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Ramos-Rodríguez M, Subirana-Granés M, Norris R, Sordi V, Fernández Á, Fuentes-Páez G, Pérez-González B, Berenguer Balaguer C, Raurell-Vila H, Chowdhury M, Corripio R, Partelli S, López-Bigas N, Pellegrini S, Montanya E, Nacher M, Falconi M, Layer R, Rovira M, González-Pérez A, Piemonti L, Pasquali L. Implications of noncoding regulatory functions in the development of insulinomas. CELL GENOMICS 2024:100604. [PMID: 38959898 DOI: 10.1016/j.xgen.2024.100604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/22/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in β cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of β cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations.
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Affiliation(s)
- Mireia Ramos-Rodríguez
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marc Subirana-Granés
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Richard Norris
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Valeria Sordi
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ángel Fernández
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain; Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, Spain
| | - Georgina Fuentes-Páez
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Beatriz Pérez-González
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Clara Berenguer Balaguer
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Helena Raurell-Vila
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Murad Chowdhury
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Raquel Corripio
- Paediatric Endocrinology Department, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Stefano Partelli
- Pancreas Translational & Research Institute, Scientific Institute San Raffaele Hospital and University Vita-Salute, Milan, Italy
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Silvia Pellegrini
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eduard Montanya
- Bellvitge Hospital-IDIBELL, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Montserrat Nacher
- Bellvitge Hospital-IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Massimo Falconi
- Pancreas Translational & Research Institute, Scientific Institute San Raffaele Hospital and University Vita-Salute, Milan, Italy
| | - Ryan Layer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA; Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
| | - Meritxell Rovira
- Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain; Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lorenzo Piemonti
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lorenzo Pasquali
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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Zhang Y, Liu S, Liu D, Zhao Z, Song H, Peng K. Identification and validation of GIMAP family genes as immune-related prognostic biomarkers in lung adenocarcinoma. Heliyon 2024; 10:e33111. [PMID: 38948046 PMCID: PMC11211882 DOI: 10.1016/j.heliyon.2024.e33111] [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: 07/26/2023] [Revised: 05/15/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024] Open
Abstract
Background The GIMAP family genes play a key role in immune function. Increasing evidence suggests that GIMAP genes were implicated in the tumorigenesis of lung adenocarcinoma (LUAD). This study aimed to investigate the clinical significance of GIMAP family genes in LUAD. Methods In this study, we explored the expression, mutation, prognostic value of GIMAP family genes and the correlation with immune microenvironment in LUAD. We further investigated the relationship between GIMAP family genes expression and immunotherapy response in GEO LUAD and melanoma cohorts. Results Among the GIMAP family genes, the expression levels of GIMAP1, GIMAP2, GIMAP4, GIMAP5, GIMAP6, GIMAP7, and GIMAP8 were significantly lower in LUAD tumor tissues than normal tissues. Most GIMAP genes were closely related to age, tumor grade and T stage, but not significantly related to sex, N stage and M stage. In the overall population, patients with high expression of GIMAP family genes had a significant longer overall survival (OS). GO and KEGG enrichment analysis showed that GIMAP family genes were highly enriched in immune-related biological process. The expression of GIMAP family genes was positively correlated with immune cell infiltration and immune checkpoint molecules. Furthermore, high expression of GIMAP family genes were correlated with therapeutic response to immunotherapy in LUAD and melanoma patients. Conclusion In this study, we identified that GIMAP family genes were significantly associated with immune cell infiltration and immune checkpoint molecules. They potentially play a critical role in anti-tumor immunity and serve as immunotherapy biomarkers.
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Affiliation(s)
- Yanyan Zhang
- Department of Infectious Diseases, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Shan Liu
- Department of Cardiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Cardiovascular Disease, Guangzhou, Guangdong, China
| | - Deyi Liu
- Department of General Practice, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhuxiang Zhao
- Department of Infectious Diseases, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Haifeng Song
- Department of Oncology, Lianzhou People's Hospital, Lianzhou, Guangdong, China
| | - Kunwei Peng
- Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy & Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Oncology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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3
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Chandrasekaran V, Wellens S, Bourguignon A, Djidrovski I, Fransen L, Ghosh S, Mazidi Z, Murphy C, Nunes C, Singh P, Zana M, Armstrong L, Dinnyés A, Grillari J, Grillari-Voglauer R, Leonard MO, Verfaillie C, Wilmes A, Zurich MG, Exner T, Jennings P, Culot M. Evaluation of the impact of iPSC differentiation protocols on transcriptomic signatures. Toxicol In Vitro 2024; 98:105826. [PMID: 38615723 DOI: 10.1016/j.tiv.2024.105826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Human induced pluripotent stem cells (iPSC) have the potential to produce desired target cell types in vitro and allow for the high-throughput screening of drugs/chemicals at population level thereby minimising the cost of drug discovery and drug withdrawals after clinical trials. There is a substantial need for the characterisation of the iPSC derived models to better understand and utilise them for toxicological relevant applications. In our study, iPSC (SBAD2 or SBAD3 lines obtained from StemBANCC project) were differentiated towards toxicologically relevant cell types: alveolar macrophages, brain capillary endothelial cells, brain cells, endothelial cells, hepatocytes, lung airway epithelium, monocytes, podocytes and renal proximal tubular cells. A targeted transcriptomic approach was employed to understand the effects of differentiation protocols on these cell types. Pearson correlation and principal component analysis (PCA) separated most of the intended target cell types and undifferentiated iPSC models as distinct groups with a high correlation among replicates from the same model. Based on PCA, the intended target cell types could also be separated into the three germ layer groups (ectoderm, endoderm and mesoderm). Differential expression analysis (DESeq2) presented the upregulated genes in each intended target cell types that allowed the evaluation of the differentiation to certain degree and the selection of key differentiation markers. In conclusion, these data confirm the versatile use of iPSC differentiated cell types as standardizable and relevant model systems for in vitro toxicology.
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Affiliation(s)
- Vidya Chandrasekaran
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Sara Wellens
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Aurore Bourguignon
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Ivo Djidrovski
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Leonie Fransen
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Sreya Ghosh
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Zahra Mazidi
- Evercyte GmbH, Vienna, Austria; Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cormac Murphy
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Carolina Nunes
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - Pranika Singh
- Edelweiss Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, 4057 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | | | - Lyle Armstrong
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - András Dinnyés
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Johannes Grillari
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Ludwig Boltzmann Institute for Traumatology in cooperation with AUVA, Vienna, Austria
| | | | - Martin O Leonard
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Marie-Gabrielle Zurich
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | | | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands.
| | - Maxime Culot
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France.
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Cui L, Shen Y, Duan S, Ding Q, Wang Y, Yang W, Chen Y. GIMAP7 inhibits epithelial-mesenchymal transition and glycolysis in lung adenocarcinoma cells via regulating the Smo/AMPK signaling pathway. Thorac Cancer 2024; 15:286-298. [PMID: 38151913 PMCID: PMC10834198 DOI: 10.1111/1759-7714.15150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND GTPase immunity-associated protein 7 (GIMAP7) has been previously recognized as a prognostic marker in pan-cancer. Our objective was to explore the function of GIMAP7 in the progression of lung adenocarcinoma (LUAD). METHODS GIMAP7 was overexpressed by transfection with GIMAP7 plasmid, and knocked down using siRNAs. The biological functions of GIMAP7 were examined by employing CCK-8, EdU, colony formation, flow cytometry, wound healing, and transwell assays. The effects of GIMAP7 on the extracellular acidification rate (ECAR), oxygen consumption rate (OCR), lactate production, and glucose uptake were evaluated. In addition, the related mRNA and protein expression was detected employing immunohistochemical, western blot, and qRT-PCR. A xenograft tumor model was established in nude mice to evaluate the effects of GIMAP7 on tumor growth. RESULTS GIMAP7 was lowly expressed in LUAD tissues and cells. GIMAP7 inhibited the proliferation, mobility, EMT, glycolysis, but promoted apoptosis in LUAD cells. Moreover, we also confirmed that GIMAP7 suppressed Smo/AMPK signaling in LUAD cells. By adding the Smo agonist SAG and AMPK agonist GSK621, the results of rescue experiments further verified that GIMAP7 played a role in LUAD inhibition through inhibition of the Smo/AMPK signaling pathway. Furthermore, the role of GIMAP7 in inhibiting tumor growth was verified in vivo. CONCLUSIONS These results demonstrate that GIMAP7 could inhibit cell proliferation, mobility and glycolysis, but accelerate apoptosis via repressing the Smo/AMPK signaling pathway in LUAD.
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Affiliation(s)
- Liyuan Cui
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yumei Shen
- Operation Room Department, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shanzhou Duan
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qifeng Ding
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yifei Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Wentao Yang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yongbing Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Greco F, Panunzio A, Tafuri A, Bernetti C, Pagliarulo V, Beomonte Zobel B, Scardapane A, Mallio CA. Radiogenomic Features of GIMAP Family Genes in Clear Cell Renal Cell Carcinoma: An Observational Study on CT Images. Genes (Basel) 2023; 14:1832. [PMID: 37895181 PMCID: PMC10606653 DOI: 10.3390/genes14101832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
GTPases of immunity-associated proteins (GIMAP) genes include seven functional genes and a pseudogene. Most of the GIMAPs have a role in the maintenance and development of lymphocytes. GIMAPs could inhibit the development of tumors by increasing the amount and antitumor activity of infiltrating immunocytes. Knowledge of key factors that affect the tumor immune microenvironment for predicting the efficacy of immunotherapy and establishing new targets in ccRCC is of great importance. A computed tomography (CT)-based radiogenomic approach was used to detect the imaging phenotypic features of GIMAP family gene expression in ccRCC. In this retrospective study we enrolled 193 ccRCC patients divided into two groups: ccRCC patients with GIMAP expression (n = 52) and ccRCC patients without GIMAP expression (n = 141). Several imaging features were evaluated on preoperative CT scan. A statistically significant correlation was found with absence of endophytic growth pattern (p = 0.049), tumor infiltration (p = 0.005), advanced age (p = 0.018), and high Fuhrman grade (p = 0.024). This study demonstrates CT imaging features of GIMAP expression in ccRCC. These results could allow the collection of data on GIMAP expression through a CT-approach and could be used for the development of a targeted therapy.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella Della Salute, Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy
| | - Andrea Panunzio
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.); (V.P.)
