MULTI-OMICS APPROACHES IN B CELL HEMATOLOGICAL DISORDERS: TOWARDS A COMPUTATIONAL MODEL

Inborn errors of immunity (IEI) are a heterogeneous group of rare genetic disorders affecting immune development, regulation, and response. A subset of these conditions, known as syndromic immunodeficiencies, involves multi-organ dysfunction and highlights the critical link between immune signaling and cellular metabolism. This doctoral thesis explores how integrated multi-omics approaches—combining transcriptomics, proteomics, lipidomics, and metabolomics—can elucidate pathogenic mechanisms underlying B-cell dysfunction in IEI, with a particular focus on PI4KA-related disorder. PI4KA encodes phosphatidylinositol 4-kinase alpha, a key enzyme in phosphoinositide metabolism and membrane signaling. Biallelic mutations in PI4KA cause a syndromic neurogastrointestinal disease often accompanied by immunodeficiency. Through the integration of multi-omics datasets and functional analyses in patient-derived EBV-transformed B cells, this work characterizes the molecular consequences of PI4KA deficiency and establishes a mechanistic model linking disrupted lipid metabolism to defective B-cell bioenergetics and immune signaling. Data from 13 patients revealed a consistent immunological phenotype characterized by B-cell lymphopenia, reduced switched memory B cells, and hypogammaglobulinemia, often associated with recurrent infections and autoimmune manifestations. Transcriptomic profiling identified altered expression of genes involved in B-cell differentiation, the mTOR and autophagy pathways, and mitochondrial oxidative metabolism. Proteomic analyses confirmed the downregulation of key components of the B-cell receptor (BCR) signaling complex and enrichment of pathways related to endoplasmic reticulum stress and cytoskeletal remodeling. Lipidomic and metabolomic data demonstrated impaired phosphatidylinositol and glycerophospholipid synthesis, accumulation of tricarboxylic acid (TCA) intermediates, and signs of mitochondrial dysfunction. Integrative computational modeling further indicated that PI4KA deficiency disrupts mitochondrial energy production, redox homeostasis, and NAD(P)+ metabolism, collectively resulting in metabolic stress and hyperactivation of the PI3K/mTOR axis. Functionally, PI4KA-mutated B cells exhibit decreased mitochondrial membrane potential, increased autophagic flux, and aberrant cytoskeleton organization, leading to impaired differentiation and antibody production. These findings define PI4KA-related disorder as a syndromic inborn error of immunity rooted in defective phosphoinositide metabolism and identify metabolic checkpoints that control B-cell homeostasis. The study underscores the power of multi-omics integration for discovering disease mechanisms and highlights computational modeling as a predictive tool for translating omics data into mechanistic insight. Overall, this research provides a systems-level framework connecting lipid signaling, mitochondrial metabolism, and immune regulation. It advances our understanding of B-cell metabolic flexibility and establishes a foundation for future precision medicine approaches targeting metabolic and signaling defects in immunodeficiencies.