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Delic S, Shuman B, Lee S, Bahmanyar S, Momany M, Onishi M. The Evolutionary Origins and Ancestral Features of Septins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586683. [PMID: 38585751 PMCID: PMC10996617 DOI: 10.1101/2024.03.25.586683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Septins are a family of membrane-associated cytoskeletal GTPases that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from rhodophyte red algae and glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the α0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that curvature-sensing is an ancestral trait of septin proteins. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.
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Affiliation(s)
- Samed Delic
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Brent Shuman
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, USA
| | - Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, North Carolina, USA
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2
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Park AY, Leney-Greene M, Lynberg M, Gabrielski JQ, Xu X, Schwarz B, Zheng L, Balasubramaniyam A, Ham H, Chao B, Zhang Y, Matthews HF, Cui J, Yao Y, Kubo S, Chanchu JM, Morawski AR, Cook SA, Jiang P, Ravell JC, Cheng YH, George A, Faruqi A, Pagalilauan AM, Bergerson JRE, Ganesan S, Chauvin SD, Aluri J, Edwards-Hicks J, Bohrnsen E, Tippett C, Omar H, Xu L, Butcher GW, Pascall J, Karakoc-Aydiner E, Kiykim A, Maecker H, Tezcan İ, Esenboga S, Heredia RJ, Akata D, Tekin S, Kara A, Kuloglu Z, Unal E, Kendirli T, Dogu F, Karabiber E, Atkinson TP, Cochet C, Filhol O, Bosio CM, Davis MM, Lifton RP, Pearce EL, Daumke O, Aytekin C, Şahin GE, Aksu AÜ, Uzel G, Koneti Rao V, Sari S, Dalgıç B, Boztug K, Cagdas D, Haskologlu S, Ikinciogullari A, Schwefel D, Vilarinho S, Baris S, Ozen A, Su HC, Lenardo MJ. GIMAP5 deficiency reveals a mammalian ceramide-driven longevity assurance pathway. Nat Immunol 2024; 25:282-293. [PMID: 38172257 PMCID: PMC11151279 DOI: 10.1038/s41590-023-01691-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/26/2023] [Indexed: 01/05/2024]
Abstract
Preserving cells in a functional, non-senescent state is a major goal for extending human healthspans. Model organisms reveal that longevity and senescence are genetically controlled, but how genes control longevity in different mammalian tissues is unknown. Here, we report a new human genetic disease that causes cell senescence, liver and immune dysfunction, and early mortality that results from deficiency of GIMAP5, an evolutionarily conserved GTPase selectively expressed in lymphocytes and endothelial cells. We show that GIMAP5 restricts the pathological accumulation of long-chain ceramides (CERs), thereby regulating longevity. GIMAP5 controls CER abundance by interacting with protein kinase CK2 (CK2), attenuating its ability to activate CER synthases. Inhibition of CK2 and CER synthase rescues GIMAP5-deficient T cells by preventing CER overaccumulation and cell deterioration. Thus, GIMAP5 controls longevity assurance pathways crucial for immune function and healthspan in mammals.
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Affiliation(s)
- Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin Q Gabrielski
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xijin Xu
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Arasu Balasubramaniyam
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Hyoungjun Ham
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brittany Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yu Zhang
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen F Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jing Cui
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jean Michel Chanchu
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aaron R Morawski
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah A Cook
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ping Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan C Ravell
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Internal Medicine, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Yan H Cheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alex George
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aiman Faruqi
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison M Pagalilauan
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sundar Ganesan
- Biological Imaging Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jahnavi Aluri
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joy Edwards-Hicks
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Caroline Tippett
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Habib Omar
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leilei Xu
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - John Pascall
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Ayca Kiykim
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - İlhan Tezcan
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Saliha Esenboga
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Raul Jimenez Heredia
- St Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Deniz Akata
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Saban Tekin
- Department of Basic Medical Sciences, Hamidiye Faculty of Medicine, Division of Medical Biology, University of Health Sciences, İstanbul, Turkey
| | - Altan Kara
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Gebze, Turkey
| | - Zarife Kuloglu
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Ankara University School of Medicine, Ankara, Türkiye
| | - Emel Unal
- Department of Pediatric Oncology, Ankara University Medical School, Ankara, Turkey
| | - Tanıl Kendirli
- Department of Pediatric Intensive Care Unit, Ankara University Medical School, Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University Medical School, Ankara, Turkey
| | - Esra Karabiber
- Department of Chest Diseases, Faculty of Medicine, Division of Adult Allergy-Immunology, Marmara University, Istanbul, Turkey
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Claude Cochet
- University Grenoble Alpes, INSERM, CEA, UMR Biosanté, Grenoble, France
| | - Odile Filhol
- University Grenoble Alpes, INSERM, CEA, UMR Biosanté, Grenoble, France
| | - Catherine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Palo Alto, CA, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erika L Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Oliver Daumke
- Department of Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gülseren Evirgen Şahin
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, University of Health Sciences, Dr Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Aysel Ünlüsoy Aksu
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, University of Health Sciences, Dr Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sinan Sari
- Department of Pediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Buket Dalgıç
- Department of Pediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Kaan Boztug
- St Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St Anna Children's Hospital, Vienna, Austria
| | - Deniz Cagdas
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Sule Haskologlu
- Department of Pediatric Immunology and Allergy, Ankara University Medical School, Ankara, Turkey
| | - Aydan Ikinciogullari
- Department of Pediatric Immunology and Allergy, Ankara University Medical School, Ankara, Turkey
| | - David Schwefel
- Department of Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Silvia Vilarinho
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Helen C Su
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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3
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Yang K, Wang Q, Wu L, Gao QC, Tang S. Development and verification of a combined diagnostic model for primary Sjögren's syndrome by integrated bioinformatics analysis and machine learning. Sci Rep 2023; 13:8641. [PMID: 37244954 DOI: 10.1038/s41598-023-35864-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/25/2023] [Indexed: 05/29/2023] Open
Abstract
Primary Sjögren's syndrome (pSS) is a chronic, systemic autoimmune disease mostly affecting the exocrine glands. This debilitating condition is complex and specific treatments remain unavailable. There is a need for the development of novel diagnostic models for early screening. Four gene profiling datasets were downloaded from the Gene Expression Omnibus database. The 'limma' software package was used to identify differentially expressed genes (DEGs). A random forest-supervised classification algorithm was used to screen disease-specific genes, and three machine learning algorithms, including artificial neural networks (ANN), random forest (RF), and support vector machines (SVM), were used to build a pSS diagnostic model. The performance of the model was measured using its area under the receiver operating characteristic curve. Immune cell infiltration was investigated using the CIBERSORT algorithm. A total of 96 DEGs were identified. By utilizing a RF classifier, a set of 14 signature genes that are pivotal in transcription regulation and disease progression in pSS were identified. Through the utilization of training and testing datasets, diagnostic models for pSS were successfully designed using ANN, RF, and SVM, resulting in AUCs of 0.972, 1.00, and 0.9742, respectively. The validation set yielded AUCs of 0.766, 0.8321, and 0.8223. It was the RF model that produced the best prediction performance out of the three models tested. As a result, an early predictive model for pSS was successfully developed with high diagnostic performance, providing a valuable resource for the screening and early diagnosis of pSS.
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Affiliation(s)
- Kun Yang
- School of Humanities and Social Sciences, Shanxi Medical University, Taiyuan, China
| | - Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Li Wu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Qi-Chao Gao
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Shan Tang
- The First Hospital of Shanxi Medical University, Taiyuan, China.
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4
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Lozano-Mendoza J, Ramírez-Montiel F, Rangel-Serrano Á, Páramo-Pérez I, Mendoza-Macías CL, Saavedra-Salazar F, Franco B, Vargas-Maya N, Jeelani G, Saito-Nakano Y, Anaya-Velázquez F, Nozaki T, Padilla-Vaca F. Attenuation of In Vitro and In Vivo Virulence Is Associated with Repression of Gene Expression of AIG1 Gene in Entamoeba histolytica. Pathogens 2023; 12:pathogens12030489. [PMID: 36986411 PMCID: PMC10051847 DOI: 10.3390/pathogens12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Entamoeba histolytica virulence results from complex host-parasite interactions implicating multiple amoebic components (e.g., Gal/GalNAc lectin, cysteine proteinases, and amoebapores) and host factors (microbiota and immune response). UG10 is a strain derived from E. histolytica virulent HM-1:IMSS strain that has lost its virulence in vitro and in vivo as determined by a decrease of hemolytic, cytopathic, and cytotoxic activities, increased susceptibility to human complement, and its inability to form liver abscesses in hamsters. We compared the transcriptome of nonvirulent UG10 and its parental HM-1:IMSS strain. No differences in gene expression of the classical virulence factors were observed. Genes downregulated in the UG10 trophozoites encode for proteins that belong to small GTPases, such as Rab and AIG1. Several protein-coding genes, including iron-sulfur flavoproteins and heat shock protein 70, were also upregulated in UG10. Overexpression of the EhAIG1 gene (EHI_180390) in nonvirulent UG10 trophozoites resulted in augmented virulence in vitro and in vivo. Cocultivation of HM-1:IMSS with E. coli O55 bacteria cells reduced virulence in vitro, and the EhAIG1 gene expression was downregulated. In contrast, virulence was increased in the monoxenic strain UG10, and the EhAIG1 gene expression was upregulated. Therefore, the EhAIG1 gene (EHI_180390) represents a novel virulence determinant in E. histolytica.
