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Raj P, Song R, Zhu H, Riediger L, Jun DJ, Liang C, Arana C, Zhang B, Gao Y, Wakeland BE, Dozmorov I, Zhou J, Kelly JA, Lauwerys BR, Guthridge JM, Olsen NJ, Nath SK, Pasare C, van Oers N, Gilkeson G, Tsao BP, Gaffney PM, Gregersen PK, James JA, Zuo X, Karp DR, Li QZ, Wakeland EK. Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus. Genome Biol 2020; 21:281. [PMID: 33213505 PMCID: PMC7677828 DOI: 10.1186/s13059-020-02184-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a clinically heterogeneous autoimmune disease characterized by the development of anti-nuclear antibodies. Susceptibility to SLE is multifactorial, with a combination of genetic and environmental risk factors contributing to disease development. Like other polygenic diseases, a significant proportion of estimated SLE heritability is not accounted for by common disease alleles analyzed by SNP array-based GWASs. Death-associated protein 1 (DAP1) was implicated as a candidate gene in a previous familial linkage study of SLE and rheumatoid arthritis, but the association has not been explored further. RESULTS We perform deep sequencing across the DAP1 genomic segment in 2032 SLE patients, and healthy controls, and discover a low-frequency functional haplotype strongly associated with SLE risk in multiple ethnicities. We find multiple cis-eQTLs embedded in a risk haplotype that progressively downregulates DAP1 transcription in immune cells. Decreased DAP1 transcription results in reduced DAP1 protein in peripheral blood mononuclear cells, monocytes, and lymphoblastoid cell lines, leading to enhanced autophagic flux in immune cells expressing the DAP1 risk haplotype. Patients with DAP1 risk allele exhibit significantly higher autoantibody titers and altered expression of the immune system, autophagy, and apoptosis pathway transcripts, indicating that the DAP1 risk allele mediates enhanced autophagy, leading to the survival of autoreactive lymphocytes and increased autoantibody. CONCLUSIONS We demonstrate how targeted sequencing captures low-frequency functional risk alleles that are missed by SNP array-based studies. SLE patients with the DAP1 genotype have distinct autoantibody and transcription profiles, supporting the dissection of SLE heterogeneity by genetic analysis.
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Affiliation(s)
- Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Linley Riediger
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Dong-Jae Jun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yajing Gao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Benjamin E Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jinchun Zhou
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Bernard R Lauwerys
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, 1200, Bruxelles, Belgium
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Nancy J Olsen
- Division of Rheumatology, Department of Medicine, Penn State Medical School, State College, PA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Chandrashekhar Pasare
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nicolai van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gary Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Betty P Tsao
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | | | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - David R Karp
- Rheumatic Diseases Division, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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