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Suresh S, Shaw AL, Pemberton JG, Scott MK, Harris NJ, Parson MAH, Jenkins ML, Rohilla P, Alvarez-Prats A, Balla T, Yip CK, Burke JE. Molecular basis for plasma membrane recruitment of PI4KA by EFR3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.587787. [PMID: 38746453 PMCID: PMC11092606 DOI: 10.1101/2024.04.30.587787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The lipid kinase phosphatidylinositol 4 kinase III alpha (PI4KIIIa/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric complex with its regulatory proteins TTC7 and FAM126. Fundamental to PI4KA activity is its targeted recruitment to the plasma membrane by the lipidated proteins EFR3A and EFR3B. Here, we report a cryo-EM structure of the C-terminus of EFR3A bound to the PI4KA-TTC7B-FAM126A complex, with extensive validation using both hydrogen deuterium exchange mass spectrometry (HDX-MS), and mutational analysis. The EFR3A C-terminus undergoes a disorder-order transition upon binding to the PI4KA complex, with an unexpected direct interaction with both TTC7B and FAM126A. Complex disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane. Multiple post-translational modifications and disease linked mutations map to this site, providing insight into how PI4KA membrane recruitment can be regulated and disrupted in human disease.
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Affiliation(s)
- Sushant Suresh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Alexandria L Shaw
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- Current address: Department of Biology, Western University, London, ON, N6A 3K7 Canada
| | - Mackenzie K Scott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Matthew AH Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Pooja Rohilla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Alejandro Alvarez-Prats
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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2
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Li S, Han T. Frequent loss of FAM126A expression in colorectal cancer results in selective FAM126B dependency. iScience 2024; 27:109646. [PMID: 38638566 PMCID: PMC11025007 DOI: 10.1016/j.isci.2024.109646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/01/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Most advanced colorectal cancer (CRC) patients cannot benefit from targeted therapy due to lack of actionable targets. By mining data from the DepMap, we identified FAM126B as a specific vulnerability in CRC cell lines exhibiting low FAM126A expression. Employing a combination of genetic perturbation and inducible protein degradation techniques, we demonstrate that FAM126A and FAM126B function in a redundant manner to facilitate the recruitment of PI4KIIIα to the plasma membrane for PI4P synthesis. Examination of data from TCGA and GTEx revealed that over 7% of CRC tumor samples exhibited loss of FAM126A expression, contrasting with uniform FAM126A expression in normal tissues. In both CRC cell lines and tumor samples, promoter hypermethylation correlated with the loss of FAM126A expression, which could be reversed by DNA methylation inhibitors. In conclusion, our study reveals that loss of FAM126A expression results in FAM126B dependency, thus proposing FAM126B as a therapeutic target for CRC treatment.
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Affiliation(s)
- Shuang Li
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ting Han
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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3
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Suresh S, Burke JE. Structural basis for the conserved roles of PI4KA and its regulatory partners and their misregulation in disease. Adv Biol Regul 2023; 90:100996. [PMID: 37979461 DOI: 10.1016/j.jbior.2023.100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
The type III Phosphatidylinositol 4-kinase alpha (PI4KA) is an essential lipid kinase that is a master regulator of phosphoinositide signalling at the plasma membrane (PM). It produces the predominant pool of phosphatidylinositol 4-phosphate (PI4P) at the PM, with this being essential in lipid transport and in regulating the PLC and PI3K signalling pathways. PI4KA is essential and is highly conserved in all eukaryotes. In yeast, the PI4KA ortholog stt4 predominantly exists as a heterodimer with its regulatory partner ypp1. In higher eukaryotes, PI4KA instead primarily forms a heterotrimer with a TTC7 subunit (ortholog of ypp1) and a FAM126 subunit. In all eukaryotes PI4KA is recruited to the plasma membrane by the protein EFR3, which does not directly bind PI4KA, but instead binds to the TTC7/ypp1 regulatory partner. Misregulation in PI4KA or its regulatory partners is involved in myriad human diseases, including loss of function mutations in neurodevelopmental and inflammatory intestinal disorders and gain of function in human cancers. This review describes an in-depth analysis of the structure function of PI4KA and its regulatory partners, with a major focus on comparing and contrasting the differences in regulation of PI4KA throughout evolution.
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Affiliation(s)
- Sushant Suresh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
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4
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Gajardo T, Bernard M, Lô M, Turck E, Leveau C, El-Daher MT, Deslys A, Panikulam P, Menche C, Kurowska M, Le Lay G, Barbier L, Moshous D, Neven B, Farin HF, Fischer A, Ménasché G, de Saint Basile G, Vargas P, Sepulveda FE. Actin dynamics regulation by TTC7A/PI4KIIIα limits DNA damage and cell death under confinement. J Allergy Clin Immunol 2023; 152:949-960. [PMID: 37390900 DOI: 10.1016/j.jaci.2023.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND The actin cytoskeleton has a crucial role in the maintenance of the immune homeostasis by controlling various cellular processes, including cell migration. Mutations in TTC7A have been described as the cause of a primary immunodeficiency associated to different degrees of gut involvement and alterations in the actin cytoskeleton dynamics. OBJECTIVES This study investigates the impact of TTC7A deficiency in immune homeostasis. In particular, the role of the TTC7A/phosphatidylinositol 4 kinase type III α pathway in the control of leukocyte migration and actin dynamics. METHODS Microfabricated devices were leveraged to study cell migration and actin dynamics of murine and patient-derived leukocytes under confinement at the single-cell level. RESULTS We show that TTC7A-deficient lymphocytes exhibit an altered cell migration and reduced capacity to deform through narrow gaps. Mechanistically, TTC7A-deficient phenotype resulted from impaired phosphoinositide signaling, leading to the downregulation of the phosphoinositide 3-kinase/AKT/RHOA regulatory axis and imbalanced actin cytoskeleton dynamics. TTC7A-associated phenotype resulted in impaired cell motility, accumulation of DNA damage, and increased cell death in dense 3-dimensional gels in the presence of chemokines. CONCLUSIONS These results highlight a novel role of TTC7A as a critical regulator of lymphocyte migration. Impairment of this cellular function is likely to contribute to the pathophysiology underlying progressive immunodeficiency in patients.
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Affiliation(s)
- Tania Gajardo
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Mathilde Bernard
- UMR 144, Institut Curie, Paris, France; Institut Pierre-Gilles de Gennes, Paris Sciences and Letters Research University, Paris, France
| | - Marie Lô
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Elisa Turck
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Claire Leveau
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Marie-Thérèse El-Daher
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Alexandre Deslys
- Leukomotion Lab, Université de Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, F-75015 Paris, France
| | - Patricia Panikulam
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Constantin Menche
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Mathieu Kurowska
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Gregoire Le Lay
- UMR 144, Institut Curie, Paris, France; Institut Pierre-Gilles de Gennes, Paris Sciences and Letters Research University, Paris, France
| | - Lucie Barbier
- UMR 144, Institut Curie, Paris, France; Institut Pierre-Gilles de Gennes, Paris Sciences and Letters Research University, Paris, France
| | - Despina Moshous
- Imagine Institute, Université de Paris Cité, Paris, France; Pediatric Immunology Hematology and Rheumatology Department, Université Paris Cité, Paris, France
| | - Bénédicte Neven
- Imagine Institute, Université de Paris Cité, Paris, France; Pediatric Immunology Hematology and Rheumatology Department, Université Paris Cité, Paris, France
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Alain Fischer
- Imagine Institute, Université de Paris Cité, Paris, France; Pediatric Immunology Hematology and Rheumatology Department, Université Paris Cité, Paris, France; Collège de France, Paris, France
| | - Gaël Ménasché
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France
| | - Geneviève de Saint Basile
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France; Centre d'Etude des Déficits Immunitaires, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Pablo Vargas
- UMR 144, Institut Curie, Paris, France; Institut Pierre-Gilles de Gennes, Paris Sciences and Letters Research University, Paris, France; Leukomotion Lab, Université de Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, F-75015 Paris, France.
| | - Fernando E Sepulveda
- Molecular Basis of Altered Immune Homeostasis Laboratory, Institut National de la Santé et de la Recherche Médicale (INSERM) Unite Mixte de Recherche (UMR) 1163, Paris, France; Imagine Institute, Université de Paris Cité, Paris, France; CNRS, Paris, France.
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5
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Barlow-Busch I, Shaw AL, Burke JE. PI4KA and PIKfyve: Essential phosphoinositide signaling enzymes involved in myriad human diseases. Curr Opin Cell Biol 2023; 83:102207. [PMID: 37453227 DOI: 10.1016/j.ceb.2023.102207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Lipid phosphoinositides are master regulators of multiple cellular functions. Misregulation of the activity of the lipid kinases that generate phosphoinositides is causative of human diseases, including cancer, neurodegeneration, developmental disorders, immunodeficiencies, and inflammatory disease. This review will present a summary of recent discoveries on the roles of two phosphoinositide kinases (PI4KA and PIKfyve), which have emerged as targets for therapeutic intervention. Phosphatidylinositol 4-kinase alpha (PI4KA) generates PI4P at the plasma membrane and PIKfyve generates PI(3,5)P2 at endo-lysosomal membranes. Both of these enzymes exist as multi-protein mega complexes that are under myriad levels of regulation. Human disease can be caused by either loss or gain-of-function of these complexes, so understanding how they are regulated will be essential in the design of therapeutics. We will summarize insight into how these enzymes are regulated by their protein-binding partners, with a major focus on the unanswered questions of how their activity is controlled.