| | - Alessandro Tafuri
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.); (V.P.)
| | - Caterina Bernetti
- Department of Medicine and Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Vincenzo Pagliarulo
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.); (V.P.)
| | - Bruno Beomonte Zobel
- Department of Medicine and Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Arnaldo Scardapane
- Dipartimento Interdisciplinare di Medicina, Sezione di Diagnostica Per Immagini, Università degli Studi di Bari “Aldo Moro”, Piazza Giulio Cesare, 11, 70124 Bari, Italy;
| | - Carlo Augusto Mallio
- Department of Medicine and Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
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Clancy J, Hoffmann CS, Pickett BE. Transcriptomics secondary analysis of severe human infection with SARS-CoV-2 identifies gene expression changes and predicts three transcriptional biomarkers in leukocytes. Comput Struct Biotechnol J 2023; 21:1403-1413. [PMID: 36785619 PMCID: PMC9908618 DOI: 10.1016/j.csbj.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
SARS-CoV-2 is the causative agent of COVID-19, which has greatly affected human health since it first emerged. Defining the human factors and biomarkers that differentiate severe SARS-CoV-2 infection from mild infection has become of increasing interest to clinicians. To help address this need, we retrieved 269 public RNA-seq human transcriptome samples from GEO that had qualitative disease severity metadata. We then subjected these samples to a robust RNA-seq data processing workflow to calculate gene expression in PBMCs, whole blood, and leukocytes, as well as to predict transcriptional biomarkers in PBMCs and leukocytes. This process involved using Salmon for read mapping, edgeR to calculate significant differential expression levels, and gene ontology enrichment using Camera. We then performed a random forest machine learning analysis on the read counts data to identify genes that best classified samples based on the COVID-19 severity phenotype. This approach produced a ranked list of leukocyte genes based on their Gini values that includes TGFBI, TTYH2, and CD4, which are associated with both the immune response and inflammation. Our results show that these three genes can potentially classify samples with severe COVID-19 with accuracy of ∼88% and an area under the receiver operating characteristic curve of 92.6--indicating acceptable specificity and sensitivity. We expect that our findings can help contribute to the development of improved diagnostics that may aid in identifying severe COVID-19 cases, guide clinical treatment, and improve mortality rates.
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Xu A, Fan Y, Liu S, Sheng L, Sun Y, Yang H. GIMAP7 induces oxidative stress and apoptosis of ovarian granulosa cells in polycystic ovary syndrome by inhibiting sonic hedgehog signalling pathway. J Ovarian Res 2022; 15:141. [PMID: 36581994 PMCID: PMC9801623 DOI: 10.1186/s13048-022-01092-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a gynaecological endocrine disease. The objective of the present study was to investigate the role of GTPase immunity-associated protein (GIMAP) 7 in PCOS. A PCOS rat model was established using dehydroepiandrosterone injection. The data showed that GIMAP7 was mainly located in granulosa cells and was abundantly expressed in the ovarian granulosa cells of PCOS rats. GIMAP7 silencing decreased blood glucose levels, HOMA-IR scores, and number of cystic follicles. In addition, GIMAP7 silencing corrected erratic oestrous cycles, inhibited apoptosis and reduced c-caspase-3 protein expression in the ovarian tissues of PCOS rats. GIMAP7 silencing reduced malondialdehyde (MDA) but increased glutathione (GSH) and superoxide dismutase (SOD) levels in the serum and ovarian tissues of PCOS rats. The effects of GIMAP7 were further investigated in human ovarian granulosa KGN cells. GIMAP7 silencing increased the viability, promoted proliferation, and increased the percentage of S-phase KGN cells. The apoptosis rate was significantly decreased by GIMAP7 silencing. GIMAP7 also inhibited oxidative stress in KGN cells, resulting in decreased levels of reactive oxygen species (ROS) and MDA and increased levels of GSH and SOD. Notably, GIMAP7 inhibited the sonic hedgehog (SHH) signalling pathway, and GIMAP7 silencing increased the expression of the SHH signalling pathway downstream genes SHH, SMO, and Gli1. Inhibition of the SHH signalling pathway using cyclopamine reduced the effect of GIMAP7 silencing on KGN cells. This study proved that GIMAP7 promotes oxidative stress and apoptosis in ovarian granulosa cells in PCOS by inhibiting the SHH signalling pathway.
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Affiliation(s)
- Anran Xu
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Yuanyuan Fan
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Song Liu
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Lianbing Sheng
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Yanyan Sun
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Huijun Yang
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
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Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. Proc Natl Acad Sci U S A 2022; 119:e2119602119. [PMID: 35733255 PMCID: PMC9245644 DOI: 10.1073/pnas.2119602119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Seadragons are widely recognized for their derived traits, which include leaf-like appendages and extreme spinal curvature. Efforts to understand the genetic basis of these unique traits and conserve these species and their relatives have been limited by genomic resource gaps. In this paper we present full, annotated genomes of leafy and weedy seadragons, which we use to uncover surprising features of gene family and genome architecture evolution that likely relate to the extravagant phenotypic traits of seadragons and their pipefish and seahorse relatives. These genomes and their analyses are important advances for the study of elaborate vertebrate traits, leveraging this diverse, morphologically exceptional group of fishes. Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations of evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent noncoding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve reorganization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and hold value for conservation of the extravagant seadragons and their relatives.
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9
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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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10
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Wu H, Dong X, Liao L, Huang L. An Integrative Analysis Identifying RAB40C as an Oncogenic Immune Protein and Prognostic Marker of Lung Squamous Cell Carcinoma. Pharmgenomics Pers Med 2022; 15:525-537. [PMID: 35645578 PMCID: PMC9135582 DOI: 10.2147/pgpm.s357166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background RAB40C, a member of the Ras oncogene family, is a protein with GTPase and GTP-binding activity and is also predicted to be important in immunomodulation. However, the link between RAB40C and lung squamous cell carcinoma (LUSC) has not yet been elucidated. Exploring the relationship between RAB40C and LUSC could help expand the repertoire of immunotherapeutic targets for LUSC and provide more effective therapeutic options for LUSC patients, which behalf of our aim for our study. Methods We analyzed the RAB40C expression in different tumor types and stages based on the TCGA database. Subsequently, we explored the differences in RAB40C expression in LUSC versus paracancerous tissues through immunohistochemical analysis. The prognostic value of RAB40C was assessed by Cox regression and Kaplan-Meier analysis. Gene set enrichment analysis-based RAB40C impact pathways and the correlation between RAB40C expression and immune infiltration were obtained using the TIMER2.0 and the CIBERSORT analytical tools. Tumor mutational load and microsatellite instability (MSI) were assessed by the Spearman correlation analysis. Finally, the close association of RAB40C with LUSC was explored by correlating immune cell infiltration with immunomodulator expression, assessing risk scores in combination with other factors, and analyzing prognostic nomogram. Results The expression of RAB40C was significantly elevated in LUSC. RAB40C expression was significantly associated with immune factors, immune-related pathways, and MSI. Moreover, RAB40C significantly negatively correlated with LUSC-associated immune infiltrating cells, CD4 memory-activated cells, γδ T cells, M1-like macrophages, and the immune regulator CD28, while it positively associated with the activation of Tregs and natural killer cells. Further, a risk model constructed from RAB40C and its associated immune genes showed that RAB40C might be an independent prognostic factor for LUSC. Conclusion RAB40C can be used as an effective prognostic biomarker and a potential immunotherapeutic target for the treatment of LUSC.
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Affiliation(s)
- Hong Wu
- Department of Pneumology, Yiwu Central Hospital, Yiwu, Zhejiang, People’s Republic of China
- Correspondence: Hong Wu, Department of Pneumology, Yiwu Central Hospital, Yiwu, Zhejiang, People’s Republic of China, Email
| | - Xuhui Dong
- Department of Pneumology, Yiwu Central Hospital, Yiwu, Zhejiang, People’s Republic of China
| | - Lixian Liao
- Department of Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Lihaoyun Huang
- Department of Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
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11
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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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12
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Huo X, Shen G, Li J, Wang M, Xie Q, Zhao F, Ren D, Dong Q, Zhao J. Identification of the GTPase IMAP family as an immune-related prognostic biomarker in the breast cancer tumor microenvironment. Gene 2021; 812:146094. [PMID: 34896519 DOI: 10.1016/j.gene.2021.146094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Breast cancer is the most common malignancy threatening women's health worldwide. The GTPase IMAP family genes are proteins belonging to the immune-associated nucleotide subfamily of the GTP-binding superfamily and nucleotide-binding proteins. However, little is known about the role of different GTPase IMAP family genes in breast cancer. METHODS We obtained differential genes from the GEPIA and UALCAN databases and then used the Kaplan-Meier plotter, The Human Protein Atlas, NetworkAnalyst, STRING, and TIMER to analyze the prognostic value, protein expression, and immune cell infiltration of the GTPase IMAP family in patients with breast cancer. RESULTS Among the GIMAP family genes, the expression levels of GIMAP1, GIMAP5, GIMAP6, GIMAP7, and GIMAP8 were significantly low in breast tumor tissues. In the overall population, patients with high expression of all genes of the GIMAP family had a significantly higher overall survival (OS), with the most significant increase correlated with the GIMAP2 gene (hazard ratio [HR] = 0.45, 95% confidence interval [CI], 0.34-0.59, P = 3.1e-09). However, patients with high expression of the GIMAP family genes in triple-negative breast cancer compared to those with low expression had a significant OS benefit, with the most pronounced benefit correlated with the GIMAP2 gene (HR = 0.37, 95% CI, 0.23-0.59, P = 1.4e-05). GIMAP7 and GIMAP8 were significantly upregulated in breast tumor tissues. The expression of genes in different GIMAP families was positively correlated with the infiltration and expression of six immune cell types (B cells, CD4+ T cells, CD8+ T cells, macrophages, neutrophils, and dendritic cells). CONCLUSION This study may provide novel insights into the selection of GIMAP family prognostic biomarkers for breast cancer.
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Affiliation(s)
- Xingfa Huo
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Guoshuang Shen
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Jinming Li
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Miaozhou Wang
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Qiqi Xie
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Fuxing Zhao
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Dengfeng Ren
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China
| | - Qiuxia Dong
- The Fifth People's Hospital of Qinghai Province, The Second Ward of Oncology, Xining 810000, China
| | - Jiuda Zhao
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining 810000, China.
