1
|
Ullrich N, Ramadani A, Paddenberg-Schubert E, Proff P, Jantsch J, Kirschneck C, Schröder A. Validation of reliable reference genes for qPCR of CD4+ T cells exposed to compressive strain. J Orofac Orthop 2024:10.1007/s00056-024-00543-0. [PMID: 39093346 DOI: 10.1007/s00056-024-00543-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/26/2024] [Indexed: 08/04/2024]
Abstract
For accurate interpretation of quantitative real-time PCR (qPCR) data, stable reference genes are essential for normalization of target genes. To date, there is no information on reliable housekeeping genes in CD4+ T cells in a three-dimensional (3D) matrix under pressure stimulation. This in vitro study describes for the first time a method for pressure stimulation of CD4+ T cells in a 3D matrix in the context of orthodontic tooth movement (OTM) and identifies a set of reliable reference genes. CD4+ T cells were isolated from murine spleen and activated with anti-CD3/-CD28 Dynabeads (Thermo Fisher, Langenselbold, Germany) on standard cell culture plates or in 3D scaffolds with or without compressive strain. Expression stability of nine potential reference genes was examined using four mathematical algorithms. Gene expression of Il2 was normalized to all potential reference genes to highlight the importance of correct normalization. Cell proliferation and the expression of the surface markers CD25 and CD69 were also determined. The 3D matrix did not inhibit proliferation after immunological activation of T cells and embedded the cells sufficiently to expose them to pressure load. Expression of ubiquitin C (Ubc) and hypoxanthine phosphoribosyltransferase (Hprt) was the most stable under all conditions tested. A combination of these two genes was suitable for normalization of qPCR data. Normalization of Il2 gene expression showed highly variable results depending on the reference gene used. Pressure reduced cell proliferation and the number of CD69-positive T cells. This study provides a basis for performing valid and reliable qPCR experiments with CD4+ T cells cultured in 3D scaffolds and exposed to compressive forces simulating OTM.
Collapse
Affiliation(s)
- Niklas Ullrich
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany.
| | - Ardita Ramadani
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany
| | | | - Peter Proff
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany
| | - Jonathan Jantsch
- Institute for Microbiology and Hygiene, University Medical Centre Regensburg, Regensburg, Germany
- Institute for Microbiology, Immunology and Hygiene, University Medical Center Cologne, Cologne, Germany
| | | | - Agnes Schröder
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany
- Institute for Microbiology and Hygiene, University Medical Centre Regensburg, Regensburg, Germany
| |
Collapse
|
2
|
Gao X, Shen Q, Roco JA, Dalton B, Frith K, Munier CML, Ballard FD, Wang K, Kelly HG, Nekrasov M, He JS, Jaeger R, Carreira P, Ellyard JI, Beattie L, Enders A, Cook MC, Zaunders JJ, Cockburn IA. Zeb2 drives the formation of CD11c + atypical B cells to sustain germinal centers that control persistent infection. Sci Immunol 2024; 9:eadj4748. [PMID: 38330097 DOI: 10.1126/sciimmunol.adj4748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
CD11c+ atypical B cells (ABCs) are an alternative memory B cell lineage associated with immunization, infection, and autoimmunity. However, the factors that drive the transcriptional program of ABCs have not been identified, and the function of this population remains incompletely understood. Here, we identified candidate transcription factors associated with the ABC population based on a human tonsillar B cell single-cell dataset. We identified CD11c+ B cells in mice with a similar transcriptomic signature to human ABCs, and using an optimized CRISPR-Cas9 knockdown screen, we observed that loss of zinc finger E-box binding homeobox 2 (Zeb2) impaired ABC formation. Furthermore, ZEB2 haplo-insufficient Mowat-Wilson syndrome (MWS) patients have decreased circulating ABCs in the blood. In Cd23Cre/+Zeb2fl/fl mice with impaired ABC formation, ABCs were dispensable for efficient humoral responses after Plasmodium sporozoite immunization but were required to control recrudescent blood-stage malaria. Immune phenotyping revealed that ABCs drive optimal T follicular helper (TFH) cell formation and germinal center (GC) responses and they reside at the red/white pulp border, likely permitting better access to pathogen antigens for presentation. Collectively, our study shows that ABC formation is dependent on Zeb2, and these cells can limit recrudescent infection by sustaining GC reactions.
