The Lupus Epigenome Relates to Genetics, Transcription and Serological Profiles with Dependency on Molecular Subtypes and Informs Drug Discovery

Objective The heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. Methods We performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. Results In a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel potential drug targets for SLE. Conclusion This study expands the number of genes associated with SLE and reveals novel pathways of disease. The findings reveal possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and the genetic architecture of DNAm in different molecular contexts. Finally, novel targets for drug development were discovered. ### Competing Interest Statement Weiliang Qiu, Cheng Zhu and Srinivas Shankara are employees of SANOFI. All other authors have no competing interests. ### Funding Statement E.C.M and O.C.P have been funded by Grants for the financing of Research, Development and Innovation (R + D + I) in Biomedicine and Health Sciences in Andalusia for the year 2021, project co-financed by 80% by funds of the FEDER Operational Program of Andalusia 2014-2020 (File Number: PECOVID-0072-2020). Funding for the preparation of this manuscript has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement no 115,565, resources composed of the financial contribution from the European Union Seventh Framework Program (FP7/2007-2013) and the EFPIA companies in kind contribution. Funding for this work has been provided by the Lupus Research Alliance/BMS Award to M.E.A.R. and the Diversity Supplement to O.C.P. This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 831434 (3TR). The JU receives support from the European Union Horizon 2020 research and innovation programme and EFPIA. ### 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: An ethical protocol was prepared, reached consensus across all partners, academic and industrial, translated into all participants languages and approved by each of the local ethical committees of the clinical recruitment centers, and all experimental protocols were approved by each of the local committees. All patients recruited to the study were aged 18 years or older and signed an informed consent form, and all methods were carried out in accordance with relevant guidelines and regulations. The study adhered to the standards set by International Conference on Harmonization and Good Clinical Practice, and to the ethical principles that have their origin in the Declaration of Helsinki (2013). The protection of the confidentiality of records that could identify the included individuals is ensured as defined by the EU Directive 2001/20/EC and the applicable national and international requirements relating to data protection in each participating country. For a list of local committees and centers involved in PRECISESADS please see Supplementary Note 1 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 and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The cohort datasets generated and analyzed during the current study are available upon request through ELIXIR platform.