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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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Bitter MC, Kapsenberg L, Silliman K, Gattuso JP, Pfister CA. Magnitude and Predictability of pH Fluctuations Shape Plastic Responses to Ocean Acidification. Am Nat 2021; 197:486-501. [PMID: 33755541 DOI: 10.1086/712930] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractPhenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus galloprovincialis. We linked differences in the magnitude and predictability of pH fluctuations in two habitats to population-specific gene expression profiles in ambient and stressful pH treatments. Our results demonstrate population-based differentiation in gene expression plasticity, whereby mussels native to a habitat exhibiting a large magnitude of pH fluctuations with low predictability display reduced phenotypic plasticity between experimentally imposed pH treatments. This work validates recent theoretical findings on evolution in fluctuating environments, suggesting that the predictability of fluctuating selection pressures may play a predominant role in shaping the phenotypic variation observed across natural populations.
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Lu S, Zhu T, Wang Z, Luo L, Wang S, Lu M, Cui Y, Zou B, Hua J. Arabidopsis immune-associated nucleotide-binding genes repress heat tolerance at the reproductive stage by inhibiting the unfolded protein response and promoting cell death. MOLECULAR PLANT 2021; 14:267-284. [PMID: 33221412 DOI: 10.1016/j.molp.2020.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/15/2020] [Accepted: 11/15/2020] [Indexed: 06/11/2023]
Abstract
Plants are vulnerable to heat stress, especially during reproductive development. The heat shock response (HSR) in the cytosol and nucleus, as well as the unfolded protein response (UPR) in the endoplasmic reticulum (ER), are two mechanisms that enable plants to survive heat stress. Excessive heat or ER stresses lead to cell death when the UPR cannot repair stress damage, but the means by which cell survival or death is determined remains unclear. In this study, we used a genome-wide association study (GWAS) to identify that a cluster of five Immune-associated nucleotide-binding protein (IAN) genes (IAN2 to IAN6) is responsible for variation in heat tolerance at the reproductive stage in Arabidopsis thaliana. These IAN genes have both unique and overlapping functions in the negative regulation of heat tolerance, and their loss of function singly or in combination confers increased heat tolerance, measured by a lower number of barren siliques and a higher seedling survival rate under heat. The loss of rice IAN1 gene function also leads to enhanced heat tolerance, suggesting a conserved function of plant IANs. Transcriptome analysis revealed enhanced expression of HSR and UPR genes, as well as reduced cell death, under heat and ER stress in the mutant of IAN6, a major effect member in Arabidopsis. Furthermore, the IAN proteins were found to promote cell death induced by heat stress, ER stress, and cell death-inducing molecules. Thus, the Arabidopsis IAN genes repress heat tolerance, probably through the HSR and UPR and by enhancing the cell death pathway. The IAN2 to IAN6 proteins are partially localized to the ER, suggesting a direct role in the UPR and UPR-mediated cell death. In addition, a natural IAN6 variant from more heat-tolerant Arabidopsis accessions confers greater heat tolerance and induces less cell death compared with the natural variant from less heat-tolerant accessions. The heat-tolerant IAN6 variant is associated with a higher maximum temperature of the warmest month at its collection sites compared with the heat-sensitive variant. Taken together, these results reveal an important role of Arabidopsis IAN2 to IAN6 genes in the regulation of the HSR, UPR, and cell death, and suggest that their natural variations have adaptive functions in heat tolerance.
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Affiliation(s)
- Shan Lu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Tianquan Zhu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhixue Wang
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lilin Luo
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Wang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Minghui Lu
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA; College of Horticulture, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Yongmei Cui
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Baohong Zou
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jian Hua
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
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Xu F, Shen J, Xu S. Integrated Bioinformatical Analysis Identifies GIMAP4 as an Immune-Related Prognostic Biomarker Associated With Remodeling in Cervical Cancer Tumor Microenvironment. Front Cell Dev Biol 2021; 9:637400. [PMID: 33553190 PMCID: PMC7858649 DOI: 10.3389/fcell.2021.637400] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor microenvironment (TME) is emerging as an essential part of cervical cancer (CC) tumorigenesis and development, becoming a hotspot of research these years. However, comprehending the specific composition of TME is still facing enormous challenges, especially the immune and stromal components. In this study, we downloaded the RNA-seq profiles and somatic mutation data of 309 CC cases from The Cancer Genome Atlas (TCGA) database, which were analyzed by integrative bioinformatical methods. Initially, ESTIMATE computational method was employed to calculate the amount of immune and stromal components. Then, based on the high- and low-immunity cohorts, we recognized the differentially expressed genes (DEGs) as well as the differentially mutated genes (DMGs). Additionally, we conducted an intersection analysis of DEGs and DMGs, ultimately determining an immune-related prognostic signature, GTPase, IMAP Family Member 4 (GIMAP4). Moreover, sequential analyses demonstrated that GIMAP4 was a protective factor in CC, positively correlated with the overall survival (OS) and negatively with distant metastasis. Besides, we utilized the Gene Set Enrichment Analysis (GSEA) to explore the enrichment-pathways in high and low-expression cohorts of GIMAP4. The results indicated that the genes of the high-expression cohort had a high enrichment in immune-related biological processes and metabolic activities in the low one. Furthermore, CIBERSORT analysis was applied to evaluate the proportion of tumor-infiltrating immune cells (TICs), illustrating that several activated TICs were strongly associated with GIMAP4 expression, which suggested that GIMAP4 had the potential to be an indicator for the immune state in TME of CC. Hence, GIMAP4 contributed to predicting the CC patients’ clinical outcomes, such as survival rate, distant metastasis and immunotherapy response. Moreover, GIMAP4 could serve as a promising biomarker for TME remodeling, suggesting the possible underlying mechanisms of tumorigenesis and CC progression, which may provide different therapeutic perceptions of CC, and therefore improve treatment.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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17
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Guillen N. Signals and signal transduction pathways in Entamoeba histolytica during the life cycle and when interacting with bacteria or human cells. Mol Microbiol 2020; 115:901-915. [PMID: 33249684 DOI: 10.1111/mmi.14657] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 01/17/2023]
Abstract
Entamoeba histolytica is the etiological agent of amebiasis in humans. This ameba parasite resides as a commensal in the intestine where it shares intestinal resources with the bacterial microbiome. In the intestinal ecosystem, the ameba encysts and eventually develops disease by invading the tissues. E. histolytica possesses cell surface receptors for the proper sensing of signals involved in encystation or sustaining parasite interaction with bacteria and human cells. Among those receptors are the Gal/GalNAc lectin, G protein-coupled receptors, and transmembrane kinases. In addition there are recently discovered, promising proteins, including orthologs of Toll-type receptors and β trefoil lectins. These proteins trigger a wide variety of signal transduction pathways; however, most of the players involved in the signaling pathways evoked in this parasite are unknown. This review provides an overview of amoebic receptors and their role in encystation, adherence to bacteria or human cells, as well as the reported intracellular signal transduction processes that they can trigger. This knowledge is essential for understanding the lifestyle of E. histolytica and its cytopathic effect on bacteria and human cells that are responsible for infection.
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Affiliation(s)
- Nancy Guillen
- Institut Pasteur, Centre National de la Recherche Scientifique, CNRS-ERL9195, Paris, France
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18
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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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19
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Systemic analyses of expression patterns and clinical features for GIMAPs family members in lung adenocarcinoma. Aging (Albany NY) 2020; 12:20413-20431. [PMID: 33115964 PMCID: PMC7655191 DOI: 10.18632/aging.103836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022]
Abstract
GTPase of immunity-associated proteins (GIMAPs) are frequently prescribed as important components of immune regulation complexes, which were known to play key roles in lung adenocarcinoma. However, little is known about the function of distinct GIMAPs in lung adenocarcinoma. To address this issue, this study investigated the biological function and pathway of GIMAPs in lung adenocarcinoma using multiple public databases. Absent expression of GIMAPs was found in lung adenocarcinoma at mRNA and protein levels. While a purity-corrected value uncovered that all GIMAPs were positively associated with the immune infiltration of lung adenocarcinoma. Furthermore, the expressions of GIMAPs were considered to be negatively associated with clinical cancer stages, patient’s gender and pathological tumor grades in patients with lung adenocarcinoma. Besides, higher mRNA expression of GIMAPs was significantly associated with longer overall survival of patients with lung adenocarcinoma. Taken together, these results may enable GIMAPs family members as diagnostic and survival biomarker candidates or even potential therapeutic targets for patients with lung adenocarcinoma.
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20
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Mégarbané A, Piquemal D, Rebillat AS, Stora S, Pierrat F, Bruno R, Noguier F, Mircher C, Ravel A, Vilaire-Meunier M, Durand S, Lefranc G. Transcriptomic study in women with trisomy 21 identifies a possible role of the GTPases of the immunity-associated proteins (GIMAP) in the protection of breast cancer. Sci Rep 2020; 10:9447. [PMID: 32523132 PMCID: PMC7286899 DOI: 10.1038/s41598-020-66469-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND People with trisomy 21 (T21) are predisposed to developing hematological tumors, but have significantly lower-than-expected age-adjusted incidence rates of having a solid tumor. MATERIAL AND METHODS To identify novel genetic factors implicated in the lower breast cancer (BC) frequency observed in women with T21 than in the general population, we compared the transcriptome pattern of women with a homogeneous T21, aged more than 30 years, with or without BC, and tumoral BC tissue of control women with a normal karyotype from the study of Varley et al. (2014). RESULTS Differential analysis of gene expression between the 15 women in the T21 without BC group and BC patients in the other groups (two women with T21 and fifteen control women, respectively) revealed 154 differentially expressed genes, of which 63 were found to have similar expression profile (up- or downregulated). Of those 63 genes, four were in the same family, namely GIMAP4, GIMAP6, GIMAP7 and GIMAP8, and were strongly upregulated in the T21 without BC group compared to the other groups. A significant decrease in mRNA levels of these genes in BC tissues compared to non-tumor breast tissues was also noted. CONCLUSION We found that the expression of some GIMAPs is significantly higher in women with T21 without BC than in patients with sporadic BC. Our findings support the hypothesis that GIMAPs may play a tumor-suppressive role against BC, and open the possibility that they may also have the same role for other solid tumors in T21 patients. The search for new prognostic factors and hopefully new therapeutic or preventive strategies against BC are discussed.
