Deconvolution of whole blood transcriptomics identifies changes in immune cell composition in patients with systemic lupus erythematosus (SLE) treated with mycophenolate mofetil
Authors: Akthar Mumina , Nair Nisha , Carter Lucy M. , Vital Edward M. , Sutton Emily , McHugh Neil ,   British Isles Lupus Assessment Group Biologics Register (BILAG BR) Consortium, Gordon Patrick , Young-Min Steven , Stevens Robert , Prabu Athiveer , Batley Mike , Gendi Nagui , Dasgupta Bhaskar , Khamashta Munther , Hewins Peter , Stratton Richard J. , Chan Antoni , De Lord Denise , King Jon , Dubey Shirish , O’Riordan Edmond , Shaffu Shireen , Laversuch Cathy , Sheeran Thomas P. , Vermaak Erin , Erb Nicola , Pyne Debasish , Jeffrey Rachel , Youssef Hazem , Al-Allaf Wahab , Regan Marian , Kaul Arvind ,   MASTERPLANS Consortium, Payne Katherine , Lunt Mark , Peek Niels , Geifman Nophar , Gavan Sean , Armitt Gillian , Doherty Patrick , Prattley Jennifer , Azadbakht Narges , Papazian Angela , Le Sueur Helen , Farrelly Carmen , Richardson Clare , Shabbir Zunnaira , Hewitt Lauren , Gordon Caroline , Young Stephen , Jayne David , Farewell Vern , Su Li , Pickering Matthew , Lightstone Elizabeth , Gilmore Alyssa , Botto Marina , Vyse Timothy , Morris David Lester , D’Cruz David , Wittmann Miriam , Emery Paul , Beresford Michael , Hedrich Christian , Midgley Angela , Gritzfeld Jenna , Ehrenstein Michael , Isenberg David , Parvaz Mariea , Dunnage Jane , Batchelor Jane , Holland Elaine , Upsall Pauline , Bruce Ian N. , Reynolds John A. 
Published: June 2023

Abstract
Background
Systemic lupus erythematosus (SLE) is a clinically and biologically heterogeneous autoimmune disease. We explored whether the deconvolution of whole blood transcriptomic data could identify differences in predicted immune cell frequency between active SLE patients, and whether these differences are associated with clinical features and/or medication use.

Methods
Patients with active SLE (BILAG-2004 Index) enrolled in the BILAG-Biologics Registry (BILAG-BR), prior to change in therapy, were studied as part of the MASTERPLANS Stratified Medicine consortium. Whole blood RNA-sequencing (RNA-seq) was conducted at enrolment into the registry. Data were deconvoluted using CIBERSORTx. Predicted immune cell frequencies were compared between active and inactive disease in the nine BILAG-2004 domains and according to immunosuppressant use (current and past).

Results
Predicted cell frequency varied between 109 patients. Patients currently, or previously, exposed to mycophenolate mofetil (MMF) had fewer inactivated macrophages (0.435% vs 1.391%, p = 0.001), naïve CD4 T cells (0.961% vs 2.251%, p = 0.002), and regulatory T cells (1.858% vs 3.574%, p = 0.007), as well as a higher proportion of memory activated CD4 T cells (1.826% vs 1.113%, p = 0.015), compared to patients never exposed to MMF. These differences remained statistically significant after adjusting for age, gender, ethnicity, disease duration, renal disease, and corticosteroid use. There were 2607 differentially expressed genes (DEGs) in patients exposed to MMF with over-representation of pathways relating to eosinophil function and erythrocyte development and function. Within CD4 + T cells, there were fewer predicted DEGs related to MMF exposure. No significant differences were observed for the other conventional immunosuppressants nor between patients according disease activity in any of the nine organ domains.

Conclusion
MMF has a significant and persisting effect on the whole blood transcriptomic signature in patients with SLE. This highlights the need to adequately adjust for background medication use in future studies using whole blood transcriptomics.