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Chen J, Chen Z, Zhang J, Zhuang W, Zheng X. Screening of reliable reference genes for the normalization of RT-qPCR in chicken gastrointestinal tract. Poult Sci 2023; 102:103169. [PMID: 37918133 PMCID: PMC10641542 DOI: 10.1016/j.psj.2023.103169] [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: 07/13/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
The application of reverse transcription quantitative real-time PCR technology for the production of gene tissue expression profiles is a widely employed approach in molecular biology research. It is imperative to ascertain internal reference genes that exhibit stable expression across diverse tissues to ensure the precision of tissue gene expression profiles. While there have been studies documenting the most suitable reference genes for various tissues in chickens, there is a dearth of research on the identification of reference genes in the gastrointestinal (GI) tract of chickens. This study utilized 4 different algorithms (Delta CT, BestKeeper, NormFinder, and Genorm) to assess the stability of 19 internal reference genes in various GI tract tissues, including individual GI tract tissues, the anterior and posterior GI tract, and the entire GI tissue. The RefFinder software was employed to comprehensively rank these genes. The research findings successfully identified the most appropriate internal reference genes for each type of GI tissue. Furthermore, TBP, DNAJC24, Polr2b, RPL13, andAp2m exhibited stable expression in the entire and posterior GI tract, whereas HMBS, TBP, Ap2m, GUSB, DNAJC24, and RPL13 demonstrated stable expression in the anterior GI tract. However, the internal reference genes commonly utilized, namely β-Actin, 18s RNA, and ALB, exhibit poor stability and are not advised for future investigations concerning gene expression in the GI region. Consequently, MUC2 and CDX1, 2 genes that specifically express in the gut, were chosen for examination to ascertain the stability of the aforementioned internal reference genes in this particular study. In summary, this study presents a relatively stable set of internal reference genes that can be employed to enhance the precision of quantifying mRNA expression levels in functional genes within the chicken GI tract.
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Affiliation(s)
- Jianfei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ziwei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jilong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Wuchao Zhuang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xiaotong Zheng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China.
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2
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Jacob P, Oertlin C, Baselet B, Westerberg LS, Frippiat JP, Baatout S. Next generation of astronauts or ESA astronaut 2.0 concept and spotlight on immunity. NPJ Microgravity 2023; 9:51. [PMID: 37380641 DOI: 10.1038/s41526-023-00294-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/15/2023] [Indexed: 06/30/2023] Open
Abstract
Although we have sent humans into space for more than 50 years, crucial questions regarding immune response in space conditions remain unanswered. There are many complex interactions between the immune system and other physiological systems in the human body. This makes it difficult to study the combined long-term effects of space stressors such as radiation and microgravity. In particular, exposure to microgravity and cosmic radiation may produce changes in the performance of the immune system at the cellular and molecular levels and in the major physiological systems of the body. Consequently, abnormal immune responses induced in the space environment may have serious health consequences, especially in future long-term space missions. In particular, radiation-induced immune effects pose significant health challenges for long-duration space exploration missions with potential risks to reduce the organism's ability to respond to injuries, infections, and vaccines, and predispose astronauts to the onset of chronic diseases (e.g., immunosuppression, cardiovascular and metabolic diseases, gut dysbiosis). Other deleterious effects encountered by radiation may include cancer and premature aging, induced by dysregulated redox and metabolic processes, microbiota, immune cell function, endotoxin, and pro-inflammatory signal production1,2. In this review, we summarize and highlight the current understanding of the effects of microgravity and radiation on the immune system and discuss knowledge gaps that future studies should address.
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Affiliation(s)
- Pauline Jacob
- Stress Immunity Pathogens Laboratory, UR 7300 SIMPA, Faculty of Medicine, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Christian Oertlin
- Karolinska Institutet, Department of Microbiology Tumor and Cell biology, Stockholm, SE-17177, Sweden
| | - Bjorn Baselet
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Lisa S Westerberg
- Karolinska Institutet, Department of Microbiology Tumor and Cell biology, Stockholm, SE-17177, Sweden
| | - Jean-Pol Frippiat
- Stress Immunity Pathogens Laboratory, UR 7300 SIMPA, Faculty of Medicine, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium.