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Affiliation(s)
- Janeth Lozano-Mendoza
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Fátima Ramírez-Montiel
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Itzel Páramo-Pérez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | | | - Faridi Saavedra-Salazar
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Naurú Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Ghulam Jeelani
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-0052, Japan
| | - Fernando Anaya-Velázquez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-0052, Japan
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
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5
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Gu Y, Lin X, Dong Y, Wood G, Seidah NG, Werstuck G, Major P, Bonert M, Kapoor A, Tang D. PCSK9 facilitates melanoma pathogenesis via a network regulating tumor immunity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:2. [PMID: 36588164 PMCID: PMC9806914 DOI: 10.1186/s13046-022-02584-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND PCSK9 regulates cholesterol homeostasis and promotes tumorigenesis. However, the relevance of these two actions and the mechanisms underlying PCSK9's oncogenic roles in melanoma and other cancers remain unclear. METHODS PCSK9's association with melanoma was analysed using the TCGA dataset. Empty vector (EV), PCSK9, gain-of-function (D374Y), and loss-of-function (Q152H) PCSK9 mutant were stably-expressed in murine melanoma B16 cells and studied for impact on B16 cell-derived oncogenesis in vitro and in vivo using syngeneic C57BL/6 and Pcsk9-/- mice. Intratumoral accumulation of cholesterol was determined. RNA-seq was performed on individual tumor types. Differentially-expressed genes (DEGs) were derived from the comparisons of B16 PCSK9, B16 D374Y, or B16 Q152H tumors to B16 EV allografts and analysed for pathway alterations. RESULTS PCSK9 expression and its network negatively correlated with the survival probability of patients with melanoma. PCSK9 promoted B16 cell proliferation, migration, and growth in soft agar in vitro, formation of tumors in C57BL/6 mice in vivo, and accumulation of intratumoral cholesterol in a manner reflecting its regulation of the low-density lipoprotein receptor (LDLR): Q152H, EV, PCSK9, and D374Y. Tumor-associated T cells, CD8 + T cells, and NK cells were significantly increased in D374Y tumors along with upregulations of multiple immune checkpoints, IFNγ, and 143 genes associated with T cell dysfunction. Overlap of 36 genes between the D374Y DEGs and the PCSK9 DEGs predicted poor prognosis of melanoma and resistance to immune checkpoint blockade (ICB) therapy. CYTH4, DENND1C, AOAH, TBC1D10C, EPSTI1, GIMAP7, and FASL (FAS ligand) were novel predictors of ICB therapy and displayed high level of correlations with multiple immune checkpoints in melanoma and across 30 human cancers. We observed FAS ligand being among the most robust biomarkers of ICB treatment and constructed two novel and effective multigene panels predicting response to ICB therapy. The profiles of allografts produced by B16 EV, PCSK9, D374Y, and Q152H remained comparable in C57BL/6 and Pcsk9-/- mice. CONCLUSIONS Tumor-derived PCSK9 plays a critical role in melanoma pathogenesis. PCSK9's oncogenic actions are associated with intratumoral cholesterol accumulation. PCSK9 systemically affects the immune system, contributing to melanoma immune evasion. Novel biomarkers derived from the PCSK9-network effectively predicted ICB therapy responses.
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Affiliation(s)
- Yan Gu
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Xiaozeng Lin
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Ying Dong
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Geoffrey Wood
- grid.34429.380000 0004 1936 8198Department of Pathology, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Nabil G. Seidah
- grid.511547.30000 0001 2106 1695Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute, University of Montreal, Montreal, QC H2W 1R7 Canada
| | - Geoff Werstuck
- grid.25073.330000 0004 1936 8227Department of Medicine, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Pierre Major
- grid.25073.330000 0004 1936 8227Department of Oncology, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Michael Bonert
- grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Anil Kapoor
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Damu Tang
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
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6
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Ismail VA, Naismith T, Kast DJ. The NTPase activity of the double FYVE domain-containing protein 1 regulates lipid droplet metabolism. J Biol Chem 2022; 299:102830. [PMID: 36574842 PMCID: PMC9881219 DOI: 10.1016/j.jbc.2022.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/26/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Lipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks and therefore play a central role in cellular metabolism. However, the molecular factors and underlying mechanisms that regulate the growth and degradation of LDs are poorly understood. It has emerged that proteins that establish contacts between LDs and the endoplasmic reticulum play a critical role in regulating LD metabolism. Recently, the autophagy-related protein, double FYVE domain-containing protein 1 (DFCP1/ZFYVE1) was shown to reside at the interface of the endoplasmic reticulum and LDs, however, little is known about the involvement of DFCP1 in autophagy and LD metabolism. Here, we show that DFCP1 is a novel NTPase that regulates free fatty acid metabolism. Specifically, we show that DFPC1-knockdown, particularly during starvation, increases cellular free fatty acids and decreases the levels of cellular TAGs, resulting in accumulated small LDs. Using selective truncations, we demonstrate that DFCP1 accumulation on LDs in cells and in vitro is regulated by a previously unknown NTPase domain. Using spectroscopic approaches, we show that this NTPase domain can dimerize and can hydrolyze both ATP and GTP. Furthermore, mutations in DFCP1 that either impact nucleotide hydrolysis or dimerization result in changes in the accumulation of DFCP1 on LDs, changes in LD density and size, and colocalization of LDs to autophagosomes. Collectively, our findings suggest that DFCP1 is an NTPase that modulates the metabolism of LDs in cells.
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Affiliation(s)
- V A Ismail
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - T Naismith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - D J Kast
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA.
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7
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Terefe E, Belay G, Han J, Hanotte O, Tijjani A. Genomic adaptation of Ethiopian indigenous cattle to high altitude. Front Genet 2022; 13:960234. [PMID: 36568400 PMCID: PMC9780680 DOI: 10.3389/fgene.2022.960234] [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: 06/02/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.
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Affiliation(s)
- Endashaw Terefe
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia,International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella, Ethiopia,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
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8
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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9
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Qin Y, Liu H, Huang X, Huang L, Liao L, Li J, Zhang L, Li W, Yang J. GIMAP7 as a Potential Predictive Marker for Pan-Cancer Prognosis and Immunotherapy Efficacy. J Inflamm Res 2022; 15:1047-1061. [PMID: 35210811 PMCID: PMC8858002 DOI: 10.2147/jir.s342503] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/02/2022] [Indexed: 01/26/2023] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Yan Qin
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, 530021, People’s Republic of China
| | - He Liu
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, 530021, People’s Republic of China
| | - Xiaoliang Huang
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People’s Republic of China
| | - Lihaoyun Huang
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People’s Republic of China
| | - Lixian Liao
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People’s Republic of China
| | - Jiasheng Li
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People’s Republic of China
| | - Lihua Zhang
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People’s Republic of China
| | - Wei Li
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, 530021, People’s Republic of China
| | - Jianrong Yang
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, 530021, People’s Republic of China
- Correspondence: Jianrong Yang; Wei Li, Health Examination Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Email ;
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10
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Komatsu M, Saito K, Miyamoto I, Koike K, Iyoda M, Nakashima D, Kasamatsu A, Shiiba M, Tanzawa H, Uzawa K. Aberrant GIMAP2 expression affects oral squamous cell carcinoma progression by promoting cell cycle and inhibiting apoptosis. Oncol Lett 2022; 23:49. [PMID: 34992682 PMCID: PMC8721858 DOI: 10.3892/ol.2021.13167] [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: 08/06/2020] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
GTPases of immunity-associated protein 2 (GIMAP2) is a GTPase family member associated with T cell survival. However, its mechanisms of action in oral squamous cell carcinoma (OSCC) remain largely unknown. Therefore, the present study aimed to elucidate the possible role of GIMAP2 in OSCC development by investigating its expression levels and molecular mechanisms in OSCC. Reverse transcription quantitative PCR, immunoblotting and immunohistochemistry indicated that GIMAP2 expression was significantly upregulated (P<0.05) in OSCC-derived cell lines and primary OSCC specimens compared with that in their normal counterparts. GIMAP2-knockdown OSCC cells exhibited decreased cell growth, which was associated with cyclin-dependent kinase (CDK)4, CDK6 and phosphorylated Rb downregulation and p53 and p21 upregulation. In addition to cell cycle arrest, GIMAP2 affected anti-apoptotic functions in GIMAP2-knockdown cells by upregulating Bcl-2 and downregulating Bax and Bak. These findings indicated that GIMAP2 may significantly influence OSCC development and apoptosis inhibition and thus is a potential biomarker of OSCC.
