iuliana Ionita-Laza, Jan Novak, Ali G. Gharavi, and Krzysztof Kiryluk

Subjects
Science
Abstract

Immunoglobulin A protects against infectious disease and contributes to autoimmune and inflammatory disorders. Here, the authors perform a genome-wide association study for serum IgA levels, identifying 20 genome-wide significant loci, providing new insights into the genetic regulation of IgA levels.

Published
2022
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2. Author Correction: Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits

Author

Lili Liu, Atlas Khan, Elena Sanchez-Rodriguez, Francesca Zanoni, Yifu Li, Nicholas Steers, Olivia Balderes, Junying Zhang, Priya Krithivasan, Robert A. LeDesma, Clara Fischman, Scott J. Hebbring, John B. Harley, Halima Moncrieffe, Leah C. Kottyan, Bahram Namjou-Khales, Theresa L. Walunas, Rachel Knevel, Soumya Raychaudhuri, Elizabeth W. Karlson, Joshua C. Denny, Ian B. Stanaway, David Crosslin, Thomas Rauen, Jürgen Floege, Frank Eitner, Zina Moldoveanu, Colin Reily, Barbora Knoppova, Stacy Hall, Justin T. Sheff, Bruce A. Julian, Robert J. Wyatt, Hitoshi Suzuki, Jingyuan Xie, Nan Chen, Xujie Zhou, Hong Zhang, Lennart Hammarström, Alexander Viktorin, Patrik K. E. Magnusson, Ning Shang, George Hripcsak, Chunhua Weng, Tatjana Rundek, Mitchell S. V. Elkind, Elizabeth C. Oelsner, R. Graham Barr, Iuliana Ionita-Laza, Jan Novak, Ali G. Gharavi, and Krzysztof Kiryluk

Subjects
Science
Published
2023
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3. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits

Author

Halima Moncrieffe, Joshua C. Denny, Soumya Raychaudhuri, R. Graham Barr, Nicholas J Steers, Chunhua Weng, Clara Fischman, John B. Harley, Tatjana Rundek, Scott J. Hebbring, Alexander Viktorin, Ian B. Stanaway, Theresa L. Walunas, Leah C. Kottyan, Ali G. Gharavi, Ning Shang, Nan Chen, Patrik K. E. Magnusson, Krzysztof Kiryluk, Stacy Hall, Lennart Hammarström, George Hripcsak, Atlas Khan, Olivia Balderes, Bruce A. Julian, David R. Crosslin, Thomas Rauen, Colin Reily, Priya Krithivasan, Rachel Knevel, Elizabeth C. Oelsner, Hitoshi Suzuki, Iuliana Ionita-Laza, Frank Eitner, Robert A. LeDesma, Zina Moldoveanu, Hong Zhang, Xu-jie Zhou, Mitchell S.V. Elkind, Francesca Zanoni, Robert J. Wyatt, Elizabeth W. Karlson, Yifu Li, Bahram Namjou-Khales, Jan Novak, Lili Liu, Justin T. Sheff, Jürgen Floege, Elena Sanchez-Rodriguez, Barbora Knoppova, Jun-Ying Zhang, and Jingyuan Xie

Subjects
Immunoglobulin A, Candidate gene, General Physics and Astronomy, Genome-wide association study, Disease, Biology, Kidney, Inflammatory bowel disease, General Biochemistry, Genetics and Molecular Biology, Nephropathy, Mice, Immune system, Antigen, medicine, Humans, Animals, Genetic Predisposition to Disease, Multidisciplinary, Glomerulonephritis, IGA, General Chemistry, Inflammatory Bowel Diseases, medicine.disease, Celiac Disease, Diabetes Mellitus, Type 2, Immunology, biology.protein, Genome-Wide Association Study
Abstract

Nature Communications 13, 6859 (2022). doi:10.1038/s41467-022-34456-6, Published by Nature Publishing Group UK, [London]

Published
2022
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4. GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy

Author

Dmitry Samsonov, Edyta Machura, Dita Maixnerova, Bénédicte Stengel, Domenico Santoro, Loreto Gesualdo, Silvana Savoldi, Raoul D. Nelson, Florian Kronenberg, Hajeong Lee, Licia Peruzzi, Gianluca Caridi, Magdalena Krajewska, Vladimir Tesar, Richard P. Lifton, William E. Smoyer, Erica Salvi, Marcin Zaniew, Magdalena Durlik, Guillaume Canaud, Heather N. Reich, Luisa Bono, Anna Köttgen, Pietro A. Canetta, Maurizio Garozzo, Marco Galliani, Bertrand Fontaine, Thomas Rauen, Renzo Mignani, Maria Szczepańska, Carmelita Marcantoni, Lili Liu, Pietro Ravani, Andrea Magnano, Aftab S. Chishti, Ulf Panzer, Dong Ki Kim, T Baczkowska, Ben Sprangers, Lucia Del Vecchio, Dorota Drozdz, Larisa Prikhodina, John B. Harley, Tomasz Liberek, Monika Pawlak-Bratkowska, Maria Stangou, Ichiei Narita, José Ballarín, Hernán Trimarchi, Barbara Moszczuk, Agnieszka Perkowska-Ptasińska, Maurizio Salvadori, Laureline Berthelot, Francesca Lugani, Katarzyna Siniewicz-Luzeńczyk, Claudia Izzi, Peter K. Gregersen, Isabella Pisani, Michelle N. Rheault, Adele Mitrotti, Ruth J. F. Loos, Xu-jie Zhou, Krzysztof Pawlaczyk, Kai-Uwe Eckardt, Giovanni Frasca, Piergiorgio Messa, Elisabet Ars, Antonio Amoroso, Evangeline Pillebout, Vito Annese, Kresimir Galesic, Tibor Kovács, Hitoshi Suzuki, Krzysztof Kiryluk, Nan Chen, Guido Gembillo, Olivia Balderes, Ciro Esposito, Małgorzata Mizerska-Wasiak, Daniel P. Gale, Sreeja Parameswaran, Michał Florczak, Jai Radhakrishnan, Alicja Dbska-Slizien, Ireneusz Habura, Matthew T. Weirauch, Belong Cho, Guillermo Hidalgo, John D. Mahan, Bruce A. Julian, Andre Franke, Alejandro Quiroga, Rosanna Coppo, Atlas Khan, Murim Choi, Giuliano Boscutti, Izabella Kuzmiuk-Glembin, Nicolas Maillard, Rosaria Polci, Jonathan Barratt, Dario Roccatello, Donna J. Claes, Marie Metzger, Chris Cotsapas, Yasar Caliskan, Raji Sreedharan, Judit Nagy, Francesca Zanoni, Monica Bodria, Dariusz Runowski, Hong Zhang, Magorzata Panczyk-Tomaszewska, Robert J. Wyatt, Claudio Ponticelli, Nikol Mladkova, Przemysław Sikora, Marcin Tkaczyk, Riccardo Magistroni, Gerald B. Appel, Ans van Wijk, Krzysztof Mucha, Barbara Bułło-Piontecka, Jan Novak, Giovanni-Giorgio Battaglia, Anna Materna-Kiryluk, Emanuela Boer, Francesco Scolari, David A. van Heel, Tomasz Hryszko, Keefe Davis, Thilini Abeygunaratne, Simone Sanna-Cherchi, Zbigniew Heleniak, Eimear E. Kenny, Sigrid Lundberg, Al-Akash Samhar, Francesco Londrino, Tetyana L. Vasylyeva, Scott E. Wenderfer, Federico Alberici, Yon Su Kim, Enrico Fiaccadori, Bruno Vogt, Gianluigi Zaza, Stanisaw Niemczyk, Patricia L. Weng, Donatella Spotti, Gian Marco Ghiggeri, Dimitrios Goumenos, Daniel Ranch, David T. Selewski, Monika Miklaszewska, Laila-Yasmin Mani, Jin-Ho Park, Jürgen Floege, Antonello Pani, Renato C. Monteiro, Leszek Paczek, Akchurin Oleh, Maddalena Marasa, Ana Huerta, Sandro Feriozzi, Simona Granata, Andrew S. Bomback, Pascal Schlosser, York Pei, Vittoria Esposito, Mahmoud Kallash, Pasquale Zamboli, Cisca Wijmenga, Daniele Cusi, Elena Sanchez-Rodriguez, Ali G. Gharavi, Francois Berthoux, Shin Goto, Natalia Krata, Leah C. Kottyan, Norbert Kwella, Iuliana Ionita-Laza, Daniel C. Cattran, Cristina Barlassina, Arif B. Ekici, Katarzyna Dyga, Philip A. Kalra, Dorota Kamińska, Jingyuan Xie, Elisa Delbarba, and Jun-Ying Zhang