- Department of Molecular Biotechnology, Gent University, Gent, Belgium.
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Murali A, Sarkar RR. Mechano-immunology in microgravity. LIFE SCIENCES IN SPACE RESEARCH 2023; 37:50-64. [PMID: 37087179 DOI: 10.1016/j.lssr.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/16/2023] [Accepted: 03/05/2023] [Indexed: 05/03/2023]
Abstract
Life on Earth has evolved to thrive in the Earth's natural gravitational field; however, as space technology advances, we must revisit and investigate the effects of unnatural conditions on human health, such as gravitational change. Studies have shown that microgravity has a negative impact on various systemic parts of humans, with the effects being more severe in the human immune system. Increasing costs, limited experimental time, and sample handling issues hampered our understanding of this field. To address the existing knowledge gap and provide confidence in modelling the phenomena, in this review, we highlight experimental works in mechano-immunology under microgravity and different computational modelling approaches that can be used to address the existing problems.
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Affiliation(s)
- Anirudh Murali
- Chemical Engineering and Process Development, CSIR - National Chemical Laboratory, Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ram Rup Sarkar
- Chemical Engineering and Process Development, CSIR - National Chemical Laboratory, Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Vahlensieck C, Thiel CS, Mosimann M, Bradley T, Caldana F, Polzer J, Lauber BA, Ullrich O. Transcriptional Response in Human Jurkat T Lymphocytes to a near Physiological Hypergravity Environment and to One Common in Routine Cell Culture Protocols. Int J Mol Sci 2023; 24:ijms24021351. [PMID: 36674869 PMCID: PMC9863927 DOI: 10.3390/ijms24021351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Cellular effects of hypergravity have been described in many studies. We investigated the transcriptional dynamics in Jurkat T cells between 20 s and 60 min of 9 g hypergravity and characterized a highly dynamic biphasic time course of gene expression response with a transition point between rapid adaptation and long-term response at approximately 7 min. Upregulated genes were shifted towards the center of the nuclei, whereby downregulated genes were shifted towards the periphery. Upregulated gene expression was mostly located on chromosomes 16-22. Protein-coding transcripts formed the majority with more than 90% of all differentially expressed genes and followed a continuous trend of downregulation, whereas retained introns demonstrated a biphasic time-course. The gene expression pattern of hypergravity response was not comparable with other stress factors such as oxidative stress, heat shock or inflammation. Furthermore, we tested a routine centrifugation protocol that is widely used to harvest cells for subsequent RNA analysis and detected a huge impact on the transcriptome compared to non-centrifuged samples, which did not return to baseline within 15 min. Thus, we recommend carefully studying the response of any cell types used for any experiments regarding the hypergravity time and levels applied during cell culture procedures and analysis.
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Affiliation(s)
- Christian Vahlensieck
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Cora Sandra Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center, 505 Odyssey Way, Exploration Park, FL 32953, USA
- UZH Space Hub, Air Force Center, Air Base Dübendorf, Überlandstrasse 270, 8600 Dübendorf, Switzerland
- Correspondence: (C.S.T.); (O.U.)
| | - Meret Mosimann
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Timothy Bradley
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Fabienne Caldana
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jennifer Polzer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Beatrice Astrid Lauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center, 505 Odyssey Way, Exploration Park, FL 32953, USA
- UZH Space Hub, Air Force Center, Air Base Dübendorf, Überlandstrasse 270, 8600 Dübendorf, Switzerland
- Ernst-Abbe-Hochschule (EAH) Jena, Department of Industrial Engineering, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Correspondence: (C.S.T.); (O.U.)
