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Islam SMM, Siddik MAB, Sørensen M, Brinchmann MF, Thompson KD, Francis DS, Vatsos IN. Insect meal in aquafeeds: A sustainable path to enhanced mucosal immunity in fish. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109625. [PMID: 38740231 DOI: 10.1016/j.fsi.2024.109625] [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: 03/15/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
The mucosal surfaces of fish, including their intestines, gills, and skin, are constantly exposed to various environmental threats, such as water quality fluctuations, pollutants, and pathogens. However, various cells and microbiota closely associated with these surfaces work in tandem to create a functional protective barrier against these conditions. Recent research has shown that incorporating specific feed ingredients into fish diets can significantly boost their mucosal and general immune response. Among the various ingredients being investigated, insect meal has emerged as one of the most promising options, owing to its high protein content and immunomodulatory properties. By positively influencing the structure and function of mucosal surfaces, insect meal (IM) has the potential to enhance the overall immune status of fish. This review provides a comprehensive overview of the potential benefits of incorporating IM into aquafeed as a feed ingredient for augmenting the mucosal immune response of fish.
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Affiliation(s)
- S M Majharul Islam
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - Muhammad A B Siddik
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3216, Australia
| | - Mette Sørensen
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | | | - Kim D Thompson
- Aquaculture Research Group, Moredun Research Institute, Edinburgh, UK
| | - David S Francis
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3216, Australia
| | - Ioannis N Vatsos
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway.
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2
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Steitz AM, Schröder C, Knuth I, Keber CU, Sommerfeld L, Finkernagel F, Jansen JM, Wagner U, Müller-Brüsselbach S, Worzfeld T, Huber M, Beutgen VM, Graumann J, Pogge von Strandmann E, Müller R, Reinartz S. TRAIL-dependent apoptosis of peritoneal mesothelial cells by NK cells promotes ovarian cancer invasion. iScience 2023; 26:108401. [PMID: 38047087 PMCID: PMC10692662 DOI: 10.1016/j.isci.2023.108401] [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: 07/06/2023] [Revised: 10/04/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
A crucial requirement for metastasis formation in ovarian high-grade serous carcinoma (HGSC) is the disruption of the protective peritoneal mesothelium. Using co-culture systems of primary human cells, we discovered that tumor-associated NK cells induce TRAIL-dependent apoptosis in mesothelial cells via death receptors DR4 and DR5 upon encounter with activated T cells. Upregulation of TRAIL expression in NK cells concomitant with enhanced cytotoxicity toward mesothelial cells was driven predominantly by T-cell-derived TNFα, as shown by affinity proteomics-based analysis of the T cell secretome in conjunction with functional studies. Consistent with these findings, we detected apoptotic mesothelial cells in the peritoneal fluid of HGSC patients. In contrast to mesothelial cells, HGSC cells express negligible levels of both DR4 and DR5 and are TRAIL resistant, indicating cell-type-selective killing by NK cells. Our data point to a cooperative action of T and NK in breaching the mesothelial barrier in HGSC patients.
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Affiliation(s)
- Anna Mary Steitz
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Clarissa Schröder
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Isabel Knuth
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Corinna U. Keber
- Institute for Pathology, Philipps University, 35043 Marburg, Germany
| | - Leah Sommerfeld
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Florian Finkernagel
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Julia M. Jansen
- Clinic for Gynecology, Gynecological Oncology, Gynecological Endocrinology, University Hospital (UKGM), 35043 Marburg, Germany
| | - Uwe Wagner
- Clinic for Gynecology, Gynecological Oncology, Gynecological Endocrinology, University Hospital (UKGM), 35043 Marburg, Germany
| | - Sabine Müller-Brüsselbach
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Thomas Worzfeld
- Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), Philipps University, 35043 Marburg, Germany
| | - Magdalena Huber
- Institute of Systems Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Vanessa M. Beutgen
- Institute of Translational Proteomics, Philipps University, 35043 Marburg, Germany
- Core Facility Translational Proteomics, Philipps University, 35043 Marburg, Germany
| | - Johannes Graumann
- Institute of Translational Proteomics, Philipps University, 35043 Marburg, Germany