Subjects
Immune system, Intestinal mucosa, Immunology, medicine, SNP, Genome-wide association study, IRF8, Biology, urologic and male genital diseases, medicine.disease, Inflammatory bowel disease, Kidney disease, Nephropathy
Abstract

IgA nephropathy (IgAN) is a progressive form of kidney disease defined by glomerular deposition of IgA. We performed a genome-wide association study involving 10,146 kidney biopsy-diagnosed IgAN cases and 28,751 matched controls across 17 international cohorts. We defined 30 independent genome-wide significant risk loci jointly explaining 11% of disease risk. A total of 16 loci were novel, including TNFSF4, REL, CD28, CXCL8/PF4V1, LY86, LYN, ANXA3, TNFSF8/15, REEP3, ZMIZ1, RELA, ETS1, IGH, IRF8, TNFRSF13B and FCAR. The SNP-based heritability of IgAN was estimated at 23%. We observed a positive genetic correlation between IgAN and total serum IgA levels, allergy, tonsillectomy, and several infections, and a negative correlation with inflammatory bowel disease. All significant non-HLA loci shared with serum IgA levels had a concordant effect on the risk of IgAN. Moreover, IgAN loci were globally enriched in gene orthologs causing abnormal IgA levels when genetically manipulated in mice. The explained heritability was enriched in the regulatory elements of cells from the immune and hematopoietic systems and intestinal mucosa, providing support for the pathogenic role of extra-renal tissues. The polygenic risk of IgAN was associated with early disease onset, increased lifetime risk of kidney failure, as well as hematuria and several other traits in a phenome-wide association study of 590,515 individuals. In the comprehensive functional annotation analysis of candidate causal genes across genome-wide significant loci, we observed the convergence of biological candidates on a common set of inflammatory signaling pathways and cytokine ligand-receptor pairs, prioritizing potential new drug targets.

Published
2021
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5. GWAS-Based Discoveries in IgA Nephropathy, Membranous Nephropathy, and Steroid-Sensitive Nephrotic Syndrome

Author

Krzysztof Kiryluk, Elena Sanchez-Rodriguez, and Christopher T. Southard

Subjects
Nephrotic Syndrome, Epidemiology, 030232 urology & nephrology, Genome-wide association study, Human leukocyte antigen, Critical Care and Intensive Care Medicine, Glomerulonephritis, Membranous, Nephropathy, 03 medical and health sciences, 0302 clinical medicine, Membranous nephropathy, medicine, Genetic predisposition, Humans, Allele, 030304 developmental biology, Genetics, 0303 health sciences, Transplantation, business.industry, Genomics of Kidney Disease, Glomerulonephritis, Glomerulonephritis, IGA, medicine.disease, Genetic architecture, Nephrology, Steroids, business, Genome-Wide Association Study
Abstract

Over the past decade, genome-wide association studies (GWAS) have emerged as a powerful tool to understand the genetic basis of complex traits in humans. The GWAS approach has been successfully applied to primary glomerular disorders, providing numerous novel insights into the genetic architecture of IgA nephropathy, membranous nephropathy, and steroid-sensitive nephrotic syndrome. IgA nephropathy appears to have a highly complex polygenic architecture, with nearly 20 genome-wide significant loci of small-to-moderate effects discovered to date. In contrast, the genetic susceptibility to membranous nephropathy and steroid-sensitive nephrotic syndrome appears to be driven by a small number of large-effect loci. The MHC locus on chromosome 6p21 is strongly associated with genetic susceptibility to all major types of immune-mediated glomerulopathies. However, a distinct set of classical HLA alleles is associated with each individual disease type, pinpointing to specific immune mechanisms underlying each of these conditions. Additional insights from the discovery of non-HLA risk loci reinforced the role of innate and adaptive immunity in the pathogenesis of these disorders, and highlighted important susceptibility overlaps between glomerular and other autoimmune and inflammatory conditions. Despite these initial successes, much larger GWAS and sequencing studies are still needed for each individual glomerular disease type. Increased power will be critical to comprehensively test for genetic effects across the full spectrum of allelic frequencies, to detect gene-gene and gene-environment interactions, and to potentially improve the performance of polygenic risk predictors. Moreover, the existing studies are limited mostly to European and East Asian populations, stressing the urgency to expand genetic discovery efforts to more diverse populations worldwide.

Published
2020

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