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Affiliation(s)
- Isobel Barlow-Busch
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Alexandria L Shaw
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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6
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McPhail JA, Burke JE. Molecular mechanisms of PI4K regulation and their involvement in viral replication. Traffic 2023; 24:131-145. [PMID: 35579216 DOI: 10.1111/tra.12841] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Lipid phosphoinositides are master signaling molecules in eukaryotic cells and key markers of organelle identity. Because of these important roles, the kinases and phosphatases that generate phosphoinositides must be tightly regulated. Viruses can manipulate this regulation, with the Type III phosphatidylinositol 4-kinases (PI4KA and PI4KB) being hijacked by many RNA viruses to mediate their intracellular replication through the formation of phosphatidylinositol 4-phosphate (PI4P)-enriched replication organelles (ROs). Different viruses have evolved unique approaches toward activating PI4K enzymes to form ROs, through both direct binding of PI4Ks and modulation of PI4K accessory proteins. This review will focus on PI4KA and PI4KB and discuss their roles in signaling, functions in membrane trafficking and manipulation by viruses. Our focus will be the molecular basis for how PI4KA and PI4KB are activated by both protein-binding partners and post-translational modifications, with an emphasis on understanding the different molecular mechanisms viruses have evolved to usurp PI4Ks. We will also discuss the chemical tools available to study the role of PI4Ks in viral infection.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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7
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Ensemble-based virtual screening of human PI4KIIIα inhibitors toward the Hepatitis C virus. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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8
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Investigating how intrinsically disordered regions contribute to protein function using HDX-MS. Biochem Soc Trans 2022; 50:1607-1617. [DOI: 10.1042/bst20220206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022]
Abstract
A large amount of the human proteome is composed of highly dynamic regions that do not adopt a single static conformation. These regions are defined as intrinsically disordered, and they are found in a third of all eukaryotic proteins. They play instrumental roles in many aspects of protein signaling, but can be challenging to characterize by biophysical methods. Intriguingly, many of these regions can adopt stable secondary structure upon interaction with a variety of binding partners, including proteins, lipids, and ligands. This review will discuss the application of Hydrogen-deuterium exchange mass spectrometry (HDX-MS) as a powerful biophysical tool that is particularly well suited for structural and functional characterization of intrinsically disordered regions in proteins. A focus will be on the theory of hydrogen exchange, and its practical application to identify disordered regions, as well as characterize how they participate in protein–protein and protein–membrane interfaces. A particular emphasis will be on how HDX-MS data can be presented specifically tailored for analysis of intrinsically disordered regions, as well as the technical aspects that are critical to consider when designing HDX-MS experiments for proteins containing intrinsically disordered regions.
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9
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Burke JE, Triscott J, Emerling BM, Hammond GRV. Beyond PI3Ks: targeting phosphoinositide kinases in disease. Nat Rev Drug Discov 2022; 22:357-386. [PMID: 36376561 PMCID: PMC9663198 DOI: 10.1038/s41573-022-00582-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
Lipid phosphoinositides are master regulators of almost all aspects of a cell's life and death and are generated by the tightly regulated activity of phosphoinositide kinases. Although extensive efforts have focused on drugging class I phosphoinositide 3-kinases (PI3Ks), recent years have revealed opportunities for targeting almost all phosphoinositide kinases in human diseases, including cancer, immunodeficiencies, viral infection and neurodegenerative disease. This has led to widespread efforts in the clinical development of potent and selective inhibitors of phosphoinositide kinases. This Review summarizes our current understanding of the molecular basis for the involvement of phosphoinositide kinases in disease and assesses the preclinical and clinical development of phosphoinositide kinase inhibitors.
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Affiliation(s)
- John E. Burke
- grid.143640.40000 0004 1936 9465Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia Canada
| | - Joanna Triscott
- grid.5734.50000 0001 0726 5157Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Brooke M. Emerling
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys, La Jolla, CA USA
| | - Gerald R. V. Hammond
- grid.21925.3d0000 0004 1936 9000Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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10
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Zhang K, Kang L, Zhang H, Bai L, Pang H, Liu Q, Zhang X, Chen D, Yu H, Lv Y, Gao M, Liu Y, Gai Z, Wang D, Li X. A synonymous mutation in PI4KA impacts the transcription and translation process of gene expression. Front Immunol 2022; 13:987666. [DOI: 10.3389/fimmu.2022.987666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Phosphatidylinositol-4-kinase alpha (PI4KIIIα), encoded by the PI4KA gene, can synthesize phosphatidylinositol-4-phosphate (PI-4-P), which serves as a specific membrane marker and is instrumental in signal transduction. PI4KA mutations can cause autosomal recessive diseases involving neurological, intestinal, and immunological conditions (OMIM:619621, 616531, 619708). We detected sepsis, severe diarrhea, and decreased immunoglobulin levels in one neonate. Two novel compound heterozygous mutations, c.5846T>C (p.Leu1949Pro) and c.3453C>T (p.Gly1151=), were identified in the neonate from the father and the mother, respectively. Sanger sequencing and reverse transcription polymerase chain reaction (RT-PCR) for peripheral blood and minigene splicing assays showed a deletion of five bases (GTGAG) with the c.3453C>T variant at the mRNA level, which could result in a truncated protein (p.Gly1151GlyfsTer17). The missense mutation c.5846T>C (p.Leu1949Pro) kinase activity was measured, and little or no catalytic activity was detected. According to the clinical characteristics and gene mutations with functional verification, our pediatricians diagnosed the child with a combined immunodeficiency and intestinal disorder close to gastrointestinal defects and immunodeficiency syndrome 2 (GIDID2; OMIM: 619708). Medicines such as immunomodulators are prescribed to balance immune dysregulation. This study is the first report of a synonymous mutation in the PI4KA gene that influences alternative splicing. Our findings expand the mutation spectrum leading to PI4KIIIa deficiency-related diseases and provide exact information for genetic counseling.
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11
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Jiang X, Huang X, Zheng G, Jia G, Li Z, Ding X, Lei L, Yuan L, Xu S, Gao N. Targeting PI4KA sensitizes refractory leukemia to chemotherapy by modulating the ERK/AMPK/OXPHOS axis. Am J Cancer Res 2022; 12:6972-6988. [PMID: 36276647 PMCID: PMC9576605 DOI: 10.7150/thno.76563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022] Open
Abstract
Background: The emergence of chemoresistance in leukemia markedly impedes chemotherapeutic efficacy and dictates poor prognosis. Recent evidence has revealed that phosphatidylinositol 4 kinase-IIIα (PI4KA) plays a critical role in tumorigenesis. However, the molecular mechanisms of PI4KA-regulated chemoresistance and leukemogenesis remain largely unknown. Methods: Liquid chromatography-mass spectrometry (LC-MS), patient samples and leukemia xenograft mouse models were used to investigate whether PI4KA was an effective target to overcome chemoresistance in leukemia. Enzyme-linked immunosorbent assay (ELISA) and molecular mechanics/generalized born surface area (MM/GBSA) method were employed to identify cepharanthine (CEP) as a novel PI4KA inhibitor. Results: High expression of PI4KA was observed in drug-resistant leukemia cells or in relapsed leukemia patients, which was correlated with poor overall survival. Depletion of PI4KA sensitized drug-resistant leukemia cells to chemotherapeutic drugs in vitro and in vivo by regulating ERK/AMPK/OXPHOS axis. We also identified cepharanthine (CEP) as a novel PI4KA inhibitor, which could undermine the stability of the PI4KA/TTC7/FAM126 complex, enhancing the sensitivity of drug-resistant leukemia cells to chemotherapeutic drugs in vitro and in vivo. Conclusions: Our study underscored the potential of therapeutic targeting of PI4KA to overcome chemoresistance in leukemia. A combination of the PI4KA inhibitor with classic chemotherapeutic agents could represent a novel therapeutic strategy for the treatment of refractory leukemia.
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Affiliation(s)
- Xiuxing Jiang
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Xiangtao Huang
- Department of Hematology, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Guoxun Zheng
- Shanghai StoneWise AI Technology Co. Ltd. Shanghai 201210, China
| | - Guanfei Jia
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Zhiqiang Li
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Xin Ding
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Ling Lei
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Liang Yuan
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China
| | - Shuangnian Xu
- Department of Hematology, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Ning Gao
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China.,Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China
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12
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Lu J, Dong W, Hammond GR, Hong Y. Hypoxia controls plasma membrane targeting of polarity proteins by dynamic turnover of PI4P and PI(4,5)P2. eLife 2022; 11:79582. [PMID: 35678383 PMCID: PMC9242647 DOI: 10.7554/elife.79582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 4,5-biphosphate (PIP2) are key phosphoinositides that determine the identity of the plasma membrane (PM) and regulate numerous key biological events there. To date, mechanisms regulating the homeostasis and dynamic turnover of PM PI4P and PIP2 in response to various physiological conditions and stresses remain to be fully elucidated. Here, we report that hypoxia in Drosophila induces acute and reversible depletion of PM PI4P and PIP2 that severely disrupts the electrostatic PM targeting of multiple polybasic polarity proteins. Genetically encoded ATP sensors confirmed that hypoxia induces acute and reversible reduction of cellular ATP levels which showed a strong real-time correlation with the levels of PM PI4P and PIP2 in cultured cells. By combining genetic manipulations with quantitative imaging assays we showed that PI4KIIIα, as well as Rbo/EFR3 and TTC7 that are essential for targeting PI4KIIIα to PM, are required for maintaining the homeostasis and dynamic turnover of PM PI4P and PIP2 under normoxia and hypoxia. Our results revealed that in cells challenged by energetic stresses triggered by hypoxia, ATP inhibition and possibly ischemia, dramatic turnover of PM PI4P and PIP2 could have profound impact on many cellular processes including electrostatic PM targeting of numerous polybasic proteins.
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Affiliation(s)
- Juan Lu
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, China [CN]
| | - Wei Dong
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, United States
| | - Gerald R Hammond
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, United States
| | - Yang Hong
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, United States
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13
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Batrouni AG, Bag N, Phan HT, Baird BA, Baskin JM. A palmitoylation code controls PI4KIIIα complex formation and PI(4,5)P2 homeostasis at the plasma membrane. J Cell Sci 2022; 135:272297. [PMID: 34569608 DOI: 10.1242/jcs.259365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα) is the major enzyme responsible for generating phosphatidylinositol (4)-phosphate [PI(4)P] at the plasma membrane. This lipid kinase forms two multicomponent complexes, both including a palmitoylated anchor, EFR3. Whereas both PI4KIIIα complexes support production of PI(4)P, the distinct functions of each complex and mechanisms underlying the interplay between them remain unknown. Here, we present roles for differential palmitoylation patterns within a tri-cysteine motif in EFR3B (Cys5, Cys7 and Cys8) in controlling the distribution of PI4KIIIα between these two complexes at the plasma membrane and corresponding functions in phosphoinositide homeostasis. Spacing of palmitoyl groups within three doubly palmitoylated EFR3B 'lipoforms' affects both interactions between EFR3B and TMEM150A, a transmembrane protein governing formation of a PI4KIIIα complex functioning in rapid phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] resynthesis following phospholipase C signaling, and EFR3B partitioning within liquid-ordered and -disordered regions of the plasma membrane. This work identifies a palmitoylation code involved in controlling protein-protein and protein-lipid interactions that affect a plasma membrane-resident lipid biosynthetic pathway.