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Affiliation(s)
- André Mégarbané
- Institut Jérôme Lejeune, CRB BioJeL, Paris, France. .,Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon.
| | | | | | | | | | | | | | | | - Aimé Ravel
- Institut Jérôme Lejeune, CRB BioJeL, Paris, France
| | | | | | - Gérard Lefranc
- Institut de Génétique Humaine, UMR 9002 CNRS-Université de Montpellier, Montpellier, France
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21
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Comparative Transcriptome Analysis of Gill Tissue in Response to Hypoxia in Silver Sillago ( Sillago sihama). Animals (Basel) 2020; 10:ani10040628. [PMID: 32268576 PMCID: PMC7222756 DOI: 10.3390/ani10040628] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/05/2020] [Accepted: 04/05/2020] [Indexed: 12/11/2022] Open
Abstract
Silver sillago (Sillago sihama) is a commercially important marine fish species in East Asia. In this study, we compared the transcriptome response to hypoxia stress in the gill tissue of S. sihama. The fish were divided into four groups, such as 1 h of hypoxia (hypoxia1h, DO = 1.5 ± 0.1 mg/L), 4 h of hypoxia (hypoxia4h, DO = 1.5 ± 0.1 mg/L), 4 h of reoxygen (reoxygen4h, DO = 8.0 ± 0.2 mg/L) after 4 h of hypoxia (DO = 1.5 mg/L), and normoxia or control (DO = 8.0 ± 0.2 mg/L) groups. Compared to the normoxia group, a total of 3550 genes were identified as differentially expressed genes (DEGs) (log2foldchange > 1 and padj < 0.05), including 1103, 1451 and 996 genes in hypoxia1h, hypoxia4h and reoxygen4h groups, respectively. Only 247 DEGs were differentially co-expressed in all treatment groups. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, DEGs were significantly enriched in steroid biosynthesis, biosynthesis of amino acids, glutathione metabolism and metabolism of xenobiotics by cytochrome P450, ferroptosis and drug metabolism-cytochrome P450 pathways. Of these, the cytochrome P450 (CYP) and glutathione S-transferase (GST) gene families were widely expressed. Our study represents the insights into the underlying molecular mechanisms of hypoxia stress.
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22
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Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH, Chain FJJ. Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes. Genome Biol Evol 2020; 11:2344-2359. [PMID: 31298693 PMCID: PMC6735750 DOI: 10.1093/gbe/evz148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfälische Wilhelms University, Münster, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, USA
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23
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Lu L, Loker ES, Zhang SM, Buddenborg SK, Bu L. Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni. BMC Genomics 2020; 21:190. [PMID: 32122294 PMCID: PMC7053062 DOI: 10.1186/s12864-020-6534-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The AIG (avrRpt2-induced gene) family of GTPases, characterized by the presence of a distinctive AIG1 domain, is mysterious in having a peculiar phylogenetic distribution, a predilection for undergoing expansion and loss, and an uncertain functional role, especially in invertebrates. AIGs are frequently represented as GIMAPs (GTPase of the immunity associated protein family), characterized by presence of the AIG1 domain along with coiled-coil domains. Here we provide an overview of the remarkably expanded AIG repertoire of the freshwater gastropod Biomphalaria glabrata, compare it with AIGs in other organisms, and detail patterns of expression in B. glabrata susceptible or resistant to infection with Schistosoma mansoni, responsible for the neglected tropical disease of intestinal schistosomiasis. RESULTS We define the 7 conserved motifs that comprise the AIG1 domain in B. glabrata and detail its association with at least 7 other domains, indicative of functional versatility of B. glabrata AIGs. AIG genes were usually found in tandem arrays in the B. glabrata genome, suggestive of an origin by segmental gene duplication. We found 91 genes with complete AIG1 domains, including 64 GIMAPs and 27 AIG genes without coiled-coils, more than known for any other organism except Danio (with > 100). We defined expression patterns of AIG genes in 12 different B. glabrata organs and characterized whole-body AIG responses to microbial PAMPs, and of schistosome-resistant or -susceptible strains of B. glabrata to S. mansoni exposure. Biomphalaria glabrata AIG genes clustered with expansions of AIG genes from other heterobranch gastropods yet showed unique lineage-specific subclusters. Other gastropods and bivalves had separate but also diverse expansions of AIG genes, whereas cephalopods seem to lack AIG genes. CONCLUSIONS The AIG genes of B. glabrata exhibit expansion in both numbers and potential functions, differ markedly in expression between strains varying in susceptibility to schistosomes, and are responsive to immune challenge. These features provide strong impetus to further explore the functional role of AIG genes in the defense responses of B. glabrata, including to suppress or support the development of medically relevant S. mansoni parasites.
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Affiliation(s)
- Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131 USA
| | - Eric S. Loker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131 USA
| | - Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131 USA
| | - Sarah K. Buddenborg
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Lijing Bu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131 USA
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24
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Sabater-Lleal M, Huffman JE, de Vries PS, Marten J, Mastrangelo MA, Song C, Pankratz N, Ward-Caviness CK, Yanek LR, Trompet S, Delgado GE, Guo X, Bartz TM, Martinez-Perez A, Germain M, de Haan HG, Ozel AB, Polasek O, Smith AV, Eicher JD, Reiner AP, Tang W, Davies NM, Stott DJ, Rotter JI, Tofler GH, Boerwinkle E, de Maat MPM, Kleber ME, Welsh P, Brody JA, Chen MH, Vaidya D, Soria JM, Suchon P, van Hylckama Vlieg A, Desch KC, Kolcic I, Joshi PK, Launer LJ, Harris TB, Campbell H, Rudan I, Becker DM, Li JZ, Rivadeneira F, Uitterlinden AG, Hofman A, Franco OH, Cushman M, Psaty BM, Morange PE, McKnight B, Chong MR, Fernandez-Cadenas I, Rosand J, Lindgren A, Gudnason V, Wilson JF, Hayward C, Ginsburg D, Fornage M, Rosendaal FR, Souto JC, Becker LC, Jenny NS, März W, Jukema JW, Dehghan A, Trégouët DA, Morrison AC, Johnson AD, O'Donnell CJ, Strachan DP, Lowenstein CJ, Smith NL. Genome-Wide Association Transethnic Meta-Analyses Identifies Novel Associations Regulating Coagulation Factor VIII and von Willebrand Factor Plasma Levels. Circulation 2019; 139:620-635. [PMID: 30586737 DOI: 10.1161/circulationaha.118.034532] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Factor VIII (FVIII) and its carrier protein von Willebrand factor (VWF) are associated with risk of arterial and venous thrombosis and with hemorrhagic disorders. We aimed to identify and functionally test novel genetic associations regulating plasma FVIII and VWF. METHODS We meta-analyzed genome-wide association results from 46 354 individuals of European, African, East Asian, and Hispanic ancestry. All studies performed linear regression analysis using an additive genetic model and associated ≈35 million imputed variants with natural log-transformed phenotype levels. In vitro gene silencing in cultured endothelial cells was performed for candidate genes to provide additional evidence on association and function. Two-sample Mendelian randomization analyses were applied to test the causal role of FVIII and VWF plasma levels on the risk of arterial and venous thrombotic events. RESULTS We identified 13 novel genome-wide significant ( P≤2.5×10-8) associations, 7 with FVIII levels ( FCHO2/TMEM171/TNPO1, HLA, SOX17/RP1, LINC00583/NFIB, RAB5C-KAT2A, RPL3/TAB1/SYNGR1, and ARSA) and 11 with VWF levels ( PDHB/PXK/KCTD6, SLC39A8, FCHO2/TMEM171/TNPO1, HLA, GIMAP7/GIMAP4, OR13C5/NIPSNAP, DAB2IP, C2CD4B, RAB5C-KAT2A, TAB1/SYNGR1, and ARSA), beyond 10 previously reported associations with these phenotypes. Functional validation provided further evidence of association for all loci on VWF except ARSA and DAB2IP. Mendelian randomization suggested causal effects of plasma FVIII activity levels on venous thrombosis and coronary artery disease risk and plasma VWF levels on ischemic stroke risk. CONCLUSIONS The meta-analysis identified 13 novel genetic loci regulating FVIII and VWF plasma levels, 10 of which we validated functionally. We provide some evidence for a causal role of these proteins in thrombotic events.
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Affiliation(s)
- Maria Sabater-Lleal
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden (M.S.-L.).,Unit of Genomics of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau, IIB-Sant Pau, Barcelona, Spain (M.S.-L., A.M.-P., J.M.S.)
| | - Jennifer E Huffman
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.).,Framingham Heart Study, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.)
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health (P.S.d.V., E.B., M.F., A.C.M.), University of Texas Health Science Center at Houston.,Department of Epidemiology (P.S.d.V., A.H., O.H.F., A.D.), Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine (J.M., J.F.W., C.H.), University of Edinburgh, Scotland
| | - Michael A Mastrangelo
- Aab Cardiovascular Research Institute, University of Rochester Medical Center, NY (M.A.M., C.J.L.)
| | - Ci Song
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.).,Framingham Heart Study, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.)
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis (N.P.)
| | - Cavin K Ward-Caviness
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C.)
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., D.V., D.M.B., L.C.B.)
| | - Stella Trompet
- Department of Geriatrics and Gerontology (S.T.), Leiden University Medical Center, the Netherlands.,Department of Cardiology (S.T., J.W.J.), Leiden University Medical Center, the Netherlands
| | - Graciela E Delgado
- Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (G.E.D., M.E.K., W.M.)
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA (X.G., J.I.R.)
| | - Traci M Bartz
- Department of Biostatistics (T.M.B., B.M.), University of Washington, Seattle
| | - Angel Martinez-Perez
- Unit of Genomics of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau, IIB-Sant Pau, Barcelona, Spain (M.S.-L., A.M.-P., J.M.S.)
| | - Marine Germain
- Institut national de la santé et de la recherche médicale (INSERM), UMR_S 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, Sorbonne Universités, Université Pierre-et-Marie-Curie, Paris, France (M.G., D.-A.T.).,ICAN Institute for Cardiometabolism and Nutrition, Paris, France (M.G., D.-A.T.)
| | - Hugoline G de Haan
- Department of Clinical Epidemiology (H.G.d.H., A.v.H.V., F.R.R.), Leiden University Medical Center, the Netherlands
| | - Ayse B Ozel
- Department of Human Genetics (A.B.O., J.Z.L., D.G.), University of Michigan, Ann Arbor
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Croatia (O.P., I.K.)
| | - Albert V Smith
- School of Public Health, Department of Biostatistics (A.V.S.), University of Michigan, Ann Arbor
| | - John D Eicher
- Framingham Heart Study, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.)
| | - Alex P Reiner
- Department of Epidemiology, (A.P.R., B.M.P., N.L.S.), University of Washington, Seattle.,Fred Hutchinson Cancer Research Center, Seattle, WA (A.P.R.)
