Endogenous retroelement activation is implicated in IFN-alpha production and anti-CCP autoantibody generation in early RA

Objectives: Endogenous retroelements (EREs) stimulate type 1 interferon (IFN-I) production but have not been explored as potential interferonogenic triggers in Rheumatoid Arthritis (RA). We investigated ERE expression in early RA (eRA), a period where IFN-I is increased. Methods: ERE expression in DMARD naive eRA whole blood (LINE1, RT-PCR) and bulk synovial tissue (LTR5, LINE1, SINE, Nanostring) was examined alongside IFN-alpha activity. Circulating lymphocyte subsets, including B cell subsets, from eRA patients and early psoriatic arthritis (PsA), were flow cytometrically sorted and similarly examined. Existing established RA and osteoarthritis (OA) synovial single-cell sequencing data was re-interrogated to identify repeat elements, and associations explored. Results: There was significant co-expression of all ERE classes and IFNA in eRA synovial tissue (n=22, p<0.0001) and significant positive associations between whole blood LINE1 expression (n=56) and circulating IFN-protein (p=0.018) and anti-CCP titres (p<0.0001). ERE expression was highest in circulating eRA B cells, particularly naive B cells compared with PsA, with ERE regulation by SAMDH1 implicated and associations with IFNA again observed. Finally, in established RA synovium, LTRs, particularly ERVK, were most increased in RA compared with OA where, for all synovial subsets (monocytes, B cells, T cells and fibroblasts), ERE expression associated with increased IFN-I signalling (p<0.001). Conclusions: Peripheral blood and synovial ERE expression is examined for the first time in eRA highlighting both a potential causal relationship between ERE and IFN-I production and an intriguing association with anti-CCP autoantibodies. This suggests EREs may contribute to RA pathophysiology with implications for future novel therapeutic strategies. ### Competing Interest Statement JDI disclosures speaker/consulting fees from AbbVie, AstraZeneca, Galapagos and Participation on a Data Safety Monitoring Board or Advisory Board for Eli Lilly. AGP discloses research funding from GSK, Pfizer, Gilead, and consulting fees from Inflection Biosciences. FAHC discloses speaker fees from AstraZeneca. The remaining authors have no competing interests. ### Funding Statement This work was funded The Medical Research Council; Academy of Medical Sciences; JGW Patterson Foundation and British Society of Rheumatology. Experimental work at Newcastle University was additionally supported by the Medical Research Council in collaboration with GSK (MR/S50239X/1). Views expressed are the authors and not necessarily those of the National Health Service, the National Institute of Health and Care Research or the Department of Health. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: For the early disease data all patients provided written, informed consent to participate in the study, which was approved by the Northeast Newcastle and North Tyneside 2 Research Ethics Committee (12/NE/0251). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data are available for the purposes of academic research on reasonable request to the corresponding author.