- Core Facility Translational Proteomics, Philipps University, 35043 Marburg, Germany
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Clinic for Hematology, Oncology and Immunology, Philipps University, 35043 Marburg, Germany
| | - Rolf Müller
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
| | - Silke Reinartz
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany
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3
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Sadhu L, Tsopoulidis N, Hasanuzzaman M, Laketa V, Way M, Fackler OT. ARPC5 isoforms and their regulation by calcium-calmodulin-N-WASP drive distinct Arp2/3-dependent actin remodeling events in CD4 T cells. eLife 2023; 12:e82450. [PMID: 37162507 PMCID: PMC10171864 DOI: 10.7554/elife.82450] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/06/2023] [Indexed: 05/11/2023] Open
Abstract
CD4 T cell activation induces nuclear and cytoplasmic actin polymerization via the Arp2/3 complex to activate cytokine expression and strengthen T cell receptor (TCR) signaling. Actin polymerization dynamics and filament morphology differ between nucleus and cytoplasm. However, it is unclear how the Arp2/3 complex mediates distinct nuclear and cytoplasmic actin polymerization in response to a common stimulus. In humans, the ARP3, ARPC1, and ARPC5 subunits of the Arp2/3 complex exist as two different isoforms, resulting in complexes with different properties. Here, we show that the Arp2/3 subunit isoforms ARPC5 and ARPC5L play a central role in coordinating distinct actin polymerization events in CD4 T cells. While ARPC5L is heterogeneously expressed in individual CD4 T cells, it specifically drives nuclear actin polymerization upon T cell activation. In contrast, ARPC5 is evenly expressed in CD4 T cell populations and is required for cytoplasmic actin dynamics. Interestingly, nuclear actin polymerization triggered by a different stimulus, DNA replication stress, specifically requires ARPC5 but not ARPC5L. TCR signaling but not DNA replication stress induces nuclear actin polymerization via nuclear calcium-calmodulin signaling and N-WASP. Diversity in the molecular properties and individual expression patterns of ARPC5 subunit isoforms thus tailors Arp2/3-mediated actin polymerization to different physiological stimuli.
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Affiliation(s)
- Lopamudra Sadhu
- Department of Infectious Diseases, Integrative Virology, University Hospital HeidelbergHeidelbergGermany
| | - Nikolaos Tsopoulidis
- Department of Infectious Diseases, Integrative Virology, University Hospital HeidelbergHeidelbergGermany
| | - Md Hasanuzzaman
- Department of Infectious Diseases, Integrative Virology, University Hospital HeidelbergHeidelbergGermany
| | - Vibor Laketa
- Department of Infectious Diseases, Virology, University Hospital HeidelbergHeidelbergGermany
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Infectious Disease, Imperial CollegeLondonUnited Kingdom
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital HeidelbergHeidelbergGermany
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4
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Wnorowski A, Wójcik J, Maj M. Gene Expression Data Mining Reveals the Involvement of GPR55 and Its Endogenous Ligands in Immune Response, Cancer, and Differentiation. Int J Mol Sci 2021; 22:ijms222413328. [PMID: 34948125 PMCID: PMC8707311 DOI: 10.3390/ijms222413328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 12/04/2022] Open
Abstract
G protein-coupled receptor 55 (GPR55) is a recently deorphanized lipid- and peptide-sensing receptor. Its lipidic endogenous agonists belong to lysoglycerophospholipids, with lysophosphatidylinositol (LPI) being the most studied. Peptide agonists derive from fragmentation of pituitary adenylate cyclase-activating polypeptide (PACAP). Although GPR55 and its ligands were implicated in several physiological and pathological conditions, their biological function remains unclear. Thus, the aim of the study was to conduct a large-scale re-analysis of publicly available gene expression datasets to identify physiological and pathological conditions affecting the expression of GPR55 and the production of its ligands. The study revealed that regulation of GPR55 occurs predominantly in the context of immune activation pointing towards the role of the receptor in response to pathogens and in immune cell lineage determination. Additionally, it was revealed that there is almost no overlap between the experimental conditions affecting the expression of GPR55 and those modulating agonist production. The capacity to synthesize LPI was enhanced in various types of tumors, indicating that cancer cells can hijack the motility-related activity of GPR55 to increase aggressiveness. Conditions favoring accumulation of PACAP-derived peptides were different than those for LPI and were mainly related to differentiation. This indicates a different function of the two agonist classes and possibly the existence of a signaling bias.