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis (W.T.)
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit and Bristol Medical School (N.M.D.), University of Bristol, UK
| | - David J Stott
- Academic Section of Geriatrics, Faculty of Medicine (J.D.S.), University of Glasgow, UK
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA (X.G., J.I.R.)
| | - Geoffrey H Tofler
- Royal North Shore Hospital, University of Sydney, Australia (G.H.T.)
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health (P.S.d.V., E.B., M.F., A.C.M.), University of Texas Health Science Center at Houston.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (E.B.)
| | - Moniek P M de Maat
- Department of Hematology (M.P.M.d.M.), Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marcus E Kleber
- Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (G.E.D., M.E.K., W.M.).,Institute of Nutrition, Friedrich-Schiller-University Jena, Mannheim, Germany (M.E.K.)
| | - Paul Welsh
- Institute of Cardiovascular and Medical Sciences (P.W.), University of Glasgow, UK
| | - Jennifer A Brody
- Department of Medicine (J.A.B., B.M.P.), University of Washington, Seattle
| | - Ming-Huei Chen
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.).,Framingham Heart Study, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.)
| | - Dhananjay Vaidya
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., D.V., D.M.B., L.C.B.)
| | - José Manuel Soria
- Unit of Genomics of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau, IIB-Sant Pau, Barcelona, Spain (M.S.-L., A.M.-P., J.M.S.)
| | - Pierre Suchon
- Laboratory of Haematology, La Timone Hospital, Marseille, France (P.S., P.-E.M.).,Institut national de la santé et de la recherche médicale (INSERM), UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille, France (P.S., P.-E.M.)
| | - Astrid van Hylckama Vlieg
- Department of Clinical Epidemiology (H.G.d.H., A.v.H.V., F.R.R.), Leiden University Medical Center, the Netherlands
| | - Karl C Desch
- Department of Pediatrics and Communicable Disease (K.D.C.), University of Michigan, Ann Arbor
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Croatia (O.P., I.K.)
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics (P.K.J., H.C., I.R., J.F.W.), University of Edinburgh, Scotland
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences National Institute on Aging, Bethesda, MD (L.J.L., T.B.H.)
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences National Institute on Aging, Bethesda, MD (L.J.L., T.B.H.)
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics (P.K.J., H.C., I.R., J.F.W.), University of Edinburgh, Scotland
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics (P.K.J., H.C., I.R., J.F.W.), University of Edinburgh, Scotland
| | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., D.V., D.M.B., L.C.B.)
| | - Jun Z Li
- Department of Human Genetics (A.B.O., J.Z.L., D.G.), University of Michigan, Ann Arbor
| | - Fernando Rivadeneira
- Department of Internal Medicine (F.R., A.G.U.), Erasmus University Medical Center, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine (F.R., A.G.U.), Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology (P.S.d.V., A.H., O.H.F., A.D.), Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Harvard H.T. Chan School of Public Health, Boston, MA (A.H.)
| | - Oscar H Franco
- Department of Epidemiology (P.S.d.V., A.H., O.H.F., A.D.), Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute of Social and Preventive Medicine, University of Bern, Switzerland (O.H.F.)
| | - Mary Cushman
- Larner College of Medicine, University of Vermont, Colchester (M.C.)
| | - Bruce M Psaty
- Department of Epidemiology, (A.P.R., B.M.P., N.L.S.), University of Washington, Seattle.,Department of Medicine (J.A.B., B.M.P.), University of Washington, Seattle.,Department of Health Services (B.M.P.), University of Washington, Seattle.,Kaiser Permanente Washington Research Institute, Kaiser Permanente Washington, Seattle (B.M.P., N.L.S.)
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France (P.S., P.-E.M.).,Institut national de la santé et de la recherche médicale (INSERM), UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille, France (P.S., P.-E.M.)
| | - Barbara McKnight
- Department of Biostatistics (T.M.B., B.M.), University of Washington, Seattle.,Cardiovascular Health Research Unit (B.M.), University of Washington, Seattle
| | - Michael R Chong
- McMaster University, Population Health Research Institute, Population Health Research Institute, Biochemistry and Biomedical Sciences, Hamilton, Canada (M.R.C.)
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and genetics, Department of Neurology, Institut d'Investigació Biomedica Sant Pau, IIB-Sant Pau, Barcelona, Spain (I.F.-C.)
| | - Jonathan Rosand
- Massachusetts General Hospital, Broad Institute, Harvard Medical School, Boston (J.R.)
| | - Arne Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (A.L.).,Department of Neurology and Rehabilitation Medicine, Neurology, Skåne University Hospital, Lund, Sweden (A.L.)
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur (V.G.).,Faculty of Medicine, University of Iceland, Reykjavik (V.G.)
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine (J.M., J.F.W., C.H.), University of Edinburgh, Scotland.,Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics (P.K.J., H.C., I.R., J.F.W.), University of Edinburgh, Scotland
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine (J.M., J.F.W., C.H.), University of Edinburgh, Scotland
| | - David Ginsburg
- Department of Human Genetics (A.B.O., J.Z.L., D.G.), University of Michigan, Ann Arbor
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health (P.S.d.V., E.B., M.F., A.C.M.), University of Texas Health Science Center at Houston.,Brown Foundation Institute of Molecular Medicine (M.F.), University of Texas Health Science Center at Houston
| | - Frits R Rosendaal
- Department of Clinical Epidemiology (H.G.d.H., A.v.H.V., F.R.R.), Leiden University Medical Center, the Netherlands.,Einthoven Laboratory of Experimental Vascular Medicine (F.R.R., J.W.J.), Leiden University Medical Center, the Netherlands
| | - Juan Carlos Souto
- Unit of Hemostasis and Thrombosis, Hospital de la Sant Creu i Sant Pau, Barcelona, Spain (J.C.S.)
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., D.V., D.M.B., L.C.B.)
| | - Nancy S Jenny
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Colchester (N.S.J.)
| | - Winfried März
- Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (G.E.D., M.E.K., W.M.).,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany (W.M.).,Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Mannheim, Germany (W.M.)
| | - J Wouter Jukema
- Department of Cardiology (S.T., J.W.J.), Leiden University Medical Center, the Netherlands.,Einthoven Laboratory of Experimental Vascular Medicine (F.R.R., J.W.J.), Leiden University Medical Center, the Netherlands.,Interuniversity Cardiology Institute of the Netherlands, Utrecht (J.W.J.)
| | - Abbas Dehghan
- Department of Epidemiology (P.S.d.V., A.H., O.H.F., A.D.), Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology and Biostatistics, Imperial College London, UK (A.D.)
| | - David-Alexandre Trégouët
- Institut national de la santé et de la recherche médicale (INSERM), UMR_S 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, Sorbonne Universités, Université Pierre-et-Marie-Curie, Paris, France (M.G., D.-A.T.).,ICAN Institute for Cardiometabolism and Nutrition, Paris, France (M.G., D.-A.T.)
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health (P.S.d.V., E.B., M.F., A.C.M.), University of Texas Health Science Center at Houston
| | - Andrew D Johnson
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.).,Framingham Heart Study, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.)
| | - Christopher J O'Donnell
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.).,Framingham Heart Study, MA (J.E.H., C.S., J.D.E., M.-H.C., A.D.J., C.J.O.).,Cardiology Section Administration, Boston VA Healthcare System, West Roxbury, MA (C.J.O.)
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, UK (D.P.S.)
| | - Charles J Lowenstein
- Aab Cardiovascular Research Institute, University of Rochester Medical Center, NY (M.A.M., C.J.L.)
| | - Nicholas L Smith
- Department of Epidemiology, (A.P.R., B.M.P., N.L.S.), University of Washington, Seattle.,Kaiser Permanente Washington Research Institute, Kaiser Permanente Washington, Seattle (B.M.P., N.L.S.).,Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, WA (N.L.S.)
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25
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Zhang W, Xu S, Wu G, Liu Y, Wang Q, Man C. Exploring the expression and preliminary function of chicken Gimap5 gene. PeerJ 2019; 7:e7618. [PMID: 31579581 PMCID: PMC6766365 DOI: 10.7717/peerj.7618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/05/2019] [Indexed: 11/20/2022] Open
Abstract
GTPase immune-associated protein 5 (Gimap5) plays a key role in maintaining T cell homeostasis, immunological tolerance and inflammatory processes. However, there are no reports on the chicken Gimap5 gene. In this study, the Gimap5 gene was first cloned from chicken and characterized its tissue expression characteristics in different developmental stages. The transcriptional activities of the Gimap5 gene in immune response were identified. The results showed that full-length cDNA sequence of Gimap5 contained 771 bp and encoded a 256-amino acid protein. The Gimap5 gene was transcribed in various tissues and different development stages. The transcriptional activities of Gimap5 gene in the most tissues increased with the development of chicken, but significantly up to peak in liver and large intestine of 10-month-old chicken. The Gimap5 gene exhibited differential transcriptional activities in immune-related tissues in immune responses, with down-regulated in liver (P < 0.01), spleen (P < 0.05) and bursa of Fabricius (P < 0.05), and up-regulated in thymus (P < 0.01). The results show that Gimap5 may be a multifunctional gene involved in tissue function, development and immune response in chicken. These data can provide the foundation for further study of Gimap5.
