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153 Biallelic PI4KA mutations Disrupt B Cell Mitochondrial Metabolism and Cause Hypogammaglobulinemia

Program: Oral and Poster Abstracts
Type: Oral
Session: 203. Lymphocytes and Acquired or Congenital Immunodeficiency Disorders: Decoding the Complex Landscape of Human Immunity: Insights From Genetic Mutations to Cellular Heterogeneity
Hematology Disease Topics & Pathways:
Diseases, Immune Disorders, immunodeficiency, immunology, metabolism, Biological Processes
Saturday, December 9, 2023: 2:30 PM

Francesco Saettini, MD1*, Fabiola Guerra2,3,4*, Mario Mauri, PhD5*, Grazia Fazio, PhD6*, Cristina Bugarin, MSc7*, Manuel Quadri2*, Stefano Rebellato4,7*, Clizia Chinello4*, Lisa Pagani4*, Federica Malighetti, MS5*, Luis González Gutiérrez-Solana8*, Vanna Denti4*, Fatemeh Emam Mousavi9,10*, Miquell Raspall-Chaure11*, Martin-Nalda Andrea12*, Estibaliz Barredo13*, David Adams14*, O'Leary Melanie15*, Precilla D’Souza14*, Ellen Macnamara14*, Sergio Rosenzweig16*, Hye Sun Kuehn16*, Jennifer Stoddard16*, Heather C Mefford17*, Giorgia Mandrile18*, Lisa Pavinato19*, Alfredo Brusco19,20*, Patricia Valentina Velez Santamaria21*, Aurora Pujol21*, Vincent Michaud22*, Agathe Roubertie23*, Zoe Nelson24*, Margaret P Adam25*, Bernice Lo26*, Holm Uhlig27,28,29*, Claire G Salter30,31*, Emma Baple31,32*, Andrew H Crosby31*, Sanil Bhatia, PhD33*, Fulvio Magni4*, Giuseppe Paglia4*, Giovanni Cazzaniga, PhD4,34, Rocco Piazza, MD, PhD35*, Andrea Biondi, MD3,4,36 and Matteo Barberis10,37,38*

1Centro Tettamanti, IRCCS San Gerardo dei Tintori, MERATE, Italy
2Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, ITA
3Pediatria, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
4Dipartimento di Medicina e Chirurgia, Università degli Studi Milano-Bicocca, Monza, Italy
5Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ITA
6Tettamanti Research Center, Monza, MB, ITA
7Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
8Hospital Infantil Niño Jesús, Madrid, España or Infant Jesus Children’s Hospital, Madrid, Spain
9Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
10Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom
11Department of Paediatric Neurology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
128. Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Institut de Recerca Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
13Neuropediatric Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
14NIH Undiagnosed Diseases Program, NIH, Bethesda
1511. Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge
16Immunology Service, DLM, NIH Clinical Center, Bethesda
17Division of Genetic Medicine, Department of Paediatrics, University of Washington, Seattle
1814. Genetic Unit and Thalassemia Center, San Luigi Gonzaga University Hospital, Orbassano, Italy
19Department of Medical Sciences, University of Turin, Torino, Italy
20Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
21Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
2218. Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, Aquitaine, France. INSERM U1211, Rare Diseases Laboratory: Genetics and Metabolism, University of Bordeaux, Talence, FRA
2319. Département de Neuropédiatrie, CIC, CHU de Montpellier, INM, Univ Montpellier, INSERM U 1298, Montpellier, France
24Vascular Anomalies Program, Seattle Children’s Hospital, Seattle
25Genetic Medicine, Department of Pediatrics, University of Washington, Seattle
26College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
27Department of Paediatrics, University of Oxford, Oxford, United Kingdom
28Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
29University of Oxford, Oxford, GBR
30Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
31RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
32Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, United Kingdom
33Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical faculty, Heinrich Heine University Düsseldorf, Duesseldorf, Germany
34Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
35Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
36Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori,, Monza, Italy
374. Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
38Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands


Biallelic mutations in the PI4KA gene cause PI4KA-related disorder, a novel condition with neurological (limb spasticity, developmental delay, intellectual disability, seizures, ataxia, nystagmus), gastrointestinal (GI; inflammatory bowel disease [IBD] and multiple intestinal atresia [MIA]) and immunological manifestations. PI4KA encodes phosphatidylinositol (PI) 4-kinase alpha, which catalyzes the first step of phosphoinositide metabolism, phosphorylating PI to PI4P (phosphatidylinositol 4-phosphate). Phosphoinositides collectively have fundamental signalling roles in the plasma membrane and other organelles. We collected comprehensive clinical and laboratory data on 13 patients and performed a multiomic strategy, combining transcriptome, proteome, lipidome and metabolome analyses of three patients' EBV-transformed cell lines to unravel the burden of B cell deficiency in PI4KA-related disorder and define the role of PI4KA in B cells.


Recurrent or severe infections (8/13) and GI (either gastroesophageal reflux disease, MIA or IBD; 6/13) manifestations were frequent. Thyroid disease (either hypo- or hyperthyroidism; 2/13), juvenile idiopathic arthritis (JIA; 1/13) and non-Hodgkin lymphoma (1/13) were reported. At last follow up 11 patients were alive. Ten had either hypogammaglobulinemia, decreased absolute numbers of B cells or decreased B cell subsets. B cell subsets showed increased transitional (4/7), decreased naive (2/7) and decreased switched memory (4/7) B cells. B cell proliferation to T independent mitogens, specifically IgM + CpG or pokeweed, was impaired in 2/2. T-cell (either CD3+, CD4+ or CD8+) lymphopenia was detected in 4/13. T-cell proliferation was maintained in 5/5. NK cells were decreased in 6/13. Ig replacement therapy (4/13) and immunosuppressive treatment (due to JIA [1/13] or IBD [2/13]) were given.

Lipidome analysis showed that different glycerophospholipids profile (i.e., phosphatidylcholine [PC], phosphatidylethanolamines [PE] and phosphatidylserine [PS]) was altered. Metabolome analysis and pathway enrichment analysis confirmed impaired phosphatidylethanolamine biosynthesis and additionally showed altered PIP metabolism and mitochondrial dysfunction (i.e., beta-oxidation of short and long fatty acids). Although the total number of mitochondria was not affected, the mitochondrial activity was significantly reduced. Integration analyses of proteomics, metabolomic and lipidomic data reveals biochemical mechanisms underlying biallelic PI4KA mutation. In particular, dysregulation of metabolic enzymes and pathways involved in glutathione metabolism and tricarboxylic acid cycle was found (Fig. 1). These metabolic impairments ultimately impacted on oxidative phosphorylation, thus disrupting mitochondrial integrity.

Gene set enrichment analysis of differentially expressed genes suggested a skewing towards naive B cell gene sets. Pathways enrichment analysis of transcriptome and proteome showed enrichment in B cell receptor (BCR) pathway and complex, PI3K/mTOR pathway and phospholipids metabolism. PI4P and its metabolite PI(4,5)P2 are determinants of PM identity, specifically controlling cytoskeletal dynamics. Deranged basal actin organization was reverted after anti-IgM stimulation. Hyperactivation of PI3K targets (pAKT473, p4EBP1 and pS6) was observed. Dysregulation of RABGAP1, RAB8B and LAMP3 mRNA prompted us to investigate autophagy. Indeed, LC3 was increased either in the presence or absence of chloroquine, showing that PI4KA mutations enhanced autophagosome formation and inhibited its degradation.


Overall, by altering the production of several key lipids, biallelic PI4KA mutations disrupt B cell metabolism causing mitochondrial dysfunction, mTOR hyperactivation, increased autophagy and deranged cytoskeleton organization. PI4KA-related disorder is a novel syndromic inborn error of immunity causing B cell deficiency and hypogammaglobulinemia.

Figure 1. Integration of proteomics, metabolomics and lipidomics reveals biochemical mechanisms underlying biallelic PI4KA mutations.

Disclosures: Biondi: Agmen: Speakers Bureau; Novartis: Speakers Bureau; Colmmune: Membership on an entity's Board of Directors or advisory committees, Research Funding; Galapagos: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees.

*signifies non-member of ASH