Integrated Multi-omics Analyses of NFKB1 patients B cells points towards an up regulation of NF-κB network inhibitors

The transcription factor NF-κB plays a pivotal role in the adaptive immune response. Pathogenic variants in NFKB1 are the most common genetic etiology of common variable immunodeficiency (CVID). Patients frequently present with impaired terminal B cell differentiation, autoimmunity, and hyperinflammatory immune dysregulation. NF-κB signaling and target gene expression are expected to be dysregulated in NFKB1 -mutated patients. Here, we performed a multi-omics characterization of B cells from a cohort of clinically affected and unaffected NFKB1 mutation carriers. Our analysis identified specific epigenetic dysregulation and gene expression differences on B cells from NFKB1 -mutated patients. We observed an aberrant expression of negative regulators of NF-κB signaling in NFKB1 mutation carriers, which may be a key factor for the autoinflammatory phenotype of these patients. Moreover, our analysis points towards a dysregulation of XBP1 and BCL3 , key players of B cell activation and proliferation at different stages of B cell differentiation. The reduced expression of negative regulators of the NF-κB network is likely to be one of several mechanisms responsible for the aberrant NF-κB signaling, which impairs the maintenance of a normal humoral immune response. In summary, our findings highlight epigenetic and gene expression changes in B cells associated with NFKB1 mutations. Our data give insight into future therapeutic opportunities for patients with NFKB1 (haplo)insufficiency. ### Competing Interest Statement B.G. is employed by the University Hospital Freiburg, Germany. During the course of this study, he received funding for research from following third parties: Deutsche Forschungsgemeinschaft (DFG); the E-rare program of the EU, managed by the DFG; the "Netzwerk Seltener Erkrankungen"of the German Ministry of Education and Research (BMBF); Merck KGaA; Takeda Pharma Vertrieb GmbH & Co. KG; Bristol-Myers Squibb GmbH & Co. KGaA; Novartis Pharma AG, and CSL Behring GmbH. This work was supported in part by the Center for Chronic Immunodeficiency (CCI), Freiburg Center for Rare Diseases (FZSE). During the last 3 years B.G. was an advisor to following companies receiv-ing fees less than 1,000 Euros: Bristol-Myers Squibb Company, Adivo Associates Germany, Pharming Group NV, Epimune GmbH, GigaGen Inc., Atheneum Partners GmbH, and less than 5,000 Euros: UCB Pharma S.A., Roche Pharma AG. * ATAC-seq : assay for Transposase-Accessible Chromatin using sequencing CSR : class switch recombination CVID : Common Variable Immunodeficiency FACS : fluorescence activated cell sorting NFKB1 : Nuclear Factor kappa B subunit 1 PBMCs : Peripheral Blood Mononuclear Cells RRBS : Reduced represented bisulfite sequencing SE : Superenhancers TFBM : transcription factor binding motifs TNF : Tumor Necrosis factor WES : whole exome sequencing WT : wild type