2020: Autophagy-related Risk Loci in Systemic Lupus Erythematous and Sjögren’s Disease

Anna Nagel¹, Bhuwan Khatri¹, Marcin Radziszewski¹, Mandi Wiley¹, Anna Stolarczyk¹, Michelle Joachims¹, Kandice Tessneer¹, Astrid Rasmussen¹, Professor Simon Bowman², Lida Radfar³, Roald Omdal⁴, Marie Wahren-Herlenius⁵, Blake Warner⁶, Torsten Witte⁷, Roland Jonsson⁸, Maureen Rischmueller⁹, Patrick Gaffney¹, Judith James¹, Lars Ronnblom¹⁰, Hal Scofield¹, Xavier Mariette¹¹, Marta Alarcon-Riquelme¹², Fai Ng¹³, Gunnel Nordmark¹⁰, Qing Sun¹⁴, Kwangwoo Kim¹⁵, Sang-Cheol Bae¹⁶, Betty Tsao¹⁴, A. Darise Farris¹ and Christopher Lessard¹, ¹Oklahoma Medical Research Foundation, Oklahoma City, OK, ²University Hospitals Birmingham, Birmingham, United Kingdom, ³University of Oklahoma Health Sciences Center, Oklahoma City, OK, ⁴Stavanger University, Stavanger, Norway, ⁵Karolinska Institutet, Stockholm, Sweden, ⁶National Institutes of Health, Bethesda, MD, ⁷MH-Hannover, Hannover, Germany, ⁸University of Bergen, Bergen, Norway, ⁹RheumatologySA, Adelaide, Australia, ¹⁰Uppsala University, Uppsala, Sweden, ¹¹Paris-Saclay University, Rueil Malmaison, Ile-de-France, France, ¹²Center for Genomics and Oncological Research (GENYO), Granada, Spain, ¹³Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom, ¹⁴Medical University of South Carolina, Charleston, SC, ¹⁵Kyung Hee University, Seoul, Republic of Korea, ¹⁶Hanyang University Medical Center, Seoul, Republic of Korea

Background/Purpose: Dysregulated autophagy is implicated in systemic lupus erythematous (SLE) and Sjögren's disease (SjD), including dysregulated expression of Autophagy-related gene 5 (ATG5) and Autophagy Related 16 Like 2 (ATG16L2) [1-3]. ATG16L2-P2RY2 and PRDM1-ATG5 loci are genome-wide significant (GWS) association in SLE [3,4]. This study aims to identify autophagy-related SLE and SjD risk variants at these loci.

Methods: Bayesian statistics of genome-wide association data (3,762 SLE cases and 6,194 population controls; 3,232 SjD cases and 17,481 population controls) defined a credible SNP set in the PRDM1-ATG5 locus [4,5]. Bioinformatic analyses (RegulomeDB, promoter capture Hi-C, eQTLs, etc.) prioritized SNPs. Luciferase assays tested allele-specific enhancer function in neutrophil-like PLB985 cells and salivary gland A235 cells. PMA/I-induced autophagosome formation was determined by LC3-I to LC3-II conversion and p62 protein aggregation, assessed using Western blotting (WB) and confocal microscopy (CF) in CRISPR/Cas9 knockout (KO) PLB985 cells.

Results: Fine-mapping of PRDM1-ATG5 SLE risk locus identified two SNPs: rs802791 located 11kb 3' from PRDM1 and rs77791277. SjD association peaked at rs526531, positioned 10kb 3' of PRDM1.Bioinformatic analyses prioritized rs533733 and rs526531 as eQTLs for ATG5 in minor salivary gland and neutrophils (p< 5x10^-2 - 5x10^-4). SNP rs533733 showed enrichment of enhancer chromatin marks in monocytes and promoter/TSS marks in neutrophils and is positioned in a topologically associated domain (TAD) 6.4kb 3' of PRDM1 that engages the ATG5 promoter region where rs9373843 (eQTL of ATG5 in neutrophil) is located.
Luciferase assay in PLB985 and A235 cells showed significant decrease in enhancer activity for rs56885418, rs3804333, rs34599047, rs34582442, and rs533733 (only in A235) risk alleles (p< 5x10^-2 - 1x10^-4). Interestingly, rs62422881 risk allele showed increased enhancer activity in A235 cells (p = 9x10^-4). CRISPR/Cas9 KO of ATG5 or ATG16L1 impaired PMA/I-induced autophagosome formation in myeloid-like and differentiated neutrophil-like PLB985 cells. In contrast, loss of ATG16L2 elevated autophagosome formation, suggesting that ATG16L2 may inhibit autophagy.

Conclusion: ATG5, ATG16L1 are critical regulators of autophagosome formation, and ATG16L2 plays a role as a negative regulator of autophagy in myeloid and neutrophil cell lines. Further, non-protein-coding GWS SNPs carried on the PRDM1-ATG5 risk locus may dysregulate autophagy in SLE and SjD by modulating ATG5 expression through chromatin-chromatin interactions with the ATG5 promoter.

References:
1. Byun YS, et al. Scientific Reports 7.1 (2017): 1-11.
2. Colafrancesco S, et al. Arthritis Research & Therapy 22.1 (2020): 1-8.
3. Lessard CJ, et al. Arthritis Rheumatol. 2016; 68(5):1197-1209.
4. Ye Xin, et al. Frontiers in immunology (2018): 2334.
5. Khatri B, et al. Ann Rheum Dis 2020;79(Suppl1):30.

Disclosures: A. Nagel, None; B. Khatri, None; M. Radziszewski, None; M. Wiley, None; A. Stolarczyk, None; M. Joachims, None; K. Tessneer, None; A. Rasmussen, None; P. Bowman, Novartis, AstraZeneca, AbbVie/Abbott, Galapagos; L. Radfar, None; R. Omdal, None; M. Wahren-Herlenius, None; B. Warner, Pfizer, Astellas Bio; T. Witte, AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Chugai, Janssen, Lilly, MSD, Mylan, Novartis, Pfizer, Roche, UCB, Galapagos; R. Jonsson, None; M. Rischmueller, None; P. Gaffney, None; J. James, Bristol-Myers Squibb(BMS), AstraZeneca, Novartis, Progentec Biosciences; L. Ronnblom, None; H. Scofield, None; X. Mariette, AstraZeneca, Bristol Myers Squibb, Galapagos, GSK, Novartis, Pfizer; M. Alarcon-Riquelme, None; F. Ng, None; G. Nordmark, None; Q. Sun, None; K. Kim, None; S. Bae, None; B. Tsao, None; A. Farris, Janssen; C. Lessard, Janssen.