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Affiliation(s)
- Alex G Batrouni
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.,Weill Institute for Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Henry T Phan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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14
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de la Cruz L, Riquelme R, Vivas O, Barria A, Jensen JB. Dishevelled coordinates phosphoinositide kinases PI4KIIIα and PIP5KIγ for efficient PtdInsP2 synthesis. J Cell Sci 2022; 135:274231. [PMID: 34982154 PMCID: PMC8919331 DOI: 10.1242/jcs.259145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/14/2021] [Indexed: 02/05/2023] Open
Abstract
Phosphatidylinositol(4,5)-bisphosphate (PtdInsP2) is an important modulator of many cellular processes, and its abundance in the plasma membrane is closely regulated. We examined the hypothesis that members of the Dishevelled scaffolding protein family can bind the lipid kinases phosphatidylinositol 4-kinase (PI4K) and phosphatidylinositol 4-phosphate 5-kinase (PIP5K), facilitating synthesis of PtdInsP2 directly from phosphatidylinositol. We used several assays for PtdInsP2 to examine the cooperative function of phosphoinositide kinases and the Dishevelled protein Dvl3 in the context of two receptor signaling cascades. Simultaneous overexpression of PI4KIIIα (also known as PI4KA) and PIP5KIγ (also known as PIP5K1C) had a synergistic effect on PtdInsP2 synthesis that was recapitulated by overexpression of Dvl3. Increasing the activity of Dvl3 by overexpression increased resting plasma membrane PtdInsP2. Knockdown of Dvl3 reduced resting plasma membrane PtdInsP2 and slowed PtdInsP2 resynthesis following receptor activation. We confirm that Dvl3 promotes coupling of PI4KIIIα and PIP5KIγ and show that this interaction is essential for efficient resynthesis of PtdInsP2 following receptor activation.
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15
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Bassot A, Mina L, Chen J, Simmen T. S-Palmitoylation of calcineurin β1 connects cellular Ca 2+ homeostasis to phosphatidylinositol 4-kinase activity at the plasma membrane. Cell Calcium 2022; 103:102545. [PMID: 35121231 DOI: 10.1016/j.ceca.2022.102545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Arthur Bassot
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G2H7 Canada
| | - Lucas Mina
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G2H7 Canada
| | - Junsheng Chen
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G2H7 Canada
| | - Thomas Simmen
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G2H7 Canada.
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16
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Zhang Q, Zhang B, Lim NKH, Zhang X, Meng S, Nyengaard JR, Huang F, Wang WA. Hyccin/FAM126A deficiency reduces glial enrichment and axonal sheath, which are rescued by overexpression of a plasma membrane-targeting PI4KIIIα in Drosophila. Biochem Biophys Res Commun 2022; 589:71-77. [PMID: 34894559 DOI: 10.1016/j.bbrc.2021.11.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/06/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Hyccin/FAM126A mutations are linked to hypomyelination and congenital cataract disease (HCC), but whether and how Hyccin/FAM126A deficiency causes hypomyelination remains undetermined. This study shows Hyccin/FAM126A expression was necessary for the expression of other components of the PI4KIIIα complex in Drosophila. Knockdown of Hyccin/FAM126A in glia reduced the enrichment of glial cells, disrupted axonal sheaths and visual ability in the visual system, and these defects could be fully rescued by overexpressing either human FAM126A or FAM126B, and partially rescued by overexpressing a plasma membrane-targeting recombinant mouse PI4KIIIα. Additionally, PI4KIIIα knockdown in glia phenocopied Hyccin/FAM126A knockdown, and this was partially rescued by overexpressing the recombinant PI4KIIIα, but not human FAM126A or FAM126B. This study establishes an animal model of HCC and indicates that Hyccin/FAM126A plays an essential role in glial enrichment and axonal sheath in a cell-autonomous manner in the visual system via controlling the expression and stabilization of the PI4KIIIα complex at the plasma membrane.
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Affiliation(s)
- Qichao Zhang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100190, China; Sino-Danish Center for Education and Research, Beijing, 100190, China; Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China; Department of Clinical Medicine, Core Center for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, 8200, Denmark
| | - Baozhu Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nastasia K H Lim
- Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China; Nuo-beta Pharmaceutical Technology (Shanghai) Co. Ltd., Shanghai, 201210, China; Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shiquan Meng
- Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China; Laboratory of Molecular Neurobiology, School of Life Sciences, Shanghai University, Shanghai, 200072, China
| | - Jens R Nyengaard
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100190, China; Sino-Danish Center for Education and Research, Beijing, 100190, China; Department of Clinical Medicine, Core Center for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, 8200, Denmark
| | - Fude Huang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100190, China; Sino-Danish Center for Education and Research, Beijing, 100190, China; Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China; Nuo-beta Pharmaceutical Technology (Shanghai) Co. Ltd., Shanghai, 201210, China.
| | - Wen-An Wang
- Department of Neurology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China; Department of Neurology, Xinhua Hospital Chongming Branch, Shanghai 202150, China.
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17
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Noack LC, Bayle V, Armengot L, Rozier F, Mamode-Cassim A, Stevens FD, Caillaud MC, Munnik T, Mongrand S, Pleskot R, Jaillais Y. A nanodomain-anchored scaffolding complex is required for the function and localization of phosphatidylinositol 4-kinase alpha in plants. THE PLANT CELL 2022; 34:302-332. [PMID: 34010411 PMCID: PMC8774046 DOI: 10.1093/plcell/koab135] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/10/2021] [Indexed: 05/24/2023]
Abstract
Phosphoinositides are low-abundant lipids that participate in the acquisition of membrane identity through their spatiotemporal enrichment in specific compartments. Phosphatidylinositol 4-phosphate (PI4P) accumulates at the plant plasma membrane driving its high electrostatic potential, and thereby facilitating interactions with polybasic regions of proteins. PI4Kα1 has been suggested to produce PI4P at the plasma membrane, but how it is recruited to this compartment is unknown. Here, we pin-point the mechanism that tethers Arabidopsis thaliana phosphatidylinositol 4-kinase alpha1 (PI4Kα1) to the plasma membrane via a nanodomain-anchored scaffolding complex. We established that PI4Kα1 is part of a complex composed of proteins from the NO-POLLEN-GERMINATION, EFR3-OF-PLANTS, and HYCCIN-CONTAINING families. Comprehensive knockout and knockdown strategies revealed that subunits of the PI4Kα1 complex are essential for pollen, embryonic, and post-embryonic development. We further found that the PI4Kα1 complex is immobilized in plasma membrane nanodomains. Using synthetic mis-targeting strategies, we demonstrate that a combination of lipid anchoring and scaffolding localizes PI4Kα1 to the plasma membrane, which is essential for its function. Together, this work opens perspectives on the mechanisms and function of plasma membrane nanopatterning by lipid kinases.
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Affiliation(s)
- Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Frédérique Rozier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Adiilah Mamode-Cassim
- Laboratoire de Biogenèse Membranaire, UMR5200, Université de Bordeaux, CNRS, 33140 Villenave d’Ornon, France
- Agroécologie, AgroSup Dijon, CNRS, INRA, University Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Floris D Stevens
- Research Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1090 GE, The Netherlands
| | - Marie-Cécile Caillaud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Teun Munnik
- Research Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1090 GE, The Netherlands
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, UMR5200, Université de Bordeaux, CNRS, 33140 Villenave d’Ornon, France
| | - Roman Pleskot
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 16502 Prague 6, Czech Republic
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18
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Verdura E, Rodríguez-Palmero A, Vélez-Santamaria V, Planas-Serra L, de la Calle I, Raspall-Chaure M, Roubertie A, Benkirane M, Saettini F, Pavinato L, Mandrile G, O'Leary M, O'Heir E, Barredo E, Chacón A, Michaud V, Goizet C, Ruiz M, Schlüter A, Rouvet I, Sala-Coromina J, Fossati C, Iascone M, Canonico F, Marcé-Grau A, de Souza P, Adams DR, Casasnovas C, Rehm HL, Mefford HC, González Gutierrez-Solana L, Brusco A, Koenig M, Macaya A, Pujol A. Biallelic PI4KA variants cause a novel neurodevelopmental syndrome with hypomyelinating leukodystrophy. Brain 2021; 144:2659-2669. [PMID: 34415322 PMCID: PMC8557332 DOI: 10.1093/brain/awab124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/14/2022] Open
Abstract
Phosphoinositides are lipids that play a critical role in processes such as cellular signalling, ion channel activity and membrane trafficking. When mutated, several genes that encode proteins that participate in the metabolism of these lipids give rise to neurological or developmental phenotypes. PI4KA is a phosphoinositide kinase that is highly expressed in the brain and is essential for life. Here we used whole exome or genome sequencing to identify 10 unrelated patients harbouring biallelic variants in PI4KA that caused a spectrum of conditions ranging from severe global neurodevelopmental delay with hypomyelination and developmental brain abnormalities to pure spastic paraplegia. Some patients presented immunological deficits or genito-urinary abnormalities. Functional analyses by western blotting and immunofluorescence showed decreased PI4KA levels in the patients’ fibroblasts. Immunofluorescence and targeted lipidomics indicated that PI4KA activity was diminished in fibroblasts and peripheral blood mononuclear cells. In conclusion, we report a novel severe metabolic disorder caused by PI4KA malfunction, highlighting the importance of phosphoinositide signalling in human brain development and the myelin sheath.