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Affiliation(s)
- Mari Komatsu
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan
| | - Kengo Saito
- Department of Molecular Virology, Chiba University, Chiba 260-8670, Japan
| | - Isao Miyamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Kazuyuki Koike
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Manabu Iyoda
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Dai Nakashima
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Atsushi Kasamatsu
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Masashi Shiiba
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Katsuhiro Uzawa
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
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11
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Coelho JC, Calhoun ED, Calhoun GN, Poole AZ. Patchy Distribution of GTPases of Immunity Associated Proteins (GIMAP) within Cnidarians and Dinoflagellates Suggests a Complex Evolutionary History. Genome Biol Evol 2022; 14:6500283. [PMID: 35015849 PMCID: PMC8857920 DOI: 10.1093/gbe/evac002] [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] [Accepted: 01/05/2022] [Indexed: 11/24/2022] Open
Abstract
GTPases of Immunity-Associated Proteins (GIMAP) are a group of small GTP-binding proteins found in a variety of organisms, including vertebrates, invertebrates, and plants. These proteins are characterized by the highly conserved AIG1 domain, and in vertebrates, have been implicated in regulation of the immune system as well as apoptosis and autophagy, though their exact mechanism of action remains unclear. Recent work on cnidarian GIMAPs suggests a conserved role in immunity, apoptosis, and autophagy—three processes involved in coral bleaching, or the breakdown of cnidarian-dinoflagellate symbiosis. Therefore, to further understand the evolution of GIMAPs in this group of organisms, the purpose of this study was to characterize GIMAP or GIMAP-like sequences utilizing publicly available genomic and transcriptomic data in species across the cnidarian phylogeny. The results revealed a patchy distribution of GIMAPs in cnidarians, with three distinct types referred to as L-GIMAP, S-GIMAP, and GIMAP-like. Additionally, GIMAPs were present in most dinoflagellate species and formed seven well-supported clades. Overall, these results elucidate the distribution of GIMAPs within two distantly related eukaryotic groups and represent the first in-depth investigation on the evolution of these proteins within both protists and basal metazoans.
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Affiliation(s)
- Jenny C Coelho
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA.,Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd, Chapel Hill, NC 27599, USA
| | - Ethan D Calhoun
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
| | - Grant N Calhoun
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
| | - Angela Z Poole
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
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12
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Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle. PLoS One 2021; 16:e0258216. [PMID: 34648531 PMCID: PMC8516222 DOI: 10.1371/journal.pone.0258216] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/21/2021] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to estimate genotype by time-lagged heat stress (HS) variance components as well as main and interaction SNP-marker effects for maternal HS during the last eight weeks of cow pregnancy, considering milk production traits recorded in the offspring generation. The HS indicator was the temperature humidity index (THI) for each week. A dummy variable with the code = 1 for the respective week for THI ≥ 60 indicated HS, otherwise, for no HS, the code = 0 was assigned. The dataset included test-day and lactation production traits from 14,188 genotyped first parity Holstein cows. After genotype quality control, 41,139 SNP markers remained for the genomic analyses. Genomic animal models without (model VC_nHS) and with in-utero HS effects (model VC_wHS) were applied to estimate variance components. Accordingly, for genome-wide associations, models GWA_nHS and GWA_wHS, respectively, were applied to estimate main and interaction SNP effects. Common genomic and residual variances for the same traits were very similar from models VC_nHS and VC_wHS. Genotype by HS interaction variances varied, depending on the week with in-utero HS. Among all traits, lactation milk yield with HS from week 5 displayed the largest proportion for interaction variances (0.07). For main effects from model GWA_wHS, 380 SNPs were suggestively associated with all production traits. For the SNP interaction effects from model GWA_wHS, we identified 31 suggestive SNPs, which were located in close distance to 62 potential candidate genes. The inferred candidate genes have various biological functions, including mechanisms of immune response, growth processes and disease resistance. Two biological processes excessively represented in the overrepresentation tests addressed lymphocyte and monocyte chemotaxis, ultimately affecting immune response. The modelling approach considering time-lagged genotype by HS interactions for production traits inferred physiological mechanisms being associated with health and immunity, enabling improvements in selection of robust animals.
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13
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Limoges MA, Cloutier M, Nandi M, Ilangumaran S, Ramanathan S. The GIMAP Family Proteins: An Incomplete Puzzle. Front Immunol 2021; 12:679739. [PMID: 34135906 PMCID: PMC8201404 DOI: 10.3389/fimmu.2021.679739] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Overview: Long-term survival of T lymphocytes in quiescent state is essential to maintain their cell numbers in secondary lymphoid organs and in peripheral circulation. In the BioBreeding diabetes-prone strain of rats (BB-DP), loss of functional GIMAP5 (GTPase of the immune associated nucleotide binding protein 5) results in profound peripheral T lymphopenia. This discovery heralded the identification of a new family of proteins initially called Immune-associated nucleotide binding protein (IAN) family. In this review we will use ‘GIMAP’ to refer to this family of proteins. Recent studies suggest that GIMAP proteins may interact with each other and also be involved in the movement of the cellular cargo along the cytoskeletal network. Here we will summarize the current knowledge on the characteristics and functions of GIMAP family of proteins.
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Affiliation(s)
- Marc-André Limoges
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Madhuparna Nandi
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
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14
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McCormack M, Talbot A, Dillon E, O’Connor I, MacCarthy E. Host Response of Atlantic Salmon ( Salmo salar) Re-Inoculated with Paramoeba perurans. Microorganisms 2021; 9:microorganisms9050993. [PMID: 34062978 PMCID: PMC8147987 DOI: 10.3390/microorganisms9050993] [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: 03/24/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 11/28/2022] Open
Abstract
In aquaculture, recurrence rates of amoebic gill disease (AGD) caused by the ectoparasite Paramoeba perurans are high and no prophylactic strategies exist for disease prevention. In this study, Atlantic salmon (Salmo salar) were initially inoculated with P. perurans and following the development of amoebic gill disease were treated with freshwater immersion on day 21 and day 35 post inoculation. Fish were re-inoculated following a negative qPCR analysis for the presence of P. perurans. The gill host immune response was investigated at 7, 14, and 18 days post re-inoculation. Differential proteome expression of immune related proteins was assessed by comparison of each time point against naïve controls. In the gill, some proteins of the innate immune system were expressed in response to gill re-colonization by P. perurans, while no features of adaptive immunity were found to be differentially expressed. Many of the proteins identified are novel in the context of AGD and their expression profiles suggest that their roles in the response to disease development and progression in single or multiple infections warrant further investigation.
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Affiliation(s)
- Michelle McCormack
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (A.T.); (I.O.); (E.M.)
- Correspondence:
| | - Anita Talbot
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (A.T.); (I.O.); (E.M.)
| | - Eugene Dillon
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland;
| | - Ian O’Connor
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (A.T.); (I.O.); (E.M.)
| | - Eugene MacCarthy
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (A.T.); (I.O.); (E.M.)
