ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis

Systemic Lupus Erythematosus (SLE) is an autoimmune disease, the pathophysiology and genetic basis of which are incompletely understood. Non-receptor tyrosine kinases (NRTKs) regulate activation, migration, and proliferation of immune cells. We report compound heterozygous deleterious variants in the kinase domains of the non-receptor tyrosine kinases (NRTK) TNK2/ACK1 in one multiplex family and PTK6/BRK in another. Experimental blockade of mouse ACK1 or BRK increases glomerular IgG deposits and circulating autoantibodies in an in vivo SLE model. In addition, we found that the patients’ ACK and BRK variants impair efferocytosis, the MERTK-mediated anti-inflammatory response to apoptotic cells, in human induced Pluripotent Stem Cells (hiPSC)-derived macrophages. Overall, our data suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement We acknowledge the use of the MSKCC Stem Cell Research Core and MSKCC Integrated Genomics Operation Core, funded by the NCI Cancer Center Support Grant (CCSG, P30 CA08748), Cycle for Survival and the Marie-Josee and Henry R. Kravis Center for Molecular Oncology. This work was supported by National Cancer Institute of the US National Institutes of Health (P30CA008748) MSKCC core grant and grants from Ludwig Institute for Cancer Research and NIH/NIAID 1R01AI130345-01 and 5R01AI124349-03 (to FG) NIH/NIAID R01-AI087644 (to MH), NIH/NCI CA58530 (to WTM), NIH/NIAID R01-AI087644 to MH, and Grants-in-Aid for Scientific Research (S) from JSPS (No. 15H05785) and Core Research for Evolutional Science and Technology from Japan Science and Technology Agency (JPMJCR14M4) (to SN). SG was supported by Fellowships from the Fondation pour la Recherche Medicale (DEA20140630127), the European Federation of Internal medicine (EFIM), the Assistance Publique-Hopitaux de Paris (Annee Recherche), and from Institut Servier. NJ was supported by Fellowships from the Arthritis Research UK Fellowship and Graham Hughes Clinical Research Fellowship; her present address: Rheumatology Department, Cambridge University Hospitals, Hills Road, Cambridge, CB2 0QQ, UK. ### 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: The study was approved by the Institutional Review Board of St Thomas' Hospital; Guy's hospital; the King's College London University and the Memorial Sloan Kettering Cancer Center. All subject samples were obtained after written informed consent from patients and their families according to the Helsinki convention (Ethics approval: 11/LO/1433). Ten multiplex families with lupus have been enrolled from Guy's and St Thomas' NHS Foundation Trust and UCL Hospital in London, UK from July 2010 to January 2012, following stringent criteria: a severe phenotype (lupus nephritis for at least 1 patient in each family), and a familial disease (≥2 family members affected in first degree). A total of 24 patients and 17 healthy controls from different ethnic origins (5 African ancestry, 4 Asian ancestry and 1 European ancestry) were selected. The patients each met the Systemic Lupus International Collaborating Clinics (SLICC) classification criteria for SLE2. Lupus nephritis was confirmed by a kidney biopsy classified per the 2004 ISN/RPS (International Society of Nephrology/Renal Pathology Society) classification and verified independently by 2 renal histopathologists. One hundred Mauritian participants were enrolled under the Ethical Clearance provided by the University of Mauritius Research Ethics Committee. Written consent with due signatures was recorded from all participants prior to partaking in the study. Consent was documented on a confidential form in duplicate, with one copy given to the participants for their records. The University of Mauritius Research Ethics Committee approved, sanctioned and fully endorsed this mode of consent recording. The ethnic backgrounds of the 100 Mauritian participants consisted of 26 Creole, 16 Franco-Mauritian, 21 Indo-Mauritian, 2 Sino-Mauritian, 24 other or undisclosed Mauritians. 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 Raw data files for the RNA sequencing analysis have been deposited in the NCBI Gene Expression Omnibus under accession number GEO: GSE118730. Further information and requests may be directed to and will be fulfilled by the corresponding author Frederic Geissmann: geissmaf@mskcc.org.