3TR (Taxonomy, Treatment, Targets and Remission) Systemic Lupus Erithematosus Study Protocol

"\- Total volume of blood (on each sampling occasion): 54,5mL.~* Whole blood will be collected in EDTA, 1 tube of 10 mL for DNA (genotyping, methylation arrays; at baseline for genotyping and at EOS visit for methylation arrays). From this, an aliquot of 0.5 mL for baseline cell numbers (cell proportions, CyTOF/flow cytometry) at all time points; capture of leukocytes for blood single cell RNA seq. at all time points and 5 mL for cell stimulations for cell metabolome (C13 to be added), and 1 tube of 10 mL for cell stimulations (CyTOF) at baseline.Tempus tube: 1 tube of 3 mL for RNA, 1 tube of 3mL for whole blood RNA seq.; to be taken at all time points. Plasma will be obtained and aliquoted from these tubes; to be obtained at all time points.~* Serum: 2 tubes of 10 mL without anticoagulant for measurements of anti-drug antibodies, hydroxychloroquine levels, cytokines and analytes, proteome, and autoantibodies; to be taken at all time points."

\- Urine: 100 mL which will be centrifuged. The pellet will be frozen, and the urine supernatant will be aliquoted;

\- Saliva: will be collect in special container for saliva microbiome and methylation;

\- Stool: One sample for microbiome to be sent to the biobank, frozen at -80 °C

"\- Tissue samples for organ-specific manifestations:~* Kidney tissue in lupus nephritis: one small fragment of the fresh kidney biopsy will be stored in a 10% dimethyl sulfoxide (DMSO) solution (slow freezing to -80 °C) until shipment.~* Skin tissue (at selected centers) from inflamed lesion and non-inflamed skin from the gluteal region will be obtained through punch biopsy and stored in a 10% dimethyl sulfoxide (DMSO) solution (slow freezing to -80 °C) until shipment.~* Synovial tissue (at selected centers) will be obtained through ultrasound-directed arthroscopy and stored in a 10% dimethyl sulfoxide (DMSO) solution (slow freezing to -80 °C) until shipment.~* Aspirate from swollen lymph nodes (at selected centers) will be obtained and stored in a 10% dimethyl sulfoxide (DMSO) solution (slow freezing to -80 °C) until shipment."