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15
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A human case of GIMAP6 deficiency: a novel primary immune deficiency. Eur J Hum Genet 2020; 29:657-662. [PMID: 33328581 PMCID: PMC7739214 DOI: 10.1038/s41431-020-00773-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 01/08/2023] Open
Abstract
The GTPase of immunity-associated proteins (GIMAPs) are a family of genes believed to contribute to lymphocyte development, signaling, and apoptosis, thus playing an important role in immune system homeostasis. While models of gene derangement have been described in both mice and immortalized cell lines, human examples of these diseases remain exceptionally rare. In this manuscript we describe the first documented human cases of a homozygous deleterious GIMAP6 variant in the GIMAP6 gene and their subsequent clinical and immunological phenotype. In order to interrogate the patients’ immune defect, we performed whole-exome sequencing, western blot, flow cytometry analysis, lymphocyte activation and proliferation studies, cytokine release assays, and apoptosis studies. We found two siblings with a predicted deleterious homozygous variant in the GIMAP6 gene with no expression of GIMAP6 protein on western blot. Patients demonstrated accelerated apoptosis, but largely normal lymphocyte subpopulations, activation and proliferation and cytokine release. There appears to be a spectrum of clinical features associated with deficiency of GIMAP6 protein, with one patient suffering lymphopenia and recurrent sinopulmonary infections, and the other clinically asymptomatic. Biallelic variants in the GIMAP6 gene have now been shown to demonstrate disease in humans. The absence of GIMAP6 protein is associated with a spectrum of clinical manifestations and much remains to be learnt about the pathogenic mechanisms underlying this disease. We suggest that biallelic variants in the gene for GIMAP6 should be considered in children with lymphopenia and recurrent sinopulmonary infections.
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16
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Zhao J, Cheng M, Gai J, Zhang R, Du T, Li Q. SPOCK2 Serves as a Potential Prognostic Marker and Correlates With Immune Infiltration in Lung Adenocarcinoma. Front Genet 2020; 11:588499. [PMID: 33244319 PMCID: PMC7683796 DOI: 10.3389/fgene.2020.588499] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 12/31/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the major types of lung cancer. Tumor-infiltrating immune cells (TIICs) are positively associated with overall survival (OS) in LUAD. The SPARC/osteonectin, cwcv and kazal-like domains proteoglycan 2 (SPOCK2) is a complex type of secreted proteoglycan involved in forming a protective barrier against viral infection. The purpose of this study was to investigate the relationship between SPOCK2 and TIICs and the prognostic role of SPOCK2 in LUAD. The GEPIA2, GEO, CPTAC, and HPA databases were analyzed to examine both the mRNA and protein expression of SPOCK2 in LUAD. GEPIA2 and the Kaplan-Meier Plotter (KM Plotter) were used to evaluate the prognostic value of SPOCK2 in LUAD patients. TCGA data were examined for a correlation between SPOCK2 expression and clinical characteristics. Gene enrichment analyses were performed to explore the underlying mechanism of SPOCK2 based on LinkedOmics. RegNetwork was used to predict the regulators of SPOCK2. The correlation between SPOCK2 and TIICs, including immune infiltration level and relative proportion was investigated via TIMER. KM Plotter was also used to evaluate the prognostic role of SPOCK2 expression in LUAD with enriched and decreased TIIC subgroups. We found SPOCK2 was significantly downregulated in LUAD compared with that in non-tumor controls and was correlated with clinical parameters. Moreover, a high SPOCK2 expression level predicted better survival. The SPOCK2-associated regulatory network was constructed. SPOCK2 influenced the TIIC infiltration level and relative proportion in LUAD. Furthermore, a high SPOCK2 expression level was associated with a favorable prognosis in enriched CD4 + T cells and macrophage subgroups in LUAD. In conclusion, a high level of SPOCK2 expression predicted favorable prognosis and was significantly correlated with TIICs in LUAD. Therefore, the expression of SPOCK2 may affect the prognosis of LUAD partly due to TIICs.
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Affiliation(s)
- Jinming Zhao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Ming Cheng
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Junda Gai
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China.,Department of Pathology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ruochen Zhang
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Tengjiao Du
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Qingchang Li
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China.,Department of Pathology, The First Affiliated Hospital of China Medical University, Shenyang, China
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17
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Bailey GF, Coelho JC, Poole AZ. Differential expression of Exaiptasia pallida GIMAP genes upon induction of apoptosis and autophagy suggests a potential role in cnidarian symbiosis and disease. J Exp Biol 2020; 223:jeb229906. [PMID: 32978315 DOI: 10.1242/jeb.229906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/15/2020] [Indexed: 01/11/2023]
Abstract
Coral reefs, one of the world's most productive and diverse ecosystems, are currently threatened by a variety of stressors that result in increased prevalence of both bleaching and disease. Therefore, understanding the molecular mechanisms involved in these responses is critical to mitigate future damage to the reefs. One group of genes that is potentially involved in cnidarian immunity and symbiosis is GTPases of immunity associated proteins (GIMAP). In vertebrates, this family of proteins is involved in regulating the fate of developing lymphocytes and interacts with proteins involved in apoptosis and autophagy. As apoptosis, autophagy and immunity have previously been shown to be involved in cnidarian symbiosis and disease, the goal of this research was to determine the role of cnidarian GIMAPs in these processes using the anemone Exaiptasia pallida To do so, GIMAP genes were characterized in the E. pallida genome and changes in gene expression were measured using qPCR in response to chemical induction of apoptosis, autophagy and treatment with the immune stimulant lipopolysaccharide (LPS) in both aposymbiotic and symbiotic anemones. The results revealed four GIMAP-like genes in E. pallida, referred to as Ep_GIMAPs Induction of apoptosis and autophagy resulted in a general downregulation of Ep_GIMAPs, but no significant changes were observed in response to LPS treatment. This indicates that Ep_GIMAPs may be involved in the regulation of apoptosis and autophagy, and therefore could play a role in cnidarian-dinoflagellate symbiosis. Overall, these results increase our knowledge on the function of GIMAPs in a basal metazoan.
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Affiliation(s)
- Grace F Bailey
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry, GA 30161, USA
| | - Jenny C Coelho
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry, GA 30161, USA
| | - Angela Z Poole
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry, GA 30161, USA
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18
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Meng Z, Ren D, Zhang K, Zhao J, Jin X, Wu H. Using ESTIMATE algorithm to establish an 8-mRNA signature prognosis prediction system and identify immunocyte infiltration-related genes in Pancreatic adenocarcinoma. Aging (Albany NY) 2020; 12:5048-5070. [PMID: 32181755 PMCID: PMC7138590 DOI: 10.18632/aging.102931] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/09/2020] [Indexed: 01/18/2023]
Abstract
OBJECTIVE The tumour microenvironment is one of the significant factors driving the carcinogenesis of Pancreatic adenocarcinoma (PAAD). However, the underlying mechanism of how the tumour microenvironment impacts the prognosis of PAAD is not completely clear. RESULTS The transcriptome and clinical data of 182 PAAD program cases were downloaded from the TCGA database. Three hundred thirty-three differentially expressed genes (DEGs) between high and low stromal groups and 314 DEGs between high and low immune score groups were identified using ESTIMATE score. Based on the 203 genes differentially expressed simultaneously in two score-related comparisons, we established an 8-mRNA signature to evaluate the prognosis of PAAD patients. Kaplan-Meier curves showed significantly worse survival for patients with high-risk scores in both the training and validation groups. The risk score was an independent prognostic factor and had a high predictive value for the prognosis of patients with PAAD. By searching the TCGA database, we showed that CA9, CXCL9, and GIMAP7 from the 8-mRNA signature were associated with the infiltration levels of immunocytes by regulating FOXO1 expression in PAAD. CONCLUSIONS Unlike traditional methods of screening for differential genes in cancer and healthy tissues, we constructed a novel 8-mRNA signature to predict the prognosis of PAAD patients by applying ESTIMATE scoring to RNA-seq-based transcriptome data. Most importantly, we identified CA9, CXCL9, and GIMAP7 from the above eight genes as regulators of immunocyte infiltration by adjusting the expression of FOXO1 in PAAD. Thus, CA9, CXCL9, and GIMAP7 might be the ideal targets of immune therapy of PAAD. METHODS ESTIMATE scoring was used to determine the stromal and immune scores of transcriptome datasets downloaded from the TCGA database. An mRNA-based prognostic signature was built for the training cohort via the LASSO Cox regression model. The signature was verified using a validation cohort. Kaplan-Meier curves and log-rank analysis were used to identify survival differences. Western blot analysis and RT-qPCR analysis were carried out to analyze the expression of specific proteins and mRNAs. IHC was performed to assess the protein levels of Forkhead box-O 1 (FOXO1), Carbonic anhydrase 9 (CA9), C-X-C motif chemokine ligand 9 (CXCL9), and GTPase, IMAP family member 7 (GIMAP7) in the tissue microarray of PAAD.