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Rapid Downregulation of H3K4me3 Binding to Immunoregulatory Genes in Altered Gravity in Primary Human M1 Macrophages. Int J Mol Sci 2022; 24:ijms24010603. [PMID: 36614046 PMCID: PMC9820304 DOI: 10.3390/ijms24010603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
The sensitivity of human immune system cells to gravity changes has been investigated in numerous studies. Human macrophages mediate innate and thus rapid immune defense on the one hand and activate T- and B-cell-based adaptive immune response on the other hand. In this process they finally act as immunoeffector cells, and are essential for tissue regeneration and remodeling. Recently, we demonstrated in the human Jurkat T cell line that genes are differentially regulated in cluster structures under altered gravity. In order to study an in vivo near system of immunologically relevant human cells under physically real microgravity, we performed parabolic flight experiments with primary human M1 macrophages under highly standardized conditions and performed chromatin immunoprecipitation DNA sequencing (ChIP-Seq) for whole-genome epigenetic detection of the DNA-binding loci of the main transcription complex RNA polymerase II and the transcription-associated epigenetic chromatin modification H3K4me3. We identified an overall downregulation of H3K4me3 binding loci in altered gravity, which were unequally distributed inter- and intrachromosomally throughout the genome. Three-quarters of all affected loci were located on the p arm of the chromosomes chr5, chr6, chr9, and chr19. The genomic distribution of the downregulated H3K4me3 loci corresponds to a substantial extent to immunoregulatory genes. In microgravity, analysis of RNA polymerase II binding showed increased binding to multiple loci at coding sequences but decreased binding to central noncoding regions. Detection of altered DNA binding of RNA polymerase II provided direct evidence that gravity changes can lead to altered transcription. Based on this study, we hypothesize that the rapid transcriptional response to changing gravitational forces is specifically encoded in the epigenetic organization of chromatin.
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6
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Thiel CS, Vahlensieck C, Ullrich O. Assoziation schneller Reaktionen der Genexpression mit Änderungen der 3D-Chromatinkonformation in veränderter Schwerkraft. FLUGMEDIZIN · TROPENMEDIZIN · REISEMEDIZIN - FTR 2022. [DOI: 10.1055/a-1928-0420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
ZUSAMMENFASSUNGDie molekularen Prinzipien bei der Transduktion von Schwerkraftänderungen in zelluläre Antwort- und Anpassungsprozesse sind bisher weitgehend unbekannt. Wir konnten in humanen Jurkat-T-Zellen zeigen, dass Gene bei veränderter Schwerkraft in Clusterstrukturen („gravity-responsive chromosomal regions“, GRCRs) differenziell reguliert werden. Durch Kombination mit Hochdurchsatz-Chromatin-Konformationsanalysen (Hi-C) konnte eine hochsignifikante Assoziation von GRCRs mit strukturellen 3D-Chromatinveränderungen identifiziert werden, die vor allem auf den kleinen Chromosomen (chr16–chr22) kolokalisieren. Wir fanden weiterhin Hinweise auf einen mechanistischen Zusammenhang zwischen Spleißprozessen und differenzieller Genexpression bei veränderter Schwerkraft. Somit haben wir erste Belege dafür gefunden, dass Änderungen der Schwerkraft in den Zellkern übertragen werden und dort 3D-Chromosomen-Konformationsänderungen hervorrufen, die mit einer schnellen Transkriptionsantwort verbunden sind. Wir vermuten, dass die schnelle genomische Antwort auf veränderte Gravitationskräfte in der Organisation des Chromatins spezifisch codiert ist.
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Affiliation(s)
- Cora S. Thiel
- Innovation Cluster Space and Aviation (UZH Space Hub), Universität Zürich, Schweiz
- Anatomisches Institut, Universität Zürich, Schweiz
- Raumfahrtmedizin, Fachbereich Wirtschaftsingenieurwesen, Ernst-Abbe-Hochschule Jena
- Weltraumbiotechnologie, Fakultät für Maschinenbau, Otto-von-Guericke-Universität Magdeburg
| | - Christian Vahlensieck
- Innovation Cluster Space and Aviation (UZH Space Hub), Universität Zürich, Schweiz
- Anatomisches Institut, Universität Zürich, Schweiz
| | - Oliver Ullrich
- Innovation Cluster Space and Aviation (UZH Space Hub), Universität Zürich, Schweiz
- Anatomisches Institut, Universität Zürich, Schweiz
- Raumfahrtmedizin, Fachbereich Wirtschaftsingenieurwesen, Ernst-Abbe-Hochschule Jena
- Weltraumbiotechnologie, Fakultät für Maschinenbau, Otto-von-Guericke-Universität Magdeburg
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7