Collapse
Affiliation(s)
- Xin Gao
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Qian Shen
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Francis Crick Institute, London, UK
| | - Jonathan A Roco
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Becan Dalton
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Katie Frith
- Sydney Children's Hospital, Randwick, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, Australia
| | | | - Fiona D Ballard
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Ke Wang
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Hannah G Kelly
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Maxim Nekrasov
- Australian Cancer Research Foundation Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Jin-Shu He
- ANU Centre for Therapeutic Discovery, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Rebecca Jaeger
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Patricia Carreira
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Julia I Ellyard
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Lynette Beattie
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anselm Enders
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Matthew C Cook
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - John J Zaunders
- Centre for Applied Medical Research, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Ian A Cockburn
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| |
Collapse
|
3
|
Rodon J, Te N, Ballester M, Segalés J, Vergara-Alert J, Bensaid A. Quantification of camelid cytokine mRNA expression in PBMCs by microfluidic qPCR technology. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 149:105061. [PMID: 37717710 DOI: 10.1016/j.dci.2023.105061] [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: 02/16/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Camelids are economically and socially important in several parts of the world and might carry pathogens with epizootic or zoonotic potential. However, biological research in these species is limited due to lack of reagents. Here, we developed RT-qPCR assays to quantify a panel of camelid innate and adaptive immune response genes, which can be monitored in a single run. The assays were validated with PHA, PMA-ionomycin, and Poly I:C-stimulated PBMCs from alpaca, dromedary camel and llama, including normalization by multiple reference genes. Further, comparative gene expression analyses for the different camelid species were performed by a unique microfluidic qPCR assay. Compared to unstimulated controls, PHA and PMA-ionomycin stimulation elicited robust Th1 and Th2 responses in PBMCs from camelid species. Additional activation of type I and type III IFN signalling pathways was described exclusively in PHA-stimulated dromedary lymphocytes, in contrast to those from alpaca and llama. We also found that PolyI:C stimulation induced robust antiviral response genes in alpaca PBMCs. The proposed methodology should be useful for the measurement of immune responses to infection or vaccination in camelid species.
Collapse
Affiliation(s)
- Jordi Rodon
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| | - Nigeer Te
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), 08140, Caldes de Montbui, Spain.
| | - Joaquim Segalés
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; Department de Sanitat i Anatomia Animals, Facultat de Veterinaria, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, 08193, Bellaterra, Catalonia, Spain.
| | - Júlia Vergara-Alert
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| | - Albert Bensaid
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| |
Collapse
|
4
|
Wu J, Yu S, Wang Y, Zhu J, Zhang Z. New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference. Front Oncol 2022; 12:1018279. [PMID: 36313673 PMCID: PMC9606464 DOI: 10.3389/fonc.2022.1018279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.
Collapse
Affiliation(s)
- Junchao Wu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sijie Yu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yalan Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,*Correspondence: Zhenhua Zhang,
| |
Collapse
|
5
|
Delgado-Benito V, Berruezo-Llacuna M, Altwasser R, Winkler W, Sundaravinayagam D, Balasubramanian S, Caganova M, Graf R, Rahjouei A, Henke MT, Driesner M, Keller L, Prigione A, Janz M, Akalin A, Di Virgilio M. PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification. J Exp Med 2021; 217:151913. [PMID: 32609329 PMCID: PMC7537392 DOI: 10.1084/jem.20200137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The establishment of protective humoral immunity is dependent on the ability of mature B cells to undergo antibody gene diversification while adjusting to the physiological stressors induced by activation with the antigen. Mature B cells diversify their antibody genes by class switch recombination (CSR) and somatic hypermutation (SHM), which are both dependent on efficient induction of activation-induced cytidine deaminase (AID). Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation and ensures efficient antibody diversification by promoting their survival and optimal function.