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Shi T, Roskin K, Baker BM, Woodle ES, Hildeman D. Advanced Genomics-Based Approaches for Defining Allograft Rejection With Single Cell Resolution. Front Immunol 2021; 12:750754. [PMID: 34721421 PMCID: PMC8551864 DOI: 10.3389/fimmu.2021.750754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Solid organ transplant recipients require long-term immunosuppression for prevention of rejection. Calcineurin inhibitor (CNI)-based immunosuppressive regimens have remained the primary means for immunosuppression for four decades now, yet little is known about their effects on graft resident and infiltrating immune cell populations. Similarly, the understanding of rejection biology under specific types of immunosuppression remains to be defined. Furthermore, development of innovative, rationally designed targeted therapeutics for mitigating or preventing rejection requires a fundamental understanding of the immunobiology that underlies the rejection process. The established use of microarray technologies in transplantation has provided great insight into gene transcripts associated with allograft rejection but does not characterize rejection on a single cell level. Therefore, the development of novel genomics tools, such as single cell sequencing techniques, combined with powerful bioinformatics approaches, has enabled characterization of immune processes at the single cell level. This can provide profound insights into the rejection process, including identification of resident and infiltrating cell transcriptomes, cell-cell interactions, and T cell receptor α/β repertoires. In this review, we discuss genomic analysis techniques, including microarray, bulk RNAseq (bulkSeq), single-cell RNAseq (scRNAseq), and spatial transcriptomic (ST) techniques, including considerations of their benefits and limitations. Further, other techniques, such as chromatin analysis via assay for transposase-accessible chromatin sequencing (ATACseq), bioinformatic regulatory network analyses, and protein-based approaches are also examined. Application of these tools will play a crucial role in redefining transplant rejection with single cell resolution and likely aid in the development of future immunomodulatory therapies in solid organ transplantation.
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Affiliation(s)
- Tiffany Shi
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Krishna Roskin
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - David Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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6
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Hanna SJ, Tatovic D, Thayer TC, Dayan CM. Insights From Single Cell RNA Sequencing Into the Immunology of Type 1 Diabetes- Cell Phenotypes and Antigen Specificity. Front Immunol 2021; 12:751701. [PMID: 34659258 PMCID: PMC8519581 DOI: 10.3389/fimmu.2021.751701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/14/2021] [Indexed: 01/10/2023] Open
Abstract
In the past few years, huge advances have been made in techniques to analyse cells at an individual level using RNA sequencing, and many of these have precipitated exciting discoveries in the immunology of type 1 diabetes (T1D). This review will cover the first papers to use scRNAseq to characterise human lymphocyte phenotypes in T1D in the peripheral blood, pancreatic lymph nodes and islets. These have revealed specific genes such as IL-32 that are differentially expressed in islet -specific T cells in T1D. scRNAseq has also revealed wider gene expression patterns that are involved in T1D and can predict its development even predating autoantibody production. Single cell sequencing of TCRs has revealed V genes and CDR3 motifs that are commonly used to target islet autoantigens, although truly public TCRs remain elusive. Little is known about BCR repertoires in T1D, but scRNAseq approaches have revealed that insulin binding BCRs commonly use specific J genes, share motifs between donors and frequently demonstrate poly-reactivity. This review will also summarise new developments in scRNAseq technology, the insights they have given into other diseases and how they could be leveraged to advance research in the type 1 diabetes field to identify novel biomarkers and targets for immunotherapy.
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Affiliation(s)
- Stephanie J. Hanna
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Danijela Tatovic
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Terri C. Thayer
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Department of Biological and Chemical Sciences, School of Natural and Social Sciences, Roberts Wesleyan College, Rochester, NY, United States
| | - Colin M. Dayan
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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7
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West AL, Miles EA, Han L, Lillycrop KA, Napier JA, Calder PC, Burdge GC. Dietary Supplementation with Transgenic Camelina sativa Oil Containing 20:5n-3 and 22:6n-3 or Fish Oil Induces Differential Changes in the Transcriptome of CD3 + T Lymphocytes. Nutrients 2021; 13:3116. [PMID: 34578993 PMCID: PMC8466821 DOI: 10.3390/nu13093116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/23/2022] Open
Abstract
Eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3) are important for leukocyte function. This study investigated whether consuming transgenic Camelina sativa (tCSO) seed oil containing both 20:5n-3 and 22:6n-3 is as effective as fish oil (FO) for increasing the 20:5n-3 and 22:6n-3 content of leukocytes and altering mitogen-induced changes to the T cell transcriptome. Healthy adults (n = 31) consumed 450 mg/day of 20:5n-3 plus 22:6n-3 from either FO or tCSO for 8 weeks. Blood was collected before and after the intervention. 20:5n-3 and 22:6n-3 incorporation from tCSO into immune cell total lipids was comparable to FO. The relative expression of the transcriptomes of mitogen-stimulated versus unstimulated T lymphocytes in a subgroup of 16 women/test oil showed 4390 transcripts were differentially expressed at Baseline (59% up-regulated), 4769 (57% up-regulated) after FO and 3443 (38% up-regulated) after tCSO supplementation. The 20 most altered transcripts after supplementation differed between test oils. The most altered pathways were associated with cell proliferation and immune function. In conclusion, 20:5n-3 and 22:6n-3 incorporation into immune cells from tCSO was comparable to FO and can modify mitogen-induced changes in the T cell transcriptome, contingent on the lipid matrix of the oil.