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Liu Y, Wu S, Jiang N, Liu W, Zhou Y, Zeng L, Zhong Q, Li Z, Fan Y. Characterization of reference genes for qRT-PCR normalization in rice-field eel (Monopterus albus) to assess differences in embryonic developmental stages, the early development of immune organs, and cells infected with rhabdovirus. FISH & SHELLFISH IMMUNOLOGY 2022; 120:92-101. [PMID: 34800657 DOI: 10.1016/j.fsi.2021.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) has become a popular technique to assess gene expression. Suitable reference genes are normally identified first to ensure accurate normalization. The aim of the present study was to select the most stable genes in embryonic developmental stages, the early development of immune organs, and cells infected with Chinese rice-field eel rhabdovirus (CrERV) of the rice-field eel (Monopterus albus). Four reference genes, including those encoding 18S ribosomal RNA (18SrRNA), beta actin (β-actin), elongation factor 1 alpha (EF1ɑ), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were assessed using geNorm, NormFinder, BestKeeper, and RefFinder software. Analyses indicated the stability ranking was 18SrRNA > β-actin > GAPDH > EF1α in the embryonic stage, with 18SrRNA as the most stable reference gene. For immunity-related organs at different developmental stages, the order in the thymus was β-actin > GAPDH > EF1α > 18SrRNA, with β-actin as the most stable gene. In both spleen and kidney tissues, the rank order was EF1ɑ > GAPDH > β-actin > 18SrRNA, with EF1α as the most stable gene. Furthermore, in rice-field eel kidney (CrE-K) cells infected with CrERV, the ranking was EF1ɑ > β-actin > GAPDH > 18SrRNA, with EF1α as the most stable gene. The results for cells infected with CrERV were verified by testing signaling pathway genes catenin beta 1 (CTNNB1) and NOTCH1 based on the above four genes after virus infection in CrE-K cells. This study laid the foundation for choosing suitable reference genes for immunity-related gene expression analysis in rice-field eel.
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Affiliation(s)
- Yuchen Liu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Shuwang Wu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Qiwang Zhong
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Yuding Fan
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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8
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Gravitational Force-Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells. Int J Mol Sci 2021; 22:ijms22179426. [PMID: 34502336 PMCID: PMC8430767 DOI: 10.3390/ijms22179426] [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: 08/11/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
The mechanisms underlying gravity perception in mammalian cells are unknown. We have recently discovered that the transcriptome of cells in the immune system, which is the most affected system during a spaceflight, responds rapidly and broadly to altered gravity. To pinpoint potential underlying mechanisms, we compared gene expression and three-dimensional (3D) chromosomal conformational changes in human Jurkat T cells during the short-term gravitational changes in parabolic flight and suborbital ballistic rocket flight experiments. We found that differential gene expression in gravity-responsive chromosomal regions, but not differentially regulated single genes, are highly conserved between different real altered gravity comparisons. These coupled gene expression effects in chromosomal regions could be explained by underlying chromatin structures. Based on a high-throughput chromatin conformation capture (Hi-C) analysis in altered gravity, we found that small chromosomes (chr16–22, with the exception of chr18) showed increased intra- and interchromosomal interactions in altered gravity, whereby large chromosomes showed decreased interactions. Finally, we detected a nonrandom overlap between Hi-C-identified chromosomal interacting regions and gravity-responsive chromosomal regions (GRCRs). We therefore demonstrate the first evidence that gravitational force-induced 3D chromosomal conformational changes are associated with rapid transcriptional response in human T cells. We propose a general model of cellular sensitivity to gravitational forces, where gravitational forces acting on the cellular membrane are rapidly and mechanically transduced through the cytoskeleton into the nucleus, moving chromosome territories to new conformation states and their genes into more expressive or repressive environments, finally resulting in region-specific differential gene expression.
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ElGindi M, Sapudom J, Ibrahim IH, Al-Sayegh M, Chen W, Garcia-Sabaté A, Teo JCM. May the Force Be with You (Or Not): The Immune System under Microgravity. Cells 2021; 10:1941. [PMID: 34440709 PMCID: PMC8391211 DOI: 10.3390/cells10081941] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
All terrestrial organisms have evolved and adapted to thrive under Earth's gravitational force. Due to the increase of crewed space flights in recent years, it is vital to understand how the lack of gravitational forces affects organisms. It is known that astronauts who have been exposed to microgravity suffer from an array of pathological conditions including an impaired immune system, which is one of the most negatively affected by microgravity. However, at the cellular level a gap in knowledge exists, limiting our ability to understand immune impairment in space. This review highlights the most significant work done over the past 10 years detailing the effects of microgravity on cellular aspects of the immune system.