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Affiliation(s)
- Zibo Meng
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Dianyun Ren
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kun Zhang
- Department of Otorhinolaryngology-Head And Neck Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jingyuan Zhao
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xin Jin
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Heshui Wu
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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19
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Song Y, Pan Y, Liu J. The relevance between the immune response-related gene module and clinical traits in head and neck squamous cell carcinoma. Cancer Manag Res 2019; 11:7455-7472. [PMID: 31496804 PMCID: PMC6689548 DOI: 10.2147/cmar.s201177] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 07/17/2019] [Indexed: 02/05/2023] Open
Abstract
Purpose Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer in the world, accounting for more than 90% of head and neck malignant tumors. However, its molecular mechanism is largely unknown. To help elucidate the potential mechanism of HNSCC tumorigenesis, we investigated the gene interaction patterns associated with tumorigenesis. Methods Weighted gene co-expression network analysis (WGCNA) can help us to predict the intrinsic relationship or correlation between gene expression. Additionally, we further explored the combination of clinical information and module construction. Results Sixteen modules were constructed, among which the key module most closely associated with clinical information was identified. By analyzing the genes in this module, we found that the latter may be related to the immune response, inflammatory response and formation of the tumor microenvironment. Sixteen hub genes were identified-ARHGAP9, SASH3, CORO1A, ITGAL, PPP1R16B, TBC1D10C, IL10RA, ITK, AKNA, PRKCB, TRAF3IP3, GIMAP4, CCR7, P2RY8, GIMAP7, and SP140. We further validated these genes at the transcriptional and translation levels. Conclusion The innovative use of a weighted network to analyze HNSCC samples provides new insights into the molecular mechanism and prognosis of HNSCC. Additionally, the hub genes we identified can be used as biomarkers and therapeutic targets of HNSCC, laying the foundation for the accurate diagnosis and treatment of HNSCC in clinical and research in the future.
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Affiliation(s)
- Yidan Song
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yihua Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jun Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
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20
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Sun J, Xu H, Qi M, Zhang C, Shi J. Identification of key genes in osteosarcoma by meta‑analysis of gene expression microarray. Mol Med Rep 2019; 20:3075-3084. [PMID: 31432118 PMCID: PMC6755242 DOI: 10.3892/mmr.2019.10543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/17/2019] [Indexed: 12/17/2022] Open
Abstract
Osteosarcoma (OS) is one of the most malignant tumors in children and young adults. To better understand the underlying mechanism, five related datasets deposited in the Gene Expression Omnibus were included in the present study. The Bioconductor ‘limma’ package was used to identify differentially expressed genes (DEGs) and the ‘Weighted Gene Co-expression Network Analysis’ package was used to construct a weighted gene co-expression network to identify key modules and hub genes, associated with OS. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes overrepresentation analyses were used for functional annotation. The results indicated that 1,405 genes were dysregulated in OS, including 927 upregulated and 478 downregulated genes, when the cut off value was set at a ≥2 fold-change and an adjusted P-value of P<0.01 was used. Functional annotation of DEGs indicated that these genes were involved in the extracellular matrix (ECM) and that they function in several processes, including biological adhesion, ECM organization, cell migration and leukocyte migration. These findings suggested that dysregulation of the ECM shaped the tumor microenvironment and modulated the OS hallmark. Genes assigned to the yellow module were positively associated with OS and could contribute to the development of OS. In conclusion, the present study has identified several key genes that are potentially druggable genes or therapeutics targets in OS. Functional annotations revealed that the dysregulation of the ECM may contribute to OS development and, therefore, provided new insights to improve our understanding of the mechanisms underlying OS.
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Affiliation(s)
- Junkui Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Hongen Xu
- Precision Medicine Center, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Muge Qi
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China
| | - Chi Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jianxiang Shi
- Precision Medicine Center, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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21
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Histological Chorioamnionitis Induces Differential Gene Expression in Human Cord Blood Mononuclear Leukocytes from Term Neonates. Sci Rep 2019; 9:5862. [PMID: 30971730 PMCID: PMC6458165 DOI: 10.1038/s41598-019-42205-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/21/2019] [Indexed: 12/15/2022] Open
Abstract
Histological chorioamnionitis (HCA) is an infection of fetal membranes and complicates 5.2% to 28.5% of all live births. HCA is associated with increased mortality and morbidity in both premature and term neonates. Exposure to HCA may have long-term consequences, including an increased risk for allergic disorders and asthma later in childhood, the mechanism(s) of which are still not yet well understood. The objective of this study was to determine the mRNA transcriptome of cord blood mononuclear leukocytes from term neonates to identify key genes and pathways involved in HCA. We found 366 differentially expressed probe IDs with exposure to HCA (198 upregulated, 168 downregulated). These transcriptomes included novel genes and pathways associated with exposure to HCA. The differential gene expression included key genes regulating inflammatory, immune, respiratory and neurological pathways, which may contribute to disorders in those pathways in neonates exposed to HCA. Our data may lead to understanding of the role of key genes and pathways identified on the long-term sequelae related to exposure to HCA, as well as to identifying potential markers and therapies to prevent HCA-associated complications.
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22
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Ou X, Wang M, Mao S, Cao J, Cheng A, Zhu D, Chen S, Jia R, Liu M, Yang Q, Wu Y, Zhao X, Zhang S, Liu Y, Yu Y, Zhang L, Chen X, Peppelenbosch MP, Pan Q. Incompatible Translation Drives a Convergent Evolution and Viral Attenuation During the Development of Live Attenuated Vaccine. Front Cell Infect Microbiol 2018; 8:249. [PMID: 30073153 PMCID: PMC6058041 DOI: 10.3389/fcimb.2018.00249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/02/2018] [Indexed: 11/13/2022] Open
Abstract
Live attenuated vaccines are widely used to protect humans or animals from pathogen infections. We have previously developed a chicken embryo-attenuated Duck Hepatitis A Virus genotype 1 (DHAV-1) vaccine (CH60 strain). This study aims to understand the mechanisms that drive a virulent strain to an attenuated virus. Here, we systematically compared five DHAV-1 chicken embryo attenuated strains and 68 virulent strains. Phylogenetic analysis indicated that duck virulent strains isolated from different geographic regions of China undergo a convergent evolution in the chicken embryos. Comparative analysis indicated that the codon usage bias of the attenuated strains were shaped by chicken codons usage bias, which essentially contributed to viral adaption in the unsuitable host driven by incompatible translation. Of note, the missense mutations in coding region and mutations in untranslated regions may also contribute to viral attenuation of DHAV-1 to some extent. Importantly, we have experimentally confirmed that the expression levels of four viral proteins (2A3pro, 2A3pro, 3Cpro, and 3Dpro) in the liver and kidney of ducks infected with an attenuated strain are significantly lower than that infected with a virulent strain, despite with similar virus load. Thus, the key mechanisms of viral attenuation revealed by this study may lead to innovative and easy approaches in designing live attenuated vaccines.
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Affiliation(s)
- Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jingyu Cao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
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23
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Pascall JC, Webb LMC, Eskelinen EL, Innocentin S, Attaf-Bouabdallah N, Butcher GW. GIMAP6 is required for T cell maintenance and efficient autophagy in mice. PLoS One 2018; 13:e0196504. [PMID: 29718959 PMCID: PMC5931655 DOI: 10.1371/journal.pone.0196504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
The GTPases of the immunity-associated proteins (GIMAP) GTPases are a family of proteins expressed strongly in the adaptive immune system. We have previously reported that in human cells one member of this family, GIMAP6, interacts with the ATG8 family member GABARAPL2, and is recruited to autophagosomes upon starvation, suggesting a role for GIMAP6 in the autophagic process. To study this possibility and the function of GIMAP6 in the immune system, we have established a mouse line in which the Gimap6 gene can be inactivated by Cre-mediated recombination. In mice bred to carry the CD2Cre transgene such that the Gimap6 gene was deleted within the T and B cell lineages there was a 50–70% reduction in peripheral CD4+ and CD8+ T cells. Analysis of splenocyte-derived proteins from these mice indicated increased levels of MAP1LC3B, particularly the lipidated LC3-II form, and S405-phosphorylation of SQSTM1. Electron microscopic measurements of Gimap6-/- CD4+ T cells indicated an increased mitochondrial/cytoplasmic volume ratio and increased numbers of autophagosomes. These results are consistent with autophagic disruption in the cells. However, Gimap6-/- T cells were largely normal in character, could be effectively activated in vitro and supported T cell-dependent antibody production. Treatment in vitro of CD4+ splenocytes from GIMAP6fl/flERT2Cre mice with 4-hydroxytamoxifen resulted in the disappearance of GIMAP6 within five days. In parallel, increased phosphorylation of SQSTM1 and TBK1 was observed. These results indicate a requirement for GIMAP6 in the maintenance of a normal peripheral adaptive immune system and a significant role for the protein in normal autophagic processes. Moreover, as GIMAP6 is expressed in a cell-selective manner, this indicates the potential existence of a cell-restricted mode of autophagic regulation.