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Affiliation(s)
- Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Pediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Valentina Vélez-Santamaria
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Neuromuscular Unit, Neurology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Irene de la Calle
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Miquel Raspall-Chaure
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Paediatric Neurology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Agathe Roubertie
- Département de Neuropédiatrie, Hôpital Gui de Chauliac Pôle Neurosciences Tête et Cou, Montpellier, France.,INSERM U1051, Institut des Neurosciences de Montpellier, Montpellier, France
| | - Mehdi Benkirane
- Laboratoire de Génétique de Maladies Rares EA7402, Institut Universitaire de Recherche Clinique, Université de Montpellier, CHU Montpellier, CEDEX 5, 34295 Montpellier, France
| | - Francesco Saettini
- Paediatric Hematology Department, Fondazione MBBM, University of Milano Bicocca, Monza, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy
| | - Giorgia Mandrile
- Thalassemia Centre and Medical Genetics Unit, San Luigi Gonzaga University Hospital, Orbassano, Italy
| | - Melanie O'Leary
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O'Heir
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Estibaliz Barredo
- Neuropediatric Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Almudena Chacón
- Neuropediatric Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Vincent Michaud
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, Aquitaine, France.,INSERM U1211, Rare Diseases Laboratory: Genetics and Metabolism, University of Bordeaux, Talence, Aquitaine, France
| | - Cyril Goizet
- INSERM U1211, Rare Diseases Laboratory: Genetics and Metabolism, University of Bordeaux, Talence, Aquitaine, France.,Reference Center for Rare Neurogenetic Diseases, Department of Medical Genetics, University Hospital Centre Bordeaux Pellegrin Hospital Group, Bordeaux, Aquitaine, France
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabelle Rouvet
- Cellular Biotechnology Department and Biobank, Hospices Civils de Lyon, CHU de Lyon, Lyon, France
| | - Julia Sala-Coromina
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Paediatric Neurology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Chiara Fossati
- Department of Paediatrics, Fondazione MBBM, Monza, Italy
| | - Maria Iascone
- Molecular Genetics Laboratory, USSD LGM, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Francesco Canonico
- Department of Neuroradiology, University of Milan-Bicocca, San Gerardo Hospital, ASST di Monza, Monza, Italy
| | - Anna Marcé-Grau
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Precilla de Souza
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.,Undiagnosed Diseases Program, The Common Fund, NIH, Bethesda, MD, USA
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Neuromuscular Unit, Neurology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Heidi L Rehm
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Paediatrics, University of Washington, Seattle, WA 98195, USA
| | - Luis González Gutierrez-Solana
- Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Pediatric Neurology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy.,Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, 10126 Turin, Italy
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares EA7402, Institut Universitaire de Recherche Clinique, Université de Montpellier, CHU Montpellier, CEDEX 5, 34295 Montpellier, France
| | - Alfons Macaya
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Paediatric Neurology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
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19
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Ulengin-Talkish I, Parson MAH, Jenkins ML, Roy J, Shih AZL, St-Denis N, Gulyas G, Balla T, Gingras AC, Várnai P, Conibear E, Burke JE, Cyert MS. Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane. Nat Commun 2021; 12:6064. [PMID: 34663815 PMCID: PMC8523714 DOI: 10.1038/s41467-021-26326-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/29/2021] [Indexed: 11/25/2022] Open
Abstract
Calcineurin, the conserved protein phosphatase and target of immunosuppressants, is a critical mediator of Ca2+ signaling. Here, to discover calcineurin-regulated processes we examined an understudied isoform, CNAβ1. We show that unlike canonical cytosolic calcineurin, CNAβ1 localizes to the plasma membrane and Golgi due to palmitoylation of its divergent C-terminal tail, which is reversed by the ABHD17A depalmitoylase. Palmitoylation targets CNAβ1 to a distinct set of membrane-associated interactors including the phosphatidylinositol 4-kinase (PI4KA) complex containing EFR3B, PI4KA, TTC7B and FAM126A. Hydrogen-deuterium exchange reveals multiple calcineurin-PI4KA complex contacts, including a calcineurin-binding peptide motif in the disordered tail of FAM126A, which we establish as a calcineurin substrate. Calcineurin inhibitors decrease PI4P production during Gq-coupled GPCR signaling, suggesting that calcineurin dephosphorylates and promotes PI4KA complex activity. In sum, this work discovers a calcineurin-regulated signaling pathway which highlights the PI4KA complex as a regulatory target and reveals that dynamic palmitoylation confers unique localization, substrate specificity and regulation to CNAβ1.
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Affiliation(s)
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexis Z L Shih
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nicole St-Denis
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, Canada
- High-Fidelity Science Communications, Summerside, PE, Canada
| | - Gergo Gulyas
- Section on Molecular Signal Transduction, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Péter Várnai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Elizabeth Conibear
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Department of Biochemistry, The University of British Columbia, Vancouver, BC, Canada
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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20
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Oncogenic KRAS is dependent upon an EFR3A-PI4KA signaling axis for potent tumorigenic activity. Nat Commun 2021; 12:5248. [PMID: 34504076 PMCID: PMC8429657 DOI: 10.1038/s41467-021-25523-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/10/2021] [Indexed: 11/15/2022] Open
Abstract
The HRAS, NRAS, and KRAS genes are collectively mutated in a fifth of all human cancers. These mutations render RAS GTP-bound and active, constitutively binding effector proteins to promote signaling conducive to tumorigenic growth. To further elucidate how RAS oncoproteins signal, we mined RAS interactomes for potential vulnerabilities. Here we identify EFR3A, an adapter protein for the phosphatidylinositol kinase PI4KA, to preferentially bind oncogenic KRAS. Disrupting EFR3A or PI4KA reduces phosphatidylinositol-4-phosphate, phosphatidylserine, and KRAS levels at the plasma membrane, as well as oncogenic signaling and tumorigenesis, phenotypes rescued by tethering PI4KA to the plasma membrane. Finally, we show that a selective PI4KA inhibitor augments the antineoplastic activity of the KRASG12C inhibitor sotorasib, suggesting a clinical path to exploit this pathway. In sum, we have discovered a distinct KRAS signaling axis with actionable therapeutic potential for the treatment of KRAS-mutant cancers. The lipid composition of the plasma membrane defines the localisation of KRAS and its oncogenic function. Here the authors show that EFR3A binds to active KRAS to recruit PI4KA and alters the lipid composition of the plasma membrane to promote KRAS oncogenic signalling and tumorigenesis.
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21
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Myeong J, de la Cruz L, Jung SR, Yeon JH, Suh BC, Koh DS, Hille B. Phosphatidylinositol 4,5-bisphosphate is regenerated by speeding of the PI 4-kinase pathway during long PLC activation. J Gen Physiol 2021; 152:211533. [PMID: 33186442 PMCID: PMC7671494 DOI: 10.1085/jgp.202012627] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023] Open
Abstract
The dynamic metabolism of membrane phosphoinositide lipids involves several cellular compartments including the ER, Golgi, and plasma membrane. There are cycles of phosphorylation and dephosphorylation and of synthesis, transfer, and breakdown. The simplified phosphoinositide cycle comprises synthesis of phosphatidylinositol in the ER, transport, and phosphorylation in the Golgi and plasma membranes to generate phosphatidylinositol 4,5-bisphosphate, followed by receptor-stimulated hydrolysis in the plasma membrane and return of the components to the ER for reassembly. Using probes for specific lipid species, we have followed and analyzed the kinetics of several of these events during stimulation of M1 muscarinic receptors coupled to the G-protein Gq. We show that during long continued agonist action, polyphosphorylated inositol lipids are initially depleted but then regenerate while agonist is still present. Experiments and kinetic modeling reveal that the regeneration results from gradual but massive up-regulation of PI 4-kinase pathways rather than from desensitization of receptors. Golgi pools of phosphatidylinositol 4-phosphate and the lipid kinase PI4KIIIα (PI4KA) contribute to this homeostatic regeneration. This powerful acceleration, which may be at the level of enzyme activity or of precursor and product delivery, reveals strong regulatory controls in the phosphoinositide cycle.
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Affiliation(s)
- Jongyun Myeong
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA
| | - Lizbeth de la Cruz
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA
| | | | - Jun-Hee Yeon
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - Byung-Chang Suh
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - Duk-Su Koh
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA
| | - Bertil Hille
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA
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22
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Salter CG, Cai Y, Lo B, Helman G, Taylor H, McCartney A, Leslie JS, Accogoli A, Zara F, Traverso M, Fasham J, Lees JA, Ferla M, Chioza BA, Wenger O, Scott E, Cross HE, Crawford J, Warshawsky I, Keisling M, Agamanolis D, Melver CW, Cox H, Elawad M, Marton T, Wakeling M, Holzinger D, Tippelt S, Munteanu M, Valcheva D, Deal C, Van Meerbeke S, Vockley CW, Butte MJ, Acar U, van der Knaap MS, Korenke GC, Kotzaeridou U, Balla T, Simons C, Uhlig HH, Crosby AH, De Camilli P, Wolf NI, Baple EL. Biallelic PI4KA variants cause neurological, intestinal and immunological disease. Brain 2021; 144:3597-3610. [PMID: 34415310 PMCID: PMC8719846 DOI: 10.1093/brain/awab313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/14/2021] [Accepted: 08/01/2021] [Indexed: 11/22/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα/PI4KA/OMIM:600286) is a lipid kinase generating phosphatidylinositol 4-phosphate (PI4P), a membrane phospholipid with critical roles in the physiology of multiple cell types. PI4KIIIα’s role in PI4P generation requires its assembly into a heterotetrameric complex with EFR3, TTC7 and FAM126. Sequence alterations in two of these molecular partners, TTC7 (encoded by TTC7A or TCC7B) and FAM126, have been associated with a heterogeneous group of either neurological (FAM126A) or intestinal and immunological (TTC7A) conditions. Here we show that biallelic PI4KA sequence alterations in humans are associated with neurological disease, in particular hypomyelinating leukodystrophy. In addition, affected individuals may present with inflammatory bowel disease, multiple intestinal atresia and combined immunodeficiency. Our cellular, biochemical and structural modelling studies indicate that PI4KA-associated phenotypical outcomes probably stem from impairment of PI4KIIIα-TTC7-FAM126's organ-specific functions, due to defective catalytic activity or altered intra-complex functional interactions. Together, these data define PI4KA gene alteration as a cause of a variable phenotypical spectrum and provide fundamental new insight into the combinatorial biology of the PI4KIIIα-FAM126-TTC7-EFR3 molecular complex.