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Affiliation(s)
- Mei ElGindi
- Laboratory for Immuno Bioengineering Research and Applications, Division of Engineering, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (M.E.); (J.S.); (I.H.I.)
| | - Jiranuwat Sapudom
- Laboratory for Immuno Bioengineering Research and Applications, Division of Engineering, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (M.E.); (J.S.); (I.H.I.)
| | - Ibrahim Hamed Ibrahim
- Laboratory for Immuno Bioengineering Research and Applications, Division of Engineering, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (M.E.); (J.S.); (I.H.I.)
| | - Mohamed Al-Sayegh
- Biology Division, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates;
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA;
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
| | - Anna Garcia-Sabaté
- Laboratory for Immuno Bioengineering Research and Applications, Division of Engineering, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (M.E.); (J.S.); (I.H.I.)
| | - Jeremy C. M. Teo
- Laboratory for Immuno Bioengineering Research and Applications, Division of Engineering, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (M.E.); (J.S.); (I.H.I.)
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA;
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
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10
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Thiel CS, Vahlensieck C, Bradley T, Tauber S, Lehmann M, Ullrich O. Metabolic Dynamics in Short- and Long-Term Microgravity in Human Primary Macrophages. Int J Mol Sci 2021; 22:ijms22136752. [PMID: 34201720 PMCID: PMC8269311 DOI: 10.3390/ijms22136752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/24/2022] Open
Abstract
Microgravity acts on cellular systems on several levels. Cells of the immune system especially react rapidly to changes in gravity. In this study, we performed a correlative metabolomics analysis on short-term and long-term microgravity effects on primary human macrophages. We could detect an increased amino acid concentration after five minutes of altered gravity, that was inverted after 11 days of microgravity. The amino acids that reacted the most to changes in gravity were tightly clustered. The observed effects indicated protein degradation processes in microgravity. Further, glucogenic and ketogenic amino acids were further degraded to Glucose and Ketoleucine. The latter is robustly accumulated in short-term and long-term microgravity but not in hypergravity. We detected highly dynamic and also robust adaptative metabolic changes in altered gravity. Metabolomic studies could contribute significantly to the understanding of gravity-induced integrative effects in human cells.
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Affiliation(s)
- Cora S. Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
- Correspondence: (C.S.T.); (O.U.)
| | - Christian Vahlensieck
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
| | - Timothy Bradley
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
| | - Svantje Tauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
| | - Martin Lehmann
- Biocenter LMU Muenchen, Department of Biology I–Botany, Großhaderner Strasse 2–4, 82152 Planegg-Martinsried, Germany;
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Medicine, Ernst-Abbe-Hochschule (EAH) Jena, Department of Industrial Engineering, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), 505 Odyssey Way, Exploration Park, FL 32953, USA
- Correspondence: (C.S.T.); (O.U.)
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11
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Choromańska A, Chwiłkowska A, Kulbacka J, Baczyńska D, Rembiałkowska N, Szewczyk A, Michel O, Gajewska-Naryniecka A, Przystupski D, Saczko J. Modifications of Plasma Membrane Organization in Cancer Cells for Targeted Therapy. Molecules 2021; 26:1850. [PMID: 33806009 PMCID: PMC8037978 DOI: 10.3390/molecules26071850] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Modifications of the composition or organization of the cancer cell membrane seem to be a promising targeted therapy. This approach can significantly enhance drug uptake or intensify the response of cancer cells to chemotherapeutics. There are several methods enabling lipid bilayer modifications, e.g., pharmacological, physical, and mechanical. It is crucial to keep in mind the significance of drug resistance phenomenon, ion channel and specific receptor impact, and lipid bilayer organization in planning the cell membrane-targeted treatment. In this review, strategies based on cell membrane modulation or reorganization are presented as an alternative tool for future therapeutic protocols.