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Affiliation(s)
- John C. Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Louise M. C. Webb
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Eeva-Liisa Eskelinen
- Department of Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Silvia Innocentin
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Noudjoud Attaf-Bouabdallah
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Geoffrey W. Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
- * E-mail:
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24
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Pinto APA, Pereira HM, Zeraik AE, Ciol H, Ferreira FM, Brandão-Neto J, DeMarco R, Navarro MVAS, Risi C, Galkin VE, Garratt RC, Araujo APU. Filaments and fingers: Novel structural aspects of the single septin from Chlamydomonas reinhardtii. J Biol Chem 2017; 292:10899-10911. [PMID: 28476887 PMCID: PMC5491775 DOI: 10.1074/jbc.m116.762229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 05/04/2017] [Indexed: 01/22/2023] Open
Abstract
Septins are filament-forming GTP-binding proteins involved in many essential cellular events related to cytoskeletal dynamics and maintenance. Septins can self-assemble into heterocomplexes, which polymerize into highly organized, cell membrane-interacting filaments. The number of septin genes varies among organisms, and although their structure and function have been thoroughly studied in opisthokonts (including animals and fungi), no structural studies have been reported for other organisms. This makes the single septin from Chlamydomonas (CrSEPT) a particularly attractive model for investigating whether functional homopolymeric septin filaments also exist. CrSEPT was detected at the base of the flagella in Chlamydomonas, suggesting that CrSEPT is involved in the formation of a membrane-diffusion barrier. Using transmission electron microscopy, we observed that recombinant CrSEPT forms long filaments with dimensions comparable with those of the canonical structure described for opisthokonts. The GTP-binding domain of CrSEPT purified as a nucleotide-free monomer that hydrolyzes GTP and readily binds its analog guanosine 5'-3-O-(thio)triphosphate. We also found that upon nucleotide binding, CrSEPT formed dimers that were stabilized by an interface involving the ligand (G-interface). Across this interface, one monomer supplied a catalytic arginine to the opposing subunit, greatly accelerating the rate of GTP hydrolysis. This is the first report of an arginine finger observed in a septin and suggests that CrSEPT may act as its own GTP-activating protein. The finger is conserved in all algal septin sequences, suggesting a possible correlation between the ability to form homopolymeric filaments and the accelerated rate of hydrolysis that it provides.
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Affiliation(s)
- Andressa P A Pinto
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil
- the Programa de Pós-graduação em Genética Evolutiva e Biologia Molecular, UFSCar, CEP 13565-905, São Carlos, SP, Brazil
| | - Humberto M Pereira
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil
| | - Ana E Zeraik
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil
| | - Heloisa Ciol
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil
| | | | - José Brandão-Neto
- the Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom, and
| | - Ricardo DeMarco
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil
| | - Marcos V A S Navarro
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil
| | - Cristina Risi
- the Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, Virginia 23501
| | - Vitold E Galkin
- the Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, Virginia 23501
| | - Richard C Garratt
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil,
| | - Ana P U Araujo
- From the Instituto de Física de São Carlos, Universidade de São Paulo, CEP: 13563-120, São Carlos, SP, Brazil,
- the Programa de Pós-graduação em Genética Evolutiva e Biologia Molecular, UFSCar, CEP 13565-905, São Carlos, SP, Brazil
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25
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Ho CH, Tsai SF. Functional and biochemical characterization of a T cell-associated anti-apoptotic protein, GIMAP6. J Biol Chem 2017; 292:9305-9319. [PMID: 28381553 DOI: 10.1074/jbc.m116.768689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 03/31/2017] [Indexed: 11/06/2022] Open
Abstract
GTPases of immunity-associated proteins (GIMAPs) are expressed in lymphocytes and regulate survival/death signaling and cell development within the immune system. We found that human GIMAP6 is expressed primarily in T cell lines. By sorting human peripheral blood mononuclear cells and performing quantitative RT-PCR, GIMAP6 was found to be expressed in CD3+ cells. In Jurkat cells that had been knocked down for GIMAP6, treatment with hydrogen peroxide, FasL, or okadaic acid significantly increased cell death/apoptosis. Exogenous expression of GMAP6 protected Huh-7 cells from apoptosis, suggesting that GIMAP6 is an anti-apoptotic protein. Furthermore, knockdown of GIMAP6 not only rendered Jurkat cells sensitive to apoptosis but also accelerated T cell activation under phorbol 12-myristate 13-acetate/ionomycin treatment conditions. Using this experimental system, we also observed a down-regulation of p65 phosphorylation (Ser-536) in GIMAP6 knockdown cells, indicating that GIMAP6 might display anti-apoptotic function through NF-κB activation. The conclusion from the study on cultured T cells was corroborated by the analysis of primary CD3+ T cells, showing that specific knockdown of GIMAP6 led to enhancement of phorbol 12-myristate 13-acetate/ionomycin-mediated activation signals. To characterize the biochemical properties of GIMAP6, we purified the recombinant GIMAP6 to homogeneity and revealed that GIMAP6 had ATPase as well as GTPase activity. We further demonstrated that the hydrolysis activity of GIMAP6 was not essential for its anti-apoptotic function in Huh-7 cells. Combining the expression data, biochemical properties, and cellular features, we conclude that GIMAP6 plays a role in modulating immune function and that it does this by controlling cell death and the activation of T cells.
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Affiliation(s)
- Ching-Huang Ho
- From the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan and
| | - Shih-Feng Tsai
- From the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan and .,the Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan
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26
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Serrano D, Ghobadi F, Boulay G, Ilangumaran S, Lavoie C, Ramanathan S. GTPase of the Immune-Associated Nucleotide Protein 5 Regulates the Lysosomal Calcium Compartment in T Lymphocytes. Front Immunol 2017; 8:94. [PMID: 28223986 PMCID: PMC5293772 DOI: 10.3389/fimmu.2017.00094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/19/2017] [Indexed: 12/20/2022] Open
Abstract
T lymphocytes from Gimap5lyp/lyp rats carrying a recessive mutation in the GTPase of immune-associated protein 5 (Gimap5) gene undergo spontaneous apoptosis. Molecular mechanisms underlying this survival defect are not yet clear. We have shown that Gimap5lyp/lyp T lymphocytes display reduced calcium influx following T cell antigen receptor (TCR) stimulation that was associated with impaired buffering of calcium by mitochondria. Here, we investigated the subcellular localization of GIMAP5 and its influence on Ca2+ response in HEK293T cells and T lymphocytes. The more abundantly expressed GIMAP5v2 localizes to the lysosome and certain endosomal vesicles. Gimap5lyp/lyp T lymphocytes showed increased accumulation of calcium in the lysosomes as evidenced by Gly-Phe β-naphthylamide (GPN) triggered Ca2+ release. As a corollary, GPN-induced Ca2+ flux was decreased in HEK293T cells expressing GIMAP5v2. Strikingly, TCR stimulation of rat, mouse, and human T lymphocytes increased lysosomal calcium content. Overall, our findings show that lysosomes modulate cellular Ca2+ response during T cell activation and that GIMAP5 regulates the lysosomal Ca2+ compartment in T lymphocytes.
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Affiliation(s)
- Daniel Serrano
- Immunology Division, Department of Pediatrics, Université de Sherbrooke , Sherbrooke, QC , Canada
| | - Farnaz Ghobadi
- Immunology Division, Department of Pediatrics, Université de Sherbrooke , Sherbrooke, QC , Canada
| | - Guylain Boulay
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada; Centre de recherche clinique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Subburaj Ilangumaran
- Immunology Division, Department of Pediatrics, Université de Sherbrooke, Sherbrooke, QC, Canada; Centre de recherche clinique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christine Lavoie
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada; Centre de recherche clinique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Sheela Ramanathan
- Immunology Division, Department of Pediatrics, Université de Sherbrooke, Sherbrooke, QC, Canada; Centre de recherche clinique, Université de Sherbrooke, Sherbrooke, QC, Canada
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27
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Aberrant activation of the GIMAP enhancer by oncogenic transcription factors in T-cell acute lymphoblastic leukemia. Leukemia 2016; 31:1798-1807. [PMID: 28028313 PMCID: PMC5529293 DOI: 10.1038/leu.2016.392] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/16/2022]
Abstract
The transcription factor TAL1/SCL is one of the most prevalent oncogenes in T-cell acute lymphoblastic leukemia (T-ALL), a malignant disorder resulting from leukemic transformation of thymus T-cell precursors. TAL1 is normally expressed in hematopoietic stem cells (HSCs) but is silenced in immature thymocytes. We hypothesize that TAL1 contributes to leukemogenesis by activating genes that are normally repressed in immature thymocytes. Herein, we identified a novel TAL1-regulated super-enhancer controlling the GIMAP locus, which resides within an insulated chromosomal locus in T-ALL cells. The GIMAP genes are expressed in HSCs and mature T-cells but are downregulated during the immature stage of thymocyte differentiation. The GIMAP enhancer is activated by TAL1, RUNX1 and GATA3 in human T-ALL cells but is repressed by E-proteins. Overexpression of human GIMAP genes in immature thymocytes alone does not induce tumorigenesis but accelerates leukemia development in zebrafish. Our results demonstrate that aberrant activation of the GIMAP enhancer contributes to T-cell leukemogenesis.