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Affiliation(s)
- Claire G Salter
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Yiying Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Bernice Lo
- Research Branch, Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Henry Taylor
- Department of surgery and Cancer, Imperial College London, London, UK
| | - Amber McCartney
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | | | | | | | - James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
| | - Joshua A Lees
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Matteo Ferla
- Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - Barry A Chioza
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | | | | | - Harold E Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Joanna Crawford
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia
| | | | | | | | | | - Helen Cox
- West Midlands Clinical Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - Mamoun Elawad
- Department of Gastroenterology, Sidra Medicine, Doha, Qatar
| | - Tamas Marton
- West Midlands Perinatal Pathology, Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Matthew Wakeling
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Dirk Holzinger
- Department of Pediatric Haematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Stephan Tippelt
- Department of Pediatric Haematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institute for Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Christin Deal
- Children's Hospital of Pittsburgh, UPMC, Division of Pediatric Allergy and Immunology, Pittsburgh, USA
| | - Sara Van Meerbeke
- Children's Hospital of Pittsburgh, UPMC, Division of Pediatric Allergy and Immunology, Pittsburgh, USA
| | - Catherine Walsh Vockley
- Children's Hospital of Pittsburgh, UPMC, Division of Genetic and Genomic Medicine, Pittsburgh, USA
| | - Manish J Butte
- Department of Paediatrics, Division of Immunology, Allergy, and Rheumatology, UCLA, Los Angeles, CA, USA
| | - Utkucan Acar
- Department of Paediatrics, Division of Immunology, Allergy, and Rheumatology, UCLA, Los Angeles, CA, USA
| | - Marjo S van der Knaap
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Center, VU University Amsterdam and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - G Christoph Korenke
- Department of Neuropediatrics, University Children's Hospital, Klinikum Oldenburg, 26133 Oldenburg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxfordshire, UK.,Department of Paediatrics, University of Oxford, Oxfordshire, UK.,Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Nicole I Wolf
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Center, VU University Amsterdam and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
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23
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Overduin M, Kervin TA. The phosphoinositide code is read by a plethora of protein domains. Expert Rev Proteomics 2021; 18:483-502. [PMID: 34351250 DOI: 10.1080/14789450.2021.1962302] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The proteins that decipher nucleic acid- and protein-based information are well known, however, those that read membrane-encoded information remain understudied. Here we report 70 different human, microbial and viral protein folds that recognize phosphoinositides (PIs), comprising the readers of a vast membrane code. AREAS COVERED Membrane recognition is best understood for FYVE, PH and PX domains, which exemplify hundreds of PI code readers. Comparable lipid interaction mechanisms may be mediated by kinases, adjacent C1 and C2 domains, trafficking arrestin, GAT and VHS modules, membrane-perturbing annexin, BAR, CHMP, ENTH, HEAT, syntaxin and Tubby helical bundles, multipurpose FERM, EH, MATH, PHD, PDZ, PROPPIN, PTB and SH2 domains, as well as systems that regulate receptors, GTPases and actin filaments, transfer lipids and assembled bacterial and viral particles. EXPERT OPINION The elucidation of how membranes are recognized has extended the genetic code to the PI code. Novel discoveries include PIP-stop and MET-stop residues to which phosphates and metabolites are attached to block phosphatidylinositol phosphate (PIP) recognition, memteins as functional membrane protein apparatuses, and lipidons as lipid "codons" recognized by membrane readers. At least 5% of the human proteome senses such membrane signals and allows eukaryotic organelles and pathogens to operate and replicate.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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24
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Compartmentalization of phosphatidylinositol 4,5-bisphosphate metabolism into plasma membrane liquid-ordered/raft domains. Proc Natl Acad Sci U S A 2021; 118:2025343118. [PMID: 33619111 DOI: 10.1073/pnas.2025343118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Possible segregation of plasma membrane (PM) phosphoinositide metabolism in membrane lipid domains is not fully understood. We exploited two differently lipidated peptide sequences, L10 and S15, to mark liquid-ordered, cholesterol-rich (Lo) and liquid-disordered, cholesterol-poor (Ld) domains of the PM, often called raft and nonraft domains, respectively. Imaging of the fluorescent labels verified that L10 segregated into cholesterol-rich Lo phases of cooled giant plasma-membrane vesicles (GPMVs), whereas S15 and the dye FAST DiI cosegregated into cholesterol-poor Ld phases. The fluorescent protein markers were used as Förster resonance energy transfer (FRET) pairs in intact cells. An increase of homologous FRET between L10 probes showed that depleting membrane cholesterol shrank Lo domains and enlarged Ld domains, whereas a decrease of L10 FRET showed that adding more cholesterol enlarged Lo and shrank Ld Heterologous FRET signals between the lipid domain probes and phosphoinositide marker proteins suggested that phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P 2] and phosphatidylinositol 4-phosphate (PtdIns4P) are present in both Lo and Ld domains. In kinetic analysis, muscarinic-receptor-activated phospholipase C (PLC) depleted PtdIns(4,5)P 2 and PtdIns4P more rapidly and produced diacylglycerol (DAG) more rapidly in Lo than in Ld Further, PtdIns(4,5)P 2 was restored more rapidly in Lo than in Ld Thus destruction and restoration of PtdIns(4,5)P 2 are faster in Lo than in Ld This suggests that Lo is enriched with both the receptor G protein/PLC pathway and the PtdIns/PI4-kinase/PtdIns4P pathway. The significant kinetic differences of lipid depletion and restoration also mean that exchange of lipids between these domains is much slower than free diffusion predicts.
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25
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Batrouni AG, Baskin JM. The chemistry and biology of phosphatidylinositol 4-phosphate at the plasma membrane. Bioorg Med Chem 2021; 40:116190. [PMID: 33965837 DOI: 10.1016/j.bmc.2021.116190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
Phosphoinositides are an important class of anionic, low abundance signaling lipids distributed throughout intracellular membranes. The plasma membrane contains three phosphoinositides: PI(4)P, PI(4,5)P2, and PI(3,4,5)P3. Of these, PI(4)P has remained the most mysterious, despite its characterization in this membrane more than a half-century ago. Fortunately, recent methodological innovations at the chemistry-biology interface have spurred a renaissance of interest in PI(4)P. Here, we describe these new toolsets and how they have revealed novel functions for the plasma membrane PI(4)P pool. We examine high-resolution structural characterization of the plasma membrane PI 4-kinase complex that produces PI(4)P, tools for modulating PI(4)P levels including isoform-selective PI 4-kinase inhibitors, and fluorescent probes for visualizing PI(4)P. Collectively, these chemical and biochemical approaches have revealed insights into how cells regulate synthesis of PI(4)P and its downstream metabolites as well as new roles for plasma membrane PI(4)P in non-vesicular lipid transport, membrane homeostasis and trafficking, and cell signaling pathways.
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Affiliation(s)
- Alex G Batrouni
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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26
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Yu H, Yong W, Gao T, Na M, Zhang Y, Kuguminkiriza IH, Kenechukwu AA, Guo Q, Zhang G, Deng X. Hormesis of low-dose inhibition of pAkt1 (Ser473) followed by a great increase of proline-rich inositol polyphosphate 5-phosphatase (PIPP) level in oocytes. In Vitro Cell Dev Biol Anim 2021; 57:342-349. [PMID: 33537929 DOI: 10.1007/s11626-021-00546-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Hormesis describes a biphasic dose-response relationship generally characterized by a low-dose excitement and a high-dose inhibition. This phenomenon has been observed in the regulation of cell, organ, and organismic level. However, hormesis has not reported in oocytes. In this study, we observed, for the first time, hormetic responses of PIPP levels in oocytes by inhibitor of Akt1 or PKCδ. The expression of PIPP was detected by qPCR, immunofluorescent (IF), and Western Blot (WB). To observe the changes of PIPP levels, we used the inhibitors against pAkt1 (Ser473) or PKCδ, SH-6 or sotrastaurin with low and/or high-dose, treated GV oocytes and cultured for 4 h, respectively. The results showed that PIPP expression was significantly enhanced when oocytes were treated with SH-6 or sotrastaurin 10 μM, but decreased with SH-6 or sotrastaurin 100 μM. We also examined the changes of PIPP levels when GV oocytes were treated with exogenous PtdIns(3,4,5)P3 or LY294002 for 4 h. Our results showed that PIPP level was enhanced much higher under the treatment of 0.1 μM PtdIns(3,4,5)P3 than that of 1 μM PtdIns(3,4,5)P3, which is consistent with the changes of PIPP when oocytes were treated with inhibitors of pAkt1 (Ser473) or PKCδ. In addition, with PIPP siRNA, we detected that down-regulated PIPP may affect distributions of Akt, Cdc25, and pCdc2 (Tyr15). Taken together, these results show that the relationships between PIPP and Akt may follow the principle of hormesis and play a key role during release of diplotene arrest in mouse oocytes.
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Affiliation(s)
- Hang Yu
- Department of Physics and Biophysics, School of Fundamental Sciences, China Medical University (CMU), Shenyang, 110122, People's Republic of China
| | - Wei Yong
- Center Laboratory of the Fourth Affiliated Hospital, China Medical University (CMU), Shenyang, 110032, People's Republic of China
| | - Teng Gao
- Center Laboratory of the Fourth Affiliated Hospital, China Medical University (CMU), Shenyang, 110032, People's Republic of China
| | - Man Na
- Center Laboratory of the Fourth Affiliated Hospital, China Medical University (CMU), Shenyang, 110032, People's Republic of China
| | - Ye Zhang
- Center Laboratory of the Fourth Affiliated Hospital, China Medical University (CMU), Shenyang, 110032, People's Republic of China
| | | | | | - Qingguo Guo
- Department of Biochemistry and Molecular Biology, CMU, Shenyang, China
| | - Guoli Zhang
- Institute of Veterinary Medicine, The Academy of Military Medical Sciences of PLA, Changchun, 130122, Jilin, People's Republic of China
| | - Xin Deng
- Center Laboratory of the Fourth Affiliated Hospital, China Medical University (CMU), Shenyang, 110032, People's Republic of China.
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27
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Balla T. Rushing to maintain plasma membrane phosphoinositide levels. J Gen Physiol 2020; 152:211537. [PMID: 33186443 PMCID: PMC7671492 DOI: 10.1085/jgp.202012793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New findings by Myeong et al. provide further details on how cells maintain their plasma membrane PI(4,5)P2 levels when stimulated via M1 muscarinic receptors
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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28
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The E3 ubiquitin ligase UBR5 interacts with TTC7A and may be associated with very early onset inflammatory bowel disease. Sci Rep 2020; 10:18648. [PMID: 33122718 PMCID: PMC7596066 DOI: 10.1038/s41598-020-73482-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/17/2020] [Indexed: 11/17/2022] Open
Abstract
Very early onset inflammatory bowel disease (VEOIBD) denotes children with onset of IBD before six years of age. A number of monogenic disorders are associated with VEOIBD including tetratricopeptide repeat domain 7A (TTC7A) deficiency. TTC7A-deficiency is characterized by apoptotic colitis in milder cases with severe intestinal atresia and immunodeficiency in cases with complete loss of protein. We used whole exome sequencing in a VEOIBD patient presenting with colitis characterized by colonic apoptosis and no identified known VEOIBD variants, to identify compound heterozygous deleterious variants in the Ubiquitin protein ligase E3 component N-recognin 5 (UBR5) gene. Functional studies demonstrated that UBR5 co-immunoprecipitates with the TTC7A and the UBR5 variants had reduced interaction between UBR5 and TTC7A. Together this implicates UBR5 in regulating TTC7A signaling in VEOIBD patients with apoptotic colitis.
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29
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Zewe JP, Miller AM, Sangappa S, Wills RC, Goulden BD, Hammond GRV. Probing the subcellular distribution of phosphatidylinositol reveals a surprising lack at the plasma membrane. J Cell Biol 2020; 219:133808. [PMID: 32211893 PMCID: PMC7054989 DOI: 10.1083/jcb.201906127] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/14/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
The polyphosphoinositides (PPIn) are central regulatory lipids that direct membrane function in eukaryotic cells. Understanding how their synthesis is regulated is crucial to revealing these lipids’ role in health and disease. PPIn are derived from the major structural lipid, phosphatidylinositol (PI). However, although the distribution of most PPIn has been characterized, the subcellular localization of PI available for PPIn synthesis is not known. Here, we used several orthogonal approaches to map the subcellular distribution of PI, including localizing exogenous fluorescent PI, as well as detecting lipid conversion products of endogenous PI after acute chemogenetic activation of PI-specific phospholipase and 4-kinase. We report that PI is broadly distributed throughout intracellular membrane compartments. However, there is a surprising lack of PI in the plasma membrane compared with the PPIn. These experiments implicate regulation of PI supply to the plasma membrane, as opposed to regulation of PPIn-kinases, as crucial to the control of PPIn synthesis and function at the PM.