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Affiliation(s)
- Annette L. West
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (A.L.W.); (E.A.M.); (P.C.C.)
| | - Elizabeth A. Miles
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (A.L.W.); (E.A.M.); (P.C.C.)
| | - Lihua Han
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK; (L.H.); (J.A.N.)
| | - Karen A. Lillycrop
- Centre for Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, UK;
| | - Johnathan A. Napier
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK; (L.H.); (J.A.N.)
| | - Philip C. Calder
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (A.L.W.); (E.A.M.); (P.C.C.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, Southampton SO16 6YD, UK
| | - Graham C. Burdge
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (A.L.W.); (E.A.M.); (P.C.C.)
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Unterweger AL, Jensen MØ, Giordanetto F, Jogini V, Rüschher A, Seuß M, Winkelmann P, Koletzko L, Shaw DE, Siebeck M, Gropp R, Beigel F, Aszodi A. Suppressing Kv1.3 Ion Channel Activity with a Novel Small Molecule Inhibitor Ameliorates Inflammation in a Humanised Mouse Model of Ulcerative Colitis. J Crohns Colitis 2021; 15:1943-1958. [PMID: 33891001 PMCID: PMC8575044 DOI: 10.1093/ecco-jcc/jjab078] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND AND AIMS The potassium channel Kv1.3 is a potentially attractive therapeutic target in T cell-mediated inflammatory diseases, as the activity of antigen-activated T cells is selectively impeded by Kv1.3 inhibition. In this study, we examined Kv1.3 as a potential therapeutic intervention point for ulcerative colitis [UC], and studied the efficacy of DES1, a small-molecule inhibitor of Kv1.3, in vitro and in vivo. METHODS Kv1.3 expression on T cells in peripheral blood mononuclear cells [PBMCs] isolated from donors with and without UC was examined by flow cytometry. In biopsies from UC patients, Kv1.3-expressing CD4+ T cells were detected by flow cytometry and immunohistochemistry. In vitro, we determined the ability of DES1 to inhibit anti-CD3-driven activation of T cells. In vivo, the efficacy of DES1 was determined in a humanised mouse model of UC and compared with infliximab and tofacitinib in head-to-head studies. RESULTS Kv1.3 expression was elevated in PBMCs from UC patients and correlated with the prevalence of TH1 and TH2 T cells. Kv1.3 expression was also detected on T cells from biopsies of UC patients. In vitro, DES1 suppressed anti-CD3-driven activation of T cells in a concentration-dependent manner. In vivo, DES1 significantly ameliorated inflammation in the UC model and most effectively so when PBMCs from donors with higher levels of activated T cells were selected for reconstitution. The efficacy of DES1 was comparable to that of either infliximab or tofacitinib. CONCLUSION Inhibition of Kv1.3 [by DES1, for instance] appears to be a potential therapeutic intervention strategy for UC patients.
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Affiliation(s)
- Anna-Lena Unterweger
- Department of General, Visceral und Transplantation Surgery, University Hospital, LMU, Munich, Germany
| | | | | | | | - Alena Rüschher
- Department of General, Visceral und Transplantation Surgery, University Hospital, LMU, Munich, Germany
| | - Marietta Seuß
- Department of General, Visceral und Transplantation Surgery, University Hospital, LMU, Munich, Germany
| | - Paula Winkelmann
- Department of General, Visceral und Transplantation Surgery, University Hospital, LMU, Munich, Germany
| | - Leandra Koletzko
- Department of Medicine II, University Hospital, LMUMunich, Germany
| | - David E Shaw
- D. E. Shaw Research, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matthias Siebeck
- Department of General, Visceral und Transplantation Surgery, University Hospital, LMU, Munich, Germany
| | - Roswitha Gropp
- Department of General, Visceral und Transplantation Surgery, University Hospital, LMU, Munich, Germany,Corresponding author: Roswitha Gropp, Department of General, Visceral and Transplantation Surgery, Hospital of the Ludwig-Maximilian University Munich, Nussbaumstr. 20, 80336 Munich, Germany.