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28
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Daumke O, Praefcke GJK. Invited review: Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily. Biopolymers 2016; 105:580-93. [PMID: 27062152 PMCID: PMC5084822 DOI: 10.1002/bip.22855] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/29/2022]
Abstract
Dynamin superfamily proteins are multidomain mechano-chemical GTPases which are implicated in nucleotide-dependent membrane remodeling events. A prominent feature of these proteins is their assembly- stimulated mechanism of GTP hydrolysis. The molecular basis for this reaction has been initially clarified for the dynamin-related guanylate binding protein 1 (GBP1) and involves the transient dimerization of the GTPase domains in a parallel head-to-head fashion. A catalytic arginine finger from the phosphate binding (P-) loop is repositioned toward the nucleotide of the same molecule to stabilize the transition state of GTP hydrolysis. Dynamin uses a related dimerization-dependent mechanism, but instead of the catalytic arginine, a monovalent cation is involved in catalysis. Still another variation of the GTP hydrolysis mechanism has been revealed for the dynamin-like Irga6 which bears a glycine at the corresponding position in the P-loop. Here, we highlight conserved and divergent features of GTP hydrolysis in dynamin superfamily proteins and show how nucleotide binding and hydrolysis are converted into mechano-chemical movements. We also describe models how the energy of GTP hydrolysis can be harnessed for diverse membrane remodeling events, such as membrane fission or fusion. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 580-593, 2016.
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Affiliation(s)
- Oliver Daumke
- Kristallographie, Max-Delbrück Centrum Für Molekulare Medizin, Robert-Rössle-Straße 10, Berlin, 13125, Germany
- Institut Für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, Berlin, 14195, Germany
| | - Gerrit J K Praefcke
- Abteilung Hämatologie/Transfusionsmedizin, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, Langen, 63225, Germany
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29
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Chen XL, Serrano D, Ghobadi F, Mayhue M, Hoebe K, Ilangumaran S, Ramanathan S. TCR and IL-7 Signaling Are Altered in the Absence of Functional GTPase of the Immune Associated Nucleotide Binding Protein 5 (GIMAP5). PLoS One 2016; 11:e0151837. [PMID: 27023180 PMCID: PMC4811415 DOI: 10.1371/journal.pone.0151837] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/05/2016] [Indexed: 01/09/2023] Open
Abstract
GTPase of the immune associated nucleotide binding protein (GIMAP) family of proteins are expressed essentially in cells of the hematopoietic system. Mutation in the founding member of this gene family, Gimap5, results in the lymphopenic phenotype in Bio-Breeding diabetes prone rats. In mice, deletion of functional Gimap5 gene affects the survival and renewal of hematopoietic stem cells in addition to the defects observed in T cells. Here we show that T cells from OTII TCR-transgenic Gimap5sph/sph mice do not proliferate in response to its cognate antigen. Furthermore, T cells from Gimap5 mutant rats and mice show decreased phosphorylation of STAT5 following stimulation with IL-7. Our results suggest that functional Gimap5 is required for optimal signaling through TCR and IL-7R in T cells.
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Affiliation(s)
- Xi-Lin Chen
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Daniel Serrano
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Farnaz Ghobadi
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Marian Mayhue
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Kasper Hoebe
- Department of Pediatrics, Division of Cellular and Molecular Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States of America
| | - Subburaj Ilangumaran
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Centre de recherche clinique, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Sheela Ramanathan
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Centre de recherche clinique, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- * E-mail:
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30
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Jokinen R, Marttinen P, Stewart JB, Neil Dear T, Battersby BJ. Tissue-specific modulation of mitochondrial DNA segregation by a defect in mitochondrial division. Hum Mol Genet 2015; 25:706-14. [PMID: 26681804 DOI: 10.1093/hmg/ddv508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/08/2015] [Indexed: 01/19/2023] Open
Abstract
Mitochondria are dynamic organelles that divide and fuse by remodeling an outer and inner membrane in response to developmental, physiological and stress stimuli. These events are coordinated by conserved dynamin-related GTPases. The dynamics of mitochondrial morphology require coordination with mitochondrial DNA (mtDNA) to ensure faithful genome transmission, however, this process remains poorly understood. Mitochondrial division is linked to the segregation of mtDNA but how it affects cases of mtDNA heteroplasmy, where two or more mtDNA variants/mutations co-exist in a cell, is unknown. Segregation of heteroplasmic human pathogenic mtDNA mutations is a critical factor in the onset and severity of human mitochondrial diseases. Here, we investigated the coupling of mitochondrial morphology to the transmission and segregation of mtDNA in mammals by taking advantage of two genetically modified mouse models: one with a dominant-negative mutation in the dynamin-related protein 1 (Drp1 or Dnm1l) that impairs mitochondrial fission and the other, heteroplasmic mice segregating two neutral mtDNA haplotypes (BALB and NZB). We show a tissue-specific response to mtDNA segregation from a defect in mitochondrial fission. Only mtDNA segregation in the hematopoietic compartment is modulated from impaired Dnm1l function. In contrast, no effect was observed in other tissues arising from the three germ layers during development and in mtDNA transmission through the female germline. Our data suggest a robust organization of a heteroplasmic mtDNA segregating unit across mammalian cell types that can overcome impaired mitochondrial division to ensure faithful transmission of the mitochondrial genome.
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Affiliation(s)
- Riikka Jokinen
- Research Programs Unit - Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Paula Marttinen
- Research Programs Unit - Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany and
| | - T Neil Dear
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Brendan J Battersby
- Research Programs Unit - Molecular Neurology, University of Helsinki, Helsinki, Finland,
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31
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Chen XL, Serrano D, Mayhue M, Hoebe K, Ilangumaran S, Ramanathan S. GIMAP5 Deficiency Is Associated with Increased AKT Activity in T Lymphocytes. PLoS One 2015; 10:e0139019. [PMID: 26440416 PMCID: PMC4595448 DOI: 10.1371/journal.pone.0139019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/07/2015] [Indexed: 01/05/2023] Open
Abstract
Long-term survival of T lymphocytes in quiescent state is essential to maintain their cell numbers in secondary lymphoid organs. In mice and in rats, the loss of functional GTPase of the immune associated nucleotide binding protein 5 (GIMAP5) causes peripheral T lymphopenia due to spontaneous death of T cells. The underlying mechanism responsible for the disruption of quiescence in Gimap5 deficient T cells remains largely unknown. In this study, we show that loss of functional Gimap5 results in increased basal activation of mammalian target of rapamycin (mTOR), independent of protein phosphatase 2A (PP2A) or AMP-activated protein kinase (AMPK). Our results suggest that the constitutive activation of the phosphoinositide 3-kinase (PI3K) pathway may be one of the consequences of the absence of functional GIMAP5.