Collapse
Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Berruezo-Llacuna
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robert Altwasser
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Wiebke Winkler
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marieta Caganova
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robin Graf
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ali Rahjouei
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marie-Thérèse Henke
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Madlen Driesner
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lisa Keller
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Alessandro Prigione
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Janz
- Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
6
|
Yu J, Su Y, Sun J, Liu J, Li Z, Zhang B. Selection of stable reference genes for gene expression analysis in sweet potato (Ipomoea batatas L.). Mol Cell Probes 2020; 53:101610. [PMID: 32522510 DOI: 10.1016/j.mcp.2020.101610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/06/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022]
Abstract
Gene expression analysis is one of the most common and important studies in biology and biomedicine. No matter for traditional blotting analysis or currently commonly used PCR strategy, all need a stable reference gene for normalizing the gene expression. To screen and select housekeeping genes as the most stable reference genes, quantitative real-time PCR (qRT-PCR) was employed to analyze the expression of sixteen commonly used reference genes (IbelF, Ibα-tubulin, IbHIS, IbCOX, IbGAPDH, IbH2B1, IbARF, IbCYC, Ibβ-tubulin, IbACT, IbEFl-a, IbG14, IbPLD, IbRPL2, IbUBQ, IbUBI) in five different tissues under two different temperature stresses in sweet potato. Data analysis by the Delta CT, geNorm, NormFinder, and BestKeeper programs revealed that IbelF is the most stable gene and IbUBI is the least stable gene as reference. Our study also shows that combination of two or more genes as reference is a better choice, rendering more substantiated expression data for comparison. This study provides evidence for selecting reference genes in sweet potato gene expression analysis.
Collapse
Affiliation(s)
- Jingjing Yu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Yu Su
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Jianying Sun
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Jingran Liu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China; Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| |
Collapse
|
7
|
Vahkal B, Yegorov S, Onyilagha C, Donner J, Reddick D, Shrivastav A, Uzonna J, Good SV. Immune System Effects of Insulin-Like Peptide 5 in a Mouse Model. Front Endocrinol (Lausanne) 2020; 11:610672. [PMID: 33519716 PMCID: PMC7841425 DOI: 10.3389/fendo.2020.610672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/16/2020] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Insulin-like peptide 5 (INSL5) is a peptide hormone with proposed actions in glucose homeostasis and appetite regulation via its cognate receptor, relaxin family peptide receptor 4 (RXFP4). Here, we look for evidence for their involvement in the immune system using a mouse model. METHODS In silico analyses: we queried public databases for evidence of expression of INSL5-RXFP4 in immune system tissues/cells (NCBI's SRA and GeoProfiles) and disorders (EMBO-EBI) and performed phylogenetic footprinting to look for evidence that they are regulated by immune-associated transcription factors (TFs). Experimental analyses: We characterized the expression and correlation of INSL5/RXFP4 and other immune system markers in central and peripheral immune organs from C57/bl6 mice in seven cohorts. We tested whether fluctuations in circulating INSL5 induce an immune response, by injecting mice with 30 μg/kg of INSL5 peptide in the peritoneum, and examining levels of immune markers and metabolic peptides in plasma. Lastly, we quantified the expression of Rxfp4 in T-cells, dendritic cells and cell lines derived from human and mouse and tested the hypothesis that co-incubation of ANA-1 cells in INSL5 and LPS alters cytokine expression. RESULTS We find Insl5 expression only in thymus (in addition to colon) where its expression was highly correlated with Il-7, a marker of thymocyte development. This result is consistent with our in silico findings that Insl5 is highly expressed in thymic DP, DN thymocytes and cortical TEC's, and with evidence that it is regulated by thymocyte-associated TF's. We find Rxfp4 expression in all immune organs, and moderately high levels in DCs, particularly splenic DCs, and evidence that it is regulated by immune-associated TF's, such as STAT's and GATA. Systemic effects: We observed significantly elevated concentrations of blood GLP-1, GIP, GCG and PYY following intraperitoneal injection of INSL5, and significantly altered expression of cytokines IL-5, IL-7, M-CSF, IL-15, IL-27 and MIP-2. Immune cell effects: Incubation of ANA-1 cells with INSL5 impeded cell growth and led to a transient elevation of IL-15 and sustained reduction in IL-1β, IL-6 and TNFα. CONCLUSION We propose that INSL5-RXFP4 play a novel role in both central and peripheral immune cell signaling.