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Affiliation(s)
- Wanting Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Sifan Xu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Guanxian Wu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Yang Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Qiuyuan Wang
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Chaolai Man
- College of Life Science and Technology, Harbin Normal University, Harbin, China
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26
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Guerin MN, Weinstein DJ, Bracht JR. Stress Adapted Mollusca and Nematoda Exhibit Convergently Expanded Hsp70 and AIG1 Gene Families. J Mol Evol 2019; 87:289-297. [PMID: 31486870 DOI: 10.1007/s00239-019-09900-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
We recently sequenced the genome of the first subterrestrial metazoan, the nematode Halicephalobus mephisto. A central finding was a dramatic expansion of genes encoding avrRpt2 induced gene (AIG1), and 70 kDa heat shock (Hsp70) domains. While the role of Hsp70 in thermotolerance is well established, the contribution of AIG1 is much more poorly characterized, though in plants some members of this family are heat-induced. Hypothesizing that this dual domain expansion may constitute a general biosignature of thermal stress adaptation, here we examine a number of genomes, finding that expansion of both AIG1 and Hsp70 is common in bivalves. Phylogenetic analysis reveals that the bivalve-specific Hsp70 protein expansion groups with H. mephisto sequences. Our identification of the same gene expansions in bivalves and a nematode implies that this biosignature may be a general stress adaptation strategy for protostomes, particularly those organisms that cannot escape their stressful environments. We hypothesize that the two families play largely complementary mechanistic roles, with Hsp70 directly refolding heat-denatured proteins while AIG1 promotes cellular and organismal survival by inhibiting apoptosis.
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Affiliation(s)
- Megan N Guerin
- Department of Biology, American University, Washington, DC, 20016, USA
| | | | - John R Bracht
- Department of Biology, American University, Washington, DC, 20016, USA.
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27
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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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28
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Falter C, Thu NBA, Pokhrel S, Reumann S. New guidelines for fluorophore application in peroxisome targeting analyses in transient plant expression systems. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:884-899. [PMID: 30791204 DOI: 10.1111/jipb.12791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Peroxisome research has been revolutionized by proteome studies combined with in vivo subcellular targeting analyses. Yellow and cyan fluorescent protein (YFP and CFP) are the classical fluorophores of plant peroxisome research. In the new transient expression system of Arabidopsis seedlings co-cultivated with Agrobacterium we detected the YFP fusion of one candidate protein in peroxisomes, but only upon co-transformation with the peroxisome marker, CFP-PTS1. The data suggested that the YFP fusion was directed to peroxisomes due to its weak heterodimerization ability with CFP-PTS1, allowing piggy-back import into peroxisomes. Indeed, if co-expressed with monomeric Cerulean-PTS1 (mCer-PTS1), the YFP fusion was no longer matrix localized. We systematically investigated the occurrence and extent of dimerization-based piggy-back import for different fluorophore combinations in five major transient plant expression systems. In Arabidopsis seedlings and tobacco leaves both untagged YFP and monomeric Venus were imported into peroxisomes if co-expressed with CFP-PTS1 but not with mCer-PTS1. By contrast, piggy-back import of cytosolic proteins was not observed in Arabidopsis and tobacco protoplasts or in onion epidermal cells for any fluorophore combination at any time point. Based on these important results we formulate new guidelines for fluorophore usage and experimental design to guarantee reliable identification of novel plant peroxisomal proteins.
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Affiliation(s)
- Christian Falter
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Nguyen Binh Anh Thu
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Saugat Pokhrel
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
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29
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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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30
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Jung S. Implications of publicly available genomic data resources in searching for therapeutic targets of obesity and type 2 diabetes. Exp Mol Med 2018; 50:1-13. [PMID: 29674722 PMCID: PMC5938056 DOI: 10.1038/s12276-018-0066-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/28/2018] [Indexed: 12/29/2022] Open
Abstract
Obesity and type 2 diabetes (T2D) are two major conditions that are related to metabolic disorders and affect a large population. Although there have been significant efforts to identify their therapeutic targets, few benefits have come from comprehensive molecular profiling. This limited availability of comprehensive molecular profiling of obesity and T2D may be due to multiple challenges, as these conditions involve multiple organs and collecting tissue samples from subjects is more difficult in obesity and T2D than in other diseases, where surgical treatments are popular choices. While there is no repository of comprehensive molecular profiling data for obesity and T2D, multiple existing data resources can be utilized to cover various aspects of these conditions. This review presents studies with available genomic data resources for obesity and T2D and discusses genome-wide association studies (GWAS), a knockout (KO)-based phenotyping study, and gene expression profiles. These studies, based on their assessed coverage and characteristics, can provide insights into how such data can be utilized to identify therapeutic targets for obesity and T2D.
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Affiliation(s)
- Sungwon Jung
- Department of Genome Medicine and Science, Gachon University School of Medicine, Incheon, Republic of Korea. .,Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, Republic of Korea.
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Small GTPase Immunity-Associated Proteins Mediate Resistance to Toxoplasma gondii Infection in Lewis Rat. Infect Immun 2018; 86:IAI.00582-17. [PMID: 29378795 DOI: 10.1128/iai.00582-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/22/2018] [Indexed: 01/12/2023] Open
Abstract
Rats vary in their susceptibilities to Toxoplasma gondii infection depending on the rat strain. Compared to the T. gondii-susceptible Brown Norway (BN) rat, the Lewis (LEW) rat is extremely resistant to T. gondii Thus, these two rat strains are ideal models for elucidating host mechanisms that are important for host resistance to T. gondii infection. Therefore, in our efforts to unravel molecular factors directing the protective early innate immune response in the LEW rat, we performed RNA sequencing analysis of the LEW versus BN rat with or without T. gondii infection. We identified three candidate small GTPase immunity-associated proteins (GIMAPs) that were upregulated (false discovery rate, 0.05) in the LEW rat in response to T. gondii infection. Subsequently, we engineered T. gondii-susceptible NR8383 rat macrophage cells for overexpression of LEW rat-derived candidate GIMAP 4, 5, and 6. By immunofluorescence analysis we observed that GIMAP 4, 5, and 6 in T. gondii-infected NR8383 cells each colocalized with GRA5, a parasite parasitophorous vacuole membrane (PVM) marker protein, suggesting their translocation to the PVM. Interestingly, overexpression of each candidate GIMAP in T. gondii-infected NR8383 cells induced translocation of LAMP1, a lysosome marker protein, to the T. gondii surface membrane. Importantly, overexpression of GIMAP 4, 5, or 6 individually inhibited intracellular T. gondii growth, with GIMAP 4 having the highest inhibitory effect. Together, our findings indicate that upregulation of GIMAP 4, 5, and 6 contributes to the robust refractoriness of the LEW rat to T. gondii through induction of lysosomal fusion to the otherwise nonfusogenic PVM.
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32
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A compendium of physical exercise-related human genes: an 'omic scale analysis. Biol Sport 2017; 35:3-11. [PMID: 30237656 PMCID: PMC6135974 DOI: 10.5114/biolsport.2018.70746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/11/2016] [Accepted: 06/05/2017] [Indexed: 12/14/2022] Open
Abstract
Regular exercise is an exogenous factor of gene regulation with numerous health benefits. The study aimed to evaluate human genes linked to physical exercise in an ‘omic scale, addressing biological questions to the generated database. Three literature databases were searched with the terms ‘exercise’, ‘fitness’, ‘physical activity’, ‘genetics’ and ‘gene expression’. For additional references, papers were scrutinized and a text-mining tool was used. Papers linking genes to exercise in humans through microarray, RNA-Seq, RT-PCR and genotyping studies were included. Genes were extracted from the collected literature, together with information on exercise protocol, experimental design, gender, age, number of individuals, analytical method, fold change and statistical data. The ‘omic scale dataset was characterized and evaluated with bioinformatics tools searching for gene expression patterns, functional meaning and gene clusters. As a result, a physical exercise-related human gene compendium was created, with data from 58 scientific papers and 5.147 genes functionally correlated with 17 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. While 50.9% of the gene set was up-regulated, 41.9% was down-regulated. 743 up- and 530 down-regulated clusters were found, some connected by regulatory networks. To summarize, up- and down-regulation was encountered, with a wide genomic distribution of the gene set and up- and down-regulated clusters possibly assembled by functional gene evolution. Physical exercise elicits a widespread response in gene expression.
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33
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Broséus J, Mourah S, Ramstein G, Bernard S, Mounier N, Cuccuini W, Gaulard P, Gisselbrecht C, Brière J, Houlgatte R, Thieblemont C. VEGF 121, is predictor for survival in activated B-cell-like diffuse large B-cell lymphoma and is related to an immune response gene signature conserved in cancers. Oncotarget 2017; 8:90808-90824. [PMID: 29207605 PMCID: PMC5710886 DOI: 10.18632/oncotarget.19385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023] Open
Abstract
Tumor microenvironment including endothelial and immune cells plays a crucial role in tumor progression and has been shown to dramatically influence cancer survival. In this study, we investigated the clinical relevance of the gene expression of key mediators of angiogenesis, VEGF isoforms 121, 165, and 189, and their receptors (VEGFR-1 and R-2) in a cohort of patients (n = 37) with relapsed/refractory diffuse large B-cell lymphoma (DLBCL) from the Collaborative Trial in Relapsed Aggressive Lymphoma (CORAL). In patients with ABC-like DLBCL, but not in patients with GCB-like DLBCL, low VEGF121 expression was associated with a significantly better survival than in those with high VEGF121 level: 4-year overall survival at 100% vs 36% (p = .011), respectively. A specific gene signature including 57 genes was correlated to VEGF121 expression level and was analyzed using a discovery process in 1,842 GSE datasets of public microarray studies. This gene signature was significantly expressed in other cancer datasets and was associated with immune response. In conclusion, low VEGF121 expression level was significantly associated with a good prognosis in relapsed/refractory ABC-like DLBCL, and with a well-conserved gene-expression profiling signature related to immune response. These findings pave the way for rationalization of drugs targeting immune response in refractory/relapsed ABC-like DLBCL.