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Affiliation(s)
- Xi-Lin Chen
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Daniel Serrano
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Marian Mayhue
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Kasper Hoebe
- Department of Pediatrics, Division of Cellular and Molecular Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States of America
| | - Subburaj Ilangumaran
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Centre de Recherche Clinique, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Sheela Ramanathan
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Centre de Recherche Clinique, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- * E-mail:
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32
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Heinonen MT, Laine AP, Söderhäll C, Gruzieva O, Rautio S, Melén E, Pershagen G, Lähdesmäki HJ, Knip M, Ilonen J, Henttinen TA, Kere J, Lahesmaa R. GIMAP GTPase family genes: potential modifiers in autoimmune diabetes, asthma, and allergy. THE JOURNAL OF IMMUNOLOGY 2015; 194:5885-94. [PMID: 25964488 DOI: 10.4049/jimmunol.1500016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/30/2015] [Indexed: 12/31/2022]
Abstract
GTPase of the immunity-associated protein (GIMAP) family members are differentially regulated during human Th cell differentiation and have been previously connected to immune-mediated disorders in animal studies. GIMAP4 is believed to contribute to the Th cell subtype-driven immunological balance via its role in T cell survival. GIMAP5 has a key role in BB-DR rat and NOD mouse lymphopenia. To elucidate GIMAP4 and GIMAP5 function and role in human immunity, we conducted a study combining genetic association in different immunological diseases and complementing functional analyses. Single nucleotide polymorphisms tagging the GIMAP haplotype variation were genotyped in Finnish type 1 diabetes (T1D) families and in a prospective Swedish asthma and allergic sensitization birth cohort. Initially, GIMAP5 rs6965571 was associated with risk for asthma and allergic sensitization (odds ratio [OR] 3.74, p = 0.00072, and OR 2.70, p = 0.0063, respectively) and protection from T1D (OR 0.64, p = 0.0058); GIMAP4 rs13222905 was associated with asthma (OR 1.28, p = 0.035) and allergic sensitization (OR 1.27, p = 0.0068). However, after false discovery rate correction for multiple testing, only the associations of GIMAP4 with allergic sensitization and GIMAP5 with asthma remained significant. In addition, transcription factor binding sites surrounding the associated loci were predicted. A gene-gene interaction in the T1D data were observed between the IL2RA rs2104286 and GIMAP4 rs9640279 (OR 1.52, p = 0.0064) and indicated between INS rs689 and GIMAP5 rs2286899. The follow-up functional analyses revealed lower IL-2RA expression upon GIMAP4 knockdown and an effect of GIMAP5 rs2286899 genotype on protein expression. Thus, the potential role of GIMAP4 and GIMAP5 as modifiers of immune-mediated diseases cannot be discarded.
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Affiliation(s)
- Mirkka T Heinonen
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland; Turku Doctoral Programme of Molecular Medicine, University of Turku, 20520 Turku Finland
| | - Antti-Pekka Laine
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland
| | - Cilla Söderhäll
- Department of Bioscience and Nutrition and Center for Innovative Medicine, Karolinska Institutet, 141 83 Huddinge, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Sini Rautio
- Department of Information and Computer Science, Aalto University, 02150 Espoo, Finland
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden; Karolinska University Hospital, Astrid Lindgren Children's Hospital, 171 76 Solna, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Harri J Lähdesmäki
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland; Folkhälsan Research Institute, 00290 Helsinki, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland; Department of Clinical Microbiology, University of Eastern Finland, 70211 Kuopio, Finland; and
| | | | - Juha Kere
- Department of Bioscience and Nutrition and Center for Innovative Medicine, Karolinska Institutet, 141 83 Huddinge, Stockholm, Sweden; Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland;
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Central role of gimap5 in maintaining peripheral tolerance and T cell homeostasis in the gut. Mediators Inflamm 2015; 2015:436017. [PMID: 25944983 PMCID: PMC4405212 DOI: 10.1155/2015/436017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/15/2014] [Indexed: 01/01/2023] Open
Abstract
Inflammatory bowel disease (IBD) including Crohn's disease and ulcerative colitis is often precipitated by an abnormal immune response to microbiota due to host genetic aberrancies. Recent studies highlight the importance of the host genome and microflora interactions in the pathogenesis of mucosal inflammation including IBD. Specifically, genome-wide (GWAS) and also next-generation sequencing (NGS)—including whole exome or genome sequencing—have uncovered a large number of susceptibility loci that predispose to autoimmune diseases and/or the two phenotypes of IBD. In addition, the generation of “IBD-prone” animal models using both reverse and forward genetic approaches has not only helped confirm the identification of susceptibility loci but also shed critical insight into the underlying molecular and cellular pathways that drive colitis development. In this review, we summarize recent findings derived from studies involving a novel early-onset model of colitis as it develops in GTPase of immunity-associated protein 5- (Gimap5-) deficient mice. In humans, GIMAP5 has been associated with autoimmune diseases although its function is poorly defined. Here, we discuss how defects in Gimap5 function impair immunological tolerance and lymphocyte survival and ultimately drive the development of CD4+ T cell-mediated early-onset colitis.
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Quantitative changes in Gimap3 and Gimap5 expression modify mitochondrial DNA segregation in mice. Genetics 2015; 200:221-35. [PMID: 25808953 DOI: 10.1534/genetics.115.175596] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/20/2015] [Indexed: 01/22/2023] Open
Abstract
Mammalian mitochondrial DNA (mtDNA) is a high-copy maternally inherited genome essential for aerobic energy metabolism. Mutations in mtDNA can lead to heteroplasmy, the co-occurence of two different mtDNA variants in the same cell, which can segregate in a tissue-specific manner affecting the onset and severity of mitochondrial dysfunction. To investigate mechanisms regulating mtDNA segregation we use a heteroplasmic mouse model with two polymorphic neutral mtDNA haplotypes (NZB and BALB) that displays tissue-specific and age-dependent selection for mtDNA haplotypes. In the hematopoietic compartment there is selection for the BALB mtDNA haplotype, a phenotype that can be modified by allelic variants of Gimap3. Gimap3 is a tail-anchored member of the GTPase of the immunity-associated protein (Gimap) family of protein scaffolds important for leukocyte development and survival. Here we show how the expression of two murine Gimap3 alleles from Mus musculus domesticus and M. m. castaneus differentially affect mtDNA segregation. The castaneus allele has incorporated a uORF (upstream open reading frame) in-frame with the Gimap3 mRNA that impairs translation and imparts a negative effect on the steady-state protein abundance. We found that quantitative changes in the expression of Gimap3 and the paralogue Gimap5, which encodes a lysosomal protein, affect mtDNA segregation in the mouse hematopoietic tissues. We also show that Gimap3 localizes to the endoplasmic reticulum and not mitochondria as previously reported. Collectively these data show that the abundance of protein scaffolds on the endoplasmic reticulum and lysosomes are important to the segregation of the mitochondrial genome in the mouse hematopoietic compartment.
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Webb LMC, Pascall JC, Hepburn L, Carter C, Turner M, Butcher GW. Generation and characterisation of mice deficient in the multi-GTPase domain containing protein, GIMAP8. PLoS One 2014; 9:e110294. [PMID: 25329815 PMCID: PMC4201521 DOI: 10.1371/journal.pone.0110294] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/17/2014] [Indexed: 02/06/2023] Open
Abstract
Background GTPases of the immunity-associated protein family (GIMAPs) are predominantly expressed in mature lymphocytes. Studies of rodents deficient in GIMAP1, GIMAP4, or GIMAP5 have demonstrated that these GTPases regulate lymphocyte survival. In contrast to the other family members, GIMAP8 contains three potential GTP-binding domains (G-domains), a highly unusual feature suggesting a novel function for this protein. To examine a role for GIMAP8 in lymphocyte biology we examined GIMAP8 expression during lymphocyte development. We also generated a mouse deficient in GIMAP8 and examined lymphocyte development and function. Principal Findings We show that GIMAP8 is expressed in the very early and late stages of T cell development in the thymus, at late stages during B cell development, and peripheral T and B cells. We find no defects in T or B lymphocyte development in the absence of GIMAP8. A marginal decrease in the number of recirculating bone marrow B cells suggests that GIMAP8 is important for the survival of mature B cells within the bone marrow niche. We also show that deletion of GIMAP8 results in a delay in apoptotic death of mature T cell in vitro in response to dexamethasone or γ-irradiation. However, despite these findings we find that GIMAP8-deficient mice mount normal primary and secondary responses to a T cell dependent antigen. Conclusions Despite its unique structure, GIMAP8 is not required for lymphocyte development but appears to have a minor role in maintaining recirculating B cells in the bone marrow niche and a role in regulating apoptosis of mature T cells.
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Affiliation(s)
- Louise M. C. Webb
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
- * E-mail:
| | - John C. Pascall
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Lucy Hepburn
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Christine Carter
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Geoffrey W. Butcher
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
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Ciucci T, Bosselut R. Gimap and T cells: a matter of life or death. Eur J Immunol 2014; 44:348-51. [PMID: 24510500 DOI: 10.1002/eji.201344375] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 12/29/2013] [Accepted: 01/13/2014] [Indexed: 11/08/2022]
Abstract
GTPase immune-associated proteins (Gimap) genes encode evolutionarily conserved GTP-binding proteins that are preferentially expressed in immune cells. Specific members have been shown to be involved in lymphocyte development, or are associated with inflammatory and autoimmune diseases. However, the function of these proteins remains poorly understood, both at the cellular and molecular levels. A new study in this issue of the European Journal of Immunology [Eur. J. Immunol. 2014. 44: 561-572] points to the distinct but partly overlapping functions of two members of this family, Gimap3 and Gimap5, and offers new insight into their potential functions in T cells.
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Affiliation(s)
- Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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