Collapse
Affiliation(s)
- Brett Vahkal
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada
- *Correspondence: Brett Vahkal, ; Sara V. Good,
| | - Sergey Yegorov
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada
| | | | | | - Dean Reddick
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada
| | | | - Jude Uzonna
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Sara V. Good
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada
- *Correspondence: Brett Vahkal, ; Sara V. Good,
| |
Collapse
|
8
|
Screening and Evaluation of Stable Reference Genes for Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Analysis in Chinese Fir Roots under Water, Phosphorus, and Nitrogen Stresses. FORESTS 2019. [DOI: 10.3390/f10121087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chinese fir (Cunninghamia lanceolata) is an economical important timber species widely planted in southeastern Asia. Decline in yield and productivity during successive rotation is believed to be linked with abiotic stress, such as drought stress and nitrogen (N) and phosphorus (P) starvation. Molecular breeding could be an option to develop tolerant genotypes. For gene expression studies using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR), stable reference genes are needed for normalization of gene expression under different experimental conditions. However, there is no internal reference genes identified for Chinese fir under abiotic stresses. Thus, nine internal reference genes based on transcriptome data were selected and analyzed in the root of Chinese fir under drought stress and N and P starvation. Data were analyzed using geNorm, NormFinder, and BestKeeper, to screen and identify the best reference genes. The results showed that the UBQ and GAPDH genes were the two most stable genes under drought stress and the Actin1 and GAPDH were the two most stable genes under P starvation. Further, it was discovered that the Actin1 and UBC were the two most stable genes under N starvation among nine candidate reference genes. The gene expression of drought stress induced expression protein 14-3-3-4, the P transporter gene ClPht1;3, and the nitrate transporter gene NRT1.1 were used to verify the stability of the selected reference genes under drought stress and P and N starvation, respectively, and the results revealed that the screened reference genes were sufficient to normalize expression of the target genes. In conclusion, the results demonstrate that the stability of reference genes was closely related to the external conditions and reference genes applied to the roots of Chinese fir under different abiotic stress treatments were different. Our data will facilitate further studies on stress ecology and gene function analysis in Chinese fir.
Collapse
|
9
|
Mosley YYC, HogenEsch H. Selection of a suitable reference gene for quantitative gene expression in mouse lymph nodes after vaccination. BMC Res Notes 2017; 10:689. [PMID: 29208024 PMCID: PMC5718095 DOI: 10.1186/s13104-017-3005-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/28/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The quantification of gene expression is an important tool in the evaluation of the immune response to vaccines. Reliable reference genes for gene expression studies in mouse draining lymph nodes after vaccination have not been reported. RESULTS The utility of seven potential reference genes was investigated using commercially available Taq-man primer/probe mixes. Results were evaluated with RefFinder, a web-based program including multiple algorithm methods such as geNorm, NormFinder, BestKeeper and the comparative delta-Ct. Further assessment was done by applying the candidate reference genes in relative expression calculations with genes related to the magnitude and longevity of the humoral immune responses. The ubiquitin C gene, Ubc, was found to be the most reliable reference gene when validated with well-known genes that are expressed at relatively low levels after vaccination. The optimal time of sample collection varied depending on the function of the target genes. CONCLUSIONS This study identified Ubc as the most reliable reference gene and provides useful information for studies examining immunological gene expression in the draining lymph nodes after vaccination in mice.
Collapse
Affiliation(s)
- Yung-Yi C Mosley
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 725 Harrison Street, West Lafayette, IN, 47907, USA.
| | - Harm HogenEsch
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 725 Harrison Street, West Lafayette, IN, 47907, USA
| |
Collapse
|
10
|
The Challenge of Stability in High-Throughput Gene Expression Analysis: Comprehensive Selection and Evaluation of Reference Genes for BALB/c Mice Spleen Samples in the Leishmania infantum Infection Model. PLoS One 2016; 11:e0163219. [PMID: 27668434 PMCID: PMC5036817 DOI: 10.1371/journal.pone.0163219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/06/2016] [Indexed: 11/23/2022] Open
Abstract
The interaction of Leishmania with BALB/c mice induces dramatic changes in transcriptome patterns in the parasite, but also in the target organs (spleen, liver…) due to its response against infection. Real-time quantitative PCR (qPCR) is an interesting approach to analyze these changes and understand the immunological pathways that lead to protection or progression of disease. However, qPCR results need to be normalized against one or more reference genes (RG) to correct for non-specific experimental variation. The development of technical platforms for high-throughput qPCR analysis, and powerful software for analysis of qPCR data, have acknowledged the problem that some reference genes widely used due to their known or suspected “housekeeping” roles, should be avoided due to high expression variability across different tissues or experimental conditions. In this paper we evaluated the stability of 112 genes using three different algorithms: geNorm, NormFinder and RefFinder in spleen samples from BALB/c mice under different experimental conditions (control and Leishmania infantum-infected mice). Despite minor discrepancies in the stability ranking shown by the three methods, most genes show very similar performance as RG (either good or poor) across this massive data set. Our results show that some of the genes traditionally used as RG in this model (i.e. B2m, Polr2a and Tbp) are clearly outperformed by others. In particular, the combination of Il2rg + Itgb2 was identified among the best scoring candidate RG for every group of mice and every algorithm used in this experimental model. Finally, we have demonstrated that using “traditional” vs rationally-selected RG for normalization of gene expression data may lead to loss of statistical significance of gene expression changes when using large-scale platforms, and therefore misinterpretation of results. Taken together, our results highlight the need for a comprehensive, high-throughput search for the most stable reference genes in each particular experimental model.