| | - Florian Beigel
- Department of Medicine II, University Hospital, LMUMunich, Germany
| | - Attila Aszodi
- Department of General, Trauma and Reconstructive Surgery, University Hospital, LMU Munich, Germany’
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9
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Ekebergh A, Mårtensson J, Ekebergh CL. Cyclopenta[ b]indole Derivative Inhibits Aurora B in Primary Cells. ACS OMEGA 2020; 5:33455-33460. [PMID: 33403307 PMCID: PMC7774273 DOI: 10.1021/acsomega.0c05491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
The Aurora family of kinases is closely involved in regulating cell division. Inhibition of Aurora A and B with small molecules is currently being investigated in clinical trials for the treatment of different cancers. It has also been evaluated as a treatment option against different autoimmune diseases in preclinical studies. Here, we present a cyclopenta[b]indole derivative capable of inhibiting Aurora B selectively in kinase assays. To evaluate the Aurora B inhibition capacity of the compound, we used a kinase IC50 assay as well as a suppression assay of proliferating primary cells. In addition, we examined if the cells had gained a phenotype characteristic for Aurora B inhibition after treatment with the compound. We found that the compound selectively inhibited Aurora B (IC50 = 1.4 μM) over Aurora A (IC50 > 30 μM). Moreover, the compound inhibited proliferating PBMCs with an IC50 = 4.2 μM, and the cells displayed reduced phosphorylation of histone H3 as well as tetraploidy, consistent with Aurora B inhibition.
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Affiliation(s)
- Andreas Ekebergh
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Jerker Mårtensson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Christine Lingblom Ekebergh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 46, Sweden
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg 413 46, Sweden
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10
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Liu B, Lindner P, Jirmo AC, Maus U, Illig T, DeLuca DS. A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. BMC Bioinformatics 2020; 21:28. [PMID: 31992182 PMCID: PMC6986093 DOI: 10.1186/s12859-020-3366-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step in the analysis process. Gene set enrichment analysis is a standard approach for summarizing differentially expressed genes into pathways or other gene groupings. Here, we explore an alternative approach to utilizing gene sets from curated databases. We examine the method of deriving custom gene sets which may be relevant to a given experiment using reference data sets from previous transcriptomics studies. We call these data-derived gene sets, "gene signatures" for the biological process tested in the previous study. We focus on the feasibility of this approach in analyzing immune-related processes, which are complicated in their nature but play an important role in the medical research. RESULTS We evaluate several statistical approaches to detecting the activity of a gene signature in a target data set. We compare the performance of the data-derived gene signature approach with comparable GO term gene sets across all of the statistical tests. A total of 61 differential expression comparisons generated from 26 transcriptome experiments were included in the analysis. These experiments covered eight immunological processes in eight types of leukocytes. The data-derived signatures were used to detect the presence of immunological processes in the test data with modest accuracy (AUC = 0.67). The performance for GO and literature based gene sets was worse (AUC = 0.59). Both approaches were plagued by poor specificity. CONCLUSIONS When investigators seek to test specific hypotheses, the data-derived signature approach can perform as well, if not better than standard gene-set based approaches for immunological signatures. Furthermore, the data-derived signatures can be generated in the cases that well-defined gene sets are lacking from pathway databases and also offer the opportunity for defining signatures in a cell-type specific manner. However, neither the data-derived signatures nor standard gene-sets can be demonstrated to reliably provide negative predictions for negative cases. We conclude that the data-derived signature approach is a useful and sometimes necessary tool, but analysts should be weary of false positives.
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Affiliation(s)
- Bin Liu
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Adan Chari Jirmo
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Department of Pediatric Pneumology,Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625 Germany
| | - Ulrich Maus
- Division of Experimental Pneumology, Hannover Medical School, Feodor-Lynen-Straße 21, Hannover, 30625 Germany
| | - Thomas Illig
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Straße, Hannover, 30625 Germany
| | - David S. DeLuca
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
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