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Affiliation(s)
- Anna Choromańska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Agnieszka Chwiłkowska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Julita Kulbacka
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Dagmara Baczyńska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Nina Rembiałkowska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Anna Szewczyk
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Olga Michel
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Agnieszka Gajewska-Naryniecka
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Dawid Przystupski
- Department of Paediatric Bone Marrow Transplantation, Oncology and Haematology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland;
| | - Jolanta Saczko
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
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Smirlis D, Dingli F, Pescher P, Prina E, Loew D, Rachidi N, Späth GF. SILAC-based quantitative proteomics reveals pleiotropic, phenotypic modulation in primary murine macrophages infected with the protozoan pathogen Leishmania donovani. J Proteomics 2019; 213:103617. [PMID: 31846769 DOI: 10.1016/j.jprot.2019.103617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/04/2019] [Accepted: 12/13/2019] [Indexed: 01/06/2023]
Abstract
Leishmaniases are major vector-borne tropical diseases responsible for great human morbidity and mortality, caused by protozoan, trypanosomatid parasites of the genus Leishmania. In the mammalian host, parasites survive and multiply within mononuclear phagocytes, especially macrophages. However, the underlying mechanisms by which Leishmania spp. affect their host are not fully understood. Herein, proteomic alterations of primary, bone marrow-derived BALB/c macrophages are documented after 72 h of infection with Leishmania donovani insect-stage promastigotes, applying a SILAC-based, quantitative proteomics approach. The protocol was optimised by combining strong anion exchange and gel electrophoresis fractionation that displayed similar depth of analysis (combined total of 6189 mouse proteins). Our analyses revealed 86 differentially modulated proteins (35 showing increased and 51 decreased abundance) in response to Leishmania donovani infection. The proteomics results were validated by analysing the abundance of selected proteins. Intracellular Leishmania donovani infection led to changes in various host cell biological processes, including primary metabolism and catabolic process, with a significant enrichment in lysosomal organisation. Overall, our analysis establishes the first proteome of bona fide primary macrophages infected ex vivo with Leishmania donovani, revealing new mechanisms acting at the host/pathogen interface. SIGNIFICANCE: Little is known on proteome changes that occur in primary macrophages after Leishmania donovani infection. This study describes a SILAC-based quantitative proteomics approach to characterise changes of bone marrow-derived macrophages infected with L. donovani promastigotes for 72 h. With the application of SILAC and the use of SAX and GEL fractionation methods, we have tested new routes for proteome quantification of primary macrophages. The protocols developed here can be applicable to other diseases and pathologies. Moreover, this study sheds important new light on the "proteomic reprogramming" of infected macrophages in response to L. donovani promastigotes that affects primary metabolism, cellular catabolic processes, and lysosomal/vacuole organisation. Thus, our study reveals key molecules and processes that act at the host/pathogen interface that may inform on new immuno- or chemotherapeutic interventions to combat leishmaniasis.
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Affiliation(s)
- Despina Smirlis
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France; Hellenic Pasteur Institute, Molecular Parasitology Laboratory, Athens, Greece.
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, Université de recherche PSL, Paris, France
| | - Pascale Pescher
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Eric Prina
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, Université de recherche PSL, Paris, France
| | - Najma Rachidi
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Gerald F Späth
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France.
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Validation of Housekeeping Genes as Reference for Reverse-Transcription-qPCR Analysis in Busulfan-Injured Microvascular Endothelial Cells. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4953806. [PMID: 30386793 PMCID: PMC6189687 DOI: 10.1155/2018/4953806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022]
Abstract
Endothelial cells (ECs) could express some important cytokines and signal molecules which play a key role in normal hematopoiesis and repopulation. Busulfan-induced vascular endothelial injury is an important feature after hematopoietic stem cell transplantation (HSCT). But the molecular mechanism of how the injured ECs affect hematopoietic reconstruction is still unknown. It is possibly through modulation of the change of some gene expression. RT-qPCR is one of the most popular methods used to accurately determine gene expression levels, based on stable reference gene (RG) selection from housekeeping genes. So our aim is to select stable RGs for more accurate measures of mRNA levels during Busulfan-induced vascular endothelial injury. In this study, 14 RGs were selected to investigate their expression stability in ECs during 72 hours of EC injury treated with Busulfan. Our results revealed extreme variation in RG stability compared by five statistical algorithms. ywhaz and alas1 were recognized as the two idlest RGs on account of the final ranking, while the two most usually used RGs (gapdh and actb) were not the most stable RGs. Next, these data were verified by testing signalling pathway genes ctnnb1, robo4, and notch1 based on the above four genes ywha, alas1, gapdh, and actb. It shows that the normalization of mRNA expression data using unstable RGs greatly affects gene fold change, which means the reliability of the biological conclusions is questionable. Based on the best RGs used, we also found that robo4 is significantly overexpressed in Busulfan-impaired ECs. In conclusion, our data reaffirms the importance of RGs selection for the valid analysis of gene expression in Busulfan-impaired ECs. And it also provides very useful guidance and basis for more accurate differential expression gene screening and future expanding biomolecule study of different drugs such as cyclophosphamide and fludarabine-injured ECs.