Collapse
|
11
|
Shi Y, Lu J, Wang Y, Wang S. Reference gene validation for quantification of gene expression during final oocyte maturation induced by diethylstilbestrol and di-(2-ethylhexyl)-phthalate in common carp. J Environ Sci (China) 2016; 46:47-54. [PMID: 27521935 DOI: 10.1016/j.jes.2015.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/28/2015] [Accepted: 12/16/2015] [Indexed: 12/17/2022]
Abstract
Final oocyte maturation is the key step to successful spawning and fertilization. Quantitative real-time PCR (qPCR) is the technique of election to quantify the abundance of functional genes in such study. Reference gene is essential for correct interpretation of qPCR data. However, an ideal universal reference gene that is stable under all experimental circumstances has not been described. Researchers should validate their reference genes while performing qPCR analysis. The expression of 6 candidate reference genes: 18s rRNA, 28s rRNA, Cathepsin Z, Elongation factor 1-α, Glyceraldehyde-3-phosphate dehydrogenase and β-actin were investigated during final oocyte maturation induced by different compounds (DES and DEHP) in common carp (Cyprinus carpio). Four softwares (Bestkeeper, geNorm, NormFinder and RefFinder) were used to screen the most stable gene in order to evaluate their expression stability. The results revealed that EF1α was highly stable expressed when final oocyte maturation was induced by DES, while gapdh was the most stable gene when final oocyte maturation was induced by DEHP. Stable expressed reference gene selection is critical for all qPCR analysis to get accurate target gene mRNA expression information.
Collapse
Affiliation(s)
- Yanyan Shi
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Jie Lu
- School of Physics and Mechanical & Electrical Engineering, Xiamen University, Xiamen 361005, China
| | - Yilei Wang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Shuhong Wang
- Fisheries College, Jimei University, Xiamen 361021, China.
| |
Collapse
|
12
|
Oturai DB, Søndergaard HB, Börnsen L, Sellebjerg F, Romme Christensen J. Identification of Suitable Reference Genes for Peripheral Blood Mononuclear Cell Subset Studies in Multiple Sclerosis. Scand J Immunol 2015; 83:72-80. [DOI: 10.1111/sji.12391] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/15/2015] [Indexed: 12/19/2022]
Affiliation(s)
- D. B. Oturai
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - H. B. Søndergaard
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - L. Börnsen
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - F. Sellebjerg
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - J. Romme Christensen
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| |
Collapse
|
13
|
Wu H, Taki FA, Zhang Y, Dobbins DL, Pan X. Evaluation and identification of reliable reference genes for toxicological study in Caenorhabditis elegans. Mol Biol Rep 2014; 41:3445-55. [PMID: 24510408 DOI: 10.1007/s11033-014-3206-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 01/27/2014] [Indexed: 12/26/2022]
Abstract
To identify reliable reference genes for toxicological studies, 16 commonly-used reference genes were selected as candidates to evaluate their expression stabilities under experimental conditions in Caenorhabditis elegans. Sixteen candidates were composed of 12 protein-coding genes and 4 non-coding RNAs, they were act-2, ama-1, arp-6, cdc-42, csq-1, eif-3.C, idhg-1, mdh, pmp-3, rbd-1, tba-1, Y45F10D.4, 18S rRNA, Ce234, U18, and U6. Larval stage 1 synchronized hermaphrodites were exposed to benzo-α-pyrene (BαP), chlorpyrifos, diazinon, gossypol, zinc oxide nanoparticles, and the vehicle control DMSO for 30 h, respectively. Expression stabilities of candidate genes were analyzed using 4 independent evaluating approaches (BestKeeper, the delta Ct approach, geNorm, and NormFinder) followed by a comprehensive method. Results showed that there were slight differences in ranking order between evaluation methods due to their different assumptions and computations. The results also showed that responses of candidate genes to different chemicals were distinct, 18S rRNA was the best for BαP and chlorpyrifos, tba-1 was the most stable gene for diazinon and gossypol treatments, while pmp-3 was more stable for zinc oxide exposure. Additionally, results demonstrated that combinations of multiple genes were more reliable than individual gene, suggesting selecting two or more candidates as reference genes may generate more reliable results for toxicological studies.