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Affiliation(s)
- Julien Broséus
- Inserm U954, Faculty of Medicine, University of Lorraine, Nancy, France.,University Hospital of Nancy, Hematology Laboratory, Nancy, France
| | - Samia Mourah
- Paris Diderot University, Sorbonne Paris Cité, Paris, France.,APHP, Saint Louis University Hospital, Pharmacology-Biologic Laboratory, Paris, France.,Inserm UMRS 976, France
| | | | - Sophie Bernard
- APHP, Saint-Louis University Hospital, Hemato-Oncology, Paris, France
| | | | - Wendy Cuccuini
- APHP, Saint-Louis University Hospital, Hematology Laboratory, Paris, France
| | - Philippe Gaulard
- Department of Pathology, APHP, Henri Mondor University Hospital, Creteil, France.,Inserm U955, University Paris-Est, Créteil, France
| | - Christian Gisselbrecht
- APHP, Saint-Louis University Hospital, Hemato-Oncology, Paris, France.,Lymphoma Study Association, Pierre-Bénite, France
| | - Josette Brière
- Department of Pathology, APHP, Saint-Louis University Hospital, Paris, France
| | - Rémi Houlgatte
- Inserm U954, Faculty of Medicine, University of Lorraine, Nancy, France.,University Hospital of Nancy, DRCI, Nancy, France
| | - Catherine Thieblemont
- Paris Diderot University, Sorbonne Paris Cité, Paris, France.,APHP, Saint-Louis University Hospital, Hemato-Oncology, Paris, France
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34
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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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35
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Klangnurak W, Tokumoto T. Fine selection of up-regulated genes during ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish. ZOOLOGICAL LETTERS 2017; 3:2. [PMID: 28265462 PMCID: PMC5330128 DOI: 10.1186/s40851-017-0065-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Two essential processes, oocyte maturation and ovulation, are independently induced, but proceed cooperatively as the final step in oogenesis before oocytes become fertilizable. Although these two processes are induced by the same maturation-inducing steroid, 17α, 20β-dihydroxy-4-pregnen-3-one (17, 20β-DHP), in zebrafish, it has been suggested that the receptor, and thus the signal transduction pathway is different for each process. Although much progress has been made in understanding the molecular mechanisms underlying the induction of oocyte maturation, the mechanisms for inducing ovulation remain under investigation. In the present study, in vivo induction techniques that permit the induction of oocyte maturation and ovulation in living zebrafish (in vivo assays) were used to select highly up-regulated genes (genes associated with ovulation). Using an in vivo assay, ovarian tissues that induced only oocyte maturation could be obtained. This made it possible for the first time to distinguish maturation-inducing genes from ovulation-inducing genes. Using a genome-wide microarray of zebrafish sequences, the gene expression levels were compared among an ethanol (EtOH)-treated group (non-activated group), a diethylstilbestrol (DES)- or testosterone (Tes)-treated group (maturation-induced group), and a 17, 20β-DHP-treated group (maturation- and ovulation-induced group). Ovulation-specific up-regulated genes were selected. The mRNA expression levels of the selected genes were measured by quantitative polymerase chain reaction (qPCR). RESULTS Among 34 genes identified, three that showed ovulation-specific increases were selected as candidates potentially associated with ovulation. The ovulation-specific up-regulation of three candidates, slc37a4a, zgc:65811 and zgc:92184 was confirmed by qPCR. CONCLUSION Our in vivo assay provides a new approach to precisely select genes associated with ovulation.
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Affiliation(s)
- Wanlada Klangnurak
- Integrated Bioscience Section, Graduate School of Science and Technology, National University Corporation Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8529 Japan
| | - Toshinobu Tokumoto
- Integrated Bioscience Section, Graduate School of Science and Technology, National University Corporation Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8529 Japan
- Department of Biology, Faculty of Science, National University Corporation Shizuoka University, Shizuoka, 422-8529 Japan
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36
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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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Cao J, Ou X, Zhu D, Ma G, Cheng A, Wang M, Chen S, Jia R, Liu M, Sun K, Yang Q, Wu Y, Chen X. The 2A2 protein of Duck hepatitis A virus type 1 induces apoptosis in primary cell culture. Virus Genes 2016; 52:780-788. [PMID: 27314270 DOI: 10.1007/s11262-016-1364-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
Duck hepatitis A virus type 1, (DHAV-1) 2A2pro, is one of the most highly conserved viral proteins within the DHAV serotypes. However, its effect on host cells is unclear. We predicted that DHAV-1 2A2pro was a GTPase-like protein based on the results of multiple sequence alignment and homologous modeling analysis. Upon transfection of a recombinant plasmid expressing DHAV-1 2A2, cells displayed fragmented nuclei, chromatin condensation, oligonucleosome-sized DNA ladder, and positive terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling staining; hence, cell death has the characteristics of apoptosis. By staining cells with fluorescein Annexin V-FITC and PI, it is possible to distinguish and quantitatively analyze nonapoptotic cells, early apoptotic cells, late apoptotic/necrotic cells, and dead cells through flow cytometry and fluorescence microscopy. The percentage of apoptotic cells gradually increased and reached a maximum after 48 h of transfection. In conclusion, apoptosis induced by this GTPase-like protein may contribute to DHAV-1 pathogenesis.
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Affiliation(s)
- Jingyu Cao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Guangpeng Ma
- China Rural Technology Development Center, Beijing, 100045, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China. .,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China. .,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Kunfeng Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
| | - Xiaoyue Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, People's Republic of China
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38
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Al-awar A, Kupai K, Veszelka M, Szűcs G, Attieh Z, Murlasits Z, Török S, Pósa A, Varga C. Experimental Diabetes Mellitus in Different Animal Models. J Diabetes Res 2016; 2016:9051426. [PMID: 27595114 PMCID: PMC4993915 DOI: 10.1155/2016/9051426] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022] Open
Abstract
Animal models have historically played a critical role in the exploration and characterization of disease pathophysiology and target identification and in the evaluation of novel therapeutic agents and treatments in vivo. Diabetes mellitus disease, commonly known as diabetes, is a group of metabolic disorders characterized by high blood glucose levels for a prolonged time. To avoid late complications of diabetes and related costs, primary prevention and early treatment are therefore necessary. Due to its chronic symptoms, new treatment strategies need to be developed, because of the limited effectiveness of the current therapies. We overviewed the pathophysiological features of diabetes in relation to its complications in type 1 and type 2 mice along with rat models, including Zucker Diabetic Fatty (ZDF) rats, BB rats, LEW 1AR1/-iddm rats, Goto-Kakizaki rats, chemically induced diabetic models, and Nonobese Diabetic mouse, and Akita mice model. The advantages and disadvantages that these models comprise were also addressed in this review. This paper briefly reviews the wide pathophysiological and molecular mechanisms associated with type 1 and type 2 diabetes, particularly focusing on the challenges associated with the evaluation and predictive validation of these models as ideal animal models for preclinical assessments and discovering new drugs and therapeutic agents for translational application in humans.
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Affiliation(s)
- Amin Al-awar
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
| | - Krisztina Kupai
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
- *Krisztina Kupai:
| | - Médea Veszelka
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
| | - Gergő Szűcs
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
| | - Zouhair Attieh
- Department of Laboratory Science and Technology, Faculty of Health Sciences, American University of Science and Technology, Alfred Naccache Avenue, Beirut 1100, Lebanon
| | | | - Szilvia Török
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
| | - Anikó Pósa
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
| | - Csaba Varga
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Kozep Fasor 52, 6726 Szeged, Hungary
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39
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Arndt T, Wedekind D, Jörns A, Tsiavaliaris G, Cuppen E, Hedrich HJ, Lenzen S. A novel Dock8 gene mutation confers diabetogenic susceptibility in the LEW.1AR1/Ztm-iddm rat, an animal model of human type 1 diabetes. Diabetologia 2015; 58:2800-9. [PMID: 26363782 DOI: 10.1007/s00125-015-3757-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/24/2015] [Indexed: 02/04/2023]
Abstract
AIMS/HYPOTHESIS The LEW.1AR1-iddm rat, an animal model of human type 1 diabetes, arose through a spontaneous mutation within the inbred strain LEW.1AR1. A susceptibility locus (Iddm8) on rat chromosome 1 (RNO1) has been identified previously, which is accompanied by autoimmune diabetes and the additional phenotype of a variable CD3(+) T cell frequency. METHODS In the present study we characterised the Iddm8 region on RNO1 in backcross strains using the genetically divergent Brown Norway (BN) and Paris (PAR) rats. Candidate genes of the Iddm8 region were sequenced for mutation analysis. RESULTS The Iddm8 region could be subdivided by single nucleotide polymorphism (SNP) analyses. In the first region, a mutation in exon 44 of the Dock8 gene was identified resulting in an amino acid exchange in the protein from glutamine to glutamate. This exchange is unique for the LEW.1AR1-iddm rat. In the second region, a SNP was detected in exon 11 of the Vwa2 gene with an exchange from arginine to tryptophan. This SNP is also present in other rat strains. CONCLUSIONS/INTERPRETATION The Dock8 mutation gave rise to a new type 1 diabetes rat model with very close similarity to type 1 diabetes in humans, providing a deepened insight into the impact of genes involved in diabetes development.
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Affiliation(s)
- Tanja Arndt
- Institute of Clinical Biochemistry, Hannover Medical School, 30623, Hannover, Germany
| | - Dirk Wedekind
- Institute for Laboratory Animal Science, Hannover Medical School, 30623, Hannover, Germany.
| | - Anne Jörns
- Institute of Clinical Biochemistry, Hannover Medical School, 30623, Hannover, Germany
| | | | - Edwin Cuppen
- Centre for Biomedical Genetics, Hubrecht Institute, Utrecht, The Netherlands
| | - Hans-Jürgen Hedrich
- Institute for Laboratory Animal Science, Hannover Medical School, 30623, Hannover, Germany
| | - Sigurd Lenzen
- Institute of Clinical Biochemistry, Hannover Medical School, 30623, Hannover, Germany.
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40
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Webb LMC, Datta P, Bell SE, Kitamura D, Turner M, Butcher GW. GIMAP1 Is Essential for the Survival of Naive and Activated B Cells In Vivo. THE JOURNAL OF IMMUNOLOGY 2015; 196:207-16. [PMID: 26621859 DOI: 10.4049/jimmunol.1501582] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/30/2015] [Indexed: 12/30/2022]
Abstract
An effective immune system depends upon regulation of lymphocyte function and homeostasis. In recent years, members of the GTPases of the immunity associated protein (GIMAP) family were proposed to regulate T cell homeostasis. In contrast, little is known about their function and mode of action in B cells. We used a combination of transgenic mice and in vivo and in vitro techniques to conditionally and electively ablate GIMAP1 in resting and activated peripheral B cells. Our data suggest that GIMAP1 is absolutely essential for the survival of peripheral B cells, irrespective of their activation state. Together with recent data showing increased expression of GIMAP1 in B cell lymphomas, our work points to the possible potential of GIMAP1 as a target for manipulation in a variety of B cell-mediated diseases.
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Affiliation(s)
- Louise M C Webb
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge CB22 3AT, United Kingdom; and
| | - Preeta Datta
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge CB22 3AT, United Kingdom; and
| | - Sarah E Bell
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge CB22 3AT, United Kingdom; and
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge CB22 3AT, United Kingdom; and
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge CB22 3AT, United Kingdom; and
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41
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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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42
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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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Forn-Cuní G, Varela M, Fernández-Rodríguez CM, Figueras A, Novoa B. Liver immune responses to inflammatory stimuli in a diet-induced obesity model of zebrafish. J Endocrinol 2015; 224:159-70. [PMID: 25371540 DOI: 10.1530/joe-14-0398] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Obesity- and metabolic syndrome-related diseases are becoming important medical challenges for the western world. Non-alcoholic fatty liver disease (NAFLD) is a manifestation of these altered conditions in the liver, and inflammation appears to be a factor that is tightly connected to its evolution. In this study, we used a diet-induced obesity approach in zebrafish (Danio rerio) based on overfeeding to analyze liver transcriptomic modulation in the disease and to determine how obesity affects the immune response against an acute inflammatory stimulus such as lipopolysaccharide (LPS). Overfed zebrafish developed an obese phenotype, showed signs of liver steatosis, and its modulation profile resembled that observed in humans, with overexpression of tac4, col4a3, col4a5, lysyl oxidases, and genes involved in retinoid metabolism. In response to LPS, healthy fish exhibited a typical host defense reaction comparable to that which occurs in mammals, whereas there was no significant gene modulation when comparing expression in the liver of LPS-stimulated and non-stimulated obese zebrafish at the same statistical level. The stimulation of obese fish represents a double-hit to the already damaged liver and can help understand the evolution of the disease. Finally, a comparison of the differential gene activation between stimulated healthy and obese zebrafish revealed the expected difference in the metabolic state between healthy and diseased liver. The differentially modulated genes are currently being studied as putative new pathological markers in NAFLD-stimulated liver in humans.
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Affiliation(s)
- Gabriel Forn-Cuní
- Instituto de Investigaciones MarinasCSIC, Eduardo Cabello 6, 36208 Vigo, SpainHospital Universitario Fundación AlcorcónMadrid, Spain
| | - Monica Varela
- Instituto de Investigaciones MarinasCSIC, Eduardo Cabello 6, 36208 Vigo, SpainHospital Universitario Fundación AlcorcónMadrid, Spain
| | - Conrado M Fernández-Rodríguez
- Instituto de Investigaciones MarinasCSIC, Eduardo Cabello 6, 36208 Vigo, SpainHospital Universitario Fundación AlcorcónMadrid, Spain
| | - Antonio Figueras
- Instituto de Investigaciones MarinasCSIC, Eduardo Cabello 6, 36208 Vigo, SpainHospital Universitario Fundación AlcorcónMadrid, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones MarinasCSIC, Eduardo Cabello 6, 36208 Vigo, SpainHospital Universitario Fundación AlcorcónMadrid, Spain
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Jokinen R, Junnila H, Battersby BJ. Gimap3: A foot-in-the-door to tissue-specific regulation of mitochondrial DNA genetics. Small GTPases 2014; 2:31-35. [PMID: 21686279 DOI: 10.4161/sgtp.2.1.14937] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/18/2011] [Accepted: 01/23/2011] [Indexed: 01/31/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a multi-copy genome encoding for proteins essential for aerobic energy metabolism. Mutations in mtDNA can lead to a variety of human diseases, from mild metabolic syndromes to severe fatal encephalomyopathies. Most mtDNA mutations co-exist with wild type genomes in a state known as heteroplasmy. The segregation of these pathogenic mutants is tissue and mutation specific, and a key determinant in the onset and severity of human mitochondrial disorders. We used a forward genetic approach in mice to identify and demonstrate that Gimap3 (GTP ase of immunity associated protein) is a key regulator of mtDNA segregation in leukocytes. The Gimap gene cluster is found only in vertebrates and appear to be a class of nucleotide-dependent dimerization GTP ases. Gimap3 is a membrane-anchored GTP ase with a critical role in T cell development. Here, we summarize our genetic findings and postulate how Gimap3 might regulate mtDNA genetics.
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Affiliation(s)
- Riikka Jokinen
- Research Program of Molecular Neurology and Institute of Biomedicine; Biomedicum Helsinki; University of Helsinki; Helsinki, Finland
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Schwefel D, Daumke O. GTP-dependent scaffold formation in the GTPase of Immunity Associated Protein family. Small GTPases 2014; 2:27-30. [PMID: 21686278 DOI: 10.4161/sgtp.2.1.14938] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/19/2011] [Accepted: 01/20/2011] [Indexed: 11/19/2022] Open
Abstract
GTP ases of Immunity-Associated Proteins (GIMAPs) are a family of guanine nucleotide binding (G) proteins which are implicated in the regulation of apoptosis in lymphocytes. GIMAPs are composed of an amino-terminal G domain and carboxy-terminal extensions of varying size. Our recent biochemical and structural analysis of a representative GIMAP family member, GIMAP2, revealed the molecular basis of GTP-dependent oligomerization which involves two interfaces in the G domain. Whereas the amphipathic helix α7 in the C-terminal extension closely folds against the G domain in the GDP-bound state, it might be released in the GTP-bound state to assemble interaction partners. We also showed that the GIMAP2 oligomer functions at the surface of lipid droplets in a Jurkat T cell line. Here, we review our recent work and discuss the GIMAP2 oligomer as a GTP-dependent protein scaffold at the surface of lipid droplets controlling apoptosis.
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Affiliation(s)
- David Schwefel
- Max-Delbrück-Centrum für Molekulare Medizin; Freie Universität Berlin
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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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Tubulin- and actin-associating GIMAP4 is required for IFN-γ secretion during Th cell differentiation. Immunol Cell Biol 2014; 93:158-66. [PMID: 25287446 PMCID: PMC4355353 DOI: 10.1038/icb.2014.86] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 09/05/2014] [Accepted: 09/06/2014] [Indexed: 12/20/2022]
Abstract
Although GTPase of the immunity-associated protein (GIMAP) family are known to be most highly expressed in the cells of the immune system, their function and role remain still poorly characterized. Small GTPases in general are known to be involved in many cellular processes in a cell type-specific manner and to contribute to specific differentiation processes. Among GIMAP family, GIMAP4 is the only member reported to have true GTPase activity, and its transcription is found to be differentially regulated during early human CD4(+) T helper (Th) lymphocyte differentiation. GIMAP4 has been previously connected mainly with T- and B-cell development and survival and T-cell apoptosis. Here we show GIMAP4 to be localized into cytoskeletal elements and with the component of the trans golgi network, which suggests it to have a function in cellular transport processes. We demonstrate that depletion of GIMAP4 with RNAi results in downregulation of endoplasmic reticulum localizing chaperone VMA21. Most importantly, we discovered that GIMAP4 regulates secretion of cytokines in early differentiating human CD4(+) Th lymphocytes and in particular the secretion of interferon-γ also affecting its downstream targets.
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Hernández-Cuevas NA, Weber C, Hon CC, Guillen N. Gene expression profiling in Entamoeba histolytica identifies key components in iron uptake and metabolism. PLoS One 2014; 9:e107102. [PMID: 25210888 PMCID: PMC4161402 DOI: 10.1371/journal.pone.0107102] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 08/12/2014] [Indexed: 01/25/2023] Open
Abstract
Entamoeba histolytica is an ameboid parasite that causes colonic dysentery and liver abscesses in humans. The parasite encounters dramatic changes in iron concentration during its invasion of the host, with relatively low levels in the intestinal lumen and then relatively high levels in the blood and liver. The liver notably contains sources of iron; therefore, the parasite's ability to use these sources might be relevant to its survival in the liver and thus the pathogenesis of liver abscesses. The objective of the present study was to identify factors involved in iron uptake, use and storage in E. histolytica. We compared the respective transcriptomes of E. histolytica trophozoites grown in normal medium (containing around 169 µM iron), low-iron medium (around 123 µM iron), iron-deficient medium (around 91 µM iron), and iron-deficient medium replenished with hemoglobin. The differentially expressed genes included those coding for the ATP-binding cassette transporters and major facilitator transporters (which share homology with bacterial siderophores and heme transporters) and genes involved in heme biosynthesis and degradation. Iron deficiency was associated with increased transcription of genes encoding a subset of cell signaling molecules, some of which have previously been linked to adaptation to the intestinal environment and virulence. The present study is the first to have assessed the transcriptome of E. histolytica grown under various iron concentrations. Our results provide insights into the pathways involved in iron uptake and metabolism in this parasite.
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Affiliation(s)
| | - Christian Weber
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Nancy Guillen
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
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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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Yano K, Carter C, Yoshida N, Abe T, Yamada A, Nitta T, Ishimaru N, Takada K, Butcher GW, Takahama Y. Gimap3 and Gimap5 cooperate to maintain T-cell numbers in the mouse. Eur J Immunol 2013; 44:561-72. [PMID: 24510501 DOI: 10.1002/eji.201343750] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/29/2013] [Accepted: 09/26/2013] [Indexed: 12/29/2022]
Abstract
Gimap3 (IAN4) and Gimap5 (IAN5) are highly homologous GTP-binding proteins of the Gimap family. Gimap3 and Gimap5, whose transcripts are abundant in mature lymphocytes, can associate with antiapoptotic Bcl-2 family proteins. While it is established that Gimap5 regulates T-cell survival, the in vivo role of Gimap3 is unclear. Here we report the preparation and characteristics of mouse strains lacking Gimap3 and/or Gimap5. We found that the number of T cells was markedly reduced in mice deficient in both Gimap3 and Gimap5. The defects in T-cell cellularity were more severe in mice lacking both Gimap3 and Gimap5 than in mice lacking only Gimap5. No defects in the cellularity of T cells were detected in mice lacking only Gimap3, whereas bone marrow cells from Gimap3-deficient mice showed reduced T-cell production in a competitive hematopoietic environment. Moreover, retroviral overexpression and short hairpin RNAs-mediated silencing of Gimap3 in bone marrow cells elevated and reduced, respectively, the number of T cells produced in irradiated mice. These results suggest that Gimap3 is a regulator of T-cell numbers in the mouse and that multiple Gimap family proteins cooperate to maintain T-cell survival.
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Affiliation(s)
- Kouta Yano
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
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