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Thiel CS, Huge A, Hauschild S, Tauber S, Lauber BA, Polzer J, Paulsen K, Lier H, Engelmann F, Schmitz B, Schütte A, Layer LE, Ullrich O. Stability of gene expression in human T cells in different gravity environments is clustered in chromosomal region 11p15.4. NPJ Microgravity 2017; 3:22. [PMID: 28868355 PMCID: PMC5579209 DOI: 10.1038/s41526-017-0028-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 12/22/2022] Open
Abstract
In the last decades, a plethora of in vitro studies with living human cells contributed a vast amount of knowledge about cellular and molecular effects of microgravity. Previous studies focused mostly on the identification of gravity-responsive genes, whereas a multi-platform analysis at an integrative level, which specifically evaluates the extent and robustness of transcriptional response to an altered gravity environment was not performed so far. Therefore, we investigated the stability of gene expression response in non-activated human Jurkat T lymphocytic cells in different gravity environments through the combination of parabolic flights with a suborbital ballistic rocket and 2D clinostat and centrifuge experiments, using strict controls for excluding all possible other factors of influence. We revealed an overall high stability of gene expression in microgravity and identified olfactory gene expression in the chromosomal region 11p15.4 as particularly robust to altered gravity. We identified that classical reference genes ABCA5, GAPDH, HPRT1, PLA2G4A, and RPL13A were stably expressed in all tested gravity conditions and platforms, while ABCA5 and GAPDH were also known to be stably expressed in U937 cells in all gravity conditions. In summary, 10-20% of all transcripts remained totally unchanged in any gravitational environment tested (between 10-4 and 9 g), 20-40% remained unchanged in microgravity (between 10-4 and 10-2 g) and 97-99% were not significantly altered in microgravity if strict exclusion criteria were applied. Therefore, we suppose a high stability of gene expression in microgravity. Comparison with other stressors suggests that microgravity alters gene expression homeostasis not stronger than other environmental factors.
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Affiliation(s)
- Cora S Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, D-39106 Magdeburg, Germany
| | - Andreas Huge
- Core Facility Genomic, Medical Faculty of Muenster, University of Muenster, Albert-Schweitzer-Campus 1, D3, Domagstrasse 3, D-48149 Muenster, Germany
| | - Swantje Hauschild
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, D-39106 Magdeburg, Germany
| | - Svantje Tauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, D-39106 Magdeburg, Germany
| | - Beatrice A Lauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jennifer Polzer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Katrin Paulsen
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hartwin Lier
- KEK GmbH, Kemberger Str. 5, D-06905 Bad Schmiedeberg, Germany
| | - Frank Engelmann
- KEK GmbH, Kemberger Str. 5, D-06905 Bad Schmiedeberg, Germany.,Ernst-Abbe-Hochschule Jena, Carl-Zeiss-Promenade 2, D-07745 Jena, Germany
| | - Burkhard Schmitz
- Airbus Defence and Space, Airbus DS GmbH, D-28199 Bremen, Germany
| | - Andreas Schütte
- Airbus Defence and Space, Airbus DS GmbH, D-28199 Bremen, Germany
| | - Liliana E Layer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, D-39106 Magdeburg, Germany.,Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Space Life Sciences, School of Life Sciences, Beijing Institute of Technology, Beijing, 100081 China
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