Collapse
Affiliation(s)
- Hongmei Wu
- School of Public Health, Wenzhou Medical College, Wenzhou, 325035, China
| | | | | | | | | |
Collapse
|
14
|
Comparative study of candidate housekeeping genes for quantification of target gene messenger RNA expression by real-time PCR in patients with inflammatory bowel disease. Inflamm Bowel Dis 2013; 19:2840-7. [PMID: 24141710 DOI: 10.1097/01.mib.0000435440.22484.e8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Mucosal expression of immunological mediators is modified in inflammatory bowel disease (IBD). Quantification of target gene messenger RNA (mRNA) transcripts depends on the normalization to a housekeeping or reference gene. Stability of housekeeping gene expression is critical for the accurate measurement of transcripts of the target gene. No studies have addressed the optimization of reference gene performance for mRNA studies in healthy intestinal mucosa and during mucosal inflammation. METHODS RNA was extracted from endoscopically obtained intestinal biopsies from healthy control subjects and patients with active IBD or non-IBD inflammatory diseases. Comparative analysis of 10 candidate housekeeping genes for quantitative real-time PCR was carried out according to predefined criteria, including use of the Web-based RefFinder platform. RESULTS We demonstrate that intestinal inflammation may significantly affect the stability of mucosal expression of housekeeping genes. Commonly used controls, such as glyceraldehyde-3-phosphate dehydrogenase, β-actin, or β2-microglobulin displayed high variability within the control group and/or between the healthy and inflamed mucosae. In contrast, we have identified novel genes with optimal stability, which may be used as appropriate housekeeping controls. The ribosomal proteins encoding genes (RPLPO and RPS9) were the most stable because their expression was not affected by interindividual differences, the presence of inflammation, or intestinal location. Normalization ofthe mRNA expression of mucosal tumor necrosis factor-α was highly dependent on the specific reference gene and varied significantly when normalized to genes with high or low stability. CONCLUSIONS Validation for optimal performance of the housekeeping gene is required for target mRNA quantification in healthy intestine and IBD-associated lesions. Suboptimal reference gene expression may explain conflicting results from published studies on IBD gene expression.
Collapse
|
15
|
Li R, Shen Y. An old method facing a new challenge: re-visiting housekeeping proteins as internal reference control for neuroscience research. Life Sci 2013; 92:747-51. [PMID: 23454168 DOI: 10.1016/j.lfs.2013.02.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/08/2013] [Accepted: 02/18/2013] [Indexed: 01/09/2023]
Abstract
The study of specific target protein expression is often performed by western blotting, a commonly used method to measure the protein expression in neuroscience research by specific antibodies. Housekeeping proteins are used as an internal control for protein loading as well as reference in the western blotting analysis. This practice is based on the belief that such housekeeping genes are considered to be ubiquitously and constitutively expressed in every tissue and produce the minimal essential transcripts necessary for normal cellular function. The most commonly used housekeeping proteins are β-actin, β-tubulin, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). However, recent studies have shown significant variation in some housekeeping genes both at the mRNA and protein levels in various neuropathological events, such as spinal cord injury and Alzheimer's diseases. Changes of housekeeping genes are also induced by non-neuronal diseases in various tissues. Therefore, these discoveries raise a potential concern regarding whether using a housekeeping protein as an internal standard for target protein analysis is an appropriate practice. This minireview will focus on (I) the effects of neuronal and non-neuronal diseases, experimental condition, and tissue-specific roles on alteration of housekeeping genes, and (II) alternative internal standards for gene and protein expression analysis.
Collapse
Affiliation(s)
- Rena Li
- Center for Hormone Advanced Science and Education, Roskamp Institute, Sarasota, FL 34243, USA.
| | | |
Collapse
|