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Affiliation(s)
- James P Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - April M Miller
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Sahana Sangappa
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Rachel C Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Brady D Goulden
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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30
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Miyamoto Y, Tanaka M, Ito H, Ooizumi H, Ohbuchi K, Mizoguchi K, Torii T, Yamauchi J. Expression of kinase-deficient MEK2 ameliorates Pelizaeus-Merzbacher disease phenotypes in mice. Biochem Biophys Res Commun 2020; 531:445-451. [PMID: 32800341 DOI: 10.1016/j.bbrc.2020.07.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 10/23/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) is characterized as a congenital hypomyelinating disorder in oligodendrocytes, myelin-forming glial cells in the central nervous system (CNS). The responsible gene of PMD is plp1, whose multiplication, deletion, or mutation is associated with PMD. We previously reported that primary oligodendrocytes overexpressing proteolipid protein 1 (PLP1) do not have the ability to differentiate morphologically, whereas inhibition of mitogen-activated protein kinase/extracellular signal-regulated protein kinase (MAPK/ERK) by its cognate siRNA or chemical inhibitor reverses their undifferentiated phenotypes. Here, we show that oligodendrocyte-specific expression of kinase-deficient dominant-inhibitory mutant (MEK2K101A) of MAPK/ERK kinase 2 (MEK2), as the direct upstream molecule of MAPK/ERK in PMD model mice, promotes myelination in CNS tissues. Expression of MEK2K101A in PMD model mice also improves Rotor-rod test performance, which is often used to assess motor coordination in a rodent model with neuropathy. These results suggest that in PMD model mice, MEK2K101A can ameliorate impairments of myelination and motor function and that the signaling through MAPK/ERK may involve potential therapeutic target molecules of PMD in vivo.
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Affiliation(s)
- Yuki Miyamoto
- Laboratory of Molecular Neuroscience and Neurology, Hachioji, Tokyo, 192-0392, Japan; Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan
| | - Marina Tanaka
- Laboratory of Molecular Neuroscience and Neurology, Hachioji, Tokyo, 192-0392, Japan
| | - Hisanaka Ito
- Laboratory of Bioorganic Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Hiroaki Ooizumi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki, Ibaraki, 200-1192, Japan
| | - Katsuya Ohbuchi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki, Ibaraki, 200-1192, Japan
| | - Kazushige Mizoguchi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki, Ibaraki, 200-1192, Japan
| | - Tomohiro Torii
- Laboratory of Ion Channel Pathophysiology, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
| | - Junji Yamauchi
- Laboratory of Molecular Neuroscience and Neurology, Hachioji, Tokyo, 192-0392, Japan; Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan.
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31
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Takeuchi Y, Tanaka M, Okura N, Fukui Y, Noguchi K, Hayashi Y, Torii T, Ooizumi H, Ohbuchi K, Mizoguchi K, Miyamoto Y, Yamauchi J. Rare Neurologic Disease-Associated Mutations of AIMP1 are Related with Inhibitory Neuronal Differentiation Which is Reversed by Ibuprofen. MEDICINES 2020; 7:medicines7050025. [PMID: 32384815 PMCID: PMC7281511 DOI: 10.3390/medicines7050025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 01/04/2023]
Abstract
Background: Hypomyelinating leukodystrophy 3 (HLD3), previously characterized as a congenital diseases associated with oligodendrocyte myelination, is increasingly regarded as primarily affecting neuronal cells. Methods: We used N1E-115 cells as the neuronal cell model to investigate whether HLD3-associated mutant proteins of cytoplasmic aminoacyl-tRNA synthase complex-interacting multifunctional protein 1 (AIMP1) aggregate in organelles and affect neuronal differentiation. Results: 292CA frame-shift type mutant proteins harboring a two-base (CA) deletion at the 292th nucleotide are mainly localized in the lysosome where they form aggregates. Similar results are observed in mutant proteins harboring the Gln39-to-Ter (Q39X) mutation. Interestingly, the frame-shift mutant-specific peptide specifically interacts with actin to block actin fiber formation. The presence of actin with 292CA mutant proteins, but not with wild type or Q39X ones, in the lysosome is detectable by immunoprecipitation of the lysosome. Furthermore, expression of 292CA or Q39X mutants in cells inhibits neuronal differentiation. Treatment with ibuprofen reverses mutant-mediated inhibitory differentiation as well as the localization in the lysosome. Conclusions: These results not only explain the cell pathological mechanisms inhibiting phenotype differentiation in cells expressing HLD3-associated mutants but also identify the first chemical that restores such cells in vitro.
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Affiliation(s)
- Yu Takeuchi
- Laboratory of Molecular Neuroscience and Neurology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (Y.T.); (M.T.); (N.O.); (Y.F.); (Y.M.)
| | - Marina Tanaka
- Laboratory of Molecular Neuroscience and Neurology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (Y.T.); (M.T.); (N.O.); (Y.F.); (Y.M.)
| | - Nanako Okura
- Laboratory of Molecular Neuroscience and Neurology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (Y.T.); (M.T.); (N.O.); (Y.F.); (Y.M.)
| | - Yasuyuki Fukui
- Laboratory of Molecular Neuroscience and Neurology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (Y.T.); (M.T.); (N.O.); (Y.F.); (Y.M.)
| | - Ko Noguchi
- Laboratory of Applied Ecology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan;
| | - Yoshihiro Hayashi
- Laboratory of Oncology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan;
| | - Tomohiro Torii
- Laboratory of Ion Channel Pathophysiology, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan;
| | - Hiroaki Ooizumi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki, Ibaraki 200-1192, Japan; (H.O.); (K.O.); (K.M.)
| | - Katsuya Ohbuchi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki, Ibaraki 200-1192, Japan; (H.O.); (K.O.); (K.M.)
| | - Kazushige Mizoguchi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki, Ibaraki 200-1192, Japan; (H.O.); (K.O.); (K.M.)
| | - Yuki Miyamoto
- Laboratory of Molecular Neuroscience and Neurology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (Y.T.); (M.T.); (N.O.); (Y.F.); (Y.M.)
- Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Setagaya, Tokyo 157-8535, Japan
| | - Junji Yamauchi
- Laboratory of Molecular Neuroscience and Neurology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (Y.T.); (M.T.); (N.O.); (Y.F.); (Y.M.)
- Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Setagaya, Tokyo 157-8535, Japan
- Correspondence: ; Tel.: (+81)-42-676-7164
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Xu C, Wan Z, Shaheen S, Wang J, Yang Z, Liu W. A PI(4,5)P2-derived "gasoline engine model" for the sustained B cell receptor activation. Immunol Rev 2020; 291:75-90. [PMID: 31402506 DOI: 10.1111/imr.12775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
To efficiently initiate activation responses against rare ligands in the microenvironment, lymphocytes employ sophisticated mechanisms involving signaling amplification. Recently, a signaling amplification mechanism initiated from phosphatidylinositol (PI) 4, 5-biphosphate [PI(4,5)P2] hydrolysis and synthesis for sustained B cell activation has been reported. Antigen and B cell receptor (BCR) recognition triggered the prompt reduction of PI(4,5)P2 density within the BCR microclusters, which led to the positive feedback for the synthesis of PI(4,5)P2 outside of the BCR microclusters. At single molecule level, the diffusion of PI(4,5)P2 was slow, allowing for the maintenance of a PI(4,5)P2 density gradient between the inside and outside of the BCR microclusters and the persistent supply of PI(4,5)P2 from outside to inside of the BCR microclusters. Here, we review studies that have contributed to uncovering the molecular mechanisms of PI(4,5)P2-derived signaling amplification model. Based on these studies, we proposed a "gasoline engine model" in which the activation of B cell signaling inside the microclusters is similar to the working principle of burning gasoline within the engine chamber of a gasoline engine. We also discuss the evidences showing the potential universality of this model and future prospects.
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Affiliation(s)
- Chenguang Xu
- Center for Life Sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Zhengpeng Wan
- Center for Life Sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Samina Shaheen
- Center for Life Sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Jing Wang
- Center for Life Sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Zhiyong Yang
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California
| | - Wanli Liu
- Center for Life Sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
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33
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Zhao Y, Diacou A, Johnston HR, Musfee FI, McDonald-McGinn DM, McGinn D, Crowley TB, Repetto GM, Swillen A, Breckpot J, Vermeesch JR, Kates WR, Digilio MC, Unolt M, Marino B, Pontillo M, Armando M, Di Fabio F, Vicari S, van den Bree M, Moss H, Owen MJ, Murphy KC, Murphy CM, Murphy D, Schoch K, Shashi V, Tassone F, Simon TJ, Shprintzen RJ, Campbell L, Philip N, Heine-Suñer D, García-Miñaúr S, Fernández L, Bearden CE, Vingerhoets C, van Amelsvoort T, Eliez S, Schneider M, Vorstman JAS, Gothelf D, Zackai E, Agopian AJ, Gur RE, Bassett AS, Emanuel BS, Goldmuntz E, Mitchell LE, Wang T, Morrow BE. Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects. Am J Hum Genet 2020; 106:26-40. [PMID: 31870554 PMCID: PMC7077921 DOI: 10.1016/j.ajhg.2019.11.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) results from non-allelic homologous recombination between low-copy repeats termed LCR22. About 60%-70% of individuals with the typical 3 megabase (Mb) deletion from LCR22A-D have congenital heart disease, mostly of the conotruncal type (CTD), whereas others have normal cardiac anatomy. In this study, we tested whether variants in the hemizygous LCR22A-D region are associated with risk for CTDs on the basis of the sequence of the 22q11.2 region from 1,053 22q11.2DS individuals. We found a significant association (FDR p < 0.05) of the CTD subset with 62 common variants in a single linkage disequilibrium (LD) block in a 350 kb interval harboring CRKL. A total of 45 of the 62 variants were associated with increased risk for CTDs (odds ratio [OR) ranges: 1.64-4.75). Associations of four variants were replicated in a meta-analysis of three genome-wide association studies of CTDs in affected individuals without 22q11.2DS. One of the replicated variants, rs178252, is located in an open chromatin region and resides in the double-elite enhancer, GH22J020947, that is predicted to regulate CRKL (CRK-like proto-oncogene, cytoplasmic adaptor) expression. Approximately 23% of patients with nested LCR22C-D deletions have CTDs, and inactivation of Crkl in mice causes CTDs, thus implicating this gene as a modifier. Rs178252 and rs6004160 are expression quantitative trait loci (eQTLs) of CRKL. Furthermore, set-based tests identified an enhancer that is predicted to target CRKL and is significantly associated with CTD risk (GH22J020946, sequence kernal association test (SKAT) p = 7.21 × 10-5) in the 22q11.2DS cohort. These findings suggest that variance in CTD penetrance in the 22q11.2DS population can be explained in part by variants affecting CRKL expression.
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Affiliation(s)
- Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alexander Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Fadi I Musfee
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas 77225, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Daniel McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - T Blaine Crowley
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Gabriela M Repetto
- Center for Genetics and Genomics, Facultad de Medicina Clinica Alemana-Universidad del Desarrollo, Santiago 7710162, Chile
| | - Ann Swillen
- Center for Human Genetics, University of Leuven (KU Leuven), Leuven 3000, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University of Leuven (KU Leuven), Leuven 3000, Belgium
| | - Joris R Vermeesch
- Center for Human Genetics, University of Leuven (KU Leuven), Leuven 3000, Belgium
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY 13202, USA; Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY 13202, USA
| | - M Cristina Digilio
- Department of Medical Genetics, Bambino Gesù Hospital, Rome 00165, Italy
| | - Marta Unolt
- Department of Medical Genetics, Bambino Gesù Hospital, Rome 00165, Italy; Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome 00185, Italy
| | - Bruno Marino
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome 00185, Italy
| | - Maria Pontillo
- Department of Neuroscience, Bambino Gesù Hospital, Rome 00165, Italy
| | - Marco Armando
- Department of Neuroscience, Bambino Gesù Hospital, Rome 00165, Italy; Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva 1211, Switzerland
| | - Fabio Di Fabio
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome 00185, Italy
| | - Stefano Vicari
- Department of Neuroscience, Bambino Gesù Hospital, Rome 00165, Italy; Department of Psychiatry, Catholic University, Rome 00153, Italy
| | - Marianne van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales CF24 4HQ, UK
| | - Hayley Moss
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales CF24 4HQ, UK
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales CF24 4HQ, UK
| | - Kieran C Murphy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin 505095, Ireland
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, King's College London, Institute of Psychiatry, Psychology, and Neuroscience, London SE5 8AF, UK; Behavioural and Developmental Psychiatry Clinical Academic Group, Behavioural Genetics Clinic, National Adult Autism and ADHD Service, South London and Maudsley Foundation National Health Service Trust, London SE5 8AZ, UK
| | - Declan Murphy
- Department of Forensic and Neurodevelopmental Sciences, King's College London, Institute of Psychiatry, Psychology, and Neuroscience, London SE5 8AF, UK; Behavioural and Developmental Psychiatry Clinical Academic Group, Behavioural Genetics Clinic, National Adult Autism and ADHD Service, South London and Maudsley Foundation National Health Service Trust, London SE5 8AZ, UK
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Flora Tassone
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Davis, CA 95817, USA
| | - Tony J Simon
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Davis, CA 95817, USA
| | | | - Linda Campbell
- School of Psychology, University of Newcastle, Newcastle 2258, Australia
| | - Nicole Philip
- Department of Medical Genetics, Aix-Marseille University, Marseille 13284, France
| | - Damian Heine-Suñer
- Genomics of Health and Unit of Molecular Diagnosis and Clinical Genetics, Son Espases University Hospital, Balearic Islands Health Research Institute, Palma de Mallorca 07120, Spain
| | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics, University Hospital La Paz, Madrid 28046, Spain
| | - Luis Fernández
- Institute of Medical and Molecular Genetics, University Hospital La Paz, Madrid 28046, Spain
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Claudia Vingerhoets
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, 6200 MD, the Netherlands
| | - Therese van Amelsvoort
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, 6200 MD, the Netherlands
| | - Stephan Eliez
- Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva 1211, Switzerland
| | - Maude Schneider
- Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva 1211, Switzerland
| | - Jacob A S Vorstman
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada; Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, M5S 1A1, Canada; Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, 3584 CG, the Netherlands
| | - Doron Gothelf
- The Child Psychiatry Unit, Edmond and Lily Sapfra Children's Hospital, Sackler Faculty of Medicine, Tel Aviv University and Sheba Medical Center, Tel Aviv, 52621, Israel
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - A J Agopian
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas 77225, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine of the University of Pennsylvania Philadelphia, PA 19104, USA; Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anne S Bassett
- Dalglish Family 22q Clinic, Clinical Genetics Research Program, Toronto M5T 1L8, Ontario Canada; Toronto General Hospital, Centre for Addiction and Mental Health, Toronto M5T 1L8, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto M5T 1L8, Ontario, Canada
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas 77225, USA
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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McPhail JA, Burke JE. Drugging the Phosphoinositide 3-Kinase (PI3K) and Phosphatidylinositol 4-Kinase (PI4K) Family of Enzymes for Treatment of Cancer, Immune Disorders, and Viral/Parasitic Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1274:203-222. [DOI: 10.1007/978-3-030-50621-6_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Pemberton JG, Kim YJ, Balla T. Integrated regulation of the phosphatidylinositol cycle and phosphoinositide-driven lipid transport at ER-PM contact sites. Traffic 2019; 21:200-219. [PMID: 31650663 DOI: 10.1111/tra.12709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Abstract
Among the structural phospholipids that form the bulk of eukaryotic cell membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the common precursor for low-abundance regulatory lipids, collectively referred to as polyphosphoinositides (PPIn). The metabolic turnover of PPIn species has received immense attention because of the essential functions of these lipids as universal regulators of membrane biology and their dysregulation in numerous human pathologies. The diverse functions of PPIn lipids occur, in part, by orchestrating the spatial organization and conformational dynamics of peripheral or integral membrane proteins within defined subcellular compartments. The emerging role of stable contact sites between adjacent membranes as specialized platforms for the coordinate control of ion exchange, cytoskeletal dynamics, and lipid transport has also revealed important new roles for PPIn species. In this review, we highlight the importance of membrane contact sites formed between the endoplasmic reticulum (ER) and plasma membrane (PM) for the integrated regulation of PPIn metabolism within the PM. Special emphasis will be placed on non-vesicular lipid transport during control of the PtdIns biosynthetic cycle as well as toward balancing the turnover of the signaling PPIn species that define PM identity.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
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36
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El-Daher MT, Lemale J, Bruneau J, Leveau C, Guerin F, Lambert N, Diana JS, Neven B, Sepulveda FE, Coulomb-L'Hermine A, Molina T, Picard C, Fischer A, de Saint Basile G. Chronic Intestinal Pseudo-Obstruction and Lymphoproliferative Syndrome as a Novel Phenotype Associated With Tetratricopeptide Repeat Domain 7A Deficiency. Front Immunol 2019; 10:2592. [PMID: 31787977 PMCID: PMC6853864 DOI: 10.3389/fimmu.2019.02592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/21/2019] [Indexed: 11/13/2022] Open
Abstract
Mutations in the tetratricopeptide repeat domain 7A (TTC7A) gene cause very early onset inflammatory bowel diseases (VOIBD) or multiple intestinal atresia associated with immune deficiency of various severities, ranging from combined immune deficiency to mild lymphopenia. In this manuscript, we report the clinical, biological and molecular features of a patient born from consanguineous parents, presenting with recurrent lymphoproliferative syndrome and pan-hypergammaglobulinemia associated with chronic intestinal pseudo obstruction (CIPO). Genetic screening revealed the novel c.974G>A (p.R325Q) mutation in homozygosity in the TTC7A gene. The patient's phenotype differs significantly from that previously associated with TTC7A deficiency in humans. It becomes closer to the one reported in the ttc7a-deficient mice that invariably develop a proliferative lymphoid and myeloid disorder. Functional studies showed that the extreme variability in the clinical phenotype couldn't be explained by the cellular phenotype. Indeed, the patient's TTC7A mutation, as well as the murine-ttc7 mutant, have the same functional impact on protein expression, DNA instability and chromatin compaction, as the other mutations that lead to classical TTC7A-associated phenotypes. Co-inheritance of genetic variants may also contribute to the unique nature of the patient's phenotype. The present case report shows that the clinical spectrum of TTC7A deficiency is much broader than previously suspected. Our findings should alert the physicians to consider screening of TTC7A mutations in patients with lymphoproliferative syndrome and hypergammaglobulinemia and/or chronic intestinal pseudo-obstruction.
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Affiliation(s)
- Marie-Thérèse El-Daher
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Paris, France.,Imagine Institute, Université de Paris, Paris, France
| | - Julie Lemale
- Pediatric Nutrition and Gastroenterology Department, Trousseau Hospital, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Julie Bruneau
- Imagine Institute, Université de Paris, Paris, France.,Department of Pathology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Claire Leveau
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Paris, France.,Imagine Institute, Université de Paris, Paris, France
| | - Frédéric Guerin
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Paris, France.,Imagine Institute, Université de Paris, Paris, France
| | - Nathalie Lambert
- Center for the Study of Primary Immunodeficiencies, Necker Enfants Malades Hospital, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Jean-Sébastien Diana
- Pediatric Hematology Department, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM UMR 1163, Paris, France
| | - Bénédicte Neven
- Pediatric Hematology Department, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM UMR 1163, Paris, France
| | - Fernando E Sepulveda
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Paris, France.,Imagine Institute, Université de Paris, Paris, France.,Centre Nationale de la Recherche Scientifique - CNRS, Villejuif, France
| | - Aurore Coulomb-L'Hermine
- Department of Pathology, Hôpital A Trousseau, Assistance-Publique des Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Thierry Molina
- Imagine Institute, Université de Paris, Paris, France.,Department of Pathology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Capucine Picard
- Imagine Institute, Université de Paris, Paris, France.,Center for the Study of Primary Immunodeficiencies, Necker Enfants Malades Hospital, Assistance Publique des Hôpitaux de Paris, Paris, France.,Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Paris, France
| | - Alain Fischer
- Imagine Institute, Université de Paris, Paris, France.,Pediatric Hematology Department, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM UMR 1163, Paris, France.,Collège de France, Paris, France
| | - Geneviève de Saint Basile
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Paris, France.,Imagine Institute, Université de Paris, Paris, France.,Center for the Study of Primary Immunodeficiencies, Necker Enfants Malades Hospital, Assistance Publique des Hôpitaux de Paris, Paris, France
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Taweecheep P, Naloka K, Matsutani M, Yakushi T, Matsushita K, Theeragool G. Superfine bacterial nanocellulose produced by reverse mutations in the bcsC gene during adaptive breeding of Komagataeibacter oboediens. Carbohydr Polym 2019; 226:115243. [PMID: 31582059 DOI: 10.1016/j.carbpol.2019.115243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022]
Abstract
Nonsense mutation in the bcsC gene occurred in the ethanol-adapted strain of Komagataeibacter oboediens MSKU 3, E3 strain, resulting in the loss of the function to produce BNC. In this study, we tried to restore the BNC-producing ability of E3 strain by the following adaptive mutation through repetitive static culture, and obtained four BNC-producing revertant strains, of which the bcsC gene had InDel mutations near the frameshift mutation region in E3 strain, resulting in several amino acid alterations compared with the BcsC of MSKU 3. Each revertant produced BNCs with different productivity on the static culture. Interestingly, one of the revertants, R37-9, produced BNC with a finer structure and narrower range of fibrils width, compared to others. The genome of R37-9 strain revealed only one amino acid substitution in the bcsC gene. Thus, we concluded that N713D mutation occurred in the bcsC gene is responsible for the finer fibrils structure.
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Affiliation(s)
- Pornchanok Taweecheep
- Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand.
| | - Kallayanee Naloka
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Minenosuke Matsutani
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Toshiharu Yakushi
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Kazunobu Matsushita
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Gunjana Theeragool
- Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand; Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
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38
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Leveau C, Gajardo T, El-Daher MT, Cagnard N, Fischer A, de Saint Basile G, Sepulveda FE. Ttc7a regulates hematopoietic stem cell functions while controlling the stress-induced response. Haematologica 2019; 105:59-70. [PMID: 31004027 PMCID: PMC6939534 DOI: 10.3324/haematol.2018.207100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/17/2019] [Indexed: 01/30/2023] Open
Abstract
The molecular machinery that regulates the balance between self-renewal and differentiation properties of hematopoietic stem cells (HSC) has yet to be characterized in detail. Here we found that the tetratricopeptide repeat domain 7 A (Ttc7a) protein, a putative scaffold protein expressed by HSC, acts as an intrinsic regulator of the proliferative response and the self-renewal potential of murine HSC in vivo. Loss of Ttc7a consistently enhanced the competitive repopulating ability of HSC and their intrinsic capacity to replenish the hematopoietic system after serial cell transplantations, relative to wildtype cells. Ttc7a-deficient HSC exhibit a different transcriptomic profile for a set of genes controlling the cellular response to stress, which was associated with increased proliferation in response to chemically induced stress in vitro and myeloablative stress in vivo. Our results therefore revealed a previously unrecognized role of Ttc7a as a critical regulator of HSC stemness. This role is related, at least in part, to regulation of the endoplasmic reticulum stress response.
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Affiliation(s)
- Claire Leveau
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Imagine Institute, Paris.,Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris
| | - Tania Gajardo
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Imagine Institute, Paris.,Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris
| | - Marie-Thérèse El-Daher
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Imagine Institute, Paris.,Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris
| | - Nicolas Cagnard
- Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris.,Bioinformatic Platform, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris.,Structure Fédérative de Recherche (SFR) Necker, INSERM US24/CNRS UMS 3633, Paris
| | - Alain Fischer
- Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris.,Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades Immunology and Pediatric Hematology Department, Paris.,Collège de France, Paris, France.,INSERM UMR1163, Paris
| | - Geneviève de Saint Basile
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Imagine Institute, Paris .,Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris.,Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Centre d'Etudes des Déficits Immunitaires, Paris
| | - Fernando E Sepulveda
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM UMR 1163, Imagine Institute, Paris .,Université Paris Descartes -Sorbonne Paris Cité, Imagine Institute, Paris.,Centre National de la Recherche Scientifique - CNRS, Paris, France
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Wu X, Luo P, Wei Z, Li Y, Huang R, Dong X, Li K, Zang S, Tang BZ. Guest-Triggered Aggregation-Induced Emission in Silver Chalcogenolate Cluster Metal-Organic Frameworks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801304. [PMID: 30693183 PMCID: PMC6343058 DOI: 10.1002/advs.201801304] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/19/2018] [Indexed: 05/21/2023]
Abstract
Utilizing aggregation-induced emission luminogens (AIEgens) as ligands has proven to be an effective strategy for constructing metal-organic frameworks (MOFs) with intense luminescent properties. However, highly luminescent AIEgen-based MOFs with adjustable emission properties are rarely achieved because of the rigid conformation of AIEgens in the crystalline state. Here, a dual-node 3D silver chalcogenolate cluster MOF (1) is designed and synthesized, where the AIE ligand shows relatively flexible and rotatable conformations. The conformations of AIE ligands in 1 are switchable by the absorption/desorption of guest molecules. As a result, 1 exhibited not only intense but also guest molecule switched luminescent properties. More importantly, the switching rate is tunable by using different guest molecules. 1 provides a unique visualized prototype to understand the mechanism of guest-triggered aggregation-induced emission in MOFs.
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Affiliation(s)
- Xiao‐Hui Wu
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Peng Luo
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Zhong Wei
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Yuan‐Yuan Li
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Ren‐Wu Huang
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Xi‐Yan Dong
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Kai Li
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Shuang‐Quan Zang
- College of Chemistry and Molecular EngineeringZhengzhou UniversityHenan450001P. R. China
| | - Ben Zhong Tang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionThe Hong Kong University of Science & TechnologyClear Water BayKowloon999077Hong KongP. R. China
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40
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Ma Q, Gabelli SB, Raben DM. Diacylglycerol kinases: Relationship to other lipid kinases. Adv Biol Regul 2019; 71:104-110. [PMID: 30348515 PMCID: PMC6347529 DOI: 10.1016/j.jbior.2018.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 04/17/2023]
Abstract
Lipid kinases regulate a wide variety of cellular functions and have emerged as one the most promising targets for drug design. Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). Despite the critical role in lipid biosynthesis, both DAG and PtdOH have been shown as bioactive lipids mediating a number of signaling pathways. Although there is increasing recognition of their role in signaling systems, our understanding of the key enzyme which regulate the balance of these two lipid messages remain limited. Solved structures provide a wealth of information for understanding the function and regulation of these enzymes. Solving the structures of mammalian DGKs by traditional NMR and X-ray crystallography approaches have been challenging and so far, there are still no three-dimensional structures of these DGKs. Despite this, some insights may be gained by examining the similarities and differences between prokaryotic DGKs and other mammalian lipid kinases. This review focuses on summarizing and comparing the structure of prokaryotic and mammalian DGKs as well as two other lipid kinases: sphingosine kinase and phosphatidylinositol-3-kinase. How these known lipid kinases structures relate to mammalian DGKs will also be discussed.
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Affiliation(s)
- Qianqian Ma
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sandra B Gabelli
- The Department of Biophysics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel M Raben
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Tian S, Zeng J, Liu X, Chen J, Zhang JZH, Zhu T. Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Phys Chem Chem Phys 2019; 21:22103-22112. [DOI: 10.1039/c9cp03598b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations and binding free energy calculations are combined to investigate the selectivity of inhibitors toward type III phosphatidylinositol 4 kinases.
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Affiliation(s)
- Shuaizhen Tian
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Jinzhe Zeng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Xiao Liu
- School of Mathematics, Physics and Statistics
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan 250357
- China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
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Jardine S, Dhingani N, Muise AM. TTC7A: Steward of Intestinal Health. Cell Mol Gastroenterol Hepatol 2018; 7:555-570. [PMID: 30553809 PMCID: PMC6406079 DOI: 10.1016/j.jcmgh.2018.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 12/15/2022]
Abstract
The increasing incidence of pediatric inflammatory bowel disease, coupled with the efficiency of whole-exome sequencing, has led to the identification of tetratricopeptide repeat domain 7A (TTC7A) as a steward of intestinal health. TTC7A deficiency is an autosomal-recessively inherited disease. In the 5 years since the original description, more than 50 patients with more than 20 distinct disease-causing TTC7A mutations have been identified. Patients show heterogenous intestinal and immunologic disease manifestations, including but not limited to multiple intestinal atresias, very early onset inflammatory bowel disease, loss of intestinal architecture, apoptotic enterocolitis, combined immunodeficiency, and various extraintestinal features related to the skin and/or hair. The focus of this review is to highlight trends in patient phenotypes and to consolidate functional data related to the role of TTC7A in maintaining intestinal homeostasis. TTC7A deficiency is fatal in approximately two thirds of patients, and, as more patients continue to be discovered, elucidating the comprehensive role of TTC7A could show druggable targets that may benefit the growing cohort of individuals suffering from inflammatory bowel disease.
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Affiliation(s)
- Sasha Jardine
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Institute for Medical Science and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Neel Dhingani
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Institute for Medical Science and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Institute for Medical Science and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada.
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43
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Structural Basis for Regulation of Phosphoinositide Kinases and Their Involvement in Human Disease. Mol Cell 2018; 71:653-673. [DOI: 10.1016/j.molcel.2018.08.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/22/2018] [Accepted: 07/30/2018] [Indexed: 01/09/2023]
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Dornan GL, Dalwadi U, Hamelin DJ, Hoffmann RM, Yip CK, Burke JE. Probing the Architecture, Dynamics, and Inhibition of the PI4KIIIα/TTC7/FAM126 Complex. J Mol Biol 2018; 430:3129-3142. [PMID: 30031006 DOI: 10.1016/j.jmb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 11/16/2022]
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα) is the lipid kinase primarily responsible for generating the lipid phosphatidylinositol 4-phosphate (PI4P) at the plasma membrane, which acts as the substrate for generation of the signaling lipids PIP2 and PIP3. PI4KIIIα forms a large heterotrimeric complex with two regulatory partners, TTC7 and FAM126. We describe using an integrated electron microscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) approach to probe the architecture and dynamics of the complex of PI4KIIIα/TTC7/FAM126. HDX-MS reveals that the majority of the PI4KIIIα sequence was protected from exchange in short deuterium pulse experiments, suggesting presence of secondary structure, even in putative unstructured regions. Negative stain electron microscopy reveals the shape and architecture of the full-length complex, revealing an overall dimer of PI4KIIIα/TTC7/FAM126 trimers. HDX-MS reveals conformational changes in the TTC7/FAM126 complex upon binding PI4KIIIα, including both at the direct TTC7-PI4KIIIα interface and at the putative membrane binding surface. Finally, HDX-MS experiments of PI4KIIIα bound to the highly potent and selective inhibitor GSK-A1 compared to that bound to the non-specific inhibitor PIK93 revealed substantial conformational changes throughout an extended region of the kinase domain. Many of these changes were distant from the putative inhibitor binding site, showing a large degree of allosteric conformational changes that occur upon inhibitor binding. Overall, our results reveal novel insight into the regulation of PI4KIIIα by its regulatory proteins TTC7/FAM126, as well as additional dynamic information on how selective inhibition of PI4KIIIα is achieved.
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Affiliation(s)
- Gillian